From 01ad718134f66b275094357e4e9818102cb892e1 Mon Sep 17 00:00:00 2001 From: XingY Date: Tue, 11 Nov 2025 20:26:31 -0800 Subject: [PATCH 1/3] Issue 54186: App actions for picklists and assay run delete don't get TransactionAuditEvent --- api/src/org/labkey/api/exp/DeleteForm.java | 22 + .../labkey/api/exp/api/ExperimentService.java | 3 +- .../org/labkey/experiment/api/ExpRunImpl.java | 2152 +- .../experiment/api/ExperimentServiceImpl.java | 18 +- .../controllers/exp/ExperimentController.java | 16693 ++++++++-------- 5 files changed, 9461 insertions(+), 9427 deletions(-) diff --git a/api/src/org/labkey/api/exp/DeleteForm.java b/api/src/org/labkey/api/exp/DeleteForm.java index 1cba049350e..c823b65435b 100644 --- a/api/src/org/labkey/api/exp/DeleteForm.java +++ b/api/src/org/labkey/api/exp/DeleteForm.java @@ -36,6 +36,28 @@ public class DeleteForm extends ProtocolIdForm implements DataRegionSelection.Da private Long _singleObjectRowId; private List _rowIds; private String _userComment; + private String _editMethod; + private String _requestSource; + + public String getRequestSource() + { + return _requestSource; + } + + public void setRequestSource(String requestSource) + { + _requestSource = requestSource; + } + + public String getEditMethod() + { + return _editMethod; + } + + public void setEditMethod(String editMethod) + { + _editMethod = editMethod; + } public void setUserComment(String userComment) { diff --git a/api/src/org/labkey/api/exp/api/ExperimentService.java b/api/src/org/labkey/api/exp/api/ExperimentService.java index f1ca905d090..a32fffb5f08 100644 --- a/api/src/org/labkey/api/exp/api/ExperimentService.java +++ b/api/src/org/labkey/api/exp/api/ExperimentService.java @@ -21,6 +21,7 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AssayProvider; +import org.labkey.api.audit.TransactionAuditProvider; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; @@ -821,7 +822,7 @@ static void validateParentAlias(Map aliasMap, Set reserv void deleteExperimentRunsByRowIds(Container container, final User user, long... runRowIds); - void deleteExperimentRunsByRowIds(Container container, final User user, @Nullable String userComment, @NotNull Collection runRowIds); + void deleteExperimentRunsByRowIds(Container container, final User user, @Nullable String userComment, @NotNull Collection runRowIds, @Nullable Map transactionDetails); void deleteExpExperimentByRowId(Container container, User user, long experimentId); diff --git a/experiment/src/org/labkey/experiment/api/ExpRunImpl.java b/experiment/src/org/labkey/experiment/api/ExpRunImpl.java index 487e579377f..dbb3747b312 100644 --- a/experiment/src/org/labkey/experiment/api/ExpRunImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpRunImpl.java @@ -1,1076 +1,1076 @@ -/* - * Copyright (c) 2008-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.labkey.experiment.api; - -import org.apache.commons.io.FileUtils; -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.cloud.CloudStoreService; -import org.labkey.api.data.Container; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; -import org.labkey.api.data.SqlExecutor; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.Table; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; -import org.labkey.api.data.dialect.SqlDialect; -import org.labkey.api.exp.ExperimentException; -import org.labkey.api.exp.ExperimentRunType; -import org.labkey.api.exp.OntologyManager; -import org.labkey.api.exp.api.DataType; -import org.labkey.api.exp.api.ExpData; -import org.labkey.api.exp.api.ExpMaterial; -import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.exp.api.ExpProtocolAction; -import org.labkey.api.exp.api.ExpProtocolApplication; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ProtocolImplementation; -import org.labkey.api.exp.api.ProvenanceService; -import org.labkey.api.exp.query.ExpRunTable; -import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.query.BatchValidationException; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryRowReference; -import org.labkey.api.security.User; -import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; -import org.labkey.api.security.permissions.UpdatePermission; -import org.labkey.api.util.FileUtil; -import org.labkey.api.util.NetworkDrive; -import org.labkey.api.view.ActionURL; -import org.labkey.api.view.UnauthorizedException; -import org.labkey.experiment.DotGraph; -import org.labkey.experiment.ExperimentRunGraph; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.Date; -import java.util.HashMap; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Map; -import java.util.Set; - -import static org.labkey.experiment.api.ExperimentServiceImpl.getExpSchema; - -public class ExpRunImpl extends ExpIdentifiableEntityImpl implements ExpRun -{ - public static final String NAMESPACE_PREFIX = "Run"; - - private boolean _populated; - private List _protocolSteps; - private Map _materialInputs = new HashMap<>(); - private Map _dataInputs = new HashMap<>(); - private List _materialOutputs = new ArrayList<>(); - private List _dataOutputs = new ArrayList<>(); - private ExpRunImpl _replacedByRun; - private Integer _maxOutputActionSequence = null; - private static final Logger LOG = LogManager.getLogger(ExpRunImpl.class); - private ExpProtocolApplication _workflowTask; - - static public List fromRuns(List runs) - { - List ret = new ArrayList<>(runs.size()); - for (ExperimentRun run : runs) - { - ret.add(new ExpRunImpl(run)); - } - return ret; - } - - // For serialization - protected ExpRunImpl() {} - - public ExpRunImpl(ExperimentRun run) - { - super(run); - if (null != run && null != run.getObjectId()) - _objectId = run.getObjectId(); - } - - @Override - public ActionURL detailsURL() - { - return _object.detailsURL(); - } - - @Override - public @Nullable QueryRowReference getQueryRowReference() - { - ExpProtocol protocol = getProtocol(); - if (protocol != null) - { - ProtocolImplementation impl = protocol.getImplementation(); - if (impl != null) - { - QueryRowReference ref = impl.getQueryRowReference(protocol, this); - if (ref != null) - return ref; - } - - ExperimentRunType type = ExperimentService.get().getExperimentRunType(protocol); - if (type != null) - { - QueryRowReference ref = type.getQueryRowReference(protocol, this); - if (ref != null) - return ref; - } - } - - return new QueryRowReference(getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Runs.name(), FieldKey.fromParts(ExpRunTable.Column.RowId), getRowId()); - } - - @Override - public Container getContainer() - { - return _object.getContainer(); - } - - @Override - public long getRowId() - { - return _object.getRowId(); - } - - @Override - public List getExperiments() - { - final String sql= " SELECT E.* FROM " + ExperimentServiceImpl.get().getTinfoExperiment() + " E " - + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoRunList() + " RL ON (E.RowId = RL.ExperimentId) " - + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoExperimentRun() + " ER ON (ER.RowId = RL.ExperimentRunId) " - + " WHERE ER.LSID = ? AND E.Hidden = ?"; - - return ExpExperimentImpl.fromExperiments(new SqlSelector(getExpSchema(), sql, _object.getLSID(), Boolean.FALSE).getArray(Experiment.class)); - } - - @Override - public @Nullable ExpExperimentImpl getBatch() - { - if (_object.getBatchId() == null) - return null; - - ExpExperimentImpl batch = ExperimentServiceImpl.get().getExpExperiment(_object.getBatchId()); - if (batch == null) - return null; - - assert checkBatch(batch); - return batch; - } - - private boolean checkBatch(ExpExperimentImpl batch) - { - List exps = getExperiments(); - if (!exps.contains(batch)) - { - LOG.warn("Expected batch '" + batch.getRowId() + "' to be in list of experiments: " + exps); - return false; - } - - if (!getProtocol().equals(batch.getBatchProtocol())) - { - LOG.warn("Expected batch '" + batch.getRowId() + "' to have same protocol as run. Expected protocol '" + getProtocol() + "', but found '" + batch.getBatchProtocol() + "'"); - return false; - } - - return true; - } - - protected void setBatchId(Long batchId) - { - assert batchId == null || checkBatch(ExperimentServiceImpl.get().getExpExperiment(batchId)); - _object.setBatchId(batchId); - } - - @Override - public ExpProtocolImpl getProtocol() - { - return ExperimentServiceImpl.get().getExpProtocol(_object.getProtocolLSID()); - } - - @Override - public boolean isFinalOutput(ExpData data) - { - ExpProtocolApplication sourceApplication = data.getSourceApplication(); - return sourceApplication != null && sourceApplication.getActionSequence() == getMaxOutputActionSequence(); - } - - private int getMaxOutputActionSequence() - { - if (_maxOutputActionSequence == null) - { - _maxOutputActionSequence = 0; - for (ExpProtocolApplication app : getProtocolApplications()) - if (!app.getDataOutputs().isEmpty() && app.getActionSequence() > _maxOutputActionSequence) - _maxOutputActionSequence = app.getActionSequence(); - } - return _maxOutputActionSequence; - } - - @Override - public List getOutputDatas(@Nullable DataType type) - { - return ExperimentServiceImpl.get().getOutputDatas(getRowId(), type); - } - - @Override - public List getInputDatas(@Nullable String inputRole, @Nullable ExpProtocol.ApplicationType applicationType) - { - SQLFragment sql = new SQLFragment(); - sql.append("SELECT exp.Data.* FROM exp.Data WHERE exp.Data.RowId IN "); - sql.append("\n(SELECT exp.DataInput.DataId FROM exp.DataInput "); - sql.append("\nINNER JOIN exp.ProtocolApplication ON exp.DataInput.TargetApplicationId = exp.ProtocolApplication.RowId"); - sql.append("\nWHERE exp.ProtocolApplication.RunId = ?"); - sql.add(getRowId()); - if (inputRole != null) - { - sql.append("\nAND exp.DataInput.Role = ? "); - sql.add(inputRole); - } - if (applicationType != null) - { - sql.append("\nAND exp.ProtocolApplication.CpasType = "); - sql.appendValue(applicationType.toString()); - } - sql.append(")"); - return ExpDataImpl.fromDatas(new SqlSelector(ExperimentService.get().getSchema(), sql).getArrayList(Data.class)); - } - - @Override - public File getFilePathRoot() - { - if (_object.getFilePathRoot() == null || FileUtil.hasCloudScheme(_object.getFilePathRoot())) - return null; - else - return new File(FileUtil.createUri(_object.getFilePathRoot(), false)); - } - - @Override - public void setFilePathRoot(File file) - { - ensureUnlocked(); - // We want "/Users/..." for local file system - _object.setFilePathRoot(file == null ? null : file.toPath().toString()); - } - - @Override - public Path getFilePathRootPath() - { - if (_object.getFilePathRoot() == null) - return null; - else if (FileUtil.hasCloudScheme(_object.getFilePathRoot())) - return CloudStoreService.get().getPathFromUrl(getContainer(), _object.getFilePathRoot()); - else - return new File(FileUtil.createUri(_object.getFilePathRoot(), false)).toPath(); - } - - @Override - public void setFilePathRootPath(Path filePathRoot) - { - ensureUnlocked(); - _object.setFilePathRoot(filePathRoot == null ? null : - FileUtil.hasCloudScheme(filePathRoot) ? - FileUtil.pathToString(filePathRoot) : - filePathRoot.toString()); - } - - @Override - public void save(User user) throws BatchValidationException - { - ExperimentServiceImpl expService = ExperimentServiceImpl.get(); - try (DbScope.Transaction t = getExpSchema().getScope().ensureTransaction()) - { - boolean newRun = getRowId() == 0; - expService.onBeforeRunSaved(getProtocol(), this, getContainer(), user); - save(user, expService.getTinfoExperimentRun(), true); - if (newRun) - expService.auditRunEvent(user, this.getProtocol(), this, null, this.getProtocol().getName() + " run loaded"); - t.addCommitTask(() -> expService.onAfterRunSaved(getProtocol(), this, getContainer(), user), DbScope.CommitTaskOption.POSTCOMMIT); - t.commit(); - } - } - - @Override - protected void save(User user, TableInfo table, boolean ensureObject) - { - assert ensureObject; - super.save(user, table, true); - ExperimentServiceImpl.get().invalidateExperimentRun(getLSID()); - } - - @Override - public void delete(User user) - { - delete(user, null); - } - - @Override - public void delete(User user, @Nullable final String auditUserComment) - { - if (!canDelete(user)) - { - throw new UnauthorizedException(); - } - ExperimentServiceImpl.get().deleteExperimentRuns(getContainer(), user, auditUserComment, Arrays.asList(this)); - } - - @Override - public void setProtocol(ExpProtocol protocol) - { - _object.setProtocolLSID(protocol.getLSID()); - } - - @Override - public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name) - { - return addProtocolApplication(user, action, appType, name, null, null, null); - } - - public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name, java.util.Date startTime, java.util.Date endTime, Integer recordCount) - { - ensureUnlocked(); - ProtocolApplication pa = new ProtocolApplication(); - if (action == null) - { - if (appType != ExpProtocol.ApplicationType.ExperimentRun) - { - throw new IllegalArgumentException("Only the ExperimentRun protocol application type is allowed to have a null protocol action."); - } - pa.setProtocolLSID(getProtocol().getLSID()); - } - else - { - pa.setProtocolLSID(action.getChildProtocol().getLSID()); - pa.setActionSequence(action.getActionSequence()); - } - pa.setName(name); - pa.setLSID(ExperimentService.get().generateGuidLSID(getContainer(), ExpProtocolApplication.class)); - pa.setCpasType(appType.toString()); - pa.setRunId(getRowId()); - pa.setStartTime(startTime); - pa.setEndTime(endTime); - pa.setRecordCount(recordCount); - - pa = Table.insert(user, ExperimentServiceImpl.get().getTinfoProtocolApplication(), pa); - return new ExpProtocolApplicationImpl(pa); - } - - @Override - public String getComments() - { - return _object.getComments(); - } - - @Override - public void setComments(String comments) - { - ensureUnlocked(); - _object.setComments(comments); - } - - @Override - public void setEntityId(String entityId) - { - ensureUnlocked(); - _object.setEntityId(entityId); - } - - @Override - public String getEntityId() - { - return _object.getEntityId(); - } - - - @Override - public void setContainer(Container container) - { - _object.setContainer(container); - } - - @Override - public void setJobId(Long jobId) - { - ensureUnlocked(); - _object.setJobId(jobId); - } - - @Override - public Long getJobId() - { - return _object.getJobId(); - } - - public void setProtocolApplications(List protocolSteps) - { - ensureUnlocked(); - _protocolSteps = protocolSteps; - } - - @Override - public @NotNull Map getMaterialInputs() - { - ensureFullyPopulated(); - return _materialInputs; - } - - @Override - public @NotNull Map getDataInputs() - { - ensureFullyPopulated(); - return _dataInputs; - } - - @Override - public List getMaterialOutputs() - { - ensureFullyPopulated(); - return _materialOutputs; - } - - @Override - public List getDataOutputs() - { - ensureFullyPopulated(); - return _dataOutputs; - } - - @Override - public List getProtocolApplications() - { - ensureFullyPopulated(); - return _protocolSteps; - } - - @Override - public @Nullable ExpProtocolApplication getProtocolApplication() - { - return findProtocolApplication(ExpProtocol.ApplicationType.ProtocolApplication); - } - - @Override - public @Nullable ExpProtocolApplication getInputProtocolApplication() - { - return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRun); - } - - private @Nullable ExpProtocolApplication findProtocolApplication(ExpProtocol.ApplicationType type) - { - for (ExpProtocolApplicationImpl expProtocolApplication : getProtocolApplications()) - { - if (type.equals(expProtocolApplication.getApplicationType())) - { - return expProtocolApplication; - } - } - return null; - } - - @Override - public @Nullable ExpProtocolApplication getOutputProtocolApplication() - { - return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRunOutput); - } - - @Override - public void deleteProtocolApplications(User user) - { - ensureUnlocked(); - deleteProtocolApplications(getOutputDatas(null), user); - } - - @Override - public void setReplacedByRun(ExpRun run) - { - ensureUnlocked(); - if (run != null && run.getRowId() < 1) - { - throw new IllegalArgumentException("Run must have already been saved to the database"); - } - _object.setReplacedByRunId(run == null ? null : run.getRowId()); - } - - @Override - public ExpRun getReplacedByRun() - { - Long id = _object.getReplacedByRunId(); - if (id == null) - { - return null; - } - if (_replacedByRun == null || _replacedByRun.getRowId() != id.intValue()) - { - _replacedByRun = ExperimentServiceImpl.get().getExpRun(id.intValue()); - } - return _replacedByRun; - } - - @Override - public List getReplacesRuns() - { - return fromRuns(new TableSelector(ExperimentServiceImpl.get().getTinfoExperimentRun(), new SimpleFilter(FieldKey.fromParts("ReplacedByRunId"), getRowId()), new Sort("Name")).getArrayList(ExperimentRun.class)); - } - - public void deleteProtocolApplications(List datasToDelete, User user) - { - if (user == null || !canDelete(user)) - { - throw new UnauthorizedException("Attempting to delete an ExperimentRun without having delete permissions for its container"); - } - final ExperimentServiceImpl svc = ExperimentServiceImpl.get(); - final SqlDialect dialect = svc.getSchema().getSqlDialect(); - - svc.invalidateExperimentRun(getLSID()); - - deleteProtocolApplicationProvenance(); - - svc.beforeDeleteData(user, getContainer(), datasToDelete); - - deleteInputObjects(svc, dialect); - - deleteAppParametersAndInputs(); - - deleteRunMaterials(user); - - deleteRunProtocolApps(); - - clearCache(); - - // Clear the cache in a commit task, which allows us to do a single clear (which is semi-expensive) if multiple - // runs are being deleted in the same transaction, like deleting a container - svc.getSchema().getScope().addCommitTask(ExperimentRunGraph.getCacheClearingCommitTask(getContainer()), DbScope.CommitTaskOption.POSTCOMMIT); - } - - @Override - public boolean canDelete(User user) - { - ExpProtocolImpl protocol = getProtocol(); - boolean isWorkflow = ExpProtocol.isSampleWorkflowProtocol(protocol.getLSID()); - if (isWorkflow && getContainer().hasPermission(user, SampleWorkflowDeletePermission.class)) - return true; - - // Issue 50776: To update lineage we need to delete existing runs - if ((ExperimentServiceImpl.get().isSampleAliquot(protocol) || ExperimentServiceImpl.get().isSampleDerivation(protocol)) && getContainer().hasPermission(user, UpdatePermission.class)) - return true; - - return !isWorkflow && getContainer().hasPermission(user, DeletePermission.class); - } - - // Clean up DataInput and MaterialInput exp.object and properties - private void deleteInputObjects(ExperimentServiceImpl svc, SqlDialect dialect) - { - SQLFragment materialSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + DataInput.lsidPrefix() + "'", - "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoDataInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", getRowId()); - - SQLFragment materialInputSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", - "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoMaterialInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", + getRowId()); - - SQLFragment dataSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + DataInput.lsidPrefix() + "'", - "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoDataInput() + " WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)", getRowId()); - - SQLFragment dataInputSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", - "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoMaterialInput() + " WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)", getRowId()); - - // Build a single UNION to help reduce DB round trips - SQLFragment unionSQL = new SQLFragment("(") - .append(materialSQL) - .append("\n UNION \n") - .append(materialInputSQL) - .append("\n UNION \n") - .append(dataSQL) - .append("\n UNION \n") - .append(dataInputSQL) - .append(")"); - - OntologyManager.deleteOntologyObjects(svc.getSchema(), unionSQL, getContainer()); - } - - private void deleteProtocolApplicationProvenance() - { - ProvenanceService pvs = ProvenanceService.get(); - pvs.deleteRunProvenance(getRowId()); - } - - private void deleteAppParametersAndInputs() - { - SQLFragment sql = new SQLFragment(); - sql.append("DELETE FROM exp.ProtocolApplicationParameter WHERE ProtocolApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); - - //per Josh: break relation between all datas with this run id and don't delete them - sql.append("UPDATE exp.Data SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); - sql.append("UPDATE exp.Material SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); - - sql.append("DELETE FROM exp.DataInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); - sql.append("DELETE FROM exp.MaterialInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); - sql.append("DELETE FROM exp.DataInput WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)").add(getRowId()).appendEOS(); - sql.append("DELETE FROM exp.MaterialInput WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)").add(getRowId()).appendEOS(); - - new SqlExecutor(getExpSchema()).execute(sql); - } - - private void deleteRunMaterials(User user) - { - for (ExpMaterial expMaterial : ExperimentServiceImpl.get().getExpMaterialsForRun(getRowId())) - { - expMaterial.delete(user); - } - } - - private void deleteRunProtocolApps() - { - new SqlExecutor(getExpSchema()).execute("DELETE FROM exp.ProtocolApplication WHERE RunId = ?", getRowId()); - } - - private synchronized void ensureFullyPopulated() - { - if (!_populated) - { - _populated = true; - ExperimentServiceImpl.get().populateRun(this); - Collections.sort(_materialOutputs); - Collections.sort(_dataOutputs); - - for (ExpProtocolApplicationImpl step : _protocolSteps) - { - Collections.sort(step.getInputDatas()); - Collections.sort(step.getOutputDatas()); - Collections.sort(step.getInputMaterials()); - Collections.sort(step.getOutputMaterials()); - } - } - } - - public void trimRunTree(Integer id, String type) throws ExperimentException - { - ensureUnlocked(); - List listPA = new ArrayList<>(); - List listM = new ArrayList<>(); - List listD = new ArrayList<>(); - Set ancestorPAStack = new LinkedHashSet<>(); - Set descendantPAStack = new LinkedHashSet<>(); - List apps = getProtocolApplications(); - - boolean found = false; - - // support focus on a starting material that is not part of the run - if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) - { - for (ExpMaterialImpl m : getMaterialInputs().keySet()) - if (m.getRowId() == id.intValue()) - { - found = true; - listM.add(m); - listPA.addAll(m.getSuccessorApps()); - descendantPAStack.addAll(m.getSuccessorApps()); - break; - } - } - if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) - { - for (ExpDataImpl d : getDataInputs().keySet()) - if (d.getRowId() == id.intValue()) - { - found = true; - listD.add(d); - listPA.addAll(d.getSuccessorApps()); - descendantPAStack.addAll(d.getSuccessorApps()); - break; - } - } - if (!found) - { - for (ExpProtocolApplicationImpl app : apps) - { - if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) - { - for (ExpMaterialImpl m : app.getOutputMaterials()) - if (m.getRowId() == id.intValue()) - { - found = true; - listM.add(m); - listPA.addAll(m.getSuccessorApps()); - descendantPAStack.addAll(m.getSuccessorApps()); - if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) - { - listPA.add(m.getSourceApplication()); - ancestorPAStack.add(m.getSourceApplication()); - } - break; - } - } - if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) - { - for (ExpDataImpl d : app.getOutputDatas()) - { - if (d.getRowId() == id.intValue()) - { - found = true; - listD.add(d); - listPA.addAll(d.getSuccessorApps()); - descendantPAStack.addAll(d.getSuccessorApps()); - if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) - { - listPA.add(d.getSourceApplication()); - ancestorPAStack.add(d.getSourceApplication()); - } - break; - } - } - } - if (type == null || DotGraph.TYPECODE_PROT_APP.equalsIgnoreCase(type)) - { - if (app.getRowId() == id.intValue()) - { - found = true; - listPA.add(app); - ancestorPAStack.add(app); - descendantPAStack.add(app); - break; - } - } - if (found) - break; - } - } - if (!found) - throw new ExperimentException("Specified node not found in Experiment Run"); - - int loopCount = 0; - while (!descendantPAStack.isEmpty()) - { - if (loopCount++ > 10000) - { - throw new IllegalStateException("Infinite loop detected for run " + getRowId()); - } - - ExpProtocolApplicationImpl pa = descendantPAStack.iterator().next(); - for (ExpMaterialImpl m : pa.getOutputMaterials()) - { - listM.add(m); - descendantPAStack.addAll(m.getSuccessorApps()); - } - for (ExpDataImpl d : pa.getOutputDatas()) - { - listD.add(d); - descendantPAStack.addAll(d.getSuccessorApps()); - } - descendantPAStack.remove(pa); - listPA.add(pa); - if (loopCount++ > 10000) - { - throw new IllegalStateException("Infinite loop detected for run " + getRowId()); - } - } - - loopCount = 0; - while (!ancestorPAStack.isEmpty()) - { - if (loopCount++ > 10000) - { - throw new IllegalStateException("Infinite loop detected for run " + getRowId()); - } - - ExpProtocolApplicationImpl pa = ancestorPAStack.iterator().next(); - if (pa.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun) - break; - for (ExpMaterialImpl m : pa.getInputMaterials()) - { - listM.add(m); - if (getMaterialInputs().containsKey(m)) - { - ExpProtocolApplication runNode = getProtocolApplications().get(0); - assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; - listPA.add(runNode); - continue; - } - if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) - ancestorPAStack.add(m.getSourceApplication()); - } - for (ExpDataImpl d : pa.getInputDatas()) - { - listD.add(d); - if (getDataInputs().containsKey(d)) - { - ExpProtocolApplication runNode = getProtocolApplications().get(0); - assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; - listPA.add(runNode); - continue; - } - if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) - ancestorPAStack.add(d.getSourceApplication()); - } - ancestorPAStack.remove(pa); - listPA.add(pa); - } - - List allPA = new ArrayList<>(); - List deletePA; - List deleteM; - List deleteD; - - setProtocolApplications(null); - - for (ExpProtocolApplicationImpl app : apps) - { - if (listPA.contains(app)) - { - allPA.add(app); - deleteM = new ArrayList<>(); - for (ExpMaterialImpl m : app.getInputMaterials()) - { - if (listM.contains(m)) - { - deletePA = new ArrayList<>(); - for (ExpProtocolApplicationImpl p : m.getSuccessorApps()) - if (!listPA.contains(p)) - deletePA.add(p); - for (ExpProtocolApplicationImpl p : deletePA) - m.getSuccessorApps().remove(p); - } - else - deleteM.add(m); - } - for (ExpMaterialImpl m : deleteM) - { - app.getInputMaterials().remove(m); - getMaterialInputs().remove(m); - } - - deleteD = new ArrayList<>(); - for (ExpDataImpl d : app.getInputDatas()) - { - if (listD.contains(d)) - { - deletePA = new ArrayList<>(); - for (ExpProtocolApplicationImpl p : d.getSuccessorApps()) - if (!listPA.contains(p)) - deletePA.add(p); - for (ExpProtocolApplicationImpl p : deletePA) - d.getSuccessorApps().remove(p); - } - else - deleteD.add(d); - } - for (ExpDataImpl d : deleteD) - { - app.getInputDatas().remove(d); - getDataInputs().remove(d); - } - - deleteM = new ArrayList<>(); - for (ExpMaterialImpl m : app.getOutputMaterials()) - { - if (!listM.contains(m)) - deleteM.add(m); - } - for (ExpMaterialImpl m : deleteM) - app.getOutputMaterials().remove(m); - - - deleteD = new ArrayList<>(); - for (ExpDataImpl d : app.getOutputDatas()) - { - if (!listD.contains(d)) - deleteD.add(d); - } - for (ExpDataImpl d : deleteD) - app.getOutputDatas().remove(d); - } - } - setProtocolApplications(allPA); - } - - @Override - public List getAllDataUsedByRun() - { - SQLFragment sql = new SQLFragment(); - sql.append("select d.* from "); - sql.append(ExperimentServiceImpl.get().getTinfoDataInput(), "di"); - sql.append(", "); - sql.append(ExperimentServiceImpl.get().getTinfoData(), "d"); - sql.append(", "); - sql.append(ExperimentServiceImpl.get().getTinfoProtocolApplication(), "pa"); - sql.append(" where di.targetapplicationid=pa.rowid and pa.runid=? and di.dataid=d.rowid"); - sql.add(getRowId()); - return ExpDataImpl.fromDatas(new SqlSelector(ExperimentServiceImpl.get().getSchema(), sql).getArrayList(Data.class)); - } - - public void clearCache() - { - _populated = false; - _dataInputs = new HashMap<>(); - _materialInputs = new HashMap<>(); - _materialOutputs = new ArrayList<>(); - _dataOutputs = new ArrayList<>(); - _protocolSteps = null; - } - - @Override - public void archiveDataFiles(User user) - { - try - { - PipeRoot pipeRoot = PipelineService.get().getPipelineRootSetting(getContainer()); - if (pipeRoot != null && pipeRoot.isValid()) - { - for (ExpData expData : getAllDataUsedByRun()) - { - File file = expData.getFile(); - // If we can find the file on disk, and it's in the assaydata directory or was created by this run, - // and there aren't any other usages, move it into an archived subdirectory. - if (NetworkDrive.exists(file) && file.isFile() && - (inAssayData(file) || isGeneratedByRun(expData)) && - !hasOtherRunUsing(expData, this)) - { - File archivedDir; - try - { - archivedDir = AssayFileWriter.ensureSubdirectory(getContainer(), AssayFileWriter.ARCHIVED_DIR_NAME).toNioPathForWrite().toFile(); - } - catch (ExperimentException e) - { - // In this case, the archived directory was not created correctly perhaps due to file permission or - // some other problem. This exception has been observed on production servers. The error is being - // ignored and the file is not archived. Archiving is a best attempt action. - LOG.warn("Unable to create an archive directory - discontinue archive and delete."); - return; - } - File targetFile = FileUtil.findUniqueFileName(file.getName(), archivedDir); - targetFile = FileUtil.getAbsoluteCaseSensitiveFile(targetFile); - FileUtils.moveFile(file, targetFile); - expData.setDataFileURI(targetFile.toURI()); - expData.save(user); - } - } - } - } - // Warn if the move fails for some reason (file is open / file deleted during archive) - catch (IOException e) - { - LOG.warn("Unable to archive file: " + e.getMessage()); - } - // Fail silently if the parent directory does not exist - archiving is a best effort action - catch (ExperimentException e) - { - LOG.warn("Unable to read parent directory: " + e.getMessage()); - } - } - - private boolean inAssayData(File file) throws ExperimentException - { - var uploadDir = AssayFileWriter.ensureUploadDirectory(getContainer()).toNioPathForWrite().toFile(); - return file.getParentFile().equals(uploadDir); - } - - /** - * Returns true if the ExpData is flagged as being generated by a run - * and the ExpData's source protocol application references this run. - */ - private boolean isGeneratedByRun(ExpData data) - { - // TODO: is using data.getRun() sufficient or must we check sourceApp.getRun() to see if the data was created by this run? - ExpProtocolApplication sourceApp = data.getSourceApplication(); - if (data.isGenerated() && sourceApp != null && this.equals(sourceApp.getRun())) - return true; - - return false; - } - - @Override - public void setCreated(Date created) - { - _object.setCreated(created); - } - - @Override - public void setCreatedBy(User user) - { - _object.setCreatedBy(user == null ? 0 : user.getUserId()); - } - - private boolean hasOtherRunUsing(ExpData originalData, ExpRun originalRun) - { - if (originalData.getDataFileUrl() != null) - { - for (ExpData data : ExperimentService.get().getAllExpDataByURL(originalData.getDataFileUrl(), null)) - { - for (ExpRun run : data.getTargetRuns()) - { - if (!run.equals(originalRun)) - { - return true; - } - } - } - } - return false; - } - - @Override - public void setWorkflowTaskId(@Nullable Long workflowTaskId) - { - _object.setWorkflowTask(workflowTaskId); - } - - @Override - public ExpProtocolApplication getWorkflowTask() - { - Long id = _object.getWorkflowTask(); - - if (id == null) { - return null; - } - - if (_workflowTask == null || _workflowTask.getRowId() != id.intValue()) - { - _workflowTask = ExperimentServiceImpl.get().getExpProtocolApplication(id); - } - - return _workflowTask; - } - - @Override - public void setWorkflowTask(ExpProtocolApplication workflowTask) - { - ensureUnlocked(); - - if (workflowTask == null) - _object.setWorkflowTask(null); - else - _object.setWorkflowTask(workflowTask.getRowId()); - } -} +/* + * Copyright (c) 2008-2019 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.labkey.experiment.api; + +import org.apache.commons.io.FileUtils; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.NotNull; +import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayFileWriter; +import org.labkey.api.cloud.CloudStoreService; +import org.labkey.api.data.Container; +import org.labkey.api.data.DbScope; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.SqlExecutor; +import org.labkey.api.data.SqlSelector; +import org.labkey.api.data.Table; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.TableSelector; +import org.labkey.api.data.dialect.SqlDialect; +import org.labkey.api.exp.ExperimentException; +import org.labkey.api.exp.ExperimentRunType; +import org.labkey.api.exp.OntologyManager; +import org.labkey.api.exp.api.DataType; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExpMaterial; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExpProtocolAction; +import org.labkey.api.exp.api.ExpProtocolApplication; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.exp.api.ProtocolImplementation; +import org.labkey.api.exp.api.ProvenanceService; +import org.labkey.api.exp.query.ExpRunTable; +import org.labkey.api.exp.query.ExpSchema; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineService; +import org.labkey.api.query.BatchValidationException; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryRowReference; +import org.labkey.api.security.User; +import org.labkey.api.security.permissions.DeletePermission; +import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; +import org.labkey.api.security.permissions.UpdatePermission; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.NetworkDrive; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.UnauthorizedException; +import org.labkey.experiment.DotGraph; +import org.labkey.experiment.ExperimentRunGraph; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Date; +import java.util.HashMap; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.labkey.experiment.api.ExperimentServiceImpl.getExpSchema; + +public class ExpRunImpl extends ExpIdentifiableEntityImpl implements ExpRun +{ + public static final String NAMESPACE_PREFIX = "Run"; + + private boolean _populated; + private List _protocolSteps; + private Map _materialInputs = new HashMap<>(); + private Map _dataInputs = new HashMap<>(); + private List _materialOutputs = new ArrayList<>(); + private List _dataOutputs = new ArrayList<>(); + private ExpRunImpl _replacedByRun; + private Integer _maxOutputActionSequence = null; + private static final Logger LOG = LogManager.getLogger(ExpRunImpl.class); + private ExpProtocolApplication _workflowTask; + + static public List fromRuns(List runs) + { + List ret = new ArrayList<>(runs.size()); + for (ExperimentRun run : runs) + { + ret.add(new ExpRunImpl(run)); + } + return ret; + } + + // For serialization + protected ExpRunImpl() {} + + public ExpRunImpl(ExperimentRun run) + { + super(run); + if (null != run && null != run.getObjectId()) + _objectId = run.getObjectId(); + } + + @Override + public ActionURL detailsURL() + { + return _object.detailsURL(); + } + + @Override + public @Nullable QueryRowReference getQueryRowReference() + { + ExpProtocol protocol = getProtocol(); + if (protocol != null) + { + ProtocolImplementation impl = protocol.getImplementation(); + if (impl != null) + { + QueryRowReference ref = impl.getQueryRowReference(protocol, this); + if (ref != null) + return ref; + } + + ExperimentRunType type = ExperimentService.get().getExperimentRunType(protocol); + if (type != null) + { + QueryRowReference ref = type.getQueryRowReference(protocol, this); + if (ref != null) + return ref; + } + } + + return new QueryRowReference(getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Runs.name(), FieldKey.fromParts(ExpRunTable.Column.RowId), getRowId()); + } + + @Override + public Container getContainer() + { + return _object.getContainer(); + } + + @Override + public long getRowId() + { + return _object.getRowId(); + } + + @Override + public List getExperiments() + { + final String sql= " SELECT E.* FROM " + ExperimentServiceImpl.get().getTinfoExperiment() + " E " + + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoRunList() + " RL ON (E.RowId = RL.ExperimentId) " + + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoExperimentRun() + " ER ON (ER.RowId = RL.ExperimentRunId) " + + " WHERE ER.LSID = ? AND E.Hidden = ?"; + + return ExpExperimentImpl.fromExperiments(new SqlSelector(getExpSchema(), sql, _object.getLSID(), Boolean.FALSE).getArray(Experiment.class)); + } + + @Override + public @Nullable ExpExperimentImpl getBatch() + { + if (_object.getBatchId() == null) + return null; + + ExpExperimentImpl batch = ExperimentServiceImpl.get().getExpExperiment(_object.getBatchId()); + if (batch == null) + return null; + + assert checkBatch(batch); + return batch; + } + + private boolean checkBatch(ExpExperimentImpl batch) + { + List exps = getExperiments(); + if (!exps.contains(batch)) + { + LOG.warn("Expected batch '" + batch.getRowId() + "' to be in list of experiments: " + exps); + return false; + } + + if (!getProtocol().equals(batch.getBatchProtocol())) + { + LOG.warn("Expected batch '" + batch.getRowId() + "' to have same protocol as run. Expected protocol '" + getProtocol() + "', but found '" + batch.getBatchProtocol() + "'"); + return false; + } + + return true; + } + + protected void setBatchId(Long batchId) + { + assert batchId == null || checkBatch(ExperimentServiceImpl.get().getExpExperiment(batchId)); + _object.setBatchId(batchId); + } + + @Override + public ExpProtocolImpl getProtocol() + { + return ExperimentServiceImpl.get().getExpProtocol(_object.getProtocolLSID()); + } + + @Override + public boolean isFinalOutput(ExpData data) + { + ExpProtocolApplication sourceApplication = data.getSourceApplication(); + return sourceApplication != null && sourceApplication.getActionSequence() == getMaxOutputActionSequence(); + } + + private int getMaxOutputActionSequence() + { + if (_maxOutputActionSequence == null) + { + _maxOutputActionSequence = 0; + for (ExpProtocolApplication app : getProtocolApplications()) + if (!app.getDataOutputs().isEmpty() && app.getActionSequence() > _maxOutputActionSequence) + _maxOutputActionSequence = app.getActionSequence(); + } + return _maxOutputActionSequence; + } + + @Override + public List getOutputDatas(@Nullable DataType type) + { + return ExperimentServiceImpl.get().getOutputDatas(getRowId(), type); + } + + @Override + public List getInputDatas(@Nullable String inputRole, @Nullable ExpProtocol.ApplicationType applicationType) + { + SQLFragment sql = new SQLFragment(); + sql.append("SELECT exp.Data.* FROM exp.Data WHERE exp.Data.RowId IN "); + sql.append("\n(SELECT exp.DataInput.DataId FROM exp.DataInput "); + sql.append("\nINNER JOIN exp.ProtocolApplication ON exp.DataInput.TargetApplicationId = exp.ProtocolApplication.RowId"); + sql.append("\nWHERE exp.ProtocolApplication.RunId = ?"); + sql.add(getRowId()); + if (inputRole != null) + { + sql.append("\nAND exp.DataInput.Role = ? "); + sql.add(inputRole); + } + if (applicationType != null) + { + sql.append("\nAND exp.ProtocolApplication.CpasType = "); + sql.appendValue(applicationType.toString()); + } + sql.append(")"); + return ExpDataImpl.fromDatas(new SqlSelector(ExperimentService.get().getSchema(), sql).getArrayList(Data.class)); + } + + @Override + public File getFilePathRoot() + { + if (_object.getFilePathRoot() == null || FileUtil.hasCloudScheme(_object.getFilePathRoot())) + return null; + else + return new File(FileUtil.createUri(_object.getFilePathRoot(), false)); + } + + @Override + public void setFilePathRoot(File file) + { + ensureUnlocked(); + // We want "/Users/..." for local file system + _object.setFilePathRoot(file == null ? null : file.toPath().toString()); + } + + @Override + public Path getFilePathRootPath() + { + if (_object.getFilePathRoot() == null) + return null; + else if (FileUtil.hasCloudScheme(_object.getFilePathRoot())) + return CloudStoreService.get().getPathFromUrl(getContainer(), _object.getFilePathRoot()); + else + return new File(FileUtil.createUri(_object.getFilePathRoot(), false)).toPath(); + } + + @Override + public void setFilePathRootPath(Path filePathRoot) + { + ensureUnlocked(); + _object.setFilePathRoot(filePathRoot == null ? null : + FileUtil.hasCloudScheme(filePathRoot) ? + FileUtil.pathToString(filePathRoot) : + filePathRoot.toString()); + } + + @Override + public void save(User user) throws BatchValidationException + { + ExperimentServiceImpl expService = ExperimentServiceImpl.get(); + try (DbScope.Transaction t = getExpSchema().getScope().ensureTransaction()) + { + boolean newRun = getRowId() == 0; + expService.onBeforeRunSaved(getProtocol(), this, getContainer(), user); + save(user, expService.getTinfoExperimentRun(), true); + if (newRun) + expService.auditRunEvent(user, this.getProtocol(), this, null, this.getProtocol().getName() + " run loaded"); + t.addCommitTask(() -> expService.onAfterRunSaved(getProtocol(), this, getContainer(), user), DbScope.CommitTaskOption.POSTCOMMIT); + t.commit(); + } + } + + @Override + protected void save(User user, TableInfo table, boolean ensureObject) + { + assert ensureObject; + super.save(user, table, true); + ExperimentServiceImpl.get().invalidateExperimentRun(getLSID()); + } + + @Override + public void delete(User user) + { + delete(user, null); + } + + @Override + public void delete(User user, @Nullable final String auditUserComment) + { + if (!canDelete(user)) + { + throw new UnauthorizedException(); + } + ExperimentServiceImpl.get().deleteExperimentRuns(getContainer(), user, auditUserComment, Arrays.asList(this), null); + } + + @Override + public void setProtocol(ExpProtocol protocol) + { + _object.setProtocolLSID(protocol.getLSID()); + } + + @Override + public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name) + { + return addProtocolApplication(user, action, appType, name, null, null, null); + } + + public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name, java.util.Date startTime, java.util.Date endTime, Integer recordCount) + { + ensureUnlocked(); + ProtocolApplication pa = new ProtocolApplication(); + if (action == null) + { + if (appType != ExpProtocol.ApplicationType.ExperimentRun) + { + throw new IllegalArgumentException("Only the ExperimentRun protocol application type is allowed to have a null protocol action."); + } + pa.setProtocolLSID(getProtocol().getLSID()); + } + else + { + pa.setProtocolLSID(action.getChildProtocol().getLSID()); + pa.setActionSequence(action.getActionSequence()); + } + pa.setName(name); + pa.setLSID(ExperimentService.get().generateGuidLSID(getContainer(), ExpProtocolApplication.class)); + pa.setCpasType(appType.toString()); + pa.setRunId(getRowId()); + pa.setStartTime(startTime); + pa.setEndTime(endTime); + pa.setRecordCount(recordCount); + + pa = Table.insert(user, ExperimentServiceImpl.get().getTinfoProtocolApplication(), pa); + return new ExpProtocolApplicationImpl(pa); + } + + @Override + public String getComments() + { + return _object.getComments(); + } + + @Override + public void setComments(String comments) + { + ensureUnlocked(); + _object.setComments(comments); + } + + @Override + public void setEntityId(String entityId) + { + ensureUnlocked(); + _object.setEntityId(entityId); + } + + @Override + public String getEntityId() + { + return _object.getEntityId(); + } + + + @Override + public void setContainer(Container container) + { + _object.setContainer(container); + } + + @Override + public void setJobId(Long jobId) + { + ensureUnlocked(); + _object.setJobId(jobId); + } + + @Override + public Long getJobId() + { + return _object.getJobId(); + } + + public void setProtocolApplications(List protocolSteps) + { + ensureUnlocked(); + _protocolSteps = protocolSteps; + } + + @Override + public @NotNull Map getMaterialInputs() + { + ensureFullyPopulated(); + return _materialInputs; + } + + @Override + public @NotNull Map getDataInputs() + { + ensureFullyPopulated(); + return _dataInputs; + } + + @Override + public List getMaterialOutputs() + { + ensureFullyPopulated(); + return _materialOutputs; + } + + @Override + public List getDataOutputs() + { + ensureFullyPopulated(); + return _dataOutputs; + } + + @Override + public List getProtocolApplications() + { + ensureFullyPopulated(); + return _protocolSteps; + } + + @Override + public @Nullable ExpProtocolApplication getProtocolApplication() + { + return findProtocolApplication(ExpProtocol.ApplicationType.ProtocolApplication); + } + + @Override + public @Nullable ExpProtocolApplication getInputProtocolApplication() + { + return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRun); + } + + private @Nullable ExpProtocolApplication findProtocolApplication(ExpProtocol.ApplicationType type) + { + for (ExpProtocolApplicationImpl expProtocolApplication : getProtocolApplications()) + { + if (type.equals(expProtocolApplication.getApplicationType())) + { + return expProtocolApplication; + } + } + return null; + } + + @Override + public @Nullable ExpProtocolApplication getOutputProtocolApplication() + { + return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRunOutput); + } + + @Override + public void deleteProtocolApplications(User user) + { + ensureUnlocked(); + deleteProtocolApplications(getOutputDatas(null), user); + } + + @Override + public void setReplacedByRun(ExpRun run) + { + ensureUnlocked(); + if (run != null && run.getRowId() < 1) + { + throw new IllegalArgumentException("Run must have already been saved to the database"); + } + _object.setReplacedByRunId(run == null ? null : run.getRowId()); + } + + @Override + public ExpRun getReplacedByRun() + { + Long id = _object.getReplacedByRunId(); + if (id == null) + { + return null; + } + if (_replacedByRun == null || _replacedByRun.getRowId() != id.intValue()) + { + _replacedByRun = ExperimentServiceImpl.get().getExpRun(id.intValue()); + } + return _replacedByRun; + } + + @Override + public List getReplacesRuns() + { + return fromRuns(new TableSelector(ExperimentServiceImpl.get().getTinfoExperimentRun(), new SimpleFilter(FieldKey.fromParts("ReplacedByRunId"), getRowId()), new Sort("Name")).getArrayList(ExperimentRun.class)); + } + + public void deleteProtocolApplications(List datasToDelete, User user) + { + if (user == null || !canDelete(user)) + { + throw new UnauthorizedException("Attempting to delete an ExperimentRun without having delete permissions for its container"); + } + final ExperimentServiceImpl svc = ExperimentServiceImpl.get(); + final SqlDialect dialect = svc.getSchema().getSqlDialect(); + + svc.invalidateExperimentRun(getLSID()); + + deleteProtocolApplicationProvenance(); + + svc.beforeDeleteData(user, getContainer(), datasToDelete); + + deleteInputObjects(svc, dialect); + + deleteAppParametersAndInputs(); + + deleteRunMaterials(user); + + deleteRunProtocolApps(); + + clearCache(); + + // Clear the cache in a commit task, which allows us to do a single clear (which is semi-expensive) if multiple + // runs are being deleted in the same transaction, like deleting a container + svc.getSchema().getScope().addCommitTask(ExperimentRunGraph.getCacheClearingCommitTask(getContainer()), DbScope.CommitTaskOption.POSTCOMMIT); + } + + @Override + public boolean canDelete(User user) + { + ExpProtocolImpl protocol = getProtocol(); + boolean isWorkflow = ExpProtocol.isSampleWorkflowProtocol(protocol.getLSID()); + if (isWorkflow && getContainer().hasPermission(user, SampleWorkflowDeletePermission.class)) + return true; + + // Issue 50776: To update lineage we need to delete existing runs + if ((ExperimentServiceImpl.get().isSampleAliquot(protocol) || ExperimentServiceImpl.get().isSampleDerivation(protocol)) && getContainer().hasPermission(user, UpdatePermission.class)) + return true; + + return !isWorkflow && getContainer().hasPermission(user, DeletePermission.class); + } + + // Clean up DataInput and MaterialInput exp.object and properties + private void deleteInputObjects(ExperimentServiceImpl svc, SqlDialect dialect) + { + SQLFragment materialSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + DataInput.lsidPrefix() + "'", + "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoDataInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", getRowId()); + + SQLFragment materialInputSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", + "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoMaterialInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", + getRowId()); + + SQLFragment dataSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + DataInput.lsidPrefix() + "'", + "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoDataInput() + " WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)", getRowId()); + + SQLFragment dataInputSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", + "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoMaterialInput() + " WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)", getRowId()); + + // Build a single UNION to help reduce DB round trips + SQLFragment unionSQL = new SQLFragment("(") + .append(materialSQL) + .append("\n UNION \n") + .append(materialInputSQL) + .append("\n UNION \n") + .append(dataSQL) + .append("\n UNION \n") + .append(dataInputSQL) + .append(")"); + + OntologyManager.deleteOntologyObjects(svc.getSchema(), unionSQL, getContainer()); + } + + private void deleteProtocolApplicationProvenance() + { + ProvenanceService pvs = ProvenanceService.get(); + pvs.deleteRunProvenance(getRowId()); + } + + private void deleteAppParametersAndInputs() + { + SQLFragment sql = new SQLFragment(); + sql.append("DELETE FROM exp.ProtocolApplicationParameter WHERE ProtocolApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); + + //per Josh: break relation between all datas with this run id and don't delete them + sql.append("UPDATE exp.Data SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); + sql.append("UPDATE exp.Material SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); + + sql.append("DELETE FROM exp.DataInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); + sql.append("DELETE FROM exp.MaterialInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); + sql.append("DELETE FROM exp.DataInput WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)").add(getRowId()).appendEOS(); + sql.append("DELETE FROM exp.MaterialInput WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)").add(getRowId()).appendEOS(); + + new SqlExecutor(getExpSchema()).execute(sql); + } + + private void deleteRunMaterials(User user) + { + for (ExpMaterial expMaterial : ExperimentServiceImpl.get().getExpMaterialsForRun(getRowId())) + { + expMaterial.delete(user); + } + } + + private void deleteRunProtocolApps() + { + new SqlExecutor(getExpSchema()).execute("DELETE FROM exp.ProtocolApplication WHERE RunId = ?", getRowId()); + } + + private synchronized void ensureFullyPopulated() + { + if (!_populated) + { + _populated = true; + ExperimentServiceImpl.get().populateRun(this); + Collections.sort(_materialOutputs); + Collections.sort(_dataOutputs); + + for (ExpProtocolApplicationImpl step : _protocolSteps) + { + Collections.sort(step.getInputDatas()); + Collections.sort(step.getOutputDatas()); + Collections.sort(step.getInputMaterials()); + Collections.sort(step.getOutputMaterials()); + } + } + } + + public void trimRunTree(Integer id, String type) throws ExperimentException + { + ensureUnlocked(); + List listPA = new ArrayList<>(); + List listM = new ArrayList<>(); + List listD = new ArrayList<>(); + Set ancestorPAStack = new LinkedHashSet<>(); + Set descendantPAStack = new LinkedHashSet<>(); + List apps = getProtocolApplications(); + + boolean found = false; + + // support focus on a starting material that is not part of the run + if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) + { + for (ExpMaterialImpl m : getMaterialInputs().keySet()) + if (m.getRowId() == id.intValue()) + { + found = true; + listM.add(m); + listPA.addAll(m.getSuccessorApps()); + descendantPAStack.addAll(m.getSuccessorApps()); + break; + } + } + if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) + { + for (ExpDataImpl d : getDataInputs().keySet()) + if (d.getRowId() == id.intValue()) + { + found = true; + listD.add(d); + listPA.addAll(d.getSuccessorApps()); + descendantPAStack.addAll(d.getSuccessorApps()); + break; + } + } + if (!found) + { + for (ExpProtocolApplicationImpl app : apps) + { + if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) + { + for (ExpMaterialImpl m : app.getOutputMaterials()) + if (m.getRowId() == id.intValue()) + { + found = true; + listM.add(m); + listPA.addAll(m.getSuccessorApps()); + descendantPAStack.addAll(m.getSuccessorApps()); + if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) + { + listPA.add(m.getSourceApplication()); + ancestorPAStack.add(m.getSourceApplication()); + } + break; + } + } + if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) + { + for (ExpDataImpl d : app.getOutputDatas()) + { + if (d.getRowId() == id.intValue()) + { + found = true; + listD.add(d); + listPA.addAll(d.getSuccessorApps()); + descendantPAStack.addAll(d.getSuccessorApps()); + if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) + { + listPA.add(d.getSourceApplication()); + ancestorPAStack.add(d.getSourceApplication()); + } + break; + } + } + } + if (type == null || DotGraph.TYPECODE_PROT_APP.equalsIgnoreCase(type)) + { + if (app.getRowId() == id.intValue()) + { + found = true; + listPA.add(app); + ancestorPAStack.add(app); + descendantPAStack.add(app); + break; + } + } + if (found) + break; + } + } + if (!found) + throw new ExperimentException("Specified node not found in Experiment Run"); + + int loopCount = 0; + while (!descendantPAStack.isEmpty()) + { + if (loopCount++ > 10000) + { + throw new IllegalStateException("Infinite loop detected for run " + getRowId()); + } + + ExpProtocolApplicationImpl pa = descendantPAStack.iterator().next(); + for (ExpMaterialImpl m : pa.getOutputMaterials()) + { + listM.add(m); + descendantPAStack.addAll(m.getSuccessorApps()); + } + for (ExpDataImpl d : pa.getOutputDatas()) + { + listD.add(d); + descendantPAStack.addAll(d.getSuccessorApps()); + } + descendantPAStack.remove(pa); + listPA.add(pa); + if (loopCount++ > 10000) + { + throw new IllegalStateException("Infinite loop detected for run " + getRowId()); + } + } + + loopCount = 0; + while (!ancestorPAStack.isEmpty()) + { + if (loopCount++ > 10000) + { + throw new IllegalStateException("Infinite loop detected for run " + getRowId()); + } + + ExpProtocolApplicationImpl pa = ancestorPAStack.iterator().next(); + if (pa.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun) + break; + for (ExpMaterialImpl m : pa.getInputMaterials()) + { + listM.add(m); + if (getMaterialInputs().containsKey(m)) + { + ExpProtocolApplication runNode = getProtocolApplications().get(0); + assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; + listPA.add(runNode); + continue; + } + if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) + ancestorPAStack.add(m.getSourceApplication()); + } + for (ExpDataImpl d : pa.getInputDatas()) + { + listD.add(d); + if (getDataInputs().containsKey(d)) + { + ExpProtocolApplication runNode = getProtocolApplications().get(0); + assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; + listPA.add(runNode); + continue; + } + if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) + ancestorPAStack.add(d.getSourceApplication()); + } + ancestorPAStack.remove(pa); + listPA.add(pa); + } + + List allPA = new ArrayList<>(); + List deletePA; + List deleteM; + List deleteD; + + setProtocolApplications(null); + + for (ExpProtocolApplicationImpl app : apps) + { + if (listPA.contains(app)) + { + allPA.add(app); + deleteM = new ArrayList<>(); + for (ExpMaterialImpl m : app.getInputMaterials()) + { + if (listM.contains(m)) + { + deletePA = new ArrayList<>(); + for (ExpProtocolApplicationImpl p : m.getSuccessorApps()) + if (!listPA.contains(p)) + deletePA.add(p); + for (ExpProtocolApplicationImpl p : deletePA) + m.getSuccessorApps().remove(p); + } + else + deleteM.add(m); + } + for (ExpMaterialImpl m : deleteM) + { + app.getInputMaterials().remove(m); + getMaterialInputs().remove(m); + } + + deleteD = new ArrayList<>(); + for (ExpDataImpl d : app.getInputDatas()) + { + if (listD.contains(d)) + { + deletePA = new ArrayList<>(); + for (ExpProtocolApplicationImpl p : d.getSuccessorApps()) + if (!listPA.contains(p)) + deletePA.add(p); + for (ExpProtocolApplicationImpl p : deletePA) + d.getSuccessorApps().remove(p); + } + else + deleteD.add(d); + } + for (ExpDataImpl d : deleteD) + { + app.getInputDatas().remove(d); + getDataInputs().remove(d); + } + + deleteM = new ArrayList<>(); + for (ExpMaterialImpl m : app.getOutputMaterials()) + { + if (!listM.contains(m)) + deleteM.add(m); + } + for (ExpMaterialImpl m : deleteM) + app.getOutputMaterials().remove(m); + + + deleteD = new ArrayList<>(); + for (ExpDataImpl d : app.getOutputDatas()) + { + if (!listD.contains(d)) + deleteD.add(d); + } + for (ExpDataImpl d : deleteD) + app.getOutputDatas().remove(d); + } + } + setProtocolApplications(allPA); + } + + @Override + public List getAllDataUsedByRun() + { + SQLFragment sql = new SQLFragment(); + sql.append("select d.* from "); + sql.append(ExperimentServiceImpl.get().getTinfoDataInput(), "di"); + sql.append(", "); + sql.append(ExperimentServiceImpl.get().getTinfoData(), "d"); + sql.append(", "); + sql.append(ExperimentServiceImpl.get().getTinfoProtocolApplication(), "pa"); + sql.append(" where di.targetapplicationid=pa.rowid and pa.runid=? and di.dataid=d.rowid"); + sql.add(getRowId()); + return ExpDataImpl.fromDatas(new SqlSelector(ExperimentServiceImpl.get().getSchema(), sql).getArrayList(Data.class)); + } + + public void clearCache() + { + _populated = false; + _dataInputs = new HashMap<>(); + _materialInputs = new HashMap<>(); + _materialOutputs = new ArrayList<>(); + _dataOutputs = new ArrayList<>(); + _protocolSteps = null; + } + + @Override + public void archiveDataFiles(User user) + { + try + { + PipeRoot pipeRoot = PipelineService.get().getPipelineRootSetting(getContainer()); + if (pipeRoot != null && pipeRoot.isValid()) + { + for (ExpData expData : getAllDataUsedByRun()) + { + File file = expData.getFile(); + // If we can find the file on disk, and it's in the assaydata directory or was created by this run, + // and there aren't any other usages, move it into an archived subdirectory. + if (NetworkDrive.exists(file) && file.isFile() && + (inAssayData(file) || isGeneratedByRun(expData)) && + !hasOtherRunUsing(expData, this)) + { + File archivedDir; + try + { + archivedDir = AssayFileWriter.ensureSubdirectory(getContainer(), AssayFileWriter.ARCHIVED_DIR_NAME).toNioPathForWrite().toFile(); + } + catch (ExperimentException e) + { + // In this case, the archived directory was not created correctly perhaps due to file permission or + // some other problem. This exception has been observed on production servers. The error is being + // ignored and the file is not archived. Archiving is a best attempt action. + LOG.warn("Unable to create an archive directory - discontinue archive and delete."); + return; + } + File targetFile = FileUtil.findUniqueFileName(file.getName(), archivedDir); + targetFile = FileUtil.getAbsoluteCaseSensitiveFile(targetFile); + FileUtils.moveFile(file, targetFile); + expData.setDataFileURI(targetFile.toURI()); + expData.save(user); + } + } + } + } + // Warn if the move fails for some reason (file is open / file deleted during archive) + catch (IOException e) + { + LOG.warn("Unable to archive file: " + e.getMessage()); + } + // Fail silently if the parent directory does not exist - archiving is a best effort action + catch (ExperimentException e) + { + LOG.warn("Unable to read parent directory: " + e.getMessage()); + } + } + + private boolean inAssayData(File file) throws ExperimentException + { + var uploadDir = AssayFileWriter.ensureUploadDirectory(getContainer()).toNioPathForWrite().toFile(); + return file.getParentFile().equals(uploadDir); + } + + /** + * Returns true if the ExpData is flagged as being generated by a run + * and the ExpData's source protocol application references this run. + */ + private boolean isGeneratedByRun(ExpData data) + { + // TODO: is using data.getRun() sufficient or must we check sourceApp.getRun() to see if the data was created by this run? + ExpProtocolApplication sourceApp = data.getSourceApplication(); + if (data.isGenerated() && sourceApp != null && this.equals(sourceApp.getRun())) + return true; + + return false; + } + + @Override + public void setCreated(Date created) + { + _object.setCreated(created); + } + + @Override + public void setCreatedBy(User user) + { + _object.setCreatedBy(user == null ? 0 : user.getUserId()); + } + + private boolean hasOtherRunUsing(ExpData originalData, ExpRun originalRun) + { + if (originalData.getDataFileUrl() != null) + { + for (ExpData data : ExperimentService.get().getAllExpDataByURL(originalData.getDataFileUrl(), null)) + { + for (ExpRun run : data.getTargetRuns()) + { + if (!run.equals(originalRun)) + { + return true; + } + } + } + } + return false; + } + + @Override + public void setWorkflowTaskId(@Nullable Long workflowTaskId) + { + _object.setWorkflowTask(workflowTaskId); + } + + @Override + public ExpProtocolApplication getWorkflowTask() + { + Long id = _object.getWorkflowTask(); + + if (id == null) { + return null; + } + + if (_workflowTask == null || _workflowTask.getRowId() != id.intValue()) + { + _workflowTask = ExperimentServiceImpl.get().getExpProtocolApplication(id); + } + + return _workflowTask; + } + + @Override + public void setWorkflowTask(ExpProtocolApplication workflowTask) + { + ensureUnlocked(); + + if (workflowTask == null) + _object.setWorkflowTask(null); + else + _object.setWorkflowTask(workflowTask.getRowId()); + } +} diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java index 16128c1d2cb..e3bc1bbb24b 100644 --- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java @@ -4201,22 +4201,28 @@ public Lsid getDataClassLsid(Container container) @Override public void deleteExperimentRunsByRowIds(Container container, final User user, long... runRowIds) { - deleteExperimentRunsByRowIds(container, user, null, Arrays.stream(runRowIds).boxed().toList()); + deleteExperimentRunsByRowIds(container, user, null, Arrays.stream(runRowIds).boxed().toList(), null); } @Override - public void deleteExperimentRunsByRowIds(Container container, final User user, @Nullable final String userComment, @NotNull Collection runRowIds) + public void deleteExperimentRunsByRowIds(Container container, final User user, @Nullable final String userComment, @NotNull Collection runRowIds, @Nullable Map transactionDetails) { - deleteExperimentRuns(container, user, userComment, getExpRuns(runRowIds)); + deleteExperimentRuns(container, user, userComment, getExpRuns(runRowIds), transactionDetails); } - public void deleteExperimentRuns(Container container, final User user, @Nullable final String userComment, @NotNull Collection runs) + public void deleteExperimentRuns(Container container, final User user, @Nullable final String userComment, @NotNull Collection runs, @Nullable Map transactionDetails) { if (runs.isEmpty()) return; try (DbScope.Transaction transaction = ensureTransaction()) { + if (transaction.getAuditEvent() == null) + { + TransactionAuditProvider.TransactionAuditEvent auditEvent = AbstractQueryUpdateService.createTransactionAuditEvent(container, QueryService.AuditAction.DELETE, transactionDetails); + AbstractQueryUpdateService.addTransactionAuditEvent(transaction, user, auditEvent); + } + AssayService assayService = AssayService.get(); // This can be slightly expensive to fetch, so don't do it multiple times if runs share protocols Map protocolImpls = new HashMap<>(); @@ -5096,13 +5102,13 @@ private void deleteRunsUsingInputs(User user, Collection dataItems, Collec if (containers.size() == 1) { Container runContainer = containers.iterator().next(); - deleteExperimentRuns(runContainer, user, null, runsToDelete); + deleteExperimentRuns(runContainer, user, null, runsToDelete, null); } else { // the slow way for (ExpRunImpl run : runsToDelete) - deleteExperimentRuns(run.getContainer(), user, null, Collections.singleton(run)); + deleteExperimentRuns(run.getContainer(), user, null, Collections.singleton(run), null); } } diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java index 945b103cf84..8bb65850ca3 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java @@ -1,8344 +1,8349 @@ -/* - * Copyright (c) 2008-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.labkey.experiment.controllers.exp; - -import jakarta.servlet.ServletException; -import jakarta.servlet.http.HttpServletRequest; -import jakarta.servlet.http.HttpServletResponse; -import jakarta.servlet.http.HttpSession; -import org.apache.commons.collections4.MapUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.lang3.Strings; -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; -import org.apache.poi.ss.usermodel.Workbook; -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.json.JSONArray; -import org.json.JSONException; -import org.json.JSONObject; -import org.labkey.api.action.ApiJsonWriter; -import org.labkey.api.action.ApiResponse; -import org.labkey.api.action.ApiSimpleResponse; -import org.labkey.api.action.ApiUsageException; -import org.labkey.api.action.ExportAction; -import org.labkey.api.action.FormHandlerAction; -import org.labkey.api.action.FormViewAction; -import org.labkey.api.action.HasViewContext; -import org.labkey.api.action.Marshal; -import org.labkey.api.action.Marshaller; -import org.labkey.api.action.MutatingApiAction; -import org.labkey.api.action.QueryViewAction; -import org.labkey.api.action.ReadOnlyApiAction; -import org.labkey.api.action.ReturnUrlForm; -import org.labkey.api.action.SimpleApiJsonForm; -import org.labkey.api.action.SimpleErrorView; -import org.labkey.api.action.SimpleResponse; -import org.labkey.api.action.SimpleViewAction; -import org.labkey.api.action.SpringActionController; -import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.actions.UploadWizardAction; -import org.labkey.api.assay.security.DesignAssayPermission; -import org.labkey.api.attachments.AttachmentParent; -import org.labkey.api.attachments.AttachmentService; -import org.labkey.api.attachments.BaseDownloadAction; -import org.labkey.api.audit.AbstractAuditTypeProvider; -import org.labkey.api.audit.AuditLogService; -import org.labkey.api.audit.DetailedAuditTypeEvent; -import org.labkey.api.audit.SampleTimelineAuditEvent; -import org.labkey.api.audit.TransactionAuditProvider; -import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.labkey.api.collections.CaseInsensitiveHashSet; -import org.labkey.api.collections.LongHashMap; -import org.labkey.api.data.ActionButton; -import org.labkey.api.data.BaseColumnInfo; -import org.labkey.api.data.ButtonBar; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.DataRegion; -import org.labkey.api.data.DataRegionSelection; -import org.labkey.api.data.DbSchema; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.DisplayColumn; -import org.labkey.api.data.ExcelWriter; -import org.labkey.api.data.MenuButton; -import org.labkey.api.data.NameGenerator; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.ShowRows; -import org.labkey.api.data.SimpleDisplayColumn; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.TSVJSONWriter; -import org.labkey.api.data.TSVWriter; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; -import org.labkey.api.dataiterator.DataIteratorContext; -import org.labkey.api.exp.AbstractParameter; -import org.labkey.api.exp.DeleteForm; -import org.labkey.api.exp.DuplicateMaterialException; -import org.labkey.api.exp.ExperimentDataHandler; -import org.labkey.api.exp.ExperimentException; -import org.labkey.api.exp.ExperimentRunForm; -import org.labkey.api.exp.ExperimentRunListView; -import org.labkey.api.exp.ExperimentRunType; -import org.labkey.api.exp.Identifiable; -import org.labkey.api.exp.Lsid; -import org.labkey.api.exp.LsidManager; -import org.labkey.api.exp.LsidType; -import org.labkey.api.exp.ObjectProperty; -import org.labkey.api.exp.OntologyManager; -import org.labkey.api.exp.ProtocolApplicationParameter; -import org.labkey.api.exp.XarContext; -import org.labkey.api.exp.api.DataClassDomainKindProperties; -import org.labkey.api.exp.api.ExpData; -import org.labkey.api.exp.api.ExpDataClass; -import org.labkey.api.exp.api.ExpExperiment; -import org.labkey.api.exp.api.ExpLineageOptions; -import org.labkey.api.exp.api.ExpMaterial; -import org.labkey.api.exp.api.ExpMaterialRunInput; -import org.labkey.api.exp.api.ExpObject; -import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.exp.api.ExpProtocolApplication; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.api.ExpRunAttachmentParent; -import org.labkey.api.exp.api.ExpRunEditor; -import org.labkey.api.exp.api.ExpRunItem; -import org.labkey.api.exp.api.ExpSampleType; -import org.labkey.api.exp.api.ExperimentJSONConverter; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ExperimentUrls; -import org.labkey.api.exp.api.NameExpressionOptionService; -import org.labkey.api.exp.api.ResolveLsidsForm; -import org.labkey.api.exp.api.SampleTypeDomainKind; -import org.labkey.api.exp.api.SampleTypeService; -import org.labkey.api.exp.list.ListService; -import org.labkey.api.exp.property.Domain; -import org.labkey.api.exp.property.DomainAuditProvider; -import org.labkey.api.exp.property.DomainKind; -import org.labkey.api.exp.property.DomainProperty; -import org.labkey.api.exp.property.DomainTemplate; -import org.labkey.api.exp.property.DomainTemplateGroup; -import org.labkey.api.exp.property.DomainUtil; -import org.labkey.api.exp.property.PropertyService; -import org.labkey.api.exp.query.ExpDataProtocolInputTable; -import org.labkey.api.exp.query.ExpInputTable; -import org.labkey.api.exp.query.ExpMaterialProtocolInputTable; -import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.exp.query.SamplesSchema; -import org.labkey.api.exp.xar.LSIDRelativizer; -import org.labkey.api.exp.xar.LsidUtils; -import org.labkey.api.files.FileContentService; -import org.labkey.api.gwt.client.AuditBehaviorType; -import org.labkey.api.inventory.InventoryService; -import org.labkey.api.module.ModuleHtmlView; -import org.labkey.api.module.ModuleLoader; -import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.pipeline.PipelineStatusFile; -import org.labkey.api.pipeline.PipelineUrls; -import org.labkey.api.pipeline.PipelineValidationException; -import org.labkey.api.qc.SampleStatusService; -import org.labkey.api.query.AbstractQueryImportAction; -import org.labkey.api.query.BatchValidationException; -import org.labkey.api.query.DetailsURL; -import org.labkey.api.query.DuplicateKeyException; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryAction; -import org.labkey.api.query.QueryDefinition; -import org.labkey.api.query.QueryException; -import org.labkey.api.query.QueryForm; -import org.labkey.api.query.QueryParam; -import org.labkey.api.query.QueryService; -import org.labkey.api.query.QuerySettings; -import org.labkey.api.query.QueryUpdateForm; -import org.labkey.api.query.QueryUpdateService; -import org.labkey.api.query.QueryUpdateServiceException; -import org.labkey.api.query.QueryView; -import org.labkey.api.query.SchemaKey; -import org.labkey.api.query.UserSchema; -import org.labkey.api.query.UserSchemaAction; -import org.labkey.api.reader.ColumnDescriptor; -import org.labkey.api.reader.DataLoader; -import org.labkey.api.reader.DataLoaderFactory; -import org.labkey.api.reader.ExcelFactory; -import org.labkey.api.search.SearchService; -import org.labkey.api.security.ActionNames; -import org.labkey.api.security.RequiresAnyOf; -import org.labkey.api.security.RequiresNoPermission; -import org.labkey.api.security.RequiresPermission; -import org.labkey.api.security.SecurableResource; -import org.labkey.api.security.User; -import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.security.permissions.DesignDataClassPermission; -import org.labkey.api.security.permissions.DesignSampleTypePermission; -import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.security.permissions.Permission; -import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; -import org.labkey.api.security.permissions.SiteAdminPermission; -import org.labkey.api.security.permissions.TroubleshooterPermission; -import org.labkey.api.security.permissions.UpdatePermission; -import org.labkey.api.settings.AppProps; -import org.labkey.api.settings.ConceptURIProperties; -import org.labkey.api.sql.LabKeySql; -import org.labkey.api.study.Dataset; -import org.labkey.api.study.StudyService; -import org.labkey.api.study.StudyUrls; -import org.labkey.api.study.publish.StudyPublishService; -import org.labkey.api.usageMetrics.SimpleMetricsService; -import org.labkey.api.util.DOM; -import org.labkey.api.util.DOM.LK; -import org.labkey.api.util.ErrorRenderer; -import org.labkey.api.util.ExceptionUtil; -import org.labkey.api.util.FileStream; -import org.labkey.api.util.FileUtil; -import org.labkey.api.util.HtmlString; -import org.labkey.api.util.HtmlStringBuilder; -import org.labkey.api.util.ImageUtil; -import org.labkey.api.util.JSoupUtil; -import org.labkey.api.util.LinkBuilder; -import org.labkey.api.util.NetworkDrive; -import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.util.Pair; -import org.labkey.api.util.ResponseHelper; -import org.labkey.api.util.SafeToRender; -import org.labkey.api.util.SessionHelper; -import org.labkey.api.util.StringExpression; -import org.labkey.api.util.StringUtilsLabKey; -import org.labkey.api.util.URLHelper; -import org.labkey.api.util.UniqueID; -import org.labkey.api.util.CsrfInput; -import org.labkey.api.view.ActionURL; -import org.labkey.api.view.BadRequestException; -import org.labkey.api.view.DataView; -import org.labkey.api.view.DataViewSnapshotSelectionForm; -import org.labkey.api.view.DetailsView; -import org.labkey.api.view.HBox; -import org.labkey.api.view.HtmlView; -import org.labkey.api.view.HttpView; -import org.labkey.api.view.InsertView; -import org.labkey.api.view.JspView; -import org.labkey.api.view.NavTree; -import org.labkey.api.view.NotFoundException; -import org.labkey.api.view.RedirectException; -import org.labkey.api.view.UnauthorizedException; -import org.labkey.api.view.UpdateView; -import org.labkey.api.view.VBox; -import org.labkey.api.view.ViewBackgroundInfo; -import org.labkey.api.view.ViewContext; -import org.labkey.api.view.ViewServlet; -import org.labkey.api.view.WebPartView; -import org.labkey.api.view.template.ClientDependency; -import org.labkey.api.view.template.PageConfig; -import org.labkey.experiment.ChooseExperimentTypeBean; -import org.labkey.experiment.ConfirmDeleteView; -import org.labkey.experiment.CustomPropertiesView; -import org.labkey.experiment.DataClassWebPart; -import org.labkey.experiment.DerivedSamplePropertyHelper; -import org.labkey.experiment.DotGraph; -import org.labkey.experiment.ExpDataFileListener; -import org.labkey.experiment.ExperimentRunDisplayColumn; -import org.labkey.experiment.ExperimentRunGraph; -import org.labkey.experiment.LineageGraphDisplayColumn; -import org.labkey.experiment.MissingFilesCheckInfo; -import org.labkey.experiment.MoveRunsBean; -import org.labkey.experiment.ParentChildView; -import org.labkey.experiment.ProtocolApplicationDisplayColumn; -import org.labkey.experiment.ProtocolDisplayColumn; -import org.labkey.experiment.ProtocolWebPart; -import org.labkey.experiment.RunGroupWebPart; -import org.labkey.experiment.SampleTypeDisplayColumn; -import org.labkey.experiment.SampleTypeWebPart; -import org.labkey.experiment.StandardAndCustomPropertiesView; -import org.labkey.experiment.XarExportPipelineJob; -import org.labkey.experiment.XarExportType; -import org.labkey.experiment.XarExporter; -import org.labkey.experiment.api.ClosureQueryHelper; -import org.labkey.experiment.api.DataClass; -import org.labkey.experiment.api.DataClassDomainKind; -import org.labkey.experiment.api.ExpDataClassAttachmentParent; -import org.labkey.experiment.api.ExpDataClassImpl; -import org.labkey.experiment.api.ExpDataImpl; -import org.labkey.experiment.api.ExpExperimentImpl; -import org.labkey.experiment.api.ExpMaterialImpl; -import org.labkey.experiment.api.ExpProtocolApplicationImpl; -import org.labkey.experiment.api.ExpProtocolImpl; -import org.labkey.experiment.api.ExpRunImpl; -import org.labkey.experiment.api.ExpSampleTypeImpl; -import org.labkey.experiment.api.Experiment; -import org.labkey.experiment.api.ExperimentServiceImpl; -import org.labkey.experiment.api.GraphAlgorithms; -import org.labkey.experiment.api.ProtocolActionStepDetail; -import org.labkey.experiment.api.SampleTypeServiceImpl; -import org.labkey.experiment.api.SampleTypeUpdateServiceDI; -import org.labkey.experiment.controllers.property.PropertyController; -import org.labkey.experiment.lineage.ExpLineageServiceImpl; -import org.labkey.experiment.pipeline.ExperimentPipelineJob; -import org.labkey.experiment.types.TypesController; -import org.labkey.experiment.xar.XarExportSelection; -import org.labkey.vfs.FileLike; -import org.labkey.vfs.FileSystemLike; -import org.springframework.beans.PropertyValue; -import org.springframework.beans.PropertyValues; -import org.springframework.validation.BindException; -import org.springframework.validation.Errors; -import org.springframework.validation.ObjectError; -import org.springframework.web.multipart.MultipartFile; -import org.springframework.web.multipart.MultipartHttpServletRequest; -import org.springframework.web.servlet.ModelAndView; - -import javax.imageio.ImageIO; -import java.awt.*; -import java.awt.image.BufferedImage; -import java.io.BufferedOutputStream; -import java.io.ByteArrayOutputStream; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; -import java.net.URI; -import java.nio.file.Files; -import java.nio.file.Path; -import java.sql.SQLException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.Collections; -import java.util.Comparator; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Map; -import java.util.Objects; -import java.util.Optional; -import java.util.Set; -import java.util.TreeSet; -import java.util.function.Function; -import java.util.stream.Collectors; - -import static java.util.stream.Collectors.toList; -import static org.labkey.api.data.DbScope.CommitTaskOption.POSTCOMMIT; -import static org.labkey.api.exp.query.ExpSchema.TableType.DataInputs; -import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM; -import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM; -import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_PROVIDER_PARAM; -import static org.labkey.api.util.DOM.A; -import static org.labkey.api.util.DOM.Attribute.action; -import static org.labkey.api.util.DOM.Attribute.href; -import static org.labkey.api.util.DOM.Attribute.id; -import static org.labkey.api.util.DOM.Attribute.method; -import static org.labkey.api.util.DOM.Attribute.name; -import static org.labkey.api.util.DOM.Attribute.size; -import static org.labkey.api.util.DOM.Attribute.src; -import static org.labkey.api.util.DOM.Attribute.target; -import static org.labkey.api.util.DOM.Attribute.type; -import static org.labkey.api.util.DOM.Attribute.value; -import static org.labkey.api.util.DOM.Attribute.width; -import static org.labkey.api.util.DOM.DIV; -import static org.labkey.api.util.DOM.IMG; -import static org.labkey.api.util.DOM.INPUT; -import static org.labkey.api.util.DOM.LI; -import static org.labkey.api.util.DOM.TABLE; -import static org.labkey.api.util.DOM.TD; -import static org.labkey.api.util.DOM.TR; -import static org.labkey.api.util.DOM.UL; -import static org.labkey.api.util.DOM.at; -import static org.labkey.api.util.DOM.cl; -import static org.labkey.experiment.ExpDataIterators.setContainerFilterForImport; -import static org.labkey.experiment.api.SampleTypeServiceImpl.SampleChangeType.update; - -public class ExperimentController extends SpringActionController -{ - private static final Logger _log = LogManager.getLogger(ExperimentController.class); - private static final DefaultActionResolver _actionResolver = new DefaultActionResolver( - ExperimentController.class - ); - private static final String GUEST_DIRECTORY_NAME = "guest"; - - public ExperimentController() - { - setActionResolver(_actionResolver); - } - - public static void ensureCorrectContainer(Container requestContainer, ExpObject object, ViewContext viewContext) - { - Container objectContainer = object.getContainer(); - if (!requestContainer.equals(objectContainer)) - { - ActionURL url = viewContext.cloneActionURL(); - url.setContainer(objectContainer); - throw new RedirectException(url); - } - } - - // Complete no-op, but leave in place in case we decide to adjust the base nav trail - private void addRootNavTrail(NavTree root) - { - // Intentionally don't add an "Experiment" node to the list because it's too overloaded. All content on the - // default action can be added to a portal page if desired. - } - - @Override - public PageConfig defaultPageConfig() - { - // set default help topic for controller - PageConfig config = super.defaultPageConfig(); - config.setHelpTopic("experiment"); - return config; - } - - @ActionNames("begin,gridView") - @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction - { - @Override - public VBox getView(Object o, BindException errors) - { - VBox result = new VBox(); - - VBox runListView = createRunListView(20); - result.addView(runListView); - - RunGroupWebPart runGroups = new RunGroupWebPart(getViewContext(), false); - runGroups.showHeader(); - result.addView(runGroups); - - result.addView(new ProtocolWebPart(false, getViewContext())); - result.addView(new SampleTypeWebPart(false, getViewContext())); - result.addView(new DataClassWebPart(false, getViewContext(), null)); - - return result; - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Experiment"); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowRunsAction extends SimpleViewAction - { - @Override - public VBox getView(Object o, BindException errors) - { - return createRunListView(100); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Experiment Runs"); - } - } - - private VBox createRunListView(int defaultMaxRows) - { - Set types = ExperimentService.get().getExperimentRunTypes(getContainer()); - ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")), getViewContext().getActionURL().clone(), Collections.emptyList()); - JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean); - - ExperimentRunListView view = ExperimentService.get().createExperimentRunWebPart(getViewContext(), bean.getSelectedFilter()); - view.setFrame(WebPartView.FrameType.NONE); - - // When paginated and the user hasn't explicitly set a maxRows, use the default maxRows size. - QuerySettings settings = view.getSettings(); - if (!settings.isMaxRowsSet() && settings.getShowRows() == ShowRows.PAGINATED) - { - settings.setMaxRows(defaultMaxRows); - } - - VBox result = new VBox(chooserView, view); - result.setFrame(WebPartView.FrameType.PORTAL); - return result; - } - - @RequiresPermission(ReadPermission.class) - @ActionNames("showRunGroups, showExperiments") - public class ShowRunGroupsAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - RunGroupWebPart webPart = new RunGroupWebPart(getViewContext(), false); - webPart.setFrame(WebPartView.FrameType.NONE); - return webPart; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - addRootNavTrail(root); - root.addChild("Run Groups"); - } - } - - public record Field(String domainURI, String domainName, String name, Container container) {} - public record MiniExpObject(Object rowId, String name) {} - public record TimelineSummary(MiniExpObject miniExpObject, String mostRecentValue) {} - public record ProblemType(String tableName, String fieldName, String pkName) { - public Object toHtml(List summaries) - { - return DOM.DIV( - DOM.H4(tableName), - DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), - DOM.THEAD(DOM.TH(pkName), DOM.TH(fieldName)), - summaries.stream().map(summary -> - DOM.TR(DOM.TD(summary.miniExpObject.name), DOM.TD(summary.mostRecentValue))) - )); - } - } - - @RequiresPermission(SiteAdminPermission.class) - public static class ReportLostFieldValuesAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - // Find all the fields that could have lost data due to issue 52666 - TableInfo t = new ExpSchema(getUser(), ContainerManager.getRoot()).getTable(ExpSchema.TableType.Fields.name(), ContainerFilter.getUnsafeEverythingFilter()); - List fields = new TableSelector(t, - new SimpleFilter(FieldKey.fromParts("StorageColumnNameMatch"), false). - addCondition(FieldKey.fromParts("DomainURI"), ":AssayDomain-Data.", CompareType.DOES_NOT_CONTAIN), - null). - getArrayList(Field.class); - - // Prep audit table for querying - UserSchema auditSchema = AuditLogService.get().createSchema(getUser(), ContainerManager.getRoot()); - - Map> sampleTypeSummaries = new HashMap<>(); - Map> dataClassSummaries = new HashMap<>(); - Map> listSummaries = new HashMap<>(); - - Map> problematicFields = new LinkedHashMap<>(); - - for (Field field : fields) - { - String domainURI = field.domainURI; - String fieldName = field.name; - Container container = field.container; - Domain domain = PropertyService.get().getDomain(container, domainURI); - if (domain != null && domain.getDomainKind() != null) - { - TableInfo table = domain.getDomainKind().getTableInfo(getUser(), container, domain, ContainerFilter.getUnsafeEverythingFilter()); - - if (table != null) - { - // Drill into sample types - if (domain.getDomainKind().getClass().equals(SampleTypeDomainKind.class)) - { - // rows that currently have no value for the field with potential for data loss - List rowsWithNull = new TableSelector(table, - new HashSet<>(List.of("RowId", "Name")), - new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), - null). - getArrayList(MiniExpObject.class); - - List fixupsNeeded = checkData( - rowsWithNull, - fieldName, - obj -> new SimpleFilter(FieldKey.fromParts("SampleId"), obj.rowId), - auditSchema.getTable(SampleTimelineAuditEvent.EVENT_TYPE, ContainerFilter.getUnsafeEverythingFilter())); - if (!fixupsNeeded.isEmpty()) - { - sampleTypeSummaries.put(new ProblemType(table.getName(), fieldName, "SampleID"), fixupsNeeded); - } - } - // and data classes/sample sources - if (domain.getDomainKind().getClass().equals(DataClassDomainKind.class)) - { - // rows samples that current have no value for the field with potential for data loss - List rowsWithNull = new TableSelector(table, - new HashSet<>(List.of("RowId", "Name")), - new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), - null). - getArrayList(MiniExpObject.class); - - List fixupsNeeded = checkData( - rowsWithNull, - fieldName, - obj -> new SimpleFilter(FieldKey.fromParts("RowPk"), Objects.toString(obj.rowId)). - addCondition(FieldKey.fromParts("SchemaName"), "exp.data"). - addCondition(FieldKey.fromParts("QueryName"), domain.getName()), - auditSchema.getTable("QueryUpdateAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); - - if (!fixupsNeeded.isEmpty()) - { - dataClassSummaries.put(new ProblemType(table.getName(), fieldName, "SourceID"), fixupsNeeded); - } - } - // and lists - if ("lists".equals(table.getUserSchema().getName())) - { - // rows samples that current have no value for the field with potential for data loss - List rowsWithNull = new ArrayList<>(); - - ColumnInfo entityIdCol = table.getColumn("EntityId"); - ColumnInfo pkCol = table.getPkColumns().get(0); - - new TableSelector(table, - List.of(entityIdCol, pkCol), - new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), - null). - forEachResults(r -> - { - Object entityId = entityIdCol.getValue(r); - Object pk = pkCol.getValue(r); - rowsWithNull.add(new MiniExpObject(entityId, pk.toString())); - }); - - - List fixupsNeeded = checkData( - rowsWithNull, - fieldName, - obj -> new SimpleFilter(FieldKey.fromParts("ListItemEntityId"), obj.rowId), - auditSchema.getTable("ListAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); - - if (!fixupsNeeded.isEmpty()) - { - listSummaries.put(new ProblemType(table.getName(), fieldName, table.getPkColumnNames().get(0)), fixupsNeeded); - } - } - - long totalRows = new TableSelector(table).getRowCount(); - long emptyRows = new TableSelector(table, new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), null).getRowCount(); - problematicFields.put(field, Pair.of(totalRows, emptyRows)); - } - else - { - problematicFields.put(field, Pair.of(null, null)); - } - } - } - - return new HtmlView("Fixups Needed", - DOM.createHtmlFragment( - DOM.H2("Potentially Problematic Fields"), - problematicFields.isEmpty() ? "No problematic fields detected!" : - DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), - DOM.THEAD(DOM.TH("Domain Name"), DOM.TH("Domain URI"), DOM.TH("Field Name"), DOM.TH("Container"), DOM.TH("Total Rows"), DOM.TH("Rows with Nulls")), - problematicFields.entrySet().stream().map(e -> { - Field f = e.getKey(); - Pair counts = e.getValue(); - return DOM.TR( - DOM.TD(f.domainName), - DOM.TD(f.domainURI), - DOM.TD(f.name), - DOM.TD(f.container.getPath()), - DOM.TD(counts.first), - DOM.TD(counts.second) - ); - } - )), - - DOM.H2("Sample Types"), - sampleTypeSummaries.isEmpty() ? "No problems detected!" : - sampleTypeSummaries.entrySet().stream().map(e -> - e.getKey().toHtml(e.getValue())), - - DOM.H2("Data Classes"), - dataClassSummaries.isEmpty() ? "No problems detected!" : - dataClassSummaries.entrySet().stream().map(e -> - e.getKey().toHtml(e.getValue())), - - DOM.H2("Lists"), - listSummaries.isEmpty() ? "No problems detected!" : - listSummaries.entrySet().stream().map(e -> - e.getKey().toHtml(e.getValue())) - )); - } - - @NotNull - private List checkData(List rowsWithNull, String fieldName, Function filterGenerator, TableInfo auditTable) - { - List fixupsNeeded = new ArrayList<>(); - - // For each sample without a value today, check the audit history - for (MiniExpObject row : rowsWithNull) - { - // Order by RowId to get them in the sequence they happened in - var events = new TableSelector(auditTable, filterGenerator.apply(row), new Sort("RowId")).getArrayList(DetailedAuditTypeEvent.class); - // Remember the most recently set value - String mostRecentValue = null; - for (DetailedAuditTypeEvent event : events) - { - Map newValues = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(event.getNewRecordMap())); - if (newValues.containsKey(fieldName)) - { - // Will be the empty string if the value was intentionally set to blank - mostRecentValue = newValues.get(fieldName); - } - } - // If the value had been set before, and its most recent insert/update wasn't setting it blank, - // it's most likely a lost value - if (mostRecentValue != null && !mostRecentValue.isEmpty()) - { - fixupsNeeded.add(new TimelineSummary(row, mostRecentValue)); - } - } - return fixupsNeeded; - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Accidentally Nulled Field Report"); - } - } - - @RequiresPermission(ReadPermission.class) - public static class CreateHiddenRunGroupAction extends MutatingApiAction - { - @Override - public ApiResponse execute(SimpleApiJsonForm form, BindException errors) throws Exception - { - JSONObject json = form.getJsonObject(); - String selectionKey = json.optString("selectionKey", null); - List runs = new ArrayList<>(); - - // Accept either an explicit list of run IDs - if (json.has("runIds")) - { - JSONArray runIds = json.getJSONArray("runIds"); - for (int i = 0; i < runIds.length(); i++) - { - ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(runIds.getInt(i)); - if (run != null) - { - runs.add(run); - } - } - } - // Or a reference to a DataRegion selection key - else if (selectionKey != null) - { - Set ids = DataRegionSelection.getSelectedIntegers(getViewContext(), selectionKey, false); - for (Long id : ids) - { - ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(id); - if (run != null) - { - runs.add(run); - } - } - } - if (runs.isEmpty()) - { - throw new NotFoundException(); - } - - ExpExperiment group = ExperimentService.get().createHiddenRunGroup(getContainer(), getUser(), runs.toArray(new ExpRun[0])); - if (selectionKey != null) - DataRegionSelection.clearAll(getViewContext(), selectionKey); - - ApiSimpleResponse response = new ApiSimpleResponse(); - response.putBean(group, "rowId", "LSID", "name", "hidden"); - return response; - } - } - - - @RequiresPermission(ReadPermission.class) - public class DetailsAction extends QueryViewAction - { - private ExpExperimentImpl _experiment; - - public DetailsAction() - { - super(ExpObjectForm.class); - } - - private Pair> createViews(ExpObjectForm form, BindException errors) - { - _experiment = ExperimentServiceImpl.get().getExpExperiment(form.getRowId()); - if (_experiment == null) - { - throw new NotFoundException("Could not find an experiment with RowId " + form.getRowId()); - } - - if (!_experiment.getContainer().equals(getContainer())) - { - throw new RedirectException(getViewContext().cloneActionURL().setContainer(_experiment.getContainer())); - } - - List protocols = _experiment.getAllProtocols(); - - Set types = new TreeSet<>(ExperimentService.get().getExperimentRunTypes(getContainer())); - ExperimentRunType selectedType = ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")); - - ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, selectedType, getViewContext().getActionURL().clone(), protocols); - JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean, errors); - - ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), bean.getSelectedFilter(), true); - runListView.getRunTable().setExperiment(_experiment); - runListView.setShowRemoveFromExperimentButton(true); - runListView.setShowDeleteButton(true); - runListView.setShowAddToRunGroupButton(true); - runListView.setShowExportButtons(true); - runListView.setShowMoveRunsButton(true); - return new Pair<>(runListView, chooserView); - } - - @Override - protected ModelAndView getHtmlView(ExpObjectForm form, BindException errors) throws Exception - { - Pair> views = createViews(form, errors); - - CustomPropertiesView customPropertiesView = new CustomPropertiesView(_experiment.getLSID(), getContainer()); - - TableInfo runGroupsTable = new ExpSchema(getUser(), getContainer()).getTable(ExpSchema.TableType.RunGroups); - - DetailsView detailsView = new DetailsView(new DataRegion(), _experiment.getRowId()); - detailsView.getDataRegion().setTable(runGroupsTable); - detailsView.getDataRegion().addColumns(runGroupsTable, "RowId,Name,Created,Modified,Contact,ExperimentDescriptionURL,Hypothesis,Comments"); - detailsView.getDataRegion().getDisplayColumn(0).setVisible(false); - detailsView.getDataRegion().getDisplayColumn(2).setWidth("60%"); - - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - ActionButton b = new ActionButton(ExperimentUrlsImpl.get().getShowUpdateURL(_experiment), "Edit"); - b.setDisplayPermission(UpdatePermission.class); - bb.add(b); - detailsView.getDataRegion().setButtonBar(bb); - if (_experiment.getBatchProtocol() != null) - { - detailsView.setTitle("Batch Details"); - detailsView.getDataRegion().addColumns(runGroupsTable, "BatchProtocolId"); - } - else - { - detailsView.setTitle("Run Group Details"); - } - - VBox runsVBox = new VBox(views.second, createInitializedQueryView(form, errors, false, null)); - runsVBox.setTitle("Experiment Runs"); - runsVBox.setFrame(WebPartView.FrameType.PORTAL); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, customPropertiesView), runsVBox); - } - - @Override - protected ExperimentRunListView createQueryView(ExpObjectForm form, BindException errors, boolean forExport, String dataRegion) - { - return createViews(form, errors).first; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - addRootNavTrail(root); - root.addChild("Run Groups", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); - root.addChild(_experiment.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ListSampleTypesAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - SampleTypeWebPart view = new SampleTypeWebPart(false, getViewContext()); - view.setFrame(WebPartView.FrameType.NONE); - view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); - - return view; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types"); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowSampleTypeAction extends SimpleViewAction - { - private ExpSampleTypeImpl _sampleType; - - @Override - public ModelAndView getView(ExpObjectForm form, BindException errors) - { - _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getRowId()); - if (_sampleType == null && form.getLsid() != null) - { - if (form.getLsid().equalsIgnoreCase("Material") || form.getLsid().equalsIgnoreCase("Sample")) - { - // Not a real sample type - just show all the materials instead - throw new RedirectException(new ActionURL(ShowAllMaterialsAction.class, getContainer())); - } - // Check if the URL specifies the LSID, and stick the bean back into the form - _sampleType = SampleTypeServiceImpl.get().getSampleType(form.getLsid()); - } - - if (_sampleType == null) - { - throw new NotFoundException("No matching sample type found"); - } - - List allScopedSampleTypes = (List) SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true); - if (!allScopedSampleTypes.contains(_sampleType)) - { - ensureCorrectContainer(getContainer(), _sampleType, getViewContext()); - } - - SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); - QuerySettings settings = schema.getSettings(getViewContext(), "Material", _sampleType.getName()); - QueryView queryView = new SampleTypeContentsView(_sampleType, schema, settings, errors); - - DetailsView detailsView = new DetailsView(getSampleTypeRegion(getViewContext()), _sampleType.getRowId()); - detailsView.getDataRegion().getDisplayColumn("Name").setURL((ActionURL)null); - detailsView.getDataRegion().getDisplayColumn("LSID").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("MaterialLSIDPrefix").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("LabelColor").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("MetricUnit").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("Category").setVisible(false); - - detailsView.setTitle("Sample Type Properties"); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).setStyle(ButtonBar.Style.separateButtons); - - Container autoLinkContainer = _sampleType.getAutoLinkTargetContainer(); - if (null != autoLinkContainer) - { - DisplayColumn autoLinkTargetColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkTargetContainer"); - autoLinkTargetColumn.setVisible(false); - - SimpleDisplayColumn displayAutoLinkTargetColumn = new SimpleDisplayColumn(); - displayAutoLinkTargetColumn.setCaption("Auto Link Target Container:"); - String path = autoLinkContainer.getPath(); - displayAutoLinkTargetColumn.setDisplayHtml(path.equals("/") ? "" : path); - detailsView.getDataRegion().addDisplayColumn(displayAutoLinkTargetColumn); - } - - DisplayColumn autoLinkCategoryColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkCategory"); - autoLinkCategoryColumn.setVisible(false); - SimpleDisplayColumn displayAutoLinkCategoryColumn = new SimpleDisplayColumn(); - displayAutoLinkCategoryColumn.setCaption("Auto Link Category:"); - displayAutoLinkCategoryColumn.setDisplayHtml(_sampleType.getAutoLinkCategory()); - detailsView.getDataRegion().addDisplayColumn(displayAutoLinkCategoryColumn); - - if (_sampleType.hasNameAsIdCol()) - { - SimpleDisplayColumn nameIdCol = new SimpleDisplayColumn(); - nameIdCol.setCaption("Has Name Id Column:"); - nameIdCol.setDisplayHtml("true"); - detailsView.getDataRegion().addDisplayColumn(nameIdCol); - } - - if (_sampleType.hasIdColumns()) - { - SimpleDisplayColumn idCols = new SimpleDisplayColumn(); - idCols.setCaption("Id Column(s):"); - String names = _sampleType.getIdCols().stream() - .filter(Objects::nonNull) - .map(DomainProperty::getName) - .collect(Collectors.joining(", ")); - if (!names.isEmpty()) - { - idCols.setDisplayHtml(PageFlowUtil.filter(names)); - detailsView.getDataRegion().addDisplayColumn(idCols); - } - } - - if (_sampleType.getParentCol() != null) - { - SimpleDisplayColumn parentCol = new SimpleDisplayColumn(PageFlowUtil.filter(_sampleType.getParentCol().getName())); - parentCol.setCaption("Parent Column:"); - detailsView.getDataRegion().addDisplayColumn(parentCol); - } - - try - { - SimpleDisplayColumn importAliasCol = new SimpleDisplayColumn(); - importAliasCol.setCaption("Parent Import Alias(es):"); - if (!_sampleType.getImportAliases().isEmpty()) - importAliasCol.setDisplayHtml(PageFlowUtil.filter(StringUtils.join(_sampleType.getImportAliases().keySet(), ", "))); - detailsView.getDataRegion().addDisplayColumn(importAliasCol); - } - catch (IOException e) - { - // unable to parse import alias map from JSON - } - - if (!getContainer().equals(_sampleType.getContainer())) - { - ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowSampleTypeURL(_sampleType); - SimpleDisplayColumn definedInCol = new SimpleDisplayColumn("" + - PageFlowUtil.filter(_sampleType.getContainer().getPath()) + - ""); - definedInCol.setCaption("Defined In:"); - detailsView.getDataRegion().addDisplayColumn(definedInCol); - } - - // Not all sample types can be edited - DomainKind domainKind = _sampleType.getDomain().getDomainKind(); - if (domainKind != null && domainKind.canEditDefinition(getUser(), _sampleType.getDomain())) - { - if (domainKind instanceof SampleTypeDomainKind) - { - ActionURL updateURL = new ActionURL(EditSampleTypeAction.class, _sampleType.getContainer()); - updateURL.addParameter("RowId", _sampleType.getRowId()); - updateURL.addReturnUrl(getViewContext().getActionURL()); - - if (!getContainer().equals(_sampleType.getContainer())) - { - String editLink = updateURL.toString(); - ActionButton updateButton = new ActionButton("Edit Type"); - updateButton.setActionType(ActionButton.Action.SCRIPT); - updateButton.setScript("if (window.confirm('This sample type is defined in the " + _sampleType.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + editLink + "' }"); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); - } - else - { - ActionButton updateButton = new ActionButton(updateURL, "Edit Type", ActionButton.Action.LINK); - updateButton.setDisplayPermission(DesignSampleTypePermission.class); - updateButton.setPrimary(true); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); - } - - ActionURL deleteURL = new ActionURL(DeleteSampleTypesAction.class, _sampleType.getContainer()); - deleteURL.addParameter("singleObjectRowId", _sampleType.getRowId()); - deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ActionButton deleteButton = new ActionButton(deleteURL, "Delete Type", ActionButton.Action.LINK); - deleteButton.setDisplayPermission(DesignSampleTypePermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(deleteButton); - } - else - { - ActionURL editURL = domainKind.urlEditDefinition(_sampleType.getDomain(), new ViewBackgroundInfo(_sampleType.getContainer(), getUser(), getViewContext().getActionURL())); - if (editURL != null) - { - editURL.addReturnUrl(getViewContext().getActionURL()); - ActionButton editTypeButton = new ActionButton(editURL, "Edit Fields"); - editTypeButton.setDisplayPermission(UpdatePermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(editTypeButton); - } - } - } - - if (_sampleType.canImportMoreSamples()) - { - TableInfo table = queryView.getTable(); - if (table != null) - { - ActionURL importURL = table.getImportDataURL(getContainer()); - if (importURL != null) - { - importURL = importURL.clone(); - importURL.addReturnUrl(getViewContext().getActionURL()); - ActionButton uploadButton = new ActionButton(importURL, "Import More Samples", ActionButton.Action.LINK); - uploadButton.setDisplayPermission(UpdatePermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(uploadButton); - } - } - } - - var publish = StudyPublishService.get(); - if (AuditLogService.get().isViewable() && publish != null) - { - ContainerFilter cf = ContainerFilter.Type.CurrentAndSubfolders.create(getContainer(), getUser()); - ActionURL linkToStudyHistoryURL = publish.getPublishHistory(getContainer(), Dataset.PublishSource.SampleType, _sampleType.getRowId(), cf); - ActionButton linkToStudyHistoryButton = new ActionButton(linkToStudyHistoryURL, "Link to Study History", ActionButton.Action.LINK); - linkToStudyHistoryButton.setDisplayPermission(InsertPermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(linkToStudyHistoryButton); - } - - return new VBox(detailsView, queryView); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - ActionURL url = ExperimentUrls.get().getShowSampleTypeListURL(getContainer()); - addRootNavTrail(root); - root.addChild("Sample Types", url); - root.addChild("Sample Type " + _sampleType.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowAllMaterialsAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - ExpSchema schema = new ExpSchema(getUser(), getContainer()); - QuerySettings settings = schema.getSettings(getViewContext(), "Materials", ExpSchema.TableType.Materials.toString()); - QueryView view = new QueryView(schema, settings, errors) - { - @Override - protected void populateButtonBar(DataView view, ButtonBar bar) - { - super.populateButtonBar(view, bar); - bar.add(SampleTypeContentsView.getDeriveSamplesButton(getContainer(),null)); - } - }; - view.setShowDetailsColumn(false); - return view; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("All Materials"); - } - } - - /** - * Only shows standard and custom properties, not parent and child samples. Used for indexing - */ - @RequiresPermission(ReadPermission.class) - public class ShowMaterialSimpleAction extends SimpleViewAction - { - protected ExpMaterialImpl _material; - - @Override - public VBox getView(ExpObjectForm form, BindException errors) throws Exception - { - Container c = getContainer(); - _material = ExperimentServiceImpl.get().getExpMaterial(form.getRowId()); - if (_material == null && form.getLsid() != null) - { - _material = ExperimentServiceImpl.get().getExpMaterial(form.getLsid()); - } - if (_material == null) - { - throw new NotFoundException("Could not find a material with RowId " + form.getRowId()); - } - - ensureCorrectContainer(getContainer(), _material, getViewContext()); - - ExpRunImpl run = _material.getRun(); - ExpProtocol sourceProtocol = _material.getSourceProtocol(); - ExpProtocolApplication sourceProtocolApplication = _material.getSourceApplication(); - - DataRegion dr = new DataRegion(); - dr.addColumns(ExperimentServiceImpl.get().getTinfoMaterial().getUserEditableColumns()); - dr.removeColumns("RowId", "RunId", "LastIndexed", "LSID", "SourceApplicationId", "CpasType"); - - //dr.addColumns(extraProps); - dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); - dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); - dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); - dr.addDisplayColumn(new LineageGraphDisplayColumn(_material, run)); - dr.addDisplayColumn(new SampleTypeDisplayColumn(_material)); - - //TODO: Can't yet edit materials uploaded from a material source - dr.setButtonBar(new ButtonBar()); - DetailsView detailsView = new DetailsView(dr, _material.getRowId()); - detailsView.setTitle("Standard Properties"); - detailsView.setFrame(WebPartView.FrameType.PORTAL); - - CustomPropertiesView cpv = new CustomPropertiesView(_material, c, getUser()); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv)); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ExpSampleType sampleType = _material.getSampleType(); - if (sampleType != null) - { - root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); - } - root.addChild("Sample " + _material.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowMaterialAction extends ShowMaterialSimpleAction - { - @Override - public VBox getView(ExpObjectForm form, BindException errors) throws Exception - { - VBox vbox = super.getView(form, errors); - - List materialsToInvestigate = new ArrayList<>(); - final Set successorRuns = new HashSet<>(); - materialsToInvestigate.add(_material); - Set investigatedMaterials = new HashSet<>(); - do - { - // Query for all the next tier of materials at once - issue 45402 - List followupRuns = ExperimentService.get().getRunsUsingMaterials(materialsToInvestigate); - - // Mark this set as investigated and reset for the next cycle - investigatedMaterials.addAll(materialsToInvestigate); - materialsToInvestigate = new ArrayList<>(); - - for (ExpRun r : followupRuns) - { - // Only expand the material outputs of the run if it's our first time visiting it - if (successorRuns.add(r)) - { - materialsToInvestigate.addAll(r.getMaterialOutputs()); - } - } - - if (successorRuns.size() > 1000) - { - // Give up - there may be a cycle or other problematic data - break; - } - - // Cull the ones we've already looked up - materialsToInvestigate.removeAll(investigatedMaterials); - } - while (!materialsToInvestigate.isEmpty()); - - HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); - ExpSampleType st = _material.getSampleType(); - if (st != null && st.getContainer() != null && st.getContainer().hasPermission(getUser(), UpdatePermission.class)) - { - // XXX: ridiculous amount of work to get a update url expression for the sample type's table. - UserSchema samplesSchema = QueryService.get().getUserSchema(getUser(), st.getContainer(), "Samples"); - QueryDefinition queryDef = samplesSchema.getQueryDefForTable(st.getName()); - StringExpression expr = queryDef.urlExpr(QueryAction.updateQueryRow, null); - if (expr != null) - { - // Since we're building a detailsURL outside the context of a "row" need to set the correct - // container context on the generated expr. - ((DetailsURL) expr).setContainerContext(st.getContainer()); - String url = expr.eval(Collections.singletonMap(new FieldKey(null, "RowId"), _material.getRowId())); - updateLinks.append(LinkBuilder.labkeyLink("edit", url)).append(" "); - } - } - - if (getContainer().hasPermission(getUser(), InsertPermission.class)) - { - ActionURL deriveURL = new ActionURL(DeriveSamplesChooseTargetAction.class, getContainer()); - deriveURL.addParameter("rowIds", _material.getRowId()); - if (st != null) - deriveURL.addParameter("targetSampleTypeId", st.getRowId()); - - updateLinks.append(LinkBuilder.labkeyLink("derive samples from this sample", deriveURL)).append(" "); - } - - vbox.addView(new HtmlView(updateLinks)); - - ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); - runListView.setShowRecordSelectors(false); - runListView.getRunTable().setRuns(successorRuns); - runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); - runListView.setAllowableContainerFilterTypes(ContainerFilter.Type.Current, ContainerFilter.Type.CurrentAndSubfolders, ContainerFilter.Type.AllFolders); - runListView.setTitle("Runs associated with this material or a derived material"); - - ParentChildView pv = new ParentChildView(_material, getViewContext()); - vbox.addView(pv); - vbox.addView(runListView); - - return vbox; - } - } - - - // - // DataClass - // - - @RequiresPermission(ReadPermission.class) - public class ListDataClassAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - DataClassWebPart view = new DataClassWebPart(false, getViewContext(), null); - view.setFrame(WebPartView.FrameType.NONE); - view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); - - return view; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - addRootNavTrail(root); - root.addChild("Data Classes"); - } - } - - public static class DataClassForm extends ExpObjectForm - { - private String _name; - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - public ExpDataClassImpl getDataClass(@Nullable Container container) - { - ExpDataClassImpl dataClass = null; - - if (getName() != null) - { - dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getName()); - if (dataClass == null) - throw new NotFoundException("No data class found for name '" + getName() + "'."); - } - else if (getRowId() > 0) - { - dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getRowId()); - } - - if (dataClass == null) - throw new NotFoundException("No data class found."); - else if (container != null && !container.equals(dataClass.getContainer())) - throw new NotFoundException("Data class is not defined in the given container."); - - return dataClass; - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowDataClassAction extends SimpleViewAction - { - private ExpDataClassImpl _dataClass; - - @Override - public ModelAndView getView(DataClassForm form, BindException errors) - { - _dataClass = form.getDataClass(null); - return new VBox(getDataClassPropertiesView(), getDataClassContentsView(errors)); - } - - private DetailsView getDataClassPropertiesView() - { - ExpSchema expSchema = new ExpSchema(getUser(), _dataClass.getContainer()); - - TableInfo table = ExpSchema.TableType.DataClasses.createTable(expSchema, null, null); - QueryUpdateForm tvf = new QueryUpdateForm(table, getViewContext(), null); - tvf.setPkVal(_dataClass.getRowId()); - DetailsView detailsView = new DetailsView(tvf); - detailsView.setTitle("Data Class Properties"); - - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - boolean inDefinitionContainer = getContainer().equals(_dataClass.getContainer()); - - DomainKind domainKind = _dataClass.getDomain().getDomainKind(); - if (domainKind != null && domainKind.canEditDefinition(getUser(), _dataClass.getDomain())) - { - ActionURL updateURL = new ActionURL(EditDataClassAction.class, _dataClass.getContainer()); - updateURL.addParameter("rowId", _dataClass.getRowId()); - updateURL.addReturnUrl(urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId())); - - if (inDefinitionContainer) - { - ActionButton updateButton = new ActionButton(updateURL, "Edit Data Class", ActionButton.Action.LINK); - updateButton.setDisplayPermission(DesignDataClassPermission.class); - updateButton.setPrimary(true); - bb.add(updateButton); - } - else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) - { - ActionButton updateButton = new ActionButton("Edit Data Class"); - updateButton.setActionType(ActionButton.Action.SCRIPT); - updateButton.setScript("if (window.confirm('This data class is defined in the " + _dataClass.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + updateURL + "' }"); - updateButton.setPrimary(true); - bb.add(updateButton); - } - - ActionURL deleteURL = new ActionURL(DeleteDataClassAction.class, _dataClass.getContainer()); - deleteURL.addParameter("singleObjectRowId", _dataClass.getRowId()); - deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - ActionButton deleteButton = new ActionButton(deleteURL, "Delete Data Class", ActionButton.Action.LINK); - - if (inDefinitionContainer) - { - deleteButton.setDisplayPermission(DesignDataClassPermission.class); - bb.add(deleteButton); - } - else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) - { - bb.add(deleteButton); - } - } - detailsView.getDataRegion().setButtonBar(bb); - - if (!inDefinitionContainer) - { - ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId()); - LinkBuilder link = LinkBuilder.simpleLink(_dataClass.getContainer().getPath(), definitionURL); - SimpleDisplayColumn definedInCol = new SimpleDisplayColumn(link.toString()); - definedInCol.setCaption("Defined In:"); - detailsView.getDataRegion().addDisplayColumn(definedInCol); - } - - return detailsView; - } - - private QueryView getDataClassContentsView(BindException errors) - { - UserSchema dataClassSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_EXP_DATA); - QuerySettings settings = dataClassSchema.getSettings(getViewContext(), QueryView.DATAREGIONNAME_DEFAULT, _dataClass.getName()); - - return new QueryView(dataClassSchema, settings, errors) - { - @Override - public @NotNull LinkedHashSet getClientDependencies() - { - LinkedHashSet resources = super.getClientDependencies(); - resources.add(ClientDependency.fromPath("Ext4")); - resources.add(ClientDependency.fromPath("dataregion/confirmDelete.js")); - return resources; - } - - @Override - public ActionButton createDeleteButton() - { - ActionButton button = super.createDeleteButton(); - if (button != null) - { - String dependencyText = ExperimentService.get() - .getObjectReferencers() - .stream() - .map(referencer -> referencer.getObjectReferenceDescription(ExpData.class)) - .collect(Collectors.joining(" or ")); - - button.setScript("LABKEY.dataregion.confirmDelete(" + - PageFlowUtil.jsString(getDataRegionName()) + ", " + - PageFlowUtil.jsString(ExpSchema.SCHEMA_EXP_DATA.toString()) + ", " + - PageFlowUtil.jsString(getQueryDef().getName()) + ", " + - "'experiment', 'getDataOperationConfirmationData.api', " + - PageFlowUtil.jsString(getSelectionKey()) + ", " + - "'data object', 'data objects', '" + dependencyText + "', {dataOperation: 'Delete'})"); - button.setRequiresSelection(true); - } - return button; - } - }; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - addRootNavTrail(root); - root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - root.addChild(_dataClass.getName()); - } - } - - @RequiresPermission(DesignDataClassPermission.class) - public class DeleteDataClassAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - super.addNavTrail(root); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - List dataClasses = getDataClasses(deleteForm); - if (!ensureCorrectContainer(dataClasses)) - { - throw new UnauthorizedException(); - } - for (ExpRun run : getRuns(dataClasses)) - { - if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new UnauthorizedException(); - } - } - for (ExpDataClass dataClass : dataClasses) - { - dataClass.delete(getUser(), deleteForm.getUserComment()); - } - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List dataClasses = getDataClasses(deleteForm); - - if (!ensureCorrectContainer(dataClasses)) - { - throw new RedirectException(ExperimentUrlsImpl.get().getDataClassListURL(getContainer(), "To delete a data class, you must be in its folder or project.")); - } - - return new ConfirmDeleteView("Data Class", ShowDataClassAction.class, dataClasses, deleteForm, getRuns(dataClasses)); - } - - private List getDataClasses(DeleteForm deleteForm) - { - List dataClasses = new ArrayList<>(); - for (long rowId : deleteForm.getIds(false)) - { - ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), rowId); - if (dataClass != null) - { - dataClasses.add(dataClass); - } - } - return dataClasses; - } - - private boolean ensureCorrectContainer(List dataClasses) - { - for (ExpDataClass dataClass : dataClasses) - { - Container sourceContainer = dataClass.getContainer(); - if (!sourceContainer.equals(getContainer())) - { - return false; - } - } - return true; - } - - private List getRuns(List dataClasses) - { - if (!dataClasses.isEmpty()) - { - List runArray = ExperimentService.get().getRunsUsingDataClasses(dataClasses); - return ExperimentService.get().runsDeletedWithInput(runArray); - } - else - { - return Collections.emptyList(); - } - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetDataClassPropertiesAction extends ReadOnlyApiAction - { - @Override - public Object execute(DataClassForm form, BindException errors) throws Exception - { - ExpDataClass dataClass = form.getDataClass(getContainer()); - if (dataClass != null) - return new DataClassDomainKindProperties(dataClass); - else - throw new NotFoundException("Data class does not exist in this container for rowId " + form.getRowId() + "."); - } - } - - @RequiresPermission(DesignDataClassPermission.class) - public static class EditDataClassAction extends SimpleViewAction - { - private ExpDataClassImpl _dataClass; - - @Override - public ModelAndView getView(DataClassForm form, BindException errors) - { - boolean create = form.getLSID() == null && form.getRowId() == 0 && form.getName() == null; - if (!create) - _dataClass = form.getDataClass(getContainer()); - - return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("dataClassDesigner")); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - - root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - if (_dataClass == null) - { - root.addChild("Create Data Class"); - } - else - { - root.addChild(_dataClass.getName(), ExperimentUrlsImpl.get().getShowDataClassURL(getContainer(), _dataClass.getRowId())); - root.addChild("Update Data Class"); - } - } - } - - @RequiresPermission(DesignDataClassPermission.class) - public static class CreateDataClassFromTemplateAction extends FormViewAction - { - private ActionURL _successUrl; - private Map _domainTemplates; - - @Override - public void validateCommand(CreateDataClassFromTemplateForm form, Errors errors) - { - String name = null; - _domainTemplates = DomainTemplateGroup.getAllTemplates(getContainer()); - - if (!_domainTemplates.containsKey(form.getDomainTemplate())) - { - errors.reject(ERROR_MSG, "Unknown template selected: " + form.getDomainTemplate()); - } - else - { - DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); - name = template.getTemplateName(); - - // Issue 40230: if template includes sample type option, verify that it exists - if (template.getOptions().containsKey("sampleSet")) - { - String sampleTypeName = template.getOptions().get("sampleSet").toString(); - ExpSampleType sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), sampleTypeName); - if (sampleType == null) - errors.reject(ERROR_MSG, "Unable to find a sample type in this container with name: " + sampleTypeName + "."); - } - } - - if (StringUtils.isBlank(name)) - errors.reject(ERROR_MSG, "DataClass template selection is required."); - else if (ExperimentService.get().getDataClass(getContainer(), getUser(), name) != null) - errors.reject(ERROR_MSG, "DataClass '" + name + "' already exists."); - - } - - @Override - public ModelAndView getView(CreateDataClassFromTemplateForm form, boolean reshow, BindException errors) - { - Set templates = DomainTemplateGroup.getTemplatesForDomainKind(getContainer(), DataClassDomainKind.NAME); - form.setAvailableDomainTemplateNames(templates); - - Set messages = new HashSet<>(); - Map groups = DomainTemplateGroup.getAllGroups(getContainer()); - for (DomainTemplateGroup g : groups.values()) - messages.addAll(g.getErrors()); - form.setXmlParseErrors(messages); - - return new JspView<>("/org/labkey/experiment/createDataClassFromTemplate.jsp", form, errors); - } - - @Override - public boolean handlePost(CreateDataClassFromTemplateForm form, BindException errors) throws Exception - { - DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); - Domain domain = DomainUtil.createDomain(template, getContainer(), getUser(), form.getName()); - - _successUrl = domain.getDomainKind().urlEditDefinition(domain, getViewContext()); - return true; - } - - @Override - public URLHelper getSuccessURL(CreateDataClassFromTemplateForm form) - { - return _successUrl; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - root.addChild("Create Data Class from Template"); - } - } - - public static class CreateDataClassFromTemplateForm extends DataClass - { - private String _domainTemplate; - private Set _availableDomainTemplateNames; - private Set _xmlParseErrors; - private final ReturnUrlForm _returnUrlForm = new ReturnUrlForm(); - - public String getDomainTemplate() - { - return _domainTemplate; - } - - public void setDomainTemplate(String domainTemplate) - { - _domainTemplate = domainTemplate; - } - - public Set getAvailableDomainTemplateNames() - { - return _availableDomainTemplateNames; - } - - public void setAvailableDomainTemplateNames(Set availableDomainTemplateNames) - { - _availableDomainTemplateNames = availableDomainTemplateNames; - } - - public Set getXmlParseErrors() - { - return _xmlParseErrors; - } - - public void setXmlParseErrors(Set xmlParseErrors) - { - _xmlParseErrors = xmlParseErrors; - } - - @Nullable - public String getReturnUrl() - { - return _returnUrlForm.getReturnUrl(); - } - - public void setReturnUrl(String s) - { - _returnUrlForm.setReturnUrl(s); - } - } - - public static class ConceptURIForm - { - private String _conceptURI; - - public String getConceptURI() - { - return _conceptURI; - } - - public void setConceptURI(String conceptURI) - { - _conceptURI = conceptURI; - } - } - - @RequiresPermission(AdminPermission.class) - public static class RemoveConceptMappingAction extends MutatingApiAction - { - @Override - public void validateForm(ConceptURIForm form, Errors errors) - { - if (form.getConceptURI() == null || ConceptURIProperties.getLookup(getContainer(), form.getConceptURI()) == null) - errors.reject(ERROR_MSG, "Concept URI not found: " + form.getConceptURI()); - } - - @Override - public Object execute(ConceptURIForm form, BindException errors) - { - ConceptURIProperties.removeLookup(getContainer(), form.getConceptURI()); - return new ApiSimpleResponse("success", true); - } - } - - @RequiresPermission(ReadPermission.class) - public static class RunAttachmentDownloadAction extends BaseDownloadAction - { - @Nullable - @Override - public Pair getAttachment(AttachmentForm form) - { - if (form.getLsid() == null || form.getName() == null) - throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); - - ExpRun run = ExperimentService.get().getExpRun(form.getLsid()); - if (run == null) - throw new NotFoundException("Run not found: " + form.getLsid()); - - if (!run.getContainer().equals(getContainer())) - { - if (run.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new RedirectException(getViewContext().cloneActionURL().setContainer(run.getContainer())); - else - throw new NotFoundException("Run not found"); - } - - AttachmentParent parent = new ExpRunAttachmentParent(run); - return new Pair<>(parent, form.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public static class DataClassAttachmentDownloadAction extends BaseDownloadAction - { - @Nullable - @Override - public Pair getAttachment(AttachmentForm form) - { - if (form.getLsid() == null || form.getName() == null) - throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); - - Lsid lsid = new Lsid(form.getLsid()); - ExpData data = ExperimentServiceImpl.get().getExpData(lsid.toString()); - if (data == null) - throw new NotFoundException("Error: Data object not found for the given LSID: " + lsid); - AttachmentParent parent = new ExpDataClassAttachmentParent(data.getContainer(), lsid); - - return new Pair<>(parent, form.getName()); - } - } - - public static class AttachmentForm extends LsidForm implements BaseDownloadAction.InlineDownloader - { - private String _name; - private boolean _inline = true; - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - @Override - public boolean isInline() - { - return _inline; - } - - public void setInline(boolean inline) - { - _inline = inline; - } - } - - // - // END DataClass actions - // - - public static ActionURL getRunGraphURL(Container c, long runId) - { - return new ActionURL(ShowRunGraphAction.class, c).addParameter("rowId", runId); - } - - - @RequiresPermission(ReadPermission.class) - public class ShowRunGraphAction extends AbstractShowRunAction - { - @Override - protected VBox createLowerView(ExpRunImpl experimentRun, BindException errors) - { - return new VBox( - createRunViewTabs(experimentRun, false, true, true), - new ExperimentRunGraphView(experimentRun, false)); - } - } - - - @RequiresPermission(ReadPermission.class) - public static class DownloadGraphAction extends SimpleViewAction - { - @Override - public ModelAndView getView(ExperimentRunForm form, BindException errors) throws Exception - { - boolean detail = form.isDetail(); - String focus = form.getFocus(); - String focusType = form.getFocusType(); - - ExpRunImpl experimentRun = (ExpRunImpl) form.lookupRun(); - ensureCorrectContainer(getContainer(), experimentRun, getViewContext()); - - ExperimentRunGraph.RunGraphFiles files; - try - { - files = ExperimentRunGraph.generateRunGraph(getViewContext(), experimentRun, detail, focus, focusType); - } - catch (ExperimentException e) - { - PageFlowUtil.streamTextAsImage(getViewContext().getResponse(), "ERROR: " + e.getMessage(), 600, 150, Color.RED); - return null; - } - - try - { - PageFlowUtil.streamFile(getViewContext().getResponse(), new File(files.getImageFile().getAbsolutePath()), false); - } - catch (FileNotFoundException e) - { - getViewContext().getResponse().sendRedirect(getViewContext().getRequest().getContextPath() + "/experiment/ExperimentRunNotFound.gif"); - } - finally - { - files.release(); - } - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - throw new UnsupportedOperationException(); - } - } - - private abstract class AbstractShowRunAction extends SimpleViewAction - { - private ExpRunImpl _experimentRun; - - @Override - public ModelAndView getView(ExperimentRunForm form, BindException errors) - { - _experimentRun = (ExpRunImpl) form.lookupRun(); - ensureCorrectContainer(getContainer(), _experimentRun, getViewContext()); - - VBox vbox = new VBox(); - - JspView detailsView = new JspView<>("/org/labkey/experiment/ExperimentRunDetails.jsp", _experimentRun); - detailsView.setTitle("Standard Properties"); - - var attachmentParent = new ExpRunAttachmentParent(_experimentRun); - var attachments = AttachmentService.get().getAttachments(attachmentParent) - .stream() - .map(att -> Pair.of(att.getName(), new ActionURL(RunAttachmentDownloadAction.class, _experimentRun.getContainer()).addParameter("name", att.getName()).addParameter("lsid", _experimentRun.getLSID()))) - .collect(toList()); - CustomPropertiesView cpv = new CustomPropertiesView(_experimentRun.getLSID(), getContainer(), attachments); - - vbox.addView(new StandardAndCustomPropertiesView(detailsView, cpv)); - - HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); - List runEditors = ExperimentService.get().getRunEditors(); - for (ExpRunEditor editor : runEditors) - { - if (editor.isProtocolEditor(form.lookupRun().getProtocol())) - { - updateLinks.append(LinkBuilder.labkeyLink("edit " + editor.getDisplayName() + " run", editor.getEditUrl(getContainer()).addParameter("rowId", form.getRowId()))); - } - } - - if (!updateLinks.isEmpty()) - { - HtmlView view = new HtmlView(updateLinks); - vbox.addView(view); - } - - VBox lowerView = createLowerView(_experimentRun, errors); - lowerView.setFrame(WebPartView.FrameType.PORTAL); - lowerView.setTitle("Run Details"); - NavTree tree = new NavTree(""); - File runRoot = _experimentRun.getFilePathRoot(); - if (NetworkDrive.exists(runRoot)) - { - if (!runRoot.isDirectory()) - { - runRoot = runRoot.getParentFile(); - } - PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(_experimentRun.getContainer()); - if (pipelineRoot != null) - { - if (pipelineRoot.isUnderRoot(runRoot)) - { - String path = pipelineRoot.relativePath(runRoot); - tree.addChild("View Files", urlProvider(PipelineUrls.class).urlBrowse(_experimentRun.getContainer(), null, path)); - } - } - } - - final String exportFilesFormId = "exportFilesForm"; - NavTree downloadFiles = new NavTree("Download all files"); - downloadFiles.setScript("document.getElementById('" + exportFilesFormId + "').submit();"); - tree.addChild(downloadFiles); - - // CONSIDER: Show modal dialog using ExperimentService.get().createRunExportView() - NavTree exportXarFiles = new NavTree("Export XAR"); - exportXarFiles.setScript("LABKEY.Experiment.exportRuns({runIds: [" + _experimentRun.getRowId() + "] });"); - tree.addChild(exportXarFiles); - - lowerView.setNavMenu(tree); - lowerView.setIsWebPart(false); - - vbox.addView(lowerView); - vbox.addView(new ExperimentRunGroupsView(getUser(), getContainer(), _experimentRun, getViewContext().getActionURL(), errors)); - - DOM.Renderable exportFilesForm = LK.FORM(at( - id, exportFilesFormId, - method, "POST", - action, new ActionURL(ExportRunFilesAction.class, _experimentRun.getContainer())), - INPUT(at(type, "hidden", - name, DataRegionSelection.DATA_REGION_SELECTION_KEY, - value, "ExportSingleRun")), - INPUT(at(type, "hidden", - name, DataRegion.SELECT_CHECKBOX_NAME, - value, _experimentRun.getRowId())), - INPUT(at(type, "hidden", - name, "zipFileName", - value, _experimentRun.getName() + ".zip"))); - - HtmlView hiddenFormView = new HtmlView(exportFilesForm); - vbox.addView(hiddenFormView); - - return vbox; - } - - protected abstract VBox createLowerView(ExpRunImpl experimentRun, BindException errors); - - @Override - public void addNavTrail(NavTree root) - { - root.addChild(_experimentRun.getName()); - } - } - - public static class ToggleRunExperimentMembershipForm - { - private int _runId; - private int _experimentId; - private boolean _included; - - public int getRunId() - { - return _runId; - } - - public void setRunId(int runId) - { - _runId = runId; - } - - public int getExperimentId() - { - return _experimentId; - } - - public void setExperimentId(int experimentId) - { - _experimentId = experimentId; - } - - public boolean isIncluded() - { - return _included; - } - - public void setIncluded(boolean included) - { - _included = included; - } - } - - @RequiresPermission(UpdatePermission.class) - public static class ToggleRunExperimentMembershipAction extends FormHandlerAction - { - @Override - public boolean handlePost(ToggleRunExperimentMembershipForm form, BindException errors) - { - ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); - // Check if the user has permission to update this run - if (run == null || !run.getContainer().hasPermission(getUser(), UpdatePermission.class)) - { - throw new NotFoundException(); - } - - ExpExperiment exp = ExperimentService.get().getExpExperiment(form.getExperimentId()); - if (exp == null) - { - throw new NotFoundException(); - } - // Check if this - if (!ExperimentService.get().getExperiments(run.getContainer(), getUser(), true, false).contains(exp)) - { - throw new NotFoundException(); - } - // Users must have permission to view, but not necessarily update, the container the holds the run group - if (!exp.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new UnauthorizedException(); - } - - if (form.isIncluded()) - { - exp.addRuns(getUser(), run); - } - else - { - exp.removeRun(getUser(), run); - } - - return true; - } - - @Override - public URLHelper getSuccessURL(ToggleRunExperimentMembershipForm form) - { - return null; - } - - @Override - public void validateCommand(ToggleRunExperimentMembershipForm target, Errors errors) - { - } - } - - private HtmlView createRunViewTabs(ExpRun expRun, boolean showGraphSummary, boolean showGraphDetail, boolean showText) - { - return new HtmlView( - TABLE(cl("labkey-tab-strip"), - TR( - createTabSpacer(false), - createTab("Graph Summary View", ExperimentUrlsImpl.get().getRunGraphURL(expRun), !showGraphSummary), - createTabSpacer(false), - createTab("Graph Detail View", ExperimentUrlsImpl.get().getRunGraphDetailURL(expRun), !showGraphDetail), - createTabSpacer(false), - createTab("Text View", ExperimentUrlsImpl.get().getRunTextURL(expRun), !showText), - createTabSpacer(true)))); - } - - private DOM.Renderable createTab(String text, ActionURL url, boolean selected) - { - return TD(cl(selected,"labkey-tab-selected", "labkey-tab"), - A(at(href, url), text)); - } - - private DOM.Renderable createTabSpacer(boolean fullWidth) - { - return TD(cl("labkey-tab-space").at(fullWidth, width, "100%"), - IMG(at(src, AppProps.getInstance().getContextPath() + "/_.gif", width, "5"))); - } - - @RequiresPermission(ReadPermission.class) - public class ShowRunTextAction extends AbstractShowRunAction - { - @Override - protected VBox createLowerView(ExpRunImpl expRun, BindException errors) - { - JspView applicationsView = new JspView<>("/org/labkey/experiment/ProtocolApplications.jsp", expRun); - applicationsView.setFrame(WebPartView.FrameType.TITLE); - applicationsView.setTitle("Protocol Applications"); - - HtmlView toggleView = createRunViewTabs(expRun, true, true, false); - - QuerySettings runDataInputsSettings = new QuerySettings(getViewContext(), "RunDataInputs", DataInputs.name()); - UsageQueryView runDataInputsView = new UsageQueryView("Data Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runDataInputsSettings, errors); - runDataInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); - - QuerySettings runDataOutputsSettings = new QuerySettings(getViewContext(), "RunDataOutputs", DataInputs.name()); - UsageQueryView runDataOutputsView = new UsageQueryView("Data Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runDataOutputsSettings, errors); - runDataOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); - - QuerySettings runMaterialInputsSetting = new QuerySettings(getViewContext(), "RunMaterialInputs", ExpSchema.TableType.MaterialInputs.name()); - UsageQueryView runMaterialInputsView = new UsageQueryView("Material Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runMaterialInputsSetting, errors); - runMaterialInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); - - QuerySettings runMaterialOutputsSettings = new QuerySettings(getViewContext(), "RunMaterialOutputs", ExpSchema.TableType.MaterialInputs.name()); - UsageQueryView runMaterialOutputsView = new UsageQueryView("Material Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runMaterialOutputsSettings, errors); - runMaterialOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); - - HBox inputsView = new HBox(runDataInputsView, runMaterialInputsView); - HBox registeredInputsView = new HBox(); - - var expService = ExperimentService.get(); - expService.getRunInputsViewProviders().forEach(provider -> - { - var queryView = provider.createView(getViewContext(), expRun, errors); - if (queryView != null) - { - registeredInputsView.addView(queryView); - } - }); - HBox outputsView = new HBox(runDataOutputsView, runMaterialOutputsView); - HBox registeredOutputsView = new HBox(); - expService.getRunOutputsViewProviders().forEach(provider -> - { - var queryView = provider.createView(getViewContext(), expRun, errors); - if (queryView != null) - { - registeredOutputsView.addView(queryView); - } - }); - - var vBox = new VBox(); - vBox.addView(toggleView); - vBox.addView(inputsView); - if (!registeredInputsView.isEmpty()) - vBox.addView(registeredInputsView); - vBox.addView(outputsView); - if (!registeredOutputsView.isEmpty()) - vBox.addView(registeredOutputsView); - vBox.addView(applicationsView); - - return vBox; - } - } - - private static class UsageQueryView extends QueryView - { - private final ExpRun _run; - private final ExpProtocol.ApplicationType _type; - - public UsageQueryView(String title, ViewContext context, ExpRun run, ExpProtocol.ApplicationType type, - QuerySettings settings, BindException errors) - { - super(new ExpSchema(context.getUser(), context.getContainer()), settings, errors); - setTitle(title); - setFrame(FrameType.TITLE); - _run = run; - _type = type; - setShowBorders(true); - setShadeAlternatingRows(true); - setShowExportButtons(false); - setShowPagination(false); - disableContainerFilterSelection(); - } - - @Override - protected TableInfo createTable() - { - String tableName = getSettings().getQueryName(); - ExpInputTable tableInfo = (ExpInputTable) getSchema().getTable(tableName, new ContainerFilter.AllFolders(getUser()), true, true); - tableInfo.setRun(_run, _type); - tableInfo.setLocked(true); - return tableInfo; - } - } - - - public static ActionURL getShowRunGraphDetailURL(Container c, long rowId) - { - ActionURL url = new ActionURL(ShowRunGraphDetailAction.class, c); - url.addParameter("rowId", rowId); - return url; - } - - - @RequiresPermission(ReadPermission.class) - public class ShowRunGraphDetailAction extends AbstractShowRunAction - { - @Override - protected VBox createLowerView(ExpRunImpl run, BindException errors) - { - ExperimentRunGraphView gw = new ExperimentRunGraphView(run, true); - if (null != getViewContext().getActionURL().getParameter("focus")) - gw.setFocus(getViewContext().getActionURL().getParameter("focus")); - if (null != getViewContext().getActionURL().getParameter("focusType")) - gw.setFocusType(getViewContext().getActionURL().getParameter("focusType")); - return new VBox(createRunViewTabs(run, true, false, true), gw); - } - } - - private abstract class AbstractDataAction extends SimpleViewAction - { - protected ExpDataImpl _data; - - @Override - public final ModelAndView getView(DataForm form, BindException errors) throws Exception - { - _data = form.lookupData(); - if (_data == null) - { - throw new NotFoundException("Could not find a data with RowId " + form.getRowId()); - } - - ensureCorrectContainer(getContainer(), _data, getViewContext()); - return getDataView(form, errors); - } - - protected abstract ModelAndView getDataView(DataForm form, BindException errors) throws Exception; - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Data " + _data.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowDataAction extends AbstractDataAction - { - @Override - public ModelAndView getDataView(DataForm form, BindException errors) - { - ExpRun run = _data.getRun(); - ExpProtocol sourceProtocol = _data.getSourceProtocol(); - ExpProtocolApplication sourceProtocolApplication = _data.getSourceApplication(); - ExpDataClass dataClass = _data.getDataClass(getUser()); - - ExpSchema schema = new ExpSchema(getUser(), getContainer()); - TableInfo table; - long pk; - if (dataClass == null) - { - table = schema.getDatasTable(); - pk = _data.getRowId(); - } - else - { - table = schema.getSchema(ExpSchema.NestedSchemas.data).getTable(dataClass.getName()); - pk = new TableSelector(table, Collections.singleton("rowId"), new SimpleFilter(FieldKey.fromParts("lsid"), _data.getLSID()), null).getObject(Integer.class); - } - - DataRegion dr = new DataRegion(); - dr.setTable(table); - List cols = table.getColumns().stream().filter(ColumnInfo::isShownInDetailsView).collect(toList()); - dr.addColumns(cols); - dr.removeColumns("RowId", "Created", "CreatedBy", "Modified", "ModifiedBy", "DataFileUrl", "Run", "LSID", "CpasType", "SourceApplicationId", "Folder", "Generated"); - dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); - dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); - dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); - dr.addDisplayColumn(new LineageGraphDisplayColumn(_data, run)); - DetailsView detailsView = new DetailsView(dr, pk); - detailsView.setTitle("Standard Properties"); - detailsView.setFrame(WebPartView.FrameType.PORTAL); - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - - ExperimentDataHandler handler = _data.findDataHandler(); - ActionURL viewDataURL = handler == null ? null : handler.getContentURL(_data); - if (viewDataURL != null) - { - bb.add(new ActionButton("View data", viewDataURL)); - } - - if (_data.isPathAccessible()) - { - bb.add(new ActionButton("View file", ExperimentUrlsImpl.get().getShowFileURL(_data, true))); - bb.add(new ActionButton("Download file", ExperimentUrlsImpl.get().getShowFileURL(_data, false))); - - if (getContainer().hasPermission(getUser(), InsertPermission.class)) - { - String relativePath = null; - PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); - if (root != null) - { - Path rootFile = root.getRootNioPath(); - Path dataFile = _data.getFilePath(); - if (dataFile != null) - { - Path pathRelative; - try - { - pathRelative = rootFile.relativize(dataFile); - if (null != pathRelative) - relativePath = pathRelative.toString(); - } - catch (IllegalArgumentException e) - { - // dataFile not relative to root - } - } - } - ActionURL browseURL = urlProvider(PipelineUrls.class).urlBrowse(getContainer(), getViewContext().getActionURL(), relativePath); - bb.add(new ActionButton("Browse in pipeline", browseURL)); - } - } - - // add links to any other exp.data that share the same dataFileUrl path - var altDataList = ExperimentService.get().getAllExpDataByURL(_data.getDataFileUrl(), getContainer()); - altDataList.removeIf(_data::equals); - if (!altDataList.isEmpty()) - { - MenuButton menu = new MenuButton("Alternate Data"); - for (ExpData altData : altDataList) - { - ExpRun altDataRun = altData.getRun(); - StringBuilder sb = new StringBuilder(altData.getName()); - if (altDataRun != null) - sb.append(" created by run '").append(altDataRun.getName()).append("' (").append(altDataRun.getProtocol().getName()).append(")"); - menu.addMenuItem(sb.toString(), altData.detailsURL()); - } - bb.add(menu); - } - - dr.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); - dr.setButtonBar(bb); - - CustomPropertiesView cpv = new CustomPropertiesView(_data.getLSID(), getContainer()); - HBox hbox = new StandardAndCustomPropertiesView(detailsView, cpv); - - VBox vbox = new VBox(hbox); - - ParentChildView pv = new ParentChildView(_data, getViewContext()); - vbox.addView(pv); - - ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); - runListView.getRunTable().setInputData(_data); - runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); - runListView.getRunTable().setLocked(true); - runListView.setTitle("Runs using this data as an input"); - vbox.addView(runListView); - - if (_data.isInlineImage() && _data.isFileOnDisk()) - { - ActionURL showFileURL = new ActionURL(ShowFileAction.class, getContainer()).addParameter("rowId", _data.getRowId()); - HtmlView imageView = new HtmlView(IMG(at(src, showFileURL))); - return new VBox(vbox, imageView); - } - return vbox; - } - } - - @RequiresPermission(AdminPermission.class) - public static class CheckDataFileAction extends MutatingApiAction - { - private ExpDataImpl _data; - - @Override - public void validateForm(DataFileForm form, Errors errors) - { - _data = form.lookupData(); - if (_data == null) - { - errors.reject(ERROR_MSG, "No ExpData found for id: " + form.getRowId()); - } - } - - @Override - public ApiResponse execute(DataFileForm form, BindException errors) - { - File dataFile = _data.getFile(); - Container dataContainer = _data.getContainer(); - boolean fileExists = _data.isFileOnDisk(); - boolean fileExistsAtCurrent = false; - File newDataFile = null; - - ApiSimpleResponse response = new ApiSimpleResponse(); - response.put("dataFileUrl", _data.getDataFileUrl()); - response.put("fileExists", fileExists); - response.put("containerPath", dataContainer.getPath()); - - if (!fileExists) - { - PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(dataContainer); - if (pipelineRoot != null && pipelineRoot.isValid() && dataFile != null) - { - newDataFile = pipelineRoot.resolvePath("/" + AssayFileWriter.DIR_NAME + "/" + dataFile.getName()); - fileExistsAtCurrent = NetworkDrive.exists(newDataFile); - response.put("fileExistsAtCurrent", fileExistsAtCurrent); - } - } - - // if the current dataFileUrl does not exist on disk and we have the file at the current - // pipeline root /assaydata dir, fix the dataFileUrl value - if (form.isAttemptFilePathFix()) - { - if (fileExistsAtCurrent) - { - ExpDataFileListener fileListener = new ExpDataFileListener(); - fileListener.fileMoved(dataFile, newDataFile, getUser(), dataContainer); - response.put("filePathFixed", true); - - // update the ExpData object so that we can get the new dataFileUrl - _data = form.lookupData(); - response.put("newDataFileUrl", _data.getDataFileUrl()); - } - else - { - response.put("filePathFixed", false); - } - } - - response.put("success", true); - return response; - } - } - - public static class DataFileForm extends DataForm - { - private boolean _attemptFilePathFix; - - public boolean isAttemptFilePathFix() - { - return _attemptFilePathFix; - } - - public void setAttemptFilePathFix(boolean attemptFilePathFix) - { - _attemptFilePathFix = attemptFilePathFix; - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowFileAction extends AbstractDataAction - { - @Override - protected ModelAndView getDataView(DataForm form, BindException errors) throws IOException - { - if (!_data.isPathAccessible()) - { - throw new NotFoundException("Data file " + _data.getDataFileUrl() + " does not exist on disk"); - } - - PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); - if (root != null && !root.isUnderRoot(_data.getFilePath())) - { - // Issue 35649: ImmPort module "publish" creates exp.data object in this container for paths that originate in a different container - FileContentService fileSvc = FileContentService.get(); - if (fileSvc == null) - throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); - - List containers = fileSvc.getContainersForFilePath(_data.getFilePath()); - if (containers.isEmpty() || containers.stream().noneMatch(c -> c.hasPermission(getUser(), ReadPermission.class))) - throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); - } - - //Issues 25667 and 31152 - if (form.isInline()) - { - ExperimentDataHandler h = _data.findDataHandler(); - if (h != null) - { - URLHelper url = h.getShowFileURL(_data); - if (url != null) - { - throw new RedirectException(url, false); - } - } - } - - try - { - Path realContent = _data.getFilePath(); - if (null == realContent) - throw new IllegalStateException("Path not found."); - - boolean inline = _data.isInlineImage() || form.isInline() || "inlineImage".equalsIgnoreCase(form.getFormat()); - if (_data.isInlineImage() && form.getMaxDimension() != null) - { - try (InputStream inputStream = Files.newInputStream(realContent)) - { - BufferedImage image = ImageIO.read(inputStream); - // If image, create a thumbnail, otherwise fall through as a regular download attempt - if (image != null) - { - int imageMax = Math.max(image.getHeight(), image.getWidth()); - if (imageMax > form.getMaxDimension().intValue()) - { - double scale = (double) form.getMaxDimension().intValue() / (double) imageMax; - ByteArrayOutputStream bOut = new ByteArrayOutputStream(); - ImageUtil.resizeImage(image, bOut, scale, 1); - PageFlowUtil.streamFileBytes(getViewContext().getResponse(), FileUtil.getFileName(realContent) + ".png", bOut.toByteArray(), !inline); - return null; - } - } - } - } - - boolean extended = "jsonTSVExtended".equalsIgnoreCase(form.getFormat()); - boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(form.getFormat()); - if ("jsonTSV".equalsIgnoreCase(form.getFormat()) || extended || ignoreTypes) - { - if (!FileUtil.hasCloudScheme(realContent)) // TODO: handle streaming from S3 to JSON - streamToJSON(FileSystemLike.wrapFile(realContent), form.getFormat(), -1, null); - return null; - } - - try (InputStream inputStream = Files.newInputStream(realContent)) - { - PageFlowUtil.streamFile(getViewContext().getResponse(), Collections.emptyMap(), FileUtil.getFileName(realContent), inputStream, !inline); - } - } - catch (IOException e) - { - try - { - // Try to write the exception back to the caller if we haven't already flushed the buffer - ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse()); - writer.writeResponse(e); - } - catch (IllegalStateException ise) - { - // Most likely that a disconnected client caused the IOException writing back the response - } - } - - return null; - } - } - - - public static class ParseForm - { - String format = "jsonTSV"; - int maxRows = -1; - - public String getFormat() - { - return format; - } - - public void setFormat(String format) - { - this.format = format; - } - - public int getMaxRows() - { - return maxRows; - } - - public void setMaxRows(int maxRow) - { - this.maxRows = maxRow; - } - } - - @RequiresNoPermission - public class ParseFileAction extends MutatingApiAction - { - @Override - public Object execute(ParseForm form, BindException errors) throws Exception - { - if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) - throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); - - MultipartFile formFile = getFileMap().get("file"); - if (formFile == null) - { - return true; - } - - FileLike tempFile = null; - try - { - tempFile = FileUtil.createTempFileLike("parse", formFile.getOriginalFilename()); - FileUtil.copyData(formFile.getInputStream(), tempFile.openOutputStream()); - streamToJSON(tempFile, form.getFormat(), form.getMaxRows(), formFile.getOriginalFilename()); - } - finally - { - if (null != tempFile) - tempFile.delete(); - } - return null; - } - } - - - // SampleTypeTest - private void streamToJSON(FileLike realContent, String format, int maxRow, String originalFileName) throws IOException - { - String lowerCaseFileName = realContent.getName().toLowerCase(); - boolean extended = "jsonTSVExtended".equalsIgnoreCase(format); - boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(format); - - JSONArray sheetsArray; - if (lowerCaseFileName.endsWith(".xls") || lowerCaseFileName.endsWith(".xlsx")) - { - try (InputStream in = realContent.openInputStream()) - { - sheetsArray = ExcelFactory.convertExcelToJSON(in, extended, maxRow); - } - } - else - { - DataLoaderFactory dlf = DataLoader.get().findFactory(realContent, null); - if (null == dlf) - { - throw new ApiUsageException("Unable to parse file " + realContent + ", it is likely of an unsupported file type"); - } - - try (InputStream in = realContent.openInputStream(); - DataLoader tabLoader = dlf.createLoader(in, true)) - { - tabLoader.setScanAheadLineCount(5000); - ColumnDescriptor[] cols = tabLoader.getColumns(); - - if (ignoreTypes) - for (ColumnDescriptor col : cols) - col.clazz = String.class; - - JSONArray rowsArray = new JSONArray(); - JSONArray headerArray = new JSONArray(); - for (ColumnDescriptor col : cols) - { - if (extended) - { - JSONObject valueObject = new JSONObject(); - valueObject.put("value", col.name); - headerArray.put(valueObject); - } - else - { - headerArray.put(col.name); - } - } - rowsArray.put(headerArray); - for (Map rowMap : tabLoader) - { - // headers count as a row to be consistent - if (maxRow > -1 && maxRow <= rowsArray.length() + 1) - break; - - JSONArray rowArray = new JSONArray(); - for (ColumnDescriptor col : cols) - { - Object value = rowMap.get(col.name); - if (extended) - { - JSONObject valueObject = new JSONObject(); - valueObject.put("value", value); - rowArray.put(valueObject); - } - else - { - rowArray.put(value); - } - } - rowsArray.put(rowArray); - } - - JSONObject sheetJSON = new JSONObject(); - sheetJSON.put("name", "flat"); - sheetJSON.put("data", rowsArray); - sheetsArray = new JSONArray(); - sheetsArray.put(sheetJSON); - } - } - - try (ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse())) - { - JSONObject workbookJSON = new JSONObject(); - workbookJSON.put("fileName", realContent.getName()); - workbookJSON.put("sheets", sheetsArray); - if (originalFileName != null) - workbookJSON.put("originalFileName", originalFileName); - writer.writeResponse(new ApiSimpleResponse(workbookJSON)); - } - } - - - public static class ConvertArraysToExcelForm - { - private String _json; - - public String getJson() - { - return _json; - } - - public void setJson(String json) - { - _json = json; - } - } - - @RequiresPermission(ReadPermission.class) - public static class ConvertArraysToExcelAction extends ExportAction - { - @Override - public void validate(ConvertArraysToExcelForm form, BindException errors) - { - if (form.getJson() == null) - { - errors.reject(ERROR_MSG, "Unable to convert to Excel - no spreadsheet data given"); - } - } - - @Override - public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception - { - try - { - JSONObject rootObject; - JSONArray sheetsArray; - if (form.getJson() == null || form.getJson().trim().isEmpty()) - { - // Create JSON so that we return an empty file - rootObject = new JSONObject(); - sheetsArray = new JSONArray(); - JSONObject sheetObject = new JSONObject(); - sheetsArray.put(sheetObject); - } - else - { - rootObject = new JSONObject(form.getJson()); - sheetsArray = rootObject.getJSONArray("sheets"); - } - String filename = rootObject.has("fileName") ? rootObject.getString("fileName") : "ExcelExport.xls"; - ExcelWriter.ExcelDocumentType docType = filename.toLowerCase().endsWith(".xlsx") ? ExcelWriter.ExcelDocumentType.xlsx : ExcelWriter.ExcelDocumentType.xls; - - try (Workbook workbook = ExcelFactory.createFromArray(sheetsArray, docType)) - { - response.setContentType(docType.getMimeType()); - ResponseHelper.setContentDisposition(response, ResponseHelper.ContentDispositionType.attachment, filename); - ResponseHelper.setPrivate(response); - workbook.write(response.getOutputStream()); - - JSONObject qInfo = rootObject.has("queryinfo") ? rootObject.getJSONObject("queryinfo") : null; - if (qInfo != null) - { - QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), - qInfo.getString("query"), getViewContext().getActionURL(), - rootObject.getString("auditMessage") + filename, - null); - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asExcel"); - } - } - } - catch (JSONException | ClassCastException e) - { - // We can get a ClassCastException if we expect an array and get a simple String, for example - ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to Excel - invalid input", e, false, false); - } - } - } - - @RequiresPermission(ReadPermission.class) - public static class ConvertArraysToTableAction extends ExportAction - { - @Override - public void validate(ConvertArraysToExcelForm form, BindException errors) - { - if (form.getJson() == null) - { - errors.reject(ERROR_MSG, "Unable to convert to table - no data given"); - } - } - - @Override - public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception - { - try - { - JSONObject rootObject; - JSONArray rowsArray; - if (form.getJson() == null || form.getJson().trim().isEmpty()) - { - // Create JSON so that we return an empty file - rootObject = new JSONObject(); - rowsArray = new JSONArray(); - } - else - { - rootObject = new JSONObject(form.getJson()); - rowsArray = rootObject.getJSONArray("rows"); - } - - TSVWriter.DELIM delimType = (!rootObject.isNull("delim") ? TSVWriter.DELIM.valueOf(rootObject.getString("delim")) : TSVWriter.DELIM.TAB); - TSVWriter.QUOTE quoteType = (!rootObject.isNull("quoteChar") ? TSVWriter.QUOTE.valueOf(rootObject.getString("quoteChar")) : TSVWriter.QUOTE.NONE); - String filenamePrefix = (!rootObject.isNull("fileNamePrefix") ? rootObject.getString("fileNamePrefix") : "Export"); - String filename = filenamePrefix + "." + delimType.extension; - String newlineChar = !rootObject.isNull("newlineChar") ? rootObject.getString("newlineChar") : "\n"; - - response.setCharacterEncoding(StringUtilsLabKey.DEFAULT_CHARSET.name()); - - try(var tsvWriter = new TSVJSONWriter(filenamePrefix, rowsArray)) - { - tsvWriter.setRowSeparator(newlineChar); - tsvWriter.setDelimiterCharacter(delimType); - tsvWriter.setQuoteCharacter(quoteType); - tsvWriter.write(response); - } - - JSONObject qInfo = rootObject.optJSONObject("queryinfo"); - if (qInfo != null) - { - QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), qInfo.getString("query"), - getViewContext().getActionURL(), - rootObject.getString("auditMessage") + filename, - rowsArray.length()); - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asDelimited"); - } - } - catch (JSONException e) - { - ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to table - invalid input", e, false, false); - } - } - } - - - public static class ConvertHtmlToExcelForm - { - private String _baseUrl; - private String _htmlFragment; - private String _name = "workbook.xls"; - - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - public String getBaseUrl() - { - return _baseUrl; - } - - public void setBaseUrl(String baseUrl) - { - _baseUrl = baseUrl; - } - - public String getHtmlFragment() - { - return _htmlFragment; - } - - public void setHtmlFragment(String htmlFragment) - { - _htmlFragment = htmlFragment; - } - } - - - @RequiresPermission(ReadPermission.class) - public static class ConvertHtmlToExcelAction extends FormViewAction - { - String _responseHtml = null; - - @Override - public void validateCommand(ConvertHtmlToExcelForm target, Errors errors) - { - } - - @Override - public ModelAndView getView(ConvertHtmlToExcelForm form, boolean reshow, BindException errors) - { - String html = - "

" + - "" + - new CsrfInput(getViewContext()) + - "
"; - return HtmlView.unsafe(html); - } - - @Override - public boolean handlePost(ConvertHtmlToExcelForm form, BindException errors) - { - ActionURL url = getViewContext().getActionURL(); - String base = url.getBaseServerURI(); - if (!base.endsWith("/")) base += "/"; - - String baseTag = ""; - SafeToRender css = PageFlowUtil.getStylesheetIncludes(getContainer()); - String htmlFragment = StringUtils.trimToEmpty(form.getHtmlFragment()); - String html = "" + baseTag + css + "" + htmlFragment + ""; - - // UNDONE: strip script - List tidyErrors = new ArrayList<>(); - String tidy = JSoupUtil.tidyHTML(html, false, tidyErrors); - - if (!tidyErrors.isEmpty()) - { - for (String err : tidyErrors) - { - errors.reject(ERROR_MSG, err); - } - return false; - } - - _responseHtml = tidy; - return true; - } - - @Override - public ModelAndView getSuccessView(ConvertHtmlToExcelForm form) - { - ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, form.getName()); - getPageConfig().setTemplate(PageConfig.Template.None); - HtmlView v = HtmlView.unsafe(_responseHtml); - v.setContentType("application/vnd.ms-excel"); - v.setFrame(WebPartView.FrameType.NONE); - return v; - } - - @Override - public URLHelper getSuccessURL(ConvertHtmlToExcelForm convertHtmlToExcelForm) - { - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - } - } - - - public static ActionURL getShowApplicationURL(Container c, long rowId) - { - ActionURL url = new ActionURL(ShowApplicationAction.class, c); - url.addParameter("rowId", rowId); - - return url; - } - - - @RequiresPermission(ReadPermission.class) - public class ShowApplicationAction extends SimpleViewAction - { - private ExpProtocolApplicationImpl _app; - private ExpRun _run; - - @Override - public ModelAndView getView(ExpObjectForm form, BindException errors) - { - _app = ExperimentServiceImpl.get().getExpProtocolApplication(form.getRowId()); - if (_app == null) - { - throw new NotFoundException("Could not find Protocol Application"); - } - _run = _app.getRun(); - if (_run == null) - { - throw new NotFoundException("No experiment run associated with Protocol Application"); - } - ensureCorrectContainer(getContainer(), _app, getViewContext()); - - ExpProtocol protocol = _app.getProtocol(); - - DataRegion dr = new DataRegion(); - dr.addColumns(ExperimentServiceImpl.get().getTinfoProtocolApplication().getUserEditableColumns()); - DetailsView detailsView = new DetailsView(dr, form.getRowId()); - dr.removeColumns("RunId", "ProtocolLSID", "RowId", "LSID"); - dr.addDisplayColumn(new ExperimentRunDisplayColumn(_run)); - dr.addDisplayColumn(new ProtocolDisplayColumn(protocol)); - dr.addDisplayColumn(new LineageGraphDisplayColumn(_app, _run)); - detailsView.setTitle("Protocol Application"); - - Container c = getContainer(); - ApplicationOutputGrid outMGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoMaterial()); - ApplicationOutputGrid outDGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoData()); - Map map = new HashMap<>(); - for (ProtocolApplicationParameter param : ExperimentService.get().getProtocolApplicationParameters(_app.getRowId())) - { - map.put(param.getOntologyEntryURI(), param); - } - - JspView> paramsView = new JspView<>("/org/labkey/experiment/Parameters.jsp", map); - paramsView.setTitle("Protocol Application Parameters"); - CustomPropertiesView cpv = new CustomPropertiesView(_app.getLSID(), c); - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), paramsView, outMGrid, outDGrid); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Experiment Run", ExperimentUrlsImpl.get().getRunGraphDetailURL(_run)); - root.addChild("Protocol Application " + _app.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowProtocolGridAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - return new ProtocolWebPart(false, getViewContext()); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Protocols"); - } - } - - @RequiresPermission(ReadPermission.class) - public class ProtocolDetailsAction extends SimpleViewAction - { - private ExpProtocolImpl _protocol; - - @Override - public ModelAndView getView(ExpObjectForm form, BindException errors) - { - _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getRowId()); - if (_protocol == null) - { - _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getLSID()); - } - - if (_protocol == null) - { - throw new NotFoundException("Unable to find a matching protocol"); - } - ensureCorrectContainer(getContainer(), _protocol, getViewContext()); - - JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", _protocol); - detailsView.setTitle("Standard Properties"); - - CustomPropertiesView cpv = new CustomPropertiesView(_protocol.getLSID(), getContainer()); - ProtocolParametersView parametersView = new ProtocolParametersView(_protocol); - - VBox protocolDetails = new VBox(); - protocolDetails.setFrame(WebPartView.FrameType.PORTAL); - protocolDetails.setTitle("Protocol Details"); - protocolDetails.addView(new ProtocolInputOutputsView(_protocol, errors)); - - JspView stepsView = new JspView<>("/org/labkey/experiment/ProtocolSteps.jsp", _protocol); - stepsView.setTitle("Protocol Steps"); - stepsView.setFrame(WebPartView.FrameType.TITLE); - protocolDetails.addView(stepsView); - - ExpSchema schema = new ExpSchema(getUser(), getContainer()); - ExperimentRunListView runView = new ExperimentRunListView(schema, ExperimentRunListView.getRunListQuerySettings(schema, getViewContext(), ExpSchema.TableType.Runs.name(), true), ExperimentRunType.ALL_RUNS_TYPE) - { - @Override - public DataView createDataView() - { - DataView result = super.createDataView(); - result.getRenderContext().setBaseFilter(new SimpleFilter(FieldKey.fromParts("Protocol", "LSID"), _protocol.getLSID())); - return result; - } - }; - - runView.setTitle("Runs Using This Protocol"); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails, runView); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); - root.addChild("Protocol: " + _protocol.getName()); - } - } - - public class ProtocolInputOutputsView extends VBox - { - ProtocolInputOutputsView(ExpProtocol protocol, Errors errors) - { - HBox inputsView = new HBox(); - addView(inputsView); - - HBox outputsView = new HBox(); - addView(outputsView); - - UserSchema expSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_NAME); - - class ProtocolInputGrid extends QueryView - { - public ProtocolInputGrid(String title, QuerySettings settings, @Nullable Errors errors) - { - super(expSchema, settings, errors); - - setFrame(FrameType.TITLE); - setTitle(title); - setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); - setShowBorders(true); - setShadeAlternatingRows(true); - setShowExportButtons(false); - setShowPagination(false); - disableContainerFilterSelection(); - } - } - - // INPUTS - - QuerySettings materialInputsSettings = expSchema.getSettings("mpi", ExpSchema.TableType.MaterialProtocolInputs.toString()); - materialInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - materialInputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) - )); - QueryView materialInputsView = new ProtocolInputGrid("Material Inputs", materialInputsSettings, errors); - inputsView.addView(materialInputsView); - - QuerySettings dataInputsSettings = expSchema.getSettings("dpi", ExpSchema.TableType.DataProtocolInputs.toString()); - dataInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - dataInputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) - )); - QueryView dataInputsView = new ProtocolInputGrid("Data Inputs", dataInputsSettings, errors); - inputsView.addView(dataInputsView); - - // OUTPUTS - - QuerySettings materialOutputsSettings = expSchema.getSettings("mpo", ExpSchema.TableType.MaterialProtocolInputs.toString()); - materialOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - materialOutputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) - )); - QueryView materialOutputsView = new ProtocolInputGrid("Material Outputs", materialOutputsSettings, errors); - outputsView.addView(materialOutputsView); - - QuerySettings dataOutputsSettings = expSchema.getSettings("dpo", ExpSchema.TableType.DataProtocolInputs.toString()); - dataOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - dataOutputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) - )); - QueryView dataOutputsView = new ProtocolInputGrid("Data Outputs", dataOutputsSettings, errors); - outputsView.addView(dataOutputsView); - } - } - - - @RequiresPermission(ReadPermission.class) - public class ProtocolPredecessorsAction extends SimpleViewAction - { - private ExpProtocol _parentProtocol; - private ProtocolActionStepDetail _actionStep; - - @Override - public ModelAndView getView(Object o, BindException errors) - { - ActionURL url = getViewContext().getActionURL(); - - String parentProtocolLSID = url.getParameter("ParentLSID"); - int actionSequence; - try - { - actionSequence = Integer.parseInt(url.getParameter("Sequence")); - } - catch (NumberFormatException e) - { - throw new NotFoundException("Could not find SequenceId " + url.getParameter("Sequence")); - } - - _parentProtocol = ExperimentService.get().getExpProtocol(parentProtocolLSID); - if (_parentProtocol == null) - { - throw new NotFoundException("Unable to find a matching protocol"); - } - - ensureCorrectContainer(getContainer(), _parentProtocol, getViewContext()); - - _actionStep = ExperimentServiceImpl.get().getProtocolActionStepDetail(parentProtocolLSID, actionSequence); - - if (_actionStep == null) - { - throw new NotFoundException("Unable to find a matching protocol action step"); - } - - ExpProtocol childProtocol = ExperimentService.get().getExpProtocol(_actionStep.getChildProtocolLSID()); - - JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", childProtocol); - detailsView.setTitle("Standard Properties"); - - CustomPropertiesView cpv = new CustomPropertiesView(childProtocol.getLSID(), getContainer()); - - ProtocolParametersView parametersView = new ProtocolParametersView(childProtocol); - - VBox protocolDetails = new VBox(); - protocolDetails.setFrame(WebPartView.FrameType.PORTAL); - protocolDetails.setTitle("Protocol Details"); - protocolDetails.addView(new ProtocolInputOutputsView(childProtocol, errors)); - protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "PredecessorChildLSID", "PredecessorSequence", "ActionSequence", "Protocol Predecessors")); - protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "ChildProtocolLSID", "ActionSequence", "PredecessorSequence", "Protocol Successors")); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); - root.addChild("Parent Protocol '" + _parentProtocol.getName() + "'", ExperimentUrlsImpl.get().getProtocolDetailsURL(_parentProtocol)); - root.addChild("Protocol Step: " + _actionStep.getName()); - } - } - - public static class DataForm - { - private boolean _inline; - private long _rowId; - private String _lsid; - private Integer _maxDimension; - private String _format; - - public boolean isInline() - { - return _inline; - } - - public void setInline(boolean inline) - { - _inline = inline; - } - - public long getRowId() - { - return _rowId; - } - - public void setRowId(long rowId) - { - _rowId = rowId; - } - - public String getLsid() - { - return _lsid; - } - - public void setLsid(String lsid) - { - _lsid = lsid; - } - - public ExpDataImpl lookupData() - { - ExpDataImpl result = ExperimentServiceImpl.get().getExpData(getRowId()); - if (result == null && getLsid() != null) - { - result = ExperimentServiceImpl.get().getExpData(getLsid()); - } - return result; - } - - public Integer getMaxDimension() - { - return _maxDimension; - } - - public void setMaxDimension(Integer maxDimension) - { - _maxDimension = maxDimension; - } - - public String getFormat() - { - return _format; - } - - public void setFormat(String format) - { - _format = format; - } - } - - public static class ExpObjectForm extends QueryViewAction.QueryExportForm - { - private long _rowId; - private String _lsid; - - public String getLsid() - { - return _lsid; - } - - public void setLsid(String lsid) - { - _lsid = lsid; - } - - public String getLSID() - { - return getLsid(); - } - - public void setLSID(String lsid) - { - setLsid(lsid); - } - - public long getRowId() - { - return _rowId; - } - - public void setRowId(long rowId) - { - _rowId = rowId; - } - } - - @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) - public class DeleteSelectedExpRunsAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - // UNDONE: Need help topic on Runs - setHelpTopic("experiment"); - super.addNavTrail(root); - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List runs = new ArrayList<>(); - - Map idToRunMap = new LongHashMap<>(); - for (long runId : deleteForm.getIds(false)) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run != null) - { - if (!run.canDelete(getUser())) - throw new UnauthorizedException("You do not have permission to delete " + - (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") - + " in " + run.getContainer()); - - runs.add(run); - idToRunMap.put(run.getRowId(), run); - } - } - - Map referencedItems = new LongHashMap<>(); - List referenceDescriptions = new ArrayList<>(); - AssayService assayService = AssayService.get(); - if (!idToRunMap.isEmpty() && assayService != null ) - { - // using the first run as a representative, since all interactions here are (I believe) using the same protocol. - ExpProtocol protocol = runs.get(0).getProtocol(); - AssayProvider provider = assayService.getProvider(protocol); - if (provider != null) - { - SchemaKey key = AssayProtocolSchema.schemaName(provider, protocol); - ExperimentService.get().getObjectReferencers() - .forEach(referencer -> { - Collection referenced = referencer.getItemsWithReferences( - idToRunMap.keySet(), - key.toString(), - "Runs" - ); - referenced.forEach(id -> referencedItems.put(id, idToRunMap.get(id))); - referenceDescriptions.add(referencer.getObjectReferenceDescription(ExpRun.class)); - } - ); - } - - } - - List> permissionDatasetRows = new ArrayList<>(); - List> noPermissionDatasetRows = new ArrayList<>(); - if (StudyPublishService.get() != null) - { - for (Dataset dataset : StudyPublishService.get().getDatasetsForAssayRuns(runs, getUser())) - { - ActionURL url = urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId()); - TableInfo t = dataset.getTableInfo(getUser()); - if (null != t && t.hasPermission(getUser(),DeletePermission.class)) - { - permissionDatasetRows.add(new Pair<>(dataset, url)); - } - else - { - noPermissionDatasetRows.add(new Pair<>(dataset, url)); - } - } - } - - return new ConfirmDeleteView( - "run", - ShowRunGraphAction.class, - runs.stream().filter(run -> !referencedItems.containsKey(run.getRowId())).toList(), - deleteForm, - Collections.emptyList(), - "dataset(s) have one or more rows which", - permissionDatasetRows, - noPermissionDatasetRows, - referencedItems.values().stream().toList(), - referenceDescriptions.stream().filter(Objects::nonNull).collect(Collectors.joining(", or "))); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - ExperimentServiceImpl.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), deleteForm.getUserComment(), deleteForm.getIds(false)); - } - } - - public static class DeleteRunForm - { - private int _runId; - - public int getRunId() - { - return _runId; - } - - public void setRunId(int runId) - { - _runId = runId; - } - } - - /** - * Separate delete action from the client API - */ - @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) - public static class DeleteRunAction extends MutatingApiAction - { - @Override - public ApiResponse execute(DeleteRunForm form, BindException errors) - { - ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); - if (run == null) - { - throw new NotFoundException("Could not find run with ID " + form.getRunId()); - } - if (!run.canDelete(getUser())) - throw new UnauthorizedException("You do not have permission to delete " - + (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") + " in this container."); - - run.delete(getUser()); - return new ApiSimpleResponse("success", true); - } - } - - - @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) - public static class DeleteRunsAction extends AbstractDeleteAPIAction - { - @Override - protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) - { - Set runIdsToDelete = new HashSet<>(form.getIds(true)); - Set runIdsCascadeDeleted = new HashSet<>(); - - if (form.isCascade()) - { - for (long runId : runIdsToDelete) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run != null) - addReplacesRuns(run, runIdsCascadeDeleted); - } - - if (!runIdsCascadeDeleted.isEmpty()) - runIdsToDelete.addAll(runIdsCascadeDeleted); - } - - ExperimentService.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), form.getUserComment(), runIdsToDelete); - - ApiSimpleResponse response = new ApiSimpleResponse("success", true); - response.put("runIdsDeleted", runIdsToDelete); - if (!runIdsCascadeDeleted.isEmpty()) - response.put("runIdsCascadeDeleted", runIdsCascadeDeleted); - return response; - } - - private void addReplacesRuns(ExpRun run, Set runIds) - { - for (ExpRun replacedRun : run.getReplacesRuns()) - { - runIds.add(replacedRun.getRowId()); - addReplacesRuns(replacedRun, runIds); - } - } - } - - private abstract static class AbstractDeleteAPIAction extends MutatingApiAction - { - @Override - public void validateForm(CascadeDeleteForm form, Errors errors) - { - if (form.getSingleObjectRowId() == null && form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "Either singleObjectRowId, dataRegionSelectionKey, or rowIds is required"); - } - - @Override - public ApiResponse execute(CascadeDeleteForm form, BindException errors) throws Exception - { - ApiSimpleResponse response; - - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - tx.addCommitTask(form::clearSelected, POSTCOMMIT); - - response = deleteObjects(form); - tx.commit(); - } - - if (null != response.get("success")) - response.put("success", !errors.hasErrors()); - - return response; - } - - protected abstract ApiSimpleResponse deleteObjects(CascadeDeleteForm form) throws Exception; - } - - public static class CascadeDeleteForm extends DeleteForm - { - private boolean _cascade; - - public boolean isCascade() - { - return _cascade; - } - - public void setCascade(boolean cascade) - { - _cascade = cascade; - } - } - - private abstract static class AbstractDeleteAction extends FormViewAction - { - @Override - public void validateCommand(DeleteForm target, Errors errors) - { - } - - @Override - public boolean handlePost(DeleteForm deleteForm, BindException errors) throws Exception - { - if (!deleteForm.isForceDelete()) - { - return false; - } - else - { - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - tx.addCommitTask(deleteForm::clearSelected, POSTCOMMIT); - - deleteObjects(deleteForm); - tx.commit(); - } - catch (BatchValidationException v) - { - v.addToErrors(errors); - } - - return !errors.hasErrors(); - } - } - - @Override - public ActionURL getSuccessURL(DeleteForm form) - { - return form.getSuccessActionURL(ExperimentUrlsImpl.get().getOverviewURL(getContainer())); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Confirm Deletion"); - } - - protected abstract void deleteObjects(DeleteForm form) throws Exception; - } - - @RequiresPermission(DesignAssayPermission.class) - public static class DeleteProtocolByRowIdsAPIAction extends AbstractDeleteAPIAction - { - @Override - protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) - { - for (ExpProtocol protocol : getProtocolsForDeletion(form)) - { - if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) - throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); - - protocol.delete(getUser(), form.getUserComment()); - } - - return new ApiSimpleResponse(); - } - } - - public static List getProtocolsForDeletion(DeleteForm form) - { - List protocols = new ArrayList<>(); - for (long protocolId : form.getIds(false)) - { - ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); - if (protocol != null) - { - protocols.add(protocol); - } - } - return protocols; - } - - @RequiresPermission(DesignAssayPermission.class) - public class DeleteProtocolByRowIdsAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - // UNDONE: Need help topic on protocols - setHelpTopic("experiment"); - super.addNavTrail(root); - } - - @Override - public ModelAndView getView(DeleteForm form, boolean reshow, BindException errors) - { - List runs = ExperimentService.get().getExpRunsForProtocolIds(false, form.getIds(false)); - List protocols = getProtocolsForDeletion(form); - String noun = "Assay Design"; - List> deleteableDatasets = new ArrayList<>(); - List> noPermissionDatasets = new ArrayList<>(); - if (AssayService.get() != null && StudyService.get() != null) - { - for (ExpProtocol protocol : protocols) - { - if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) - throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); - - if (AssayService.get().getProvider(protocol) == null) - { - noun = "Protocol"; - } - for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(protocol.getRowId(), Dataset.PublishSource.Assay)) - { - Pair entry = new Pair<>(dataset, urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId())); - if (dataset.canDeleteDefinition(getUser())) - { - deleteableDatasets.add(entry); - } - else - { - noPermissionDatasets.add(entry); - } - } - } - } - - return new ConfirmDeleteView(noun, ProtocolDetailsAction.class, protocols, form, runs, "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); - } - - @Override - protected void deleteObjects(DeleteForm form) - { - for (ExpProtocol protocol : getProtocolsForDeletion(form)) - { - protocol.delete(getUser(), form.getUserComment()); - } - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetDataOperationConfirmationDataAction extends ReadOnlyApiAction - { - @Override - public void validateForm(DataOperationConfirmationForm form, Errors errors) - { - if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey"); - if (form.getDataOperation() == null) - errors.reject(ERROR_REQUIRED, "An operation type must be provided."); - } - - @Override - public Object execute(DataOperationConfirmationForm form, BindException errors) - { - Collection requestIds = form.getIds(false); - ExperimentServiceImpl service = ExperimentServiceImpl.get(); - List allData = service.getExpDatas(requestIds); - - Set notAllowedIds = new HashSet<>(); - if (form.getDataOperation() == ExpDataImpl.DataOperations.Delete) - service.getObjectReferencers().forEach(referencer -> - notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "exp.data"))); - - Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allData); - - Collection containers = new HashSet<>(); - Collection notPermittedIds = new ArrayList<>(); - Class permClass = form.getDataOperation().getPermissionClass(); - for (ExpDataImpl expData : allData) - { - Container c = expData.getContainer(); - if (c.hasPermission(getUser(), ReadPermission.class)) - containers.add(c); - if (permClass != null && !c.hasPermission(getUser(), permClass)) - notPermittedIds.add(expData.getRowId()); - } - - NameExpressionOptionService svc = NameExpressionOptionService.get(); - response.put("containers", containers.stream().map(c -> Map.of( - "id", c.getEntityId(), - "path", (Object) c.getPath(), - "permitted", permClass == null || c.hasPermission(getUser(), permClass), - "canEditName", svc.getAllowUserSpecificNamesValue(c) - )).toList()); - - response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); - - return success(response); - } - } - - - public static class DataOperationConfirmationForm extends DataViewSnapshotSelectionForm - { - private ExpDataImpl.DataOperations _dataOperation; - - public ExpDataImpl.DataOperations getDataOperation() - { - return _dataOperation; - } - - public void setDataOperation(ExpDataImpl.DataOperations dataOperation) - { - _dataOperation = dataOperation; - } - - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetMaterialOperationConfirmationDataAction extends ReadOnlyApiAction - { - @Override - public void validateForm(MaterialOperationConfirmationForm form, Errors errors) - { - if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); - if (form.getSampleOperation() == null) - errors.reject(ERROR_REQUIRED, "An operation type must be provided."); - } - - @Override - public Object execute(MaterialOperationConfirmationForm form, BindException errors) - { - Set requestIds = form.getIds(false); - ExperimentServiceImpl service = ExperimentServiceImpl.get(); - List allMaterials = service.getExpMaterials(requestIds); - - Set notAllowedIds = new HashSet<>(); - // We prevent deletion if a sample is used as a parent, has assay data, is used in a job, etc. - if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) - service.getObjectReferencers().forEach(referencer -> - notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "samples"))); - - if (SampleStatusService.get().supportsSampleStatus()) - notAllowedIds.addAll(service.findIdsNotPermittedForOperation(allMaterials, form.getSampleOperation())); - - Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allMaterials); - - Collection containers = new HashSet<>(); - Collection notPermittedIds = new ArrayList<>(); - Class permClass = form.getSampleOperation().getPermissionClass(); - for (ExpMaterial material : allMaterials) - { - Container c = material.getContainer(); - if (c.hasPermission(getUser(), ReadPermission.class)) - containers.add(c); - if (permClass != null && !c.hasPermission(getUser(), permClass)) - notPermittedIds.add(material.getRowId()); - } - - NameExpressionOptionService svc = NameExpressionOptionService.get(); - - response.put("containers", containers.stream().map(c -> Map.of( - "id", c.getEntityId(), - "path", (Object) c.getPath(), - "permitted", permClass == null || c.hasPermission(getUser(), permClass), - "canEditName", svc.getAllowUserSpecificNamesValue(c) - )).toList()); - - response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); - - if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) - // String 'associatedDatasets' must be synced to its handling in confirmDelete.js, confirmDelete() - response.put("associatedDatasets", ExperimentServiceImpl.includeLinkedToStudyText(allMaterials, requestIds, getUser(), getContainer())); - - return success(response); - } - } - - public static class MaterialOperationConfirmationForm extends DataViewSnapshotSelectionForm - { - private SampleTypeService.SampleOperations _sampleOperation; - - public SampleTypeService.SampleOperations getSampleOperation() - { - return _sampleOperation; - } - - public void setSampleOperation(SampleTypeService.SampleOperations sampleOperation) - { - _sampleOperation = sampleOperation; - } - } - - @RequiresPermission(DeletePermission.class) - public class DeleteSelectedDataAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - // UNDONE: Need help topic on Datas - setHelpTopic("experiment"); - super.addNavTrail(root); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) throws Exception - { - List datas = getDatas(deleteForm, false); - - for (ExpRun run : getRuns(datas)) - { - if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) - throw new UnauthorizedException(); - } - - // Issue 32076: Delete the exp.Data objects using QueryUpdateService so trigger scripts will be executed - Map, List> byDataClass = datas.stream().collect(Collectors.groupingBy(d -> Optional.ofNullable(d.getDataClass(null)))); - for (Optional opt : byDataClass.keySet()) - { - SchemaKey schemaKey; - String queryName; - ExpDataClass dc = opt.orElse(null); - List ds = byDataClass.get(opt); - if (dc == null) - { - // Reference to exp.Data table - schemaKey = ExpSchema.SCHEMA_EXP; - queryName = ExpSchema.TableType.Data.name(); - } - else - { - // Reference to exp.data. table - schemaKey = ExpSchema.SCHEMA_EXP_DATA; - queryName = dc.getName(); - } - - UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), schemaKey); - if (schema == null) - throw new IllegalStateException("Failed to get schema '" + schemaKey + "'"); - - TableInfo table = schema.getTable(queryName); - if (table == null) - throw new IllegalStateException("Failed to get table '" + queryName + "' in schema '" + schemaKey + "'"); - - QueryUpdateService qus = table.getUpdateService(); - if (qus == null) - throw new IllegalStateException(); - - qus.deleteRows(getUser(), getContainer(), toKeys(ds), null, null); - } - } - - protected List> toKeys(List datas) - { - return datas.stream().map(d -> CaseInsensitiveHashMap.of("rowId", d.getRowId())).collect(toList()); - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - if (errors.hasErrors()) - return new SimpleErrorView(errors, false); - - List datas = getDatas(deleteForm, false); - List runs = getRuns(datas); - - return new ConfirmDeleteView("Data", ShowDataAction.class, datas, deleteForm, runs); - } - - private List getRuns(List datas) - { - List runArray = ExperimentService.get().getRunsUsingDatas(datas); - return new ArrayList<>(ExperimentService.get().runsDeletedWithInput(runArray)); - } - - private List getDatas(DeleteForm deleteForm, boolean clear) - { - List datas = new ArrayList<>(); - for (long dataId : deleteForm.getIds(clear)) - { - ExpData data = ExperimentService.get().getExpData(dataId); - if (data != null) - { - datas.add(data); - } - } - return datas; - } - } - - @RequiresPermission(DeletePermission.class) - public class DeleteSelectedExperimentsAction extends AbstractDeleteAction - { - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - for (ExpExperiment exp : lookupExperiments(deleteForm)) - { - exp.delete(getUser()); - } - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List experiments = lookupExperiments(deleteForm); - - List runs = new ArrayList<>(); - boolean allBatches = true; - for (ExpExperiment experiment : experiments) - { - // Deleting a batch also deletes all of its runs - if (experiment.getBatchProtocol() != null) - { - runs.addAll(experiment.getRuns()); - } - else - { - allBatches = false; - } - } - - return new ConfirmDeleteView(allBatches ? "batch" : "run group", DetailsAction.class, experiments, deleteForm, runs); - } - - private List lookupExperiments(DeleteForm deleteForm) - { - List experiments = new ArrayList<>(); - for (long experimentId : deleteForm.getIds(false)) - { - ExpExperiment experiment = ExperimentService.get().getExpExperiment(experimentId); - if (experiment != null) - { - experiments.add(experiment); - } - } - return experiments; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - super.addNavTrail(root); - } - } - - @RequiresPermission(DesignSampleTypePermission.class) - public class DeleteSampleTypesAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - super.addNavTrail(root); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - List sampleTypes = getSampleTypes(deleteForm); - if (sampleTypes.isEmpty()) - { - throw new NotFoundException("No sample types found for ids provided."); - } - if (!ensureCorrectContainer(sampleTypes)) - { - throw new UnauthorizedException(); - } - - for (ExpRun run : getRuns(sampleTypes)) - { - if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new UnauthorizedException(); - } - } - - for (ExpSampleType source : sampleTypes) - { - Domain domain = source.getDomain(); - if (!domain.getDomainKind().canDeleteDefinition(getUser(), domain)) - { - throw new UnauthorizedException(); - } - - source.delete(getUser(), deleteForm.getUserComment()); - } - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List sampleTypes = getSampleTypes(deleteForm); - if (!ensureCorrectContainer(sampleTypes)) - { - throw new RedirectException(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer(), "To delete a sample type, you must be in its folder or project.")); - } - - List> deleteableDatasets = new ArrayList<>(); - List> noPermissionDatasets = new ArrayList<>(); - if (StudyService.get() != null && StudyPublishService.get() != null) - { - for (ExpSampleType sampleType: sampleTypes) - { - for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(sampleType.getRowId(), Dataset.PublishSource.SampleType)) - { - ActionURL datasetURL = StudyService.get().getDatasetURL(getContainer(), dataset.getDatasetId()); - Pair entry = new Pair<>(dataset, datasetURL); - if (dataset.canDeleteDefinition(getUser())) - { - deleteableDatasets.add(entry); - } - else - { - noPermissionDatasets.add(entry); - } - } - } - } - return new ConfirmDeleteView("Sample Type", ShowSampleTypeAction.class, sampleTypes, deleteForm, getRuns(sampleTypes), "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); - } - - private List getSampleTypes(DeleteForm deleteForm) - { - List sources = new ArrayList<>(); - for (long rowId : deleteForm.getIds(false)) - { - ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId); - if (sampleType != null) - { - sources.add(sampleType); - } - } - return sources; - } - - private boolean ensureCorrectContainer(List sampleTypes) - { - for (ExpSampleType source : sampleTypes) - { - Container sourceContainer = source.getContainer(); - if (!sourceContainer.equals(getContainer())) - { - return false; - } - } - return true; - } - - private List getRuns(List sampleTypes) - { - if (!sampleTypes.isEmpty()) - { - List runArray = ExperimentService.get().getRunsUsingSampleTypes(sampleTypes.toArray(new ExpSampleType[0])); - return ExperimentService.get().runsDeletedWithInput(runArray); - } - else - { - return Collections.emptyList(); - } - } - } - - private DataRegion getSampleTypeRegion(ViewContext model) - { - TableInfo tableInfo = ExperimentServiceImpl.get().getTinfoSampleType(); - - QuerySettings settings = new QuerySettings(model, "SampleType"); - settings.setSelectionKey(DataRegionSelection.getSelectionKey(tableInfo.getSchema().getName(), tableInfo.getName(), "SampleType", settings.getDataRegionName())); - - DataRegion dr = new DataRegion(); - dr.setSettings(settings); - dr.addColumns(tableInfo.getUserEditableColumns()); - dr.removeColumns("lastindexed"); - dr.getDisplayColumn(0).setVisible(false); - - dr.getDisplayColumn("idcol1").setVisible(false); - dr.getDisplayColumn("idcol2").setVisible(false); - dr.getDisplayColumn("idcol3").setVisible(false); - dr.getDisplayColumn("lsid").setVisible(false); - dr.getDisplayColumn("materiallsidprefix").setVisible(false); - dr.getDisplayColumn("parentcol").setVisible(false); - - ActionURL url = new ActionURL(ShowSampleTypeAction.class, model.getContainer()); - dr.getDisplayColumn(1).setURL(url.addParameter("rowId", "${RowId}")); - dr.setShowRecordSelectors(getContainer().hasOneOf(getUser(), DeletePermission.class, UpdatePermission.class)); - - return dr; - } - - @RequiresPermission(ReadPermission.class) - @ActionNames("getSampleType,getSampleTypeApi") // Referenced in labkey-ui-components components/samples/actions.ts TODO: migrate getSampleTypeApi -> getSampleType - public static class GetSampleTypeAction extends ReadOnlyApiAction - { - @Override - public void validateForm(SampleTypeForm form, Errors errors) - { - if (form.getRowId() == null && form.getLSID() == null) - errors.reject(ERROR_REQUIRED, "RowId or LSID must be provided"); - } - - @Override - public Object execute(SampleTypeForm form, BindException errors) throws Exception - { - ExpSampleTypeImpl st = form.getSampleType(getContainer()); - - return getSampleTypeResponse(st); - } - } - - @NotNull - private static ApiSimpleResponse getSampleTypeResponse(ExpSampleType st) throws IOException - { - Map sampleType = new HashMap<>(); - sampleType.put("name", st.getName()); - sampleType.put("nameExpression", st.getNameExpression()); - sampleType.put("labelColor", st.getLabelColor()); - sampleType.put("metricUnit", st.getMetricUnit()); - sampleType.put("description", st.getDescription()); - sampleType.put("importAliases", st.getImportAliasMap()); - sampleType.put("lsid", st.getLSID()); - sampleType.put("rowId", st.getRowId()); - sampleType.put("domainId", st.getDomain().getTypeId()); - sampleType.put("category", st.getCategory()); - - return new ApiSimpleResponse(Map.of("sampleSet", sampleType, "success", true)); - } - - public static class DataTypesWithRequiredLineageForm - { - private Integer _parentDataTypeRowId; - private boolean _sampleParent; - - public Integer getParentDataTypeRowId() - { - return _parentDataTypeRowId; - } - - public void setParentDataTypeRowId(Integer parentDataTypeRowId) - { - this._parentDataTypeRowId = parentDataTypeRowId; - } - - public boolean isSampleParent() - { - return _sampleParent; - } - - public void setSampleParent(boolean sampleParent) - { - _sampleParent = sampleParent; - } - } - - @RequiresPermission(ReadPermission.class) - public static class GetDataTypesWithRequiredLineageAction extends ReadOnlyApiAction - { - @Override - public void validateForm(DataTypesWithRequiredLineageForm form, Errors errors) - { - if (form.getParentDataTypeRowId() == null) - errors.reject(ERROR_REQUIRED, "ParentDataTypeRowId must be provided"); - } - - @Override - public Object execute(DataTypesWithRequiredLineageForm form, BindException errors) throws Exception - { - return getDataTypesWithRequiredLineageResponse(form.getParentDataTypeRowId(), form.isSampleParent(), getContainer(), getUser()); - } - } - @NotNull - private static ApiSimpleResponse getDataTypesWithRequiredLineageResponse(Integer parentDataType, boolean isSampleParent, Container container, User user) - { - Pair, Set> requiredLineages = ExperimentServiceImpl.get().getDataTypesWithRequiredLineage(parentDataType, isSampleParent, container, user); - return new ApiSimpleResponse(Map.of("sampleTypes", requiredLineages.first, "dataClasses", requiredLineages.second,"success", true)); - } - - @RequiresPermission(DesignSampleTypePermission.class) - public static class EditSampleTypeAction extends SimpleViewAction - { - private ExpSampleTypeImpl _sampleType; - - @Override - public ModelAndView getView(SampleTypeForm form, BindException errors) - { - boolean create = form.getLSID() == null && form.getRowId() == null; - if (!create) - _sampleType = form.getSampleType(getContainer()); - - return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("sampleTypeDesigner")); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - if (_sampleType == null) - { - root.addChild("Create Sample Type"); - } - else - { - root.addChild(_sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(_sampleType)); - root.addChild("Update Sample Type"); - } - } - } - - public static class SampleTypeForm extends ReturnUrlForm - { - private Integer rowId; - private String lsid; - - public Integer getRowId() - { - return rowId; - } - - public void setRowId(Integer rowId) - { - this.rowId = rowId; - } - - public String getLSID() - { - return this.lsid; - } - - public void setLSID(String lsid) - { - this.lsid = lsid; - } - - public ExpSampleTypeImpl getSampleType(Container container) throws NotFoundException - { - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getLSID()); - if (sampleType == null) - sampleType = SampleTypeServiceImpl.get().getSampleType(getRowId()); - - if (sampleType == null) - { - throw new NotFoundException("Sample type not found: " + (getLSID() != null ? getLSID() : getRowId())); - } - - if (!container.equals(sampleType.getContainer())) - { - throw new NotFoundException("Sample type is not defined in the given container."); - } - - return sampleType; - } - } - - @RequiresPermission(InsertPermission.class) - public static class ImportSamplesAction extends AbstractExpDataImportAction - { - ExpSampleTypeImpl _sampleType; - boolean _isCrossTypeImport = false; - - @Override - public void validateForm(QueryForm queryForm, Errors errors) - { - _form = queryForm; - _insertOption = queryForm.getInsertOption(); - _isCrossTypeImport = getOptionParamValue(Params.crossTypeImport); - _form.setSchemaName(getTargetSchemaName()); - if (_isCrossTypeImport) - { - _form.setQueryName(getPipelineTargetQueryName()); - } - super.validateForm(queryForm, errors); - if (queryForm.getQueryName() == null) - errors.reject(ERROR_REQUIRED, "Sample type name is required"); - else - { - if (!_isCrossTypeImport) - { - _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), queryForm.getQueryName()); - if (_sampleType == null) - { - errors.reject(ERROR_GENERIC, "Sample type '" + queryForm.getQueryName() + " not found."); - } - } - } - } - - private String getTargetSchemaName() - { - return getOptionParamValue(Params.crossTypeImport) ? ExpSchema.SCHEMA_NAME : "samples"; - } - - @Override - protected UserSchema getTargetSchema() - { - return getOptionParamValue(Params.crossTypeImport) ? QueryService.get().getUserSchema(getUser(), getContainer(), getTargetSchemaName()) : super.getTargetSchema(); - } - - @Override - protected String getPipelineTargetQueryName() - { - return getOptionParamValue(Params.crossTypeImport) ? "materials" : super.getPipelineTargetQueryName(); - } - - @Override - protected Map getRenamedColumns() - { - Map renamedColumns = super.getRenamedColumns(); - renamedColumns.putAll(SampleTypeUpdateServiceDI.SAMPLE_ALT_IMPORT_NAME_COLS); - return renamedColumns; - } - - @Override - protected @Nullable Set getLineageImportAliases() throws IOException - { - Set aliases = new CaseInsensitiveHashSet(); - // Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import - aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT); - aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL); - boolean crossTypeImport = getOptionParamValue(AbstractQueryImportAction.Params.crossTypeImport); - // Issue 51894: We need to stop conversion to numbers for alias fields for all type - // If there are aliases defined for one type that are number fields in another type, this will prevent - // conversion to numbers during the initial partitioning, but the conversion will happen when the partition - // file is loaded. - if (crossTypeImport) - { - List sampleTypes = SampleTypeServiceImpl.get().getSampleTypes(getContainer(), true); - for (ExpSampleTypeImpl sampleType : sampleTypes) - aliases.addAll(sampleType.getImportAliases().keySet()); - } - else - { - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), _form.getQueryName()); - aliases.addAll(sampleType.getImportAliases().keySet()); - } - return aliases; - } - - @Override - protected int importData( - DataLoader dl, - FileStream file, - String originalName, - BatchValidationException errors, - @Nullable AuditBehaviorType auditBehaviorType, - TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, - @Nullable String auditUserComment - ) throws IOException - { - initContext(dl, errors, auditBehaviorType, auditUserComment); - - TableInfo tInfo = _target; - QueryUpdateService updateService = _updateService; - if (getOptionParamValue(Params.crossTypeImport)) - { - tInfo = ExperimentService.get().createMaterialTable(new SamplesSchema(getUser(), getContainer()), ContainerFilter.current(this), null); - updateService = tInfo.getUpdateService(); - } - - int count = importData(dl, tInfo, updateService, _context, auditEvent, getUser(), getContainer()); - - if (getOptionParamValue(Params.crossTypeImport)) - { - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeImport"); - if (_context.getInsertOption() == QueryUpdateService.InsertOption.UPDATE) - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeUpdate"); - else if (_context.getInsertOption() == QueryUpdateService.InsertOption.MERGE) - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeMerge"); - } - - return count; - } - - @Override - public ModelAndView getView(QueryForm form, BindException errors) throws Exception - { - initRequest(form); - setHelpTopic("importSampleSets"); // page-wide help topic - setImportHelpTopic("importSampleSets"); // importOptions help topic - setTypeName("samples"); - return getDefaultImportView(form, errors); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ActionURL url = _form.urlFor(QueryAction.executeQuery); - if (_form.getQueryName() != null && url != null) - root.addChild(_form.getQueryName(), url); - root.addChild("Import Data"); - } - - @Override - protected JSONObject createSuccessResponse(int rowCount) - { - JSONObject json = super.createSuccessResponse(rowCount); - if (!_context.getResponseInfo().isEmpty()) - { - for (String key : _context.getResponseInfo().keySet()) - json.put(key, _context.getResponseInfo().get(key)); - } - return json; - } - - } - - public abstract static class AbstractExpDataImportAction extends AbstractQueryImportAction - { - protected QueryForm _form; - protected DataIteratorContext _context; - - @Override - public void validateForm(QueryForm form, Errors errors) - { - QueryDefinition query = form.getQueryDef(); - if (query.getContainerFilter() != null && query.getContainerFilter().getType() != null) - { - // cross folder import not supported - if (query.getContainerFilter().getType() != ContainerFilter.Type.Current) - errors.reject(ERROR_GENERIC, "ContainerFilter is not supported for import actions."); - } - } - - @Override - protected void initRequest(QueryForm form) throws ServletException - { - QueryDefinition query = form.getQueryDef(); - setContainerFilterForImport(query, getContainer(), getUser()); - List qpe = new ArrayList<>(); - TableInfo t = query.getTable(form.getSchema(), qpe, true); - - if (!qpe.isEmpty()) - throw qpe.get(0); - if (!getOptionParamValue(Params.crossTypeImport) && null != t) - { - setTarget(t); - setShowMergeOption(t.supportsInsertOption(QueryUpdateService.InsertOption.MERGE)); - setShowUpdateOption(t.supportsInsertOption(QueryUpdateService.InsertOption.UPDATE)); - } - - _auditBehaviorType = form.getAuditBehavior(); - _auditUserComment = form.getAuditUserComment(); - } - - @Override - protected Map getRenamedColumns() - { - final String renameParamPrefix = "importAlias."; - Map renameColumns = new CaseInsensitiveHashMap<>(); - PropertyValue[] pvs = _form.getInitParameters().getPropertyValues(); - for (PropertyValue pv : pvs) - { - String paramName = pv.getName(); - if (!paramName.startsWith(renameParamPrefix) || pv.getValue() == null) - continue; - - renameColumns.put(paramName.substring(renameParamPrefix.length()), (String) pv.getValue()); - } - return renameColumns; - } - - @Override - protected Set getLineageImportAliases() throws IOException - { - ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), _form.getQueryName()); - return new CaseInsensitiveHashSet(dataClass.getImportAliases().keySet()); - } - - protected void initContext(DataLoader dl, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, @Nullable String auditUserComment) - { - _context = createDataIteratorContext(_insertOption, getOptionParamsMap(), getLookupResolutionType(), auditBehaviorType, auditUserComment, errors, null, getContainer()); - - if (_context.isCrossFolderImport() && !getContainer().hasProductFolders()) - _context.setCrossFolderImport(false); - } - - @Override - protected int importData(DataLoader dl, FileStream file, String originalName, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, @Nullable String auditUserComment) throws IOException - { - initContext(dl, errors, auditBehaviorType, auditUserComment); - return importData(dl, _target, _updateService, _context, auditEvent, getUser(), getContainer()); - } - - @Override - protected String getQueryImportProviderName() - { - PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_PROVIDER_PARAM); - return pv == null ? null : (String) pv.getValue(); - } - - @Override - protected String getQueryImportDescription() - { - PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM); - return pv == null ? null : (String) pv.getValue(); - } - - @Override - protected String getQueryImportJobNotificationProviderName() - { - PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM); - return pv == null ? null : (String) pv.getValue(); - } - - @Override - protected boolean isBackgroundImportSupported() - { - return true; - } - - @Override - protected boolean allowLineageColumns() - { - return true; - } - - } - - @RequiresPermission(InsertPermission.class) - public static class ImportDataAction extends AbstractExpDataImportAction - { - @Override - public void validateForm(QueryForm queryForm, Errors errors) - { - _form = queryForm; - _form.setSchemaName("exp.data"); - _insertOption = queryForm.getInsertOption(); - super.validateForm(queryForm, errors); - if (queryForm.getQueryName() == null) - errors.reject(ERROR_REQUIRED, "Data class name is required"); - else - { - ExpDataClass dataClass = ExperimentService.get().getDataClass(getContainer(), getUser(), queryForm.getQueryName()); - if (dataClass == null) - { - errors.reject(ERROR_GENERIC, "Data class '" + queryForm.getQueryName() + " not found."); - } - } - } - - @Override - public ModelAndView getView(QueryForm form, BindException errors) throws Exception - { - initRequest(form); - setHelpTopic("dataClass"); // page wide help topic - setImportHelpTopic("dataClass#ui"); // importOptions help topic - setTypeName("data"); - return getDefaultImportView(form, errors); - } - - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - ActionURL url = _form.urlFor(QueryAction.executeQuery); - if (_form.getQueryName() != null && url != null) - root.addChild(_form.getQueryName(), url); - root.addChild("Import Data"); - } - - } - - @RequiresPermission(UpdatePermission.class) - public class ShowUpdateAction extends SimpleViewAction - { - @Override - public ModelAndView getView(ExperimentForm form, BindException errors) - { - form.refreshFromDb(); - Experiment exp = form.getBean(); - if (exp == null) - { - throw new NotFoundException(); - } - ensureCorrectContainer(getContainer(), ExperimentService.get().getExpExperiment(exp.getRowId()), getViewContext()); - - return new ExperimentUpdateView(new DataRegion(), form, errors); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - addRootNavTrail(root); - root.addChild("Update Run Group"); - } - } - - @RequiresPermission(UpdatePermission.class) - public static class UpdateAction extends FormHandlerAction - { - private Experiment _exp; - - @Override - public void validateCommand(ExperimentForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ExperimentForm form, BindException errors) throws Exception - { - form.doUpdate(); - form.refreshFromDb(); - _exp = form.getBean(); - return true; - } - - @Override - public ActionURL getSuccessURL(ExperimentForm experimentForm) - { - return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), ExperimentService.get().getExpExperiment(_exp.getRowId())); - } - } - - public static class ExportBean - { - private final LSIDRelativizer _selectedRelativizer; - private final XarExportType _selectedExportType; - private final String _fileName; - private final String _dataRegionSelectionKey; - private final String _error; - private final Long _expRowId; - private final Long _protocolId; - private final ActionURL _postURL; - private final Set _roles; - - public ExportBean(LSIDRelativizer selectedRelativizer, XarExportType selectedExportType, String fileName, ExportOptionsForm form, Set roles, ActionURL postURL) - { - _selectedRelativizer = selectedRelativizer; - _selectedExportType = selectedExportType; - _fileName = fileName; - _dataRegionSelectionKey = form.getDataRegionSelectionKey(); - _error = form.getError(); - _expRowId = form.getExpRowId(); - _postURL = postURL; - _roles = roles; - _protocolId = form.getProtocolId(); - } - - public LSIDRelativizer getSelectedRelativizer() - { - return _selectedRelativizer; - } - - public XarExportType getSelectedExportType() - { - return _selectedExportType; - } - - public String getError() - { - return _error; - } - - public String getFileName() - { - return _fileName; - } - - public Set getRoles() - { - return _roles; - } - - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - public ActionURL getPostURL() - { - return _postURL; - } - - public Long getProtocolId() - { - return _protocolId; - } - - public Long getExpRowId() - { - return _expRowId; - } - } - - - private String fixupExportName(String runName) - { - runName = runName.replace('/', '-'); - runName = runName.replace('\\', '-'); - return runName; - } - - public static class ExportOptionsForm extends ExperimentRunListForm - { - private String _error; - private XarExportType _exportType; - private LSIDRelativizer _lsidOutputType; - private String _xarFileName; - private String _zipFileName; - private String _fileExportType; - private Long _protocolId; - private Integer _sampleTypeId; - private long[] _dataIds; - private String[] _roles = new String[0]; - - public String getError() - { - return _error; - } - - public void setError(String error) - { - _error = error; - } - - public XarExportType getExportType() - { - return _exportType; - } - - public LSIDRelativizer getLsidOutputType() - { - return _lsidOutputType; - } - - public String getFileExportType() - { - return _fileExportType; - } - - public void setFileExportType(String fileExportType) - { - _fileExportType = fileExportType; - } - - public String getXarFileName() - { - return _xarFileName; - } - - public void setXarFileName(String xarFileName) - { - _xarFileName = xarFileName; - } - - public String getZipFileName() - { - return _zipFileName; - } - - public void setZipFileName(String zipFileName) - { - _zipFileName = zipFileName; - } - - public void setExportType(XarExportType exportType) - { - _exportType = exportType; - } - - public void setLsidOutputType(LSIDRelativizer lsidOutputType) - { - _lsidOutputType = lsidOutputType; - } - - public Long getProtocolId() - { - return _protocolId; - } - - public void setProtocolId(Long protocolId) - { - _protocolId = protocolId; - } - - public String[] getRoles() - { - return _roles; - } - - public void setRoles(String[] roles) - { - _roles = roles; - } - - public Integer getSampleTypeId() - { - return _sampleTypeId; - } - - public void setSampleTypeId(Integer sampleTypeId) - { - _sampleTypeId = sampleTypeId; - } - - public long[] getDataIds() - { - return _dataIds; - } - - public void setDataIds(long[] dataIds) - { - _dataIds = dataIds; - } - - public List lookupProtocols(ViewContext context, boolean clearSelection) - { - List protocols = new ArrayList<>(); - - if (_protocolId != null) - { - ExpProtocol protocol = ExperimentService.get().getExpProtocol(_protocolId.intValue()); - if (protocol == null || !protocol.getContainer().equals(context.getContainer())) - { - throw new NotFoundException(); - } - protocols.add(protocol); - return protocols; - } - - for (Long protocolId : DataRegionSelection.getSelectedIntegers(context, clearSelection)) - { - try - { - ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); - if (protocol == null || !protocol.getContainer().equals(context.getContainer())) - { - throw new NotFoundException(); - } - protocols.add(protocol); - } - catch (NumberFormatException e) - { - throw new NotFoundException("Invalid protocol id: " + protocolId); - } - } - if (protocols.isEmpty()) - { - throw new NotFoundException("No protocols selected"); - } - return protocols; - } - } - - private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable String fileName) - throws ExperimentException, IOException, PipelineValidationException - { - return exportXAR(selection, null, null, fileName); - } - - private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable LSIDRelativizer lsidRelativizer, @Nullable XarExportType exportType, @Nullable String fileName) - throws ExperimentException, IOException, PipelineValidationException - { - if (lsidRelativizer == null) - lsidRelativizer = LSIDRelativizer.FOLDER_RELATIVE; - - if (exportType == null) - exportType = XarExportType.BROWSER_DOWNLOAD; - - if (fileName == null || fileName.isEmpty()) - fileName = "export.xar"; - - fileName = fixupExportName(fileName); - String xarXmlFileName = null; - if (Strings.CI.endsWith(fileName, ".xar")) - xarXmlFileName = fileName + ".xml"; - - switch (exportType) - { - case BROWSER_DOWNLOAD: - XarExporter exporter = new XarExporter(lsidRelativizer, selection, getUser(), xarXmlFileName, null, getContainer()); - - getViewContext().getResponse().setContentType("application/zip"); - ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, fileName); - ResponseHelper.setPrivate(getViewContext().getResponse()); - - exporter.writeAsArchive(getViewContext().getResponse().getOutputStream()); - return null; - case PIPELINE_FILE: - if (!PipelineService.get().hasValidPipelineRoot(getContainer())) - { - throw new IllegalStateException("You must set a valid pipeline root before you can export a XAR to it."); - } - PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); - XarExportPipelineJob job = new XarExportPipelineJob(getViewBackgroundInfo(), pipeRoot, fileName, lsidRelativizer, selection, xarXmlFileName); - PipelineService.get().queueJob(job); - PipelineStatusFile status = PipelineService.get().getStatusFile(job.getJobGUID()); - return PageFlowUtil.urlProvider(PipelineUrls.class).statusDetails(getContainer(), status.getRowId()); - default: - throw new IllegalArgumentException("Unknown export type: " + exportType); - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportProtocolsAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - List protocols = form.lookupProtocols(getViewContext(), false); - - long[] ids = new long[protocols.size()]; - for (int i = 0; i < ids.length; i++) - { - ids[i] = protocols.get(i).getRowId(); - } - XarExportSelection selection = new XarExportSelection(); - selection.addProtocolIds(ids); - - exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); - - if (form.getDataRegionSelectionKey() != null) - { - // Clear the selection - form.lookupProtocols(getViewContext(), true); - } - return true; - } - } - - public abstract static class AbstractExportAction extends FormViewAction - { - protected ActionURL _resultURL; - - @Override - public void validateCommand(ExportOptionsForm target, Errors errors) - { - } - - @Override - public ActionURL getSuccessURL(ExportOptionsForm exportOptionsForm) - { - return _resultURL; - } - - @Override - public ModelAndView getSuccessView(ExportOptionsForm exportOptionsForm) - { - return null; - } - - @Override - public ModelAndView getView(ExportOptionsForm form, boolean reshow, BindException errors) throws Exception - { - // FormViewAction can reinvoke getView() in response to a POST if we're not redirecting the browser, - // so avoid double-creating the export - if ("get".equalsIgnoreCase(getViewContext().getRequest().getMethod())) - handlePost(form, errors); - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - } - - public List lookupRuns(ExportOptionsForm form) - { - Set runIds; - if (form.getRunIds() != null && form.getRunIds().length > 0) - runIds = new HashSet<>(Arrays.asList(form.getRunIds())); - else - runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); - - if (runIds.isEmpty()) - { - throw new NotFoundException(); - } - List result = new ArrayList<>(); - - for (long id : runIds) - { - ExpRun run = ExperimentService.get().getExpRun(id); - if (run == null || !run.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new NotFoundException("Could not find run " + id); - } - result.add(run); - } - return result; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportRunsAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - XarExportSelection selection = new XarExportSelection(); - if (form.getExpRowId() != null) - { - ExpExperiment experiment = ExperimentService.get().getExpExperiment(form.getExpRowId()); - if (experiment != null && !experiment.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new NotFoundException("Run group " + form.getExpRowId()); - } - selection.addExperimentIds(experiment.getRowId()); - } - selection.addRuns(lookupRuns(form)); - - _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - return true; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportSampleTypeAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - Integer rowId = form.getSampleTypeId(); - if (rowId == null) - { - throw new NotFoundException("No sampleTypeId parameter specified"); - } - ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId.intValue()); - if (sampleType == null) - { - throw new NotFoundException("No such sample type with RowId " + rowId); - } - if (!sampleType.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new UnauthorizedException(); - } - - XarExportSelection selection = new XarExportSelection(); - selection.addSampleType(sampleType); - - _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), FileUtil.makeLegalName(sampleType.getName() + ".xar")); - return true; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportRunFilesAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - XarExportSelection selection = new XarExportSelection(); - selection.setIncludeXarXml(false); - if ("role".equalsIgnoreCase(form.getFileExportType())) - { - selection.addRoles(form.getRoles()); - } - selection.addRuns(lookupRuns(form)); - - _resultURL = exportXAR(selection, form.getZipFileName()); - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - return true; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportFilesAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - long[] dataIds = form.getDataIds(); - if (dataIds == null || dataIds.length == 0) - { - throw new NotFoundException(); - } - - try - { - for (long id : dataIds) - { - ExpData data = ExperimentService.get().getExpData(id); - if (data == null || !data.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new NotFoundException("Could not find file " + id); - } - } - - XarExportSelection selection = new XarExportSelection(); - selection.setIncludeXarXml(false); - selection.addDataIds(dataIds); - - _resultURL = exportXAR(selection, form.getZipFileName()); - return true; - } - catch (NumberFormatException e) - { - throw new NotFoundException(Arrays.toString(dataIds)); - } - } - } - - public static class ExperimentRunListForm implements DataRegionSelection.DataSelectionKeyForm - { - private String _dataRegionSelectionKey; - private Long _expRowId; - private Long[] _runIds; - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String key) - { - _dataRegionSelectionKey = key; - } - - public Long getExpRowId() - { - return _expRowId; - } - - public void setExpRowId(Long expRowId) - { - _expRowId = expRowId; - } - - public Long[] getRunIds() - { - return _runIds; - } - - public void setRunIds(Long[] runIds) - { - _runIds = runIds; - } - - public ExpExperiment lookupExperiment() - { - return getExpRowId() == null ? null : ExperimentService.get().getExpExperiment(getExpRowId().intValue()); - } - } - - private void addSelectedRunsToExperiment(ExpExperiment exp, String dataRegionSelectionKey) - { - Collection runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), dataRegionSelectionKey, true); - List runs = new ArrayList<>(); - for (long runId : runIds) - { - ExpRun run = ExperimentServiceImpl.get().getExpRun(runId); - if (run != null) - { - runs.add(run); - } - } - exp.addRuns(getUser(), runs.toArray(new ExpRun[0])); - } - - - @RequiresPermission(InsertPermission.class) - public class AddRunsToExperimentAction extends FormHandlerAction - { - @Override - public void validateCommand(ExperimentRunListForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ExperimentRunListForm form, BindException errors) - { - addSelectedRunsToExperiment(form.lookupExperiment(), form.getDataRegionSelectionKey()); - return true; - } - - @Override - public ActionURL getSuccessURL(ExperimentRunListForm form) - { - return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); - } - } - - @RequiresPermission(DeletePermission.class) - public static class RemoveSelectedExpRunsAction extends FormHandlerAction - { - @Override - public void validateCommand(ExperimentRunListForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ExperimentRunListForm form, BindException errors) - { - ExpExperiment exp = form.lookupExperiment(); - if (exp == null || !exp.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new NotFoundException("Could not find run group with RowId " + form.getExpRowId()); - } - - for (long runId : DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false)) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run == null || !run.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new NotFoundException("Could not find run with RowId " + runId); - } - exp.removeRun(getUser(), run); - } - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - return true; - } - - @Override - public ActionURL getSuccessURL(ExperimentRunListForm form) - { - return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); - } - } - - public static ActionURL getResolveLsidURL(Container c, @NotNull String type, @NotNull String lsid) - { - ActionURL url = new ActionURL(ResolveLSIDAction.class, c); - url.addParameter("type", type); - url.addParameter("lsid", lsid); - - return url; - } - - - @RequiresPermission(ReadPermission.class) - public static class ResolveLSIDAction extends SimpleViewAction - { - @Override - public ModelAndView getView(LsidForm form, BindException errors) - { - String message = ""; - if (!PageFlowUtil.empty(form.getLsid())) - { - try - { - String lsid = Lsid.canonical(form.getLsid().trim()); - ActionURL url = LsidManager.get().getDisplayURL(lsid); - if (url == null && form.getType() != null) - { - url = switch (form.getType().toLowerCase()) - { - case "data" -> LsidType.Data.getDisplayURL(new Lsid(lsid)); - case "material" -> LsidType.Material.getDisplayURL(new Lsid(lsid)); - default -> url; - }; - } - if (null != url) - { - throw new RedirectException(url); - } - message = "Could not map LSID to URL"; - } - catch (IllegalArgumentException e) - { - message = "Invalid LSID"; - } - } - - return new HtmlView("Enter LSID", - DOM.createHtmlFragment( - message, - DOM.FORM(at(action, getViewContext().cloneActionURL().setAction(ResolveLSIDAction.class)), - "LSID: ", - DOM.INPUT(at(type, "text", name, "lsid", size, "80", value, form.getLsid())), - PageFlowUtil.button("Go").submit(true)))); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Resolve LSID"); - } - } - - public static class LsidForm - { - private String _lsid; - - public String getType() - { - return _type; - } - - public void setType(String type) - { - _type = type; - } - - private String _type; - - public void setLsid(String lsid) - { - _lsid = lsid; - } - - public String getLsid() - { - return _lsid; - } - } - - public static class SetFlagForm extends LsidForm - { - private String _comment; - private boolean _redirect = true; - - public String getComment() - { - return _comment; - } - - public void setComment(String comment) - { - _comment = comment; - } - - public boolean isRedirect() - { - return _redirect; - } - - public void setRedirect(boolean redirect) - { - _redirect = redirect; - } - } - - /** - * Check for update on the object itself - */ - @RequiresNoPermission - public static class SetFlagAction extends FormHandlerAction - { - @Override - public void validateCommand(SetFlagForm target, Errors errors) - { - } - - @Override - public boolean handlePost(SetFlagForm form, BindException errors) throws Exception - { - String lsid = form.getLsid(); - if (lsid == null) - throw new NotFoundException(); - ExpObject obj = ExperimentService.get().findObjectFromLSID(lsid); - if (obj == null) - throw new NotFoundException(); - Container container = obj.getContainer(); - if (!container.hasPermission(getUser(), UpdatePermission.class)) - { - throw new UnauthorizedException(); - } - - obj.setComment(getUser(), form.getComment()); - return true; - } - - @Override - public URLHelper getSuccessURL(SetFlagForm form) - { - return null; - } - } - - @RequiresPermission(InsertPermission.class) - public class DeriveSamplesChooseTargetAction extends SimpleViewAction - { - private List _materials; - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; - if (sampleType != null) - { - root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); - } - root.addChild("Derive Samples"); - } - - @Override - public void validate(DeriveMaterialForm form, BindException errors) - { - _materials = form.lookupMaterials(); - if (_materials.isEmpty()) - { - throw new NotFoundException("Could not find any matching materials"); - } - } - - @Override - public ModelAndView getView(DeriveMaterialForm form, BindException errors) - { - Container c = getContainer(); - PipeRoot root = PipelineService.get().findPipelineRoot(c); - - if (root == null || !root.isValid()) - { - ActionURL pipelineURL = urlProvider(PipelineUrls.class).urlSetup(c); - return new HtmlView(DIV("You must ", - DOM.A(DOM.at(href, pipelineURL), "configure a valid pipeline root for this folder"), - " before deriving samples.")); - } - else - { - Set materialInputRoles = new TreeSet<>(ExperimentService.get().getMaterialInputRoles(getContainer(), getUser())); - Map materialsWithRoles = new LinkedHashMap<>(); - for (ExpMaterial material : _materials) - { - materialsWithRoles.put(material, null); - } - - List sampleTypes = getUploadableSampleTypes(); - - DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), sampleTypes, materialsWithRoles, form.getOutputCount(), materialInputRoles, null); - return new JspView<>("/org/labkey/experiment/deriveSamplesChooseTarget.jsp", bean); - } - } - } - - public static class DeriveSamplesChooseTargetBean implements DataRegionSelection.DataSelectionKeyForm - { - private String _dataRegionSelectionKey; - - private final Integer _targetSampleTypeId; - private final List _sampleTypes; - private final Map _sourceMaterials; - private final int _sampleCount; - private final Collection _inputRoles; - private final DerivedSamplePropertyHelper _propertyHelper; - - public static final String CUSTOM_ROLE = "--CUSTOM--"; - - public DeriveSamplesChooseTargetBean(String dataRegionSelectionKey, Integer targetSampleTypeId, List sampleTypes, Map sourceMaterials, int sampleCount, Collection inputRoles, DerivedSamplePropertyHelper helper) - { - _dataRegionSelectionKey = dataRegionSelectionKey; - _targetSampleTypeId = targetSampleTypeId; - _sampleTypes = sampleTypes; - _sourceMaterials = sourceMaterials; - _sampleCount = sampleCount; - _inputRoles = inputRoles; - _propertyHelper = helper; - } - - public Integer getTargetSampleTypeId() - { - return _targetSampleTypeId; - } - - public DerivedSamplePropertyHelper getPropertyHelper() - { - return _propertyHelper; - } - - public int getSampleCount() - { - return _sampleCount; - } - - public Map getSourceMaterials() - { - return _sourceMaterials; - } - - public List getSampleTypes() - { - return _sampleTypes; - } - - public Collection getInputRoles() - { - return _inputRoles; - } - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String key) - { - _dataRegionSelectionKey = key; - } - } - - private List getUploadableSampleTypes() - { - // Make a copy so we can modify it - List sampleTypes = new ArrayList<>(SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true)); - sampleTypes.removeIf(sampleType -> !sampleType.canImportMoreSamples()); - return sampleTypes; - } - - @RequiresPermission(InsertPermission.class) - public class DeriveSamplesAction extends FormViewAction - { - private List _materials; - private ActionURL _successUrl; - private final Map _inputMaterials = new LinkedHashMap<>(); - - @Override - public ModelAndView getView(DeriveMaterialForm form, boolean reshow, BindException errors) - { - _materials = form.lookupMaterials(); - if (_materials.isEmpty()) - { - throw new NotFoundException("Could not find any matching materials"); - } - - Container c = getContainer(); - - if (form.getOutputCount() <= 0) - { - form.setOutputCount(1); - } - - if (form.getTargetSampleTypeId() == 0) - throw new NotFoundException("Target sample type required for the derived samples"); - - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); - if (sampleType == null) - throw new NotFoundException("Could not find sample type with rowId " + form.getTargetSampleTypeId()); - - InsertView insertView = new InsertView(new DataRegion(), errors); - - DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), c, getUser()); - helper.addSampleColumns(insertView, getUser()); - - int[] rowIds = form.getRowIds(); - for (int i = 0; i < rowIds.length; i++) - { - insertView.getDataRegion().addHiddenFormField("rowIds", Integer.toString(rowIds[i])); - insertView.getDataRegion().addHiddenFormField("inputRole" + i, form.getInputRole(i) == null ? "" : form.getInputRole(i)); - insertView.getDataRegion().addHiddenFormField("customRole" + i, form.getCustomRole(i) == null ? "" : form.getCustomRole(i)); - } - - insertView.getDataRegion().addHiddenFormField("targetSampleTypeId", Integer.toString(form.getTargetSampleTypeId())); - insertView.getDataRegion().addHiddenFormField("outputCount", Integer.toString(form.getOutputCount())); - if (form.getDataRegionSelectionKey() != null) - insertView.getDataRegion().addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, form.getDataRegionSelectionKey()); - insertView.setInitialValues(ViewServlet.adaptParameterMap(getViewContext().getRequest().getParameterMap())); - ButtonBar bar = new ButtonBar(); - bar.setStyle(ButtonBar.Style.separateButtons); - ActionButton submitButton = new ActionButton(DeriveSamplesAction.class, "Submit"); - submitButton.setActionType(ActionButton.Action.POST); - bar.add(submitButton); - insertView.getDataRegion().setButtonBar(bar); - insertView.setTitle("Output Samples"); - - Map materialsWithRoles = new LinkedHashMap<>(); - List materials = form.lookupMaterials(); - for (int i = 0; i < materials.size(); i++) - { - materialsWithRoles.put(materials.get(i), form.determineLabel(i)); - } - - DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), getUploadableSampleTypes(), materialsWithRoles, form.getOutputCount(), Collections.emptyList(), helper); - JspView view = new JspView<>("/org/labkey/experiment/summarizeMaterialInputs.jsp", bean); - view.setTitle("Input Samples"); - - return new VBox(view, insertView); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; - if (sampleType != null) - { - root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); - } - root.addChild("Derive Samples"); - } - - @Override - public void validateCommand(DeriveMaterialForm form, Errors errors) - { - List materials = form.lookupMaterials(); - - List lockedSamples = new ArrayList<>(); - for (int i = 0; i < materials.size(); i++) - { - ExpMaterial m = materials.get(i); - if (!m.isOperationPermitted(SampleTypeService.SampleOperations.EditLineage)) - { - lockedSamples.add(m); - } - String inputRole = form.determineLabel(i); - if (inputRole == null || inputRole.isEmpty()) - { - ExpSampleType st = m.getSampleType(); - inputRole = st != null ? st.getName() : ExpMaterialRunInput.DEFAULT_ROLE; - } - _inputMaterials.put(materials.get(i), inputRole); - } - - if (!lockedSamples.isEmpty()) - { - errors.reject(ERROR_MSG, SampleTypeService.get().getOperationNotPermittedMessage(lockedSamples, SampleTypeService.SampleOperations.EditLineage)); - } - } - - @Override - public boolean handlePost(DeriveMaterialForm form, BindException errors) - { - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); - - DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), getContainer(), getUser()); - - Map, Map> allProperties; - try - { - boolean valid = true; - for (Map.Entry> entry : helper.getPostedPropertyValues(getViewContext().getRequest()).entrySet()) - valid = UploadWizardAction.validatePostedProperties(getViewContext(), entry.getValue(), errors) && valid; - if (!valid) - return false; - - allProperties = helper.getSampleProperties(getViewContext().getRequest(), _inputMaterials.keySet()); - } - catch (DuplicateMaterialException e) - { - errors.addError(new ObjectError(e.getColName(), null, null, e.getMessage())); - return false; - } - catch (ExperimentException e) - { - errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); - return false; - } - - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - Map outputMaterials = new HashMap<>(); - int i = 0; - for (Map.Entry, Map> entry : allProperties.entrySet()) - { - Lsid lsid = entry.getKey().first; - String name = entry.getKey().second; - assert name != null; - - ExpMaterialImpl outputMaterial = ExperimentServiceImpl.get().createExpMaterial(getContainer(), lsid.toString(), name); - if (sampleType != null) - { - outputMaterial.setCpasType(sampleType.getLSID()); - } - outputMaterial.save(getUser()); - - if (sampleType != null) - { - Map pvs = new HashMap<>(); - for (Map.Entry propertyEntry : entry.getValue().entrySet()) - pvs.put(propertyEntry.getKey().getName(), propertyEntry.getValue()); - outputMaterial.setProperties(getUser(), pvs, false); - } - - outputMaterials.put(outputMaterial, helper.getSampleNames().get(i++)); - } - - ExperimentService.get().deriveSamples(_inputMaterials, outputMaterials, getViewBackgroundInfo(), _log); - - tx.commit(); - - // automatically link samples to study, if configured - StudyPublishService.get().autoLinkDerivedSamples(sampleType, outputMaterials.keySet().stream().map(ExpObject::getRowId).collect(toList()), getContainer(), getUser()); - - _successUrl = ExperimentUrlsImpl.get().getShowSampleURL(getContainer(), outputMaterials.keySet().iterator().next()); - - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - } - catch (Exception e) - { - errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); - return false; - } - - return true; - } - - @Override - public URLHelper getSuccessURL(DeriveMaterialForm deriveMaterialForm) - { - return _successUrl; - } - } - - public static class DeriveMaterialForm implements HasViewContext, DataRegionSelection.DataSelectionKeyForm - { - private String _dataRegionSelectionKey; - private int _outputCount = 1; - private int _targetSampleTypeId; - private int[] _rowIds; - private String _name; - - private ViewContext _context; - - @Override - public void setViewContext(ViewContext context) - { - _context = context; - } - - @Override - public ViewContext getViewContext() - { - return _context; - } - - public List lookupMaterials() - { - List result = new ArrayList<>(); - for (int rowId : getRowIds()) - { - ExpMaterial material = ExperimentService.get().getExpMaterial(rowId); - if (material != null) - { - if (material.getContainer().hasPermission(_context.getUser(), ReadPermission.class)) - { - result.add(material); - } - else - { - throw new UnauthorizedException(); - } - } - else - { - throw new NotFoundException("No material with RowId " + rowId); - } - } - result.sort(Comparator.comparing(Identifiable::getName)); - return result; - } - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String dataRegionSelectionKey) - { - _dataRegionSelectionKey = dataRegionSelectionKey; - } - - public int[] getRowIds() - { - if (_rowIds == null) - { - _rowIds = PageFlowUtil.toInts(DataRegionSelection.getSelected(getViewContext(), getDataRegionSelectionKey(), false)); - } - return _rowIds; - } - - public void setRowIds(int[] rowIds) - { - _rowIds = rowIds; - } - - public int getOutputCount() - { - return _outputCount; - } - - public void setOutputCount(int outputCount) - { - _outputCount = outputCount; - } - - public int getTargetSampleTypeId() - { - return _targetSampleTypeId; - } - - public void setTargetSampleTypeId(int targetSampleTypeId) - { - _targetSampleTypeId = targetSampleTypeId; - } - - public String getInputRole(int i) - { - return _context.getRequest().getParameter("inputRole" + i); - } - - public String getCustomRole(int i) - { - return _context.getRequest().getParameter("customRole" + i); - } - - public String determineLabel(int index) - { - String result = getInputRole(index); - if (DeriveSamplesChooseTargetBean.CUSTOM_ROLE.equals(result)) - { - result = getCustomRole(index); - } - if (result != null) - { - result = result.trim(); - } - return result; - } - } - - - public static class ExpInput - { - public String role; - public int rowId; - public Lsid lsid; - } - - public static class DerivationSpec - { - public String role; - public Map values; - } - - public static class DerivationForm - { - public List dataInputs; - public List materialInputs; - - public int dataOutputCount; - public Lsid targetDataClass; - public Map dataDefault; - public List dataOutputs; - - public int materialOutputCount; - public Lsid targetSampleType; - public Map materialDefault; - public List materialOutputs; - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(InsertPermission.class) - public static class DeriveAction extends MutatingApiAction - { - @Override - public void validateForm(DerivationForm form, Errors errors) - { - if (errors.hasErrors()) - return; - - if (form.materialOutputCount > 0 && form.materialOutputs != null && !form.materialOutputs.isEmpty()) - errors.reject(ERROR_MSG, "Either 'materialOutputCount' or 'materialOutputs' property can be specified, but not both."); - - if (form.dataOutputCount > 0 && form.dataOutputs != null && !form.dataOutputs.isEmpty()) - errors.reject(ERROR_MSG, "Either 'dataOutputCount' or 'dataOutputs' property can be specified, but not both."); - - boolean hasMaterialOutputs = form.materialOutputCount > 0 || form.materialOutputs != null && !form.materialOutputs.isEmpty(); - boolean hasDataOutputs = form.dataOutputCount > 0 || form.dataOutputs != null && !form.dataOutputs.isEmpty(); - - if (!hasMaterialOutputs && !hasDataOutputs) - errors.reject(ERROR_MSG, "At least one data output or material output is required"); - - if (hasMaterialOutputs && form.targetSampleType == null) - errors.reject(ERROR_MSG, "targetSampleType lsid required for material outputs"); - - if (hasDataOutputs && form.targetDataClass == null) - errors.reject(ERROR_MSG, "targetDataClass lsid required for data outputs"); - } - - @Override - public Object execute(DerivationForm form, BindException errors) throws Exception - { - // Find material inputs - Map materialInputs = new LinkedHashMap<>(); - if (form.materialInputs != null) - { - for (ExpInput in : form.materialInputs) - { - ExpMaterial m = null; - if (in.lsid != null) - { - m = ExperimentService.get().getExpMaterial(in.lsid.toString()); - if (m == null) - errors.reject(ERROR_MSG, "Can't resolve sample '" + in.lsid + "'"); - } - else if (in.rowId > 0) - { - m = ExperimentService.get().getExpMaterial(in.rowId); - if (m == null) - errors.reject(ERROR_MSG, "Can't resolve sample '" + in.rowId + "'"); - } - - if (m == null) - { - errors.reject(ERROR_MSG, "Material input lsid or rowId required"); - continue; - } - - ExpSampleType st = m.getSampleType(); - if (st == null) - { - errors.reject(ERROR_MSG, "Material input is not a member of a SampleType"); - continue; - } - - String role = in.role; - if (role == null || role.isEmpty()) - { - role = st.getName(); - } - materialInputs.put(m, role); - } - } - - // Find input data - Map dataInputs = new LinkedHashMap<>(); - if (form.dataInputs != null) - { - for (ExpInput in : form.dataInputs) - { - ExpData d = null; - if (in.lsid != null) - { - d = ExperimentService.get().getExpData(in.lsid.toString()); - if (d == null) - errors.reject(ERROR_MSG, "Can't resolve data '" + in.lsid + "'"); - } - else if (in.rowId > 0) - { - d = ExperimentService.get().getExpData(in.rowId); - if (d == null) - errors.reject(ERROR_MSG, "Can't resolve data '" + in.rowId + "'"); - } - - if (d == null) - { - errors.reject(ERROR_MSG, "Data input lsid or rowId required"); - continue; - } - - ExpDataClass dc = d.getDataClass(getUser()); - if (dc == null) - { - errors.reject(ERROR_MSG, "Data input is not a member of a DataClass"); - continue; - } - - String role = in.role; - if (role == null || role.isEmpty()) - { - role = dc.getName(); - } - dataInputs.put(d, role); - } - } - - ExpSampleType outSampleType; - if (form.targetSampleType != null) - { - // TODO: check in scope and has permission - outSampleType = SampleTypeService.get().getSampleType(form.targetSampleType.toString()); - if (outSampleType == null) - errors.reject(ERROR_MSG, "Sample type not found: " + form.targetSampleType.toString()); - } - else - { - outSampleType = null; - } - - ExpDataClass outDataClass; - if (form.targetDataClass != null) - { - // TODO: check in scope and has permission - outDataClass = ExperimentServiceImpl.get().getDataClass(form.targetDataClass.toString()); - if (outDataClass == null) - errors.reject(ERROR_MSG, "DataClass not found: " + form.targetDataClass.toString()); - } - else - { - outDataClass = null; - } - - if (errors.hasErrors()) - return null; - - // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names - // Create "MaterialInputs/" columns with a value containing a comma-separated list of Material names - final Map> parentInputNames = new HashMap<>(); - Set inputTypes = new CaseInsensitiveHashSet(); - for (ExpMaterial material : materialInputs.keySet()) - { - ExpSampleType st = material.getSampleType(); - String keyName = ExpMaterial.MATERIAL_INPUT_PARENT + "/" + st.getName(); - inputTypes.add(keyName); - parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(material.getName()); - } - - // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names - // Create "DataInputs/" columns with a value containing a comma-separated list of ExpData names - for (ExpData d : dataInputs.keySet()) - { - ExpDataClass dc = d.getDataClass(getUser()); - String keyName = ExpData.DATA_INPUT_PARENT + "/" + dc.getName(); - inputTypes.add(keyName); - parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(d.getName()); - } - - - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - Set requiredParentTypes = new CaseInsensitiveHashSet(); - - // output materials - Map outputMaterials = new HashMap<>(); - int materialOutputCount = Math.max(form.materialOutputCount, form.materialOutputs != null ? form.materialOutputs.size() : 0); - if (materialOutputCount > 0 && outSampleType != null) - { - requiredParentTypes.addAll(outSampleType.getRequiredImportAliases().values()); - DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.materialDefault, form.materialOutputs, materialOutputCount, ExpMaterial.DEFAULT_CPAS_TYPE) - { - @Override - protected TableInfo createTable() - { - SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); - return schema.getTable(outSampleType.getName()); - } - - @Override - protected List getExpObject(List> insertedRows) - { - List rowIds = insertedRows.stream().map(r -> MapUtils.getLong(r,"rowid")).collect(toList()); - return ExperimentService.get().getExpMaterials(rowIds); - } - }; - - outputMaterials = derived.createOutputs(); - } - - - // create output data - Map outputData = new HashMap<>(); - int dataOutputCount = Math.max(form.dataOutputCount, form.dataOutputs != null ? form.dataOutputs.size() : 0); - if (dataOutputCount > 0 && outDataClass != null) - { - requiredParentTypes.addAll(outDataClass.getRequiredImportAliases().values()); - DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.dataDefault, form.dataOutputs, dataOutputCount, ExpData.DEFAULT_CPAS_TYPE) - { - @Override - protected TableInfo createTable() - { - ExpSchema expSchema = new ExpSchema(getUser(), getContainer()); - UserSchema dataSchema = expSchema.getUserSchema(ExpSchema.NestedSchemas.data.name()); - return dataSchema.getTable(outDataClass.getName()); - } - - @Override - protected List getExpObject(List> insertedRows) - { - List lsids = insertedRows.stream().map(r -> (String) r.get("lsid")).collect(toList()); - return ExperimentService.get().getExpDatasByLSID(lsids); - } - }; - - outputData = derived.createOutputs(); - } - - if (outputMaterials.isEmpty() && outputData.isEmpty()) - throw new IllegalStateException("Expected to create " + materialOutputCount + " materials and " + dataOutputCount + " datas"); - - boolean hasMissingRequiredParent = false; - for (String required : requiredParentTypes) - { - if (!inputTypes.contains(required)) - { - hasMissingRequiredParent = true; - break; - } - } - if (hasMissingRequiredParent) - throw new IllegalStateException("Inputs are required: " + String.join(",", requiredParentTypes)); - - // finally, create the derived run if there are any parents - ExpRun run = null; - if (!materialInputs.isEmpty() || !dataInputs.isEmpty()) - run = ExperimentService.get().derive(materialInputs, dataInputs, outputMaterials, outputData, new ViewBackgroundInfo(getContainer(), getUser(), null), _log); - tx.commit(); - - StringBuilder successMessage = new StringBuilder("Created "); - if (!outputMaterials.isEmpty()) - successMessage.append(outputMaterials.size()).append(" materials"); - if (!outputData.isEmpty()) - successMessage.append(outputData.size()).append(" data"); - - JSONObject ret; - if (run != null) - ret = ExperimentJSONConverter.serializeRun(run, null, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); - else - ret = ExperimentJSONConverter.serializeRunOutputs(outputData.keySet(), outputMaterials.keySet(), getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); - - return success(successMessage.toString(), ret); - } - } - - // Helper class that prepares and executes the QueryUpdateService.insertRows() on the data or material table. - private abstract class DerivedOutputs - { - private final @NotNull Map> _parentInputNames; - private final @Nullable Map _defaultValues; - private final @Nullable List _values; - private final int _outputCount; - private final String _rolePrefix; - - - public DerivedOutputs(@NotNull Map> parentInputNames, @Nullable Map defaultValues, @Nullable List values, int outputCount, String rolePrefix) - { - _parentInputNames = parentInputNames; - _defaultValues = defaultValues; - _values = values; - _outputCount = outputCount; - _rolePrefix = rolePrefix; - } - - public Pair>, List> prepareRows() - { - List> rows = new ArrayList<>(); - List roles = new ArrayList<>(); - int unknownOutputDataCount = 0; - - for (int i = 0; i < _outputCount; i++) - { - Map row = new CaseInsensitiveHashMap<>(); - if (_defaultValues != null) - row.putAll(_defaultValues); - DerivationSpec spec = _values != null && i < _values.size() ? _values.get(i) : null; - String role = null; - if (spec != null) - { - row.putAll(spec.values); - role = spec.role; - } - - // NOTE: Input parents are added to each row, but are only used for name generation and not for derivation. - // NOTE: We will derive the inserted samples in a single derivation run after the sample/date have been inserted. - row.putAll(_parentInputNames); - - rows.add(row); - - if (StringUtils.trimToNull(role) == null) - { - role = _rolePrefix + (unknownOutputDataCount == 0 ? "" : Integer.toString(unknownOutputDataCount + 1)); - unknownOutputDataCount++; - } - roles.add(role); - } - return Pair.of(rows, roles); - } - - protected abstract TableInfo createTable(); - - protected abstract List getExpObject(List> insertedRows); - - public Map createOutputs() throws BatchValidationException, DuplicateKeyException, SQLException, QueryUpdateServiceException - { - Pair>, List> pair = prepareRows(); - List> rows = pair.first; - List roles = pair.second; - - TableInfo table = createTable(); - QueryUpdateService qus = table.getUpdateService(); - if (qus == null) - throw new IllegalStateException(); - - Map configParams = new HashMap<>(); - // Skip derivation during insert -- DeriveAction will call ExperimentService.get().derive() after samples are inserted - configParams.put(SampleTypeUpdateServiceDI.Options.SkipDerivation, true); - - BatchValidationException qusErrors = new BatchValidationException(); - List> insertedRows = qus.insertRows(getUser(), getContainer(), rows, qusErrors, configParams, null); - if (qusErrors.hasErrors()) - throw qusErrors; - - if (insertedRows.size() != roles.size()) - throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); - - List outputs = getExpObject(insertedRows); - if (outputs.size() != roles.size()) - throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); - - Map outputMap = new HashMap<>(); - for (int i = 0; i < outputs.size(); i++) - { - String role = roles.get(i); - T data = outputs.get(i); - outputMap.put(data, role); - } - - return outputMap; - } - } - } - - public static class CreateExperimentForm extends ExperimentForm implements DataRegionSelection.DataSelectionKeyForm - { - private boolean _addSelectedRuns; - private String _dataRegionSelectionKey; - - public boolean isAddSelectedRuns() - { - return _addSelectedRuns; - } - - public void setAddSelectedRuns(boolean addSelectedRuns) - { - _addSelectedRuns = addSelectedRuns; - } - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String dataRegionSelectionKey) - { - _dataRegionSelectionKey = dataRegionSelectionKey; - } - } - - @RequiresPermission(InsertPermission.class) - @ActionNames("createRunGroup, createExperiment") - public class CreateRunGroupAction extends FormViewAction - { - @Override - public ModelAndView getView(CreateExperimentForm form, boolean reshow, BindException errors) - { - // HACK - convert ExperimentForm to not be a BeanViewForm - form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); - form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - - DataRegion drg = new DataRegion(); - - drg.addHiddenFormField(ActionURL.Param.returnUrl, getViewContext().getRequest().getParameter(ActionURL.Param.returnUrl.name())); - drg.addHiddenFormField("addSelectedRuns", Boolean.toString("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns")))); - form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - // Fix issue 27562 - include session-stored selection - if (form.getDataRegionSelectionKey() != null) - { - for (String rowId : DataRegionSelection.getSelected(getViewContext(), form.getDataRegionSelectionKey(), false)) - { - drg.addHiddenFormField(DataRegion.SELECT_CHECKBOX_NAME, rowId); - } - } - drg.addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - - drg.addColumns(ExperimentServiceImpl.get().getTinfoExperiment(), "RowId,Name,LSID,ContactId,ExperimentDescriptionURL,Hypothesis,Comments,Created"); - - DisplayColumn col = drg.getDisplayColumn("RowId"); - col.setVisible(false); - drg.getDisplayColumn("LSID").setVisible(false); - drg.getDisplayColumn("Created").setVisible(false); - - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - ActionButton insertButton = new ActionButton(new ActionURL(CreateRunGroupAction.class, getContainer()), "Submit", ActionButton.Action.POST); - bb.add(insertButton); - - drg.setButtonBar(bb); - - return new InsertView(drg, errors); - } - - - @Override - public boolean handlePost(CreateExperimentForm form, BindException errors) throws Exception - { - // This is strange... but the "Create new run group..." menu item on the run grid always POSTs, probably to - // allow for long lists of run IDs. This "noPost" parameter on the initial POST is used to inform the action - // that it wants to display the form, not try to save anything yet. - if (!"true".equals(getViewContext().getRequest().getParameter("noPost"))) - { - form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); - form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - - Experiment exp = form.getBean(); - if (exp.getName() == null || exp.getName().trim().isEmpty()) - { - errors.reject(ERROR_MSG, "You must specify a name for the experiment"); - } - else - { - int maxNameLength = ExperimentService.get().getTinfoExperimentRun().getColumn("Name").getScale(); - if (exp.getName().length() > maxNameLength) - { - errors.reject(ERROR_MSG, "Name of the experiment must be " + maxNameLength + " characters or less."); - } - } - - String lsid; - int suffix = 1; - do - { - String template = "urn:lsid:" + XarContext.LSID_AUTHORITY_SUBSTITUTION + ":Experiment.Folder-" + XarContext.CONTAINER_ID_SUBSTITUTION + ":" + exp.getName(); - if (suffix > 1) - { - template = template + suffix; - } - suffix++; - lsid = LsidUtils.resolveLsidFromTemplate(template, new XarContext("Experiment Creation", getContainer(), getUser()), ExpExperiment.DEFAULT_CPAS_TYPE); - } - while (ExperimentService.get().getExpExperiment(lsid) != null); - exp.setLSID(lsid); - exp.setContainer(getContainer()); - - if (errors.getErrorCount() == 0) - { - ExpExperimentImpl wrapper = new ExpExperimentImpl(exp); - wrapper.save(getUser()); - - if (form.isAddSelectedRuns()) - { - addSelectedRunsToExperiment(wrapper, form.getDataRegionSelectionKey()); - } - - if (form.getReturnUrl() != null) - { - throw new RedirectException(form.getReturnUrl()); - } - throw new RedirectException(ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); - } - } - return true; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - root.addChild("Create Run Group"); - } - - @Override - public URLHelper getSuccessURL(CreateExperimentForm createExperimentForm) - { - return null; // null is used to show the form in the case where IDs are POSTed from the grid - } - - @Override - public void validateCommand(CreateExperimentForm target, Errors errors) { } - } - - public static class MoveRunsForm implements DataRegionSelection.DataSelectionKeyForm - { - private String _targetContainerId; - private String _dataRegionSelectionKey; - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String key) - { - _dataRegionSelectionKey = key; - } - - public String getTargetContainerId() - { - return _targetContainerId; - } - - public void setTargetContainerId(String targetContainerId) - { - _targetContainerId = targetContainerId; - } - } - - @RequiresPermission(DeletePermission.class) - public class MoveRunsLocationAction extends SimpleViewAction - { - @Override - public ModelAndView getView(MoveRunsForm form, BindException errors) - { - ActionURL moveURL = new ActionURL(MoveRunsAction.class, getContainer()); - PipelineRootContainerTree ct = new PipelineRootContainerTree(getUser(), moveURL) - { - private boolean _clickHandlerRegistered = false; - - @Override - protected void renderCellContents(StringBuilder html, Container c, ActionURL url, boolean hasRoot) - { - boolean renderLink = hasRoot && !c.equals(getContainer()); - - if (renderLink) - { - html.append(""); - } - html.append(PageFlowUtil.filter(c.getName())); - if (renderLink) - { - html.append(""); - } - - if (!_clickHandlerRegistered) - { - HttpView.currentPageConfig().addHandlerForQuerySelector("a.move-target-container", "click", "moveTo(this.attributes.getNamedItem('data-objectid').value);" ); - _clickHandlerRegistered = true; - } - } - }; - ct.setInitialLevel(1); - - MoveRunsBean bean = new MoveRunsBean(ct, form.getDataRegionSelectionKey()); - JspView result = new JspView<>("/org/labkey/experiment/moveRunsLocation.jsp", bean); - result.setTitle("Choose Destination Folder"); - result.setFrame(WebPartView.FrameType.PORTAL); - return result; - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Move Runs"); - } - } - - - @RequiresPermission(DeletePermission.class) - public class MoveRunsAction extends FormHandlerAction - { - private Container _targetContainer; - - @Override - public void validateCommand(MoveRunsForm target, Errors errors) - { - } - - @Override - public boolean handlePost(MoveRunsForm form, BindException errors) - { - _targetContainer = ContainerManager.getForId(form.getTargetContainerId()); - if (_targetContainer == null || !_targetContainer.hasPermission(getUser(), InsertPermission.class)) - { - throw new UnauthorizedException(); - } - - Set runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); - List runs = new ArrayList<>(); - for (Long runId : runIds) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run != null) - { - runs.add(run); - } - } - - ViewBackgroundInfo info = getViewBackgroundInfo(); - info.setContainer(_targetContainer); - - try - { - ExperimentService.get().moveRuns(info, getContainer(), runs); - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - } - catch (IOException e) - { - throw new NotFoundException("Failed to initialize move. Check that the pipeline root is configured correctly. " + e); - } - return true; - } - - @Override - public ActionURL getSuccessURL(MoveRunsForm form) - { - return urlProvider(PipelineUrls.class).urlBegin(_targetContainer); - } - } - - public static class ShowExternalDocsForm - { - private String _objectURI; - private String _propertyURI; - - public String getObjectURI() - { - return _objectURI; - } - - public void setObjectURI(String objectURI) - { - _objectURI = objectURI; - } - - public String getPropertyURI() - { - return _propertyURI; - } - - public void setPropertyURI(String propertyURI) - { - _propertyURI = propertyURI; - } - } - - @RequiresPermission(ReadPermission.class) - public static class ShowExternalDocsAction extends SimpleViewAction - { - @Override - public ModelAndView getView(ShowExternalDocsForm form, BindException errors) throws Exception - { - Map props = OntologyManager.getPropertyObjects(getContainer(), form.getObjectURI()); - ObjectProperty prop = props.get(form.getPropertyURI()); - if (prop == null || !getContainer().equals(prop.getContainer())) - { - throw new NotFoundException(); - } - URI uri = new URI(prop.getStringValue()); - File f = new File(uri); - if (!f.exists()) - { - throw new NotFoundException(); - } - - PageFlowUtil.streamFile(getViewContext().getResponse(), new File(f.getAbsolutePath()), false); - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - } - } - - - // TODO: DotGraph has been adding a "runId" parameter, but ShowGraphMoreListAction - public static ActionURL getShowGraphMoreListURL(Container c, @Nullable Long runId, @NotNull String objtype) - { - ActionURL url = new ActionURL(ShowGraphMoreListAction.class, c); - - if (null != runId) - url.addParameter("runId", runId); - - url.addParameter("objtype", objtype); - - return url; - } - - - @RequiresPermission(ReadPermission.class) - public static class ShowGraphMoreListAction extends SimpleViewAction - { - private ExperimentRunForm _form; - - @Override - public ModelAndView getView(ExperimentRunForm form, BindException errors) - { - _form = form; - return new GraphMoreGrid(getContainer(), errors, getViewContext().getActionURL()); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild(new NavTree("Experiments", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer()))); - ExpRun run = ExperimentService.get().getExpRun(_form.getRowId()); - if (run != null) - { - root.addChild(new NavTree("Experiment Run", ExperimentUrlsImpl.get().getRunGraphURL(_form.lookupRun()))); - } - root.addChild(new NavTree("Selected Protocol Applications")); - } - } - - @RequiresPermission(DesignAssayPermission.class) - public class AssayXarFileAction extends MutatingApiAction - { - - @Override - public Object execute(Object o, BindException errors) throws Exception - { - ApiSimpleResponse response = new ApiSimpleResponse(); - - if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) - throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); - - if (!PipelineService.get().hasValidPipelineRoot(getContainer())) - { - return false; - } - - MultipartFile formFile = getFileMap().get("file"); - if (formFile == null) - { - errors.reject(ERROR_MSG, "No file was posted by the browser."); - return false; - } - - byte[] bytes = formFile.getBytes(); - if (bytes.length == 0) - { - errors.reject(ERROR_MSG, "No file was posted by the browser."); - return false; - } - - PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); - FileLike systemDir = pipeRoot.ensureSystemDirectory(); - FileLike uploadDir = systemDir.resolveChild("UploadedXARs"); - FileUtil.createDirectories(uploadDir); - if (!uploadDir.isDirectory()) - { - errors.reject(ERROR_MSG, "Unable to create a 'system/UploadedXARs' directory under the pipeline root"); - return false; - } - String userDirName = getUser().getEmail(); - if (userDirName == null || userDirName.isEmpty()) - { - userDirName = GUEST_DIRECTORY_NAME; - } - FileLike userDir = uploadDir.resolveChild(userDirName); - FileUtil.createDirectories(userDir); - if (!userDir.isDirectory()) - { - errors.reject(ERROR_MSG, "Unable to create an 'UploadedXARs/" + userDirName + "' directory under the pipeline root"); - return false; - } - - FileLike xarFile = userDir.resolveChild(formFile.getOriginalFilename()); - - // As this is multi-part will need to use finally to close, to prevent a stream closure exception - try (OutputStream out = new BufferedOutputStream(xarFile.openOutputStream())) - { - out.write(bytes); - } - catch (IOException e) - { - errors.reject(ERROR_MSG, "Unable to write uploaded XAR file to " + xarFile); - return false; - } - //noinspection EmptyCatchBlock - - ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), xarFile, - "Uploaded file", true, pipeRoot); - PipelineService.get().queueJob(job); - - response.put("success", true); - return response; - } - } - - @RequiresPermission(InsertPermission.class) - public class ImportXarFileAction extends FormHandlerAction - { - @Override - public void validateCommand(ImportXarForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ImportXarForm form, BindException errors) throws Exception - { - for (FileLike f : form.getValidatedFiles(getContainer())) - { - if (f.isFile()) - { - ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); - - // TODO: Configure module resources with the appropriate log location per container - if (form.getModule() != null) - { - FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); - job.setLogFile(logFile); - } - - PipelineService.get().queueJob(job); - } - else - { - throw new NotFoundException("Expected a file but found a directory: " + f.getName()); - } - } - - return true; - } - - @Override - public URLHelper getSuccessURL(ImportXarForm importXarForm) - { - return getContainer().getStartURL(getUser()); - } - } - - - @RequiresPermission(InsertPermission.class) - public class ImportXarAction extends MutatingApiAction - { - @Override - public Object execute(ImportXarForm form, BindException errors) throws Exception - { - ApiSimpleResponse response = new ApiSimpleResponse(); - - List> archives = new ArrayList<>(); - for (FileLike f : form.getValidatedFiles(getContainer())) - { - Map archive = new HashMap<>(); - ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); - - // TODO: Configure module resources with the appropriate log location per container - if (form.getModule() != null) - { - FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); - job.setLogFile(logFile); - } - - PipelineService.get().queueJob(job); - - archive.put("file", f.getName()); - archive.put("job", job.getJobGUID()); - archive.put("path", form.getPath()); // echo back the public path - - archives.add(archive); - } - - response.put("success", true); - response.put("archives", archives); - - return response; - } - } - - - /** - * User: jeckels - * Date: Jan 27, 2008 - */ - public static class ExperimentUrlsImpl implements ExperimentUrls - { - public ActionURL getOverviewURL(Container c) - { - return new ActionURL(BeginAction.class, c); - } - - @Override - public ActionURL getExperimentDetailsURL(Container c, ExpExperiment expExperiment) - { - return new ActionURL(DetailsAction.class, c).addParameter("rowId", expExperiment.getRowId()); - } - - public ActionURL getShowSampleURL(Container c, ExpMaterial material) - { - return getMaterialDetailsBaseURL(c, null).addParameter("rowId", material.getRowId()); - } - - @Override - public ActionURL getExportProtocolURL(Container container, ExpProtocol protocol) - { - return new ActionURL(ExperimentController.ExportProtocolsAction.class, container). - addParameter("protocolId", protocol.getRowId()). - addParameter("xarFileName", protocol.getName() + ".xar"); - } - - @Override - public ActionURL getMoveRunsLocationURL(Container container) - { - return new ActionURL(ExperimentController.MoveRunsLocationAction.class, container); - } - - @Override - public ActionURL getProtocolDetailsURL(ExpProtocol protocol) - { - return new ActionURL(ProtocolDetailsAction.class, protocol.getContainer()).addParameter("rowId", protocol.getRowId()); - } - - @Override - public ActionURL getProtocolApplicationDetailsURL(ExpProtocolApplication app) - { - return getShowApplicationURL(app.getContainer(), app.getRowId()); - } - - public ActionURL getProtocolGridURL(Container c) - { - return new ActionURL(ShowProtocolGridAction.class, c); - } - - public ActionURL getRunGraphDetailURL(ExpRun run) - { - return getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpData focus) - { - return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_DATA); - } - - public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpMaterial focus) - { - return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_MATERIAL); - } - - public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpProtocolApplication focus) - { - return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_PROT_APP); - } - - private ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpObject focus, String typeCode) - { - ActionURL result = getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); - result.addParameter("detail", "true"); - if (focus != null) - { - result.addParameter("focus", typeCode + focus.getRowId()); - } - return result; - } - - @Override - public ActionURL getRunGraphURL(Container container, long runId) - { - return ExperimentController.getRunGraphURL(container, runId); - } - - @Override - public ActionURL getRunGraphURL(ExpRun run) - { - return getRunGraphURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getRunTextURL(Container c, long runId) - { - return new ActionURL(ShowRunTextAction.class, c).addParameter("rowId", runId); - } - - @Override - public ActionURL getRunTextURL(ExpRun run) - { - return getRunTextURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getDeleteExperimentsURL(Container container, URLHelper returnUrl) - { - return new ActionURL(DeleteSelectedExperimentsAction.class, container).addReturnUrl(returnUrl); - } - - @Override - public ActionURL getDeleteProtocolURL(@NotNull ExpProtocol protocol, URLHelper returnUrl) - { - ActionURL result = new ActionURL(DeleteProtocolByRowIdsAction.class, protocol.getContainer()); - result.addParameter("singleObjectRowId", protocol.getRowId()); - if (returnUrl != null) - { - result.addReturnUrl(returnUrl); - } - return result; - } - - @Override - public ActionURL getAddRunsToExperimentURL(Container c, ExpExperiment exp) - { - return new ActionURL(AddRunsToExperimentAction.class, c).addParameter("expRowId", exp.getRowId()); - } - - @Override - public ActionURL getShowRunsURL(Container c, ExperimentRunType type) - { - ActionURL result = new ActionURL(ShowRunsAction.class, c); - result.addParameter("experimentRunFilter", type.getDescription()); - return result; - } - - public ActionURL getShowExperimentsURL(Container c) - { - return new ActionURL(ShowRunGroupsAction.class, c); - } - - @Override - public ActionURL getShowSampleTypeListURL(Container c) - { - return getShowSampleTypeListURL(c, null); - } - - @Override - public ActionURL getShowSampleTypeURL(ExpSampleType sampleType) - { - return getShowSampleTypeURL(sampleType, sampleType.getContainer()); - } - - @Override - public ActionURL getShowSampleTypeURL(ExpSampleType sampleType, Container container) - { - return new ActionURL(ShowSampleTypeAction.class, container).addParameter("rowId", sampleType.getRowId()); - } - - public ActionURL getExperimentListURL(Container container) - { - return new ActionURL(ShowRunGroupsAction.class, container); - } - - public ActionURL getShowSampleTypeListURL(Container c, String errorMessage) - { - ActionURL url = new ActionURL(ListSampleTypesAction.class, c); - if (errorMessage != null) - { - url.addParameter("errorMessage", errorMessage); - } - return url; - } - - @Override - public ActionURL getDataClassListURL(Container c) - { - return getDataClassListURL(c, null); - } - - public ActionURL getDataClassListURL(Container c, String errorMessage) - { - ActionURL url = new ActionURL(ListDataClassAction.class, c); - if (errorMessage != null) - { - url.addParameter("errorMessage", errorMessage); - } - return url; - } - - @Override - public ActionURL getDeleteDatasURL(Container c, URLHelper returnUrl) - { - ActionURL url = new ActionURL(DeleteSelectedDataAction.class, c); - if (returnUrl != null) - url.addReturnUrl(returnUrl); - return url; - } - - public ActionURL getDeleteSelectedExperimentsURL(Container c, URLHelper returnUrl) - { - ActionURL result = new ActionURL(DeleteSelectedExperimentsAction.class, c); - if (returnUrl != null) - result.addReturnUrl(returnUrl); - return result; - } - - @Override - public ActionURL getDeleteSelectedExpRunsURL(Container container, URLHelper returnUrl) - { - return new ActionURL(DeleteSelectedExpRunsAction.class, container).addReturnUrl(returnUrl); - } - - public ActionURL getShowUpdateURL(ExpExperiment experiment) - { - return new ActionURL(ShowUpdateAction.class, experiment.getContainer()).addParameter("rowId", experiment.getRowId()); - } - - @Override - public ActionURL getRemoveSelectedExpRunsURL(Container container, URLHelper returnUrl, ExpExperiment exp) - { - return new ActionURL(RemoveSelectedExpRunsAction.class, container).addReturnUrl(returnUrl).addParameter("expRowId", exp.getRowId()); - } - - @Override - public ActionURL getCreateRunGroupURL(Container container, URLHelper returnUrl, boolean addSelectedRuns) - { - ActionURL result = new ActionURL(CreateRunGroupAction.class, container); - if (returnUrl != null) - { - result.addReturnUrl(returnUrl); - } - if (addSelectedRuns) - { - result.addParameter("addSelectedRuns", "true"); - } - return result; - } - - - public static ExperimentUrlsImpl get() - { - return (ExperimentUrlsImpl) urlProvider(ExperimentUrls.class); - } - - public ActionURL getDownloadGraphURL(ExpRun run, boolean detail, String focus, String focusType) - { - ActionURL result = new ActionURL(DownloadGraphAction.class, run.getContainer()); - result.addParameter("rowId", run.getRowId()).addParameter("detail", detail); - if (focus != null) - { - result.addParameter("focus", focus); - } - if (focusType != null) - { - result.addParameter("focusType", focusType); - } - return result; - } - - public ActionURL getBeginURL(Container container) - { - return new ActionURL(BeginAction.class, container); - } - - @Override - public ActionURL getDomainEditorURL(Container container, String domainURI, boolean createOrEdit) - { - Domain domain = PropertyService.get().getDomain(container, domainURI); - if (domain != null) - return getDomainEditorURL(container, domain); - - ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); - url.addParameter("domainURI", domainURI); - if (createOrEdit) - url.addParameter("createOrEdit", true); - return url; - } - - @Override - public ActionURL getDomainEditorURL(Container container, Domain domain) - { - ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); - url.addParameter("domainId", domain.getTypeId()); - return url; - } - - @Override - public ActionURL getCreateDataClassURL(Container container) - { - return new ActionURL(EditDataClassAction.class, container); - } - - @Override - public ActionURL getShowDataClassURL(Container container, long rowId) - { - ActionURL url = new ActionURL(ShowDataClassAction.class, container); - url.addParameter("rowId", rowId); - return url; - } - - @Override - public ActionURL getShowFileURL(ExpData data, boolean inline) - { - ActionURL result = getShowFileURL(data.getContainer()).addParameter("rowId", data.getRowId()); - if (inline) - { - result.addParameter("inline", inline); - } - return result; - } - - @Override - public ActionURL getMaterialDetailsURL(ExpMaterial material) - { - return getMaterialDetailsURL(material.getContainer(), material.getRowId()); - } - - @Override - public ActionURL getMaterialDetailsURL(Container c, long materialRowId) - { - return getMaterialDetailsBaseURL(c, null).addParameter("rowId", materialRowId); - } - - @Override - public ActionURL getMaterialDetailsBaseURL(Container c, @Nullable String materialIdFieldKey) - { - return new ActionURL(ShowMaterialAction.class, c); - } - - @Override - public ActionURL getCreateSampleTypeURL(Container container) - { - return new ActionURL(EditSampleTypeAction.class, container); - } - - @Override - public ActionURL getImportSamplesURL(Container container, String sampleTypeName) - { - ActionURL url = new ActionURL(ImportSamplesAction.class, container); - url.addParameter("query.queryName", sampleTypeName); - url.addParameter("schemaName", "exp.materials"); - return url; - } - - @Override - public ActionURL getImportDataURL(Container container, String dataClassName) - { - ActionURL url = new ActionURL(ImportDataAction.class, container); - url.addParameter("query.queryName", dataClassName); - url.addParameter("schemaName", "exp.data"); - return url; - } - - @Override - public ActionURL getDataDetailsURL(ExpData data) - { - return new ActionURL(ShowDataAction.class, data.getContainer()).addParameter("rowId", data.getRowId()); - } - - @Override - public ActionURL getShowFileURL(Container c) - { - return new ActionURL(ShowFileAction.class, c); - } - - @Override - public ActionURL getSetFlagURL(Container container) - { - return new ActionURL(SetFlagAction.class, container); - } - - @Override - public ActionURL getShowRunGraphURL(ExpRun run) - { - return ExperimentController.getRunGraphURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getRepairTypeURL(Container container) - { - return new ActionURL(TypesController.RepairAction.class, container); - } - - @Override - public ActionURL getUpdateMaterialQueryRowAction(Container c, TableInfo table) - { - ActionURL url = new ActionURL(UpdateMaterialQueryRowAction.class, c); - url.addParameter("schemaName", "samples"); - url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); - - return url; - } - - @Override - public ActionURL getInsertMaterialQueryRowAction(Container c, TableInfo table) - { - ActionURL url = new ActionURL(InsertMaterialQueryRowAction.class, c); - url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); - - return url; - } - - @Override - public ActionURL getDataClassAttachmentDownloadAction(Container c) - { - return new ActionURL(ExperimentController.DataClassAttachmentDownloadAction.class, c); - } - - } - - private static abstract class BaseResolveLsidApiAction extends ReadOnlyApiAction - { - protected Set _seeds; - - @Override - public void validateForm(F form, Errors errors) - { - if (null != form.getLsids()) - { - _seeds = new LinkedHashSet<>(form.getLsids().size()); - for (String lsid : form.getLsids()) - { - Identifiable id = LsidManager.get().getObject(lsid); - if (id == null) - throw new NotFoundException("Unable to resolve object: " + lsid); - - // ensure the user has read permission in the seed container - if (!getContainer().equals(id.getContainer())) - { - if (!id.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new UnauthorizedException("User does not have permission to read object: " + lsid); - } - - _seeds.add(id); - } - } - else - { - throw new ApiUsageException("Starting lsids required"); - } - } - } - - @RequiresPermission(ReadPermission.class) - public static class ResolveAction extends BaseResolveLsidApiAction - { - @Override - public Object execute(ResolveLsidsForm form, BindException errors) - { - var settings = new ExperimentJSONConverter.Settings(form.isIncludeProperties(), form.isIncludeInputsAndOutputs(), form.isIncludeRunSteps()); - var data = _seeds.stream().map(n -> ExperimentJSONConverter.serialize(n, getUser(), settings)).collect(toList()); - return new ApiSimpleResponse("data", data); - } - } - - @RequiresPermission(ReadPermission.class) - public static class LineageAction extends BaseResolveLsidApiAction - { - @Override - public Object execute(ExpLineageOptions options, BindException errors) throws Exception - { - ExpLineageServiceImpl.get().streamLineage(getContainer(), getUser(), getViewContext().getResponse(), _seeds, options); - return null; - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class RebuildEdgesAction extends MutatingApiAction - { - @Override - public Object execute(ExperimentRunForm form, BindException errors) - { - if (form.getRowId() != 0 || form.getLsid() != null) - { - ExpRun run = form.lookupRun(); - if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new UnauthorizedException("Not permitted"); - - ExperimentServiceImpl.get().syncRunEdges(run); - } - else - { - // should this require site admin permissions? - ExperimentServiceImpl.get().rebuildAllRunEdges(); - } - return success(); - } - } - - private static class VerifyEdgesForm extends ExperimentRunForm - { - private Integer _limit; - - public Integer getLimit() - { - return _limit; - } - - public void setLimit(Integer limit) - { - _limit = limit; - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class VerifyEdgesAction extends ReadOnlyApiAction - { - @Override - public Object execute(VerifyEdgesForm form, BindException errors) - { - if (form.getRowId() != 0 || form.getLsid() != null) - { - ExpRun run = form.lookupRun(); - if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new UnauthorizedException("Not permitted"); - - ExperimentServiceImpl.get().verifyRunEdges(run); - } - else - { - ExperimentServiceImpl.get().verifyAllEdges(getContainer(), form.getLimit()); - } - return success(); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class RebuildAncestorsAction extends MutatingApiAction - { - @Override - public Object execute(Object form, BindException errors) - { - ClosureQueryHelper.truncateAndRecreate(); - return success(); - } - } - - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class CheckDataClassesIndexedAction extends ReadOnlyApiAction - { - @Override - public Object execute(Object o, BindException errors) throws Exception - { - List> notInIndex = new ArrayList<>(100); - - List list = ExperimentService.get().getDataClasses(getContainer(), getUser(), false); - for (ExpDataClass dc : list) - { - for (ExpData d : dc.getDatas()) - { - String docId = d.getDocumentId(); - if (docId != null) - { - SearchService.SearchHit hit = SearchService.get().find(docId); - if (hit == null) - { - JSONObject props = ExperimentJSONConverter.serializeData(d, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); - props.put("docid", docId); - notInIndex.add(props.toMap()); - } - } - } - } - - return success(notInIndex); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class CheckEdgesAction extends ReadOnlyApiAction - { - @Override - public Object execute(Object o, BindException errors) throws Exception - { - List result; - DbSchema schema = ExperimentService.get().getSchema(); - TableInfo edgeTable = schema.getTable("Edge"); - - if (null != edgeTable.getColumn("fromObjectId")) - { - var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") - .resultSetStream() - .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) - .collect(toList()); - var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); - result = cycles.stream().map(e -> new Integer[]{e.first, e.second}).collect(toList()); - } - else - { - var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromLsid, toLsid FROM exp.Edge") - .resultSetStream() - .map(r -> { try { return new Pair<>(r.getString(1), r.getString(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) - .collect(toList()); - var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); - result = cycles.stream().map(e -> new String[]{e.first, e.second}).collect(toList()); - } - - JSONObject ret = new JSONObject(); - ret.put("result", result); - ret.put("success", true); - return ret; - } - } - - @RequiresPermission(UpdatePermission.class) - public static class UpdateMaterialQueryRowAction extends UserSchemaAction - { - @Override - protected QueryForm createQueryForm(ViewContext context) - { - QueryForm form = new QueryForm("samples", null); - form.setViewContext(getViewContext()); - form.bindParameters(getViewContext().getBindPropertyValues()); - return form; - } - - @Override - public BindException bindParameters(PropertyValues m) throws Exception - { - BindException bind = super.bindParameters(m); - - QueryUpdateForm tableForm = (QueryUpdateForm)bind.getTarget(); - - int sampleId; - try - { - sampleId = Integer.parseInt((String) tableForm.getPkVal()); - } - catch (NumberFormatException e) - { - throw new NotFoundException("Invalid RowId: " + tableForm.getPkVal()); - } - - ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); - if (material == null) - throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); - - return bind; - } - - @Override - public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) - { - int sampleId = Integer.parseInt((String) tableForm.getPkVal()); - - ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); - if (material == null) - throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); - - boolean isAliquot = !StringUtils.isEmpty(material.getAliquotedFromLSID()); - - TableInfo tableInfo = tableForm.getTable(); - Map scopedFields = new CaseInsensitiveHashMap<>(); - for (DomainProperty dp : tableInfo.getDomain().getProperties()) - { - if (!ExpSchema.DerivationDataScopeType.All.name().equalsIgnoreCase(dp.getDerivationDataScope())) - scopedFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); - } - - for (var column : tableInfo.getColumns()) - { - String columnName = column.getName(); - if (scopedFields.containsKey(columnName)) - { - boolean isAliquotField = scopedFields.get(columnName); - boolean show = (isAliquot && isAliquotField) || (!isAliquot && !isAliquotField); - ((BaseColumnInfo)column).setUserEditable(show); - ((BaseColumnInfo)column).setHidden(!show); - } - } - - ButtonBar bb = createSubmitCancelButtonBar(tableForm); - UpdateView view = new UpdateView(tableForm, errors); - view.getDataRegion().setButtonBar(bb); - return view; - } - - @Override - public boolean handlePost(QueryUpdateForm tableForm, BindException errors) - { - doInsertUpdate(tableForm, errors, false); - return 0 == errors.getErrorCount(); - } - - @Override - public void addNavTrail(NavTree root) - { - super.addNavTrail(root); - root.addChild("Edit " + _form.getQueryName()); - } - } - - @RequiresPermission(InsertPermission.class) - public static class InsertMaterialQueryRowAction extends UserSchemaAction - { - @Override - protected QueryForm createQueryForm(ViewContext context) - { - QueryForm form = new QueryForm("samples", null); - form.setViewContext(getViewContext()); - form.bindParameters(getViewContext().getBindPropertyValues()); - - return form; - } - - @Override - public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) - { - TableInfo tableInfo = tableForm.getTable(); - Map propertyFields = new CaseInsensitiveHashMap<>(); - for (DomainProperty dp : tableInfo.getDomain().getProperties()) - { - propertyFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); - } - - for (var column : tableInfo.getColumns()) - { - String columnName = column.getName(); - if (propertyFields.containsKey(columnName)) - { - boolean isAliquotField = propertyFields.get(columnName); - ((BaseColumnInfo)column).setUserEditable(!isAliquotField); - ((BaseColumnInfo)column).setHidden(isAliquotField); - } - } - - InsertView view = new InsertView(tableForm, errors); - view.getDataRegion().setButtonBar(createSubmitCancelButtonBar(tableForm)); - return view; - } - - @Override - public boolean handlePost(QueryUpdateForm tableForm, BindException errors) - { - doInsertUpdate(tableForm, errors, true); - return 0 == errors.getErrorCount(); - } - - @Override - public void addNavTrail(NavTree root) - { - super.addNavTrail(root); - root.addChild("Insert " + _form.getQueryName()); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class SaveFindIdsAction extends ReadOnlyApiAction - { - - public static final String FIND_BY_IDS_SESSION_KEY_PREFIX = "findByIds"; - - @Override - public Object execute(FindByIdsForm form, BindException errors) throws Exception - { - HttpServletRequest request = getViewContext().getRequest(); - String key = form.getSessionKey(); - boolean removePrevious = false; - - if (key == null) - { - removePrevious = true; - key = FIND_BY_IDS_SESSION_KEY_PREFIX + "_" + UniqueID.getServerSessionScopedUID(); - } - - if (request != null) - { - if (removePrevious) - SessionHelper.clearAttributesWithPrefix(request, FIND_BY_IDS_SESSION_KEY_PREFIX); - HttpSession session = request.getSession(false); - if (session != null) - { - @SuppressWarnings("unchecked") - List existingIds = (List) session.getAttribute(key); - - // deduplicate from existing ids - if (existingIds != null && form.getSessionKey() != null) - { - existingIds.addAll(form.getIds().stream().filter(id -> !existingIds.contains(id)).toList()); - session.setAttribute(key, existingIds); - } - else - { - session.setAttribute(key, form.getIds()); - } - return success("Saved ids to session key", key); - } - } - - return new SimpleResponse<>(false, "Unable to save to session. Session or request may be null."); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class SaveOrderedSamplesQueryAction extends ReadOnlyApiAction - { - private static final String SAMPLE_ID_PREFIX = "s:"; - private static final String UNIQUE_ID_PREFIX = "u:"; - - private List _ids; - private Map> _uniqueIdLsids; - - @Override - public void validateForm(FindByIdsForm form, Errors errors) - { - if (form.getSessionKey() == null) - errors.reject(ERROR_REQUIRED, "sessionKey must be provided"); - else - { - _ids = getFindIdsFromSession(form.getSessionKey()); - if (_ids == null || _ids.isEmpty()) - errors.reject(ERROR_REQUIRED, "No ids found corresponding to session key " + form.getSessionKey()); - } - } - - private void ensureUniqueIdLsids() - { - boolean hasUniqueId = _ids.stream().anyMatch(s -> s.startsWith(UNIQUE_ID_PREFIX)); - if (hasUniqueId && _uniqueIdLsids == null) - { - List uniqueIds = _ids.stream().map(s -> s.substring(UNIQUE_ID_PREFIX.length())).toList(); - _uniqueIdLsids = ExperimentService.get().getUniqueIdLsids(uniqueIds, getUser(), getContainer()); - } - } - - @Override - public Object execute(FindByIdsForm form, BindException errors) throws Exception - { - ensureUniqueIdLsids(); - - SQLFragment select = getOrderedRowsSql(); - // need to set the key field so selections are possible - // need the SampleTypeUnits so we will display using that unit - String metadata = - """ - - - - - true - true - - - true - - - true - - -
- """; - QueryDefinition def = QueryService.get().saveSessionQuery(getViewContext(), getContainer(), ExperimentServiceImpl.getExpSchema().getName(), select.getSQL(), metadata); - return success("Session query created", Map.of("queryName", def.getName(), "ids", _ids)); - } - - - private List getFindIdsFromSession(String sessionKey) - { - HttpServletRequest request = getViewContext().getRequest(); - List ids = new ArrayList<>(); - if (request != null) - { - HttpSession session = request.getSession(false); - if (session != null) - { - ids = (List) session.getAttribute(sessionKey); - } - } - return ids; - } - - private SQLFragment getOrderedRowsSql() - { - boolean isFMEnabled = InventoryService.isFreezerManagementEnabled(getContainer()); - String samplesTable = isFMEnabled ? "inventory.SampleItems" : "exp.materials"; - List orderedIdCols = new ArrayList<>(Arrays.asList("Id AS ProvidedID", "RowId", "Ordinal")); - List sampleColumns = new ArrayList<>(); - if (!isFMEnabled) - { - sampleColumns.addAll(Arrays.asList( - "S.Name AS SampleID", - "S.MaterialExpDate AS ExpirationDate", - "S.SampleSet as SampleType", - "S.SampleState", - "S.isAliquot", - "S.Created", - "S.CreatedBy" - )); - } - else - { - sampleColumns.addAll(Arrays.asList( - "S.Name AS SampleID", - "S.MaterialExpDate AS ExpirationDate", - "S.LabelColor", - "S.SampleSet", - "S.SampleState", - "S.StoredAmount", - "S.Units", - "S.SampleTypeUnits", - "S.FreezeThawCount", - "S.StorageStatus", - "S.CheckedOutBy", - "S.StorageLocation", - "S.StorageRow", - "S.StorageCol", - "S.StoragePositionNumber", - "S.IsAliquot", - "S.Created", - "S.CreatedBy" - )); - } - - - String sampleIdComma = ""; - String uniqueIdComma = ""; - int index = 1; - SQLFragment sampleIdValuesSql = new SQLFragment(); - SQLFragment uniqueIdValuesSql = new SQLFragment(); - for (String id : _ids) - { - if (id.startsWith(SAMPLE_ID_PREFIX)) - { - sampleIdValuesSql.append(sampleIdComma).append("\t(").appendValue(index); - sampleIdValuesSql.append(", "); - sampleIdValuesSql.append(LabKeySql.quoteString(id.substring(SAMPLE_ID_PREFIX.length()))); - sampleIdValuesSql.append(", "); - sampleIdValuesSql.append(LabKeySql.quoteString("null")); - sampleIdValuesSql.append(")"); - sampleIdComma = "\n,"; - } - else if (id.startsWith(UNIQUE_ID_PREFIX)) - { - String idClean = id.substring(UNIQUE_ID_PREFIX.length()); - - List lsids = _uniqueIdLsids.get(idClean); - if (lsids != null) - { - for (String lsid : lsids) - { - uniqueIdValuesSql.append(uniqueIdComma).append("\t(").appendValue(index); - uniqueIdValuesSql.append(", "); - uniqueIdValuesSql.append(LabKeySql.quoteString(idClean)); - uniqueIdValuesSql.append(", "); - uniqueIdValuesSql.append(LabKeySql.quoteString(lsid)); - uniqueIdValuesSql.append(")"); - uniqueIdComma = "\n,"; - } - } - } - index++; - } - - boolean haveData = !sampleIdValuesSql.isEmpty() || !_uniqueIdLsids.isEmpty(); - SQLFragment sql = new SQLFragment(); - if (!sampleIdValuesSql.isEmpty()) - { - sql.append("WITH _ordered_ids_ AS (\nSELECT * FROM (VALUES\n"); - sql.append(sampleIdValuesSql); - sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter - } - if (!uniqueIdValuesSql.isEmpty()) - { - if (!sampleIdValuesSql.isEmpty()) - sql.append(",\n"); - else - sql.append("WITH "); - - sql.append("_ordered_unique_ids_ AS (\nSELECT * FROM (VALUES\n"); - sql.append(uniqueIdValuesSql); - sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter - } - - sql.append("SELECT "); - sql.append("\n\tOID.").append(StringUtils.join(orderedIdCols, ",\n\tOID.")); - sql.append(",\n\t").append(StringUtils.join( sampleColumns, ",\n\t")); - sql.append("\nFROM\n("); - if (!sampleIdValuesSql.isEmpty()) - { - sql.append("SELECT\n\tM.RowId,\n\t_ordered_ids_.column1 as Ordinal,\n\t_ordered_ids_.column2 as Id,\n\t_ordered_ids_.column2 as lsid"); - sql.append("\nFROM _ordered_ids_\n"); - sql.append("INNER JOIN exp.materials M ON _ordered_ids_.column2 = M.Name"); - sql.append("\n"); - } - if (!uniqueIdValuesSql.isEmpty()) - { - if (!sampleIdValuesSql.isEmpty()) - sql.append("\nUNION ALL\n\n"); - - sql.append("SELECT\n\tM.RowId,\n\t_ordered_unique_ids_.column1 as Ordinal,\n\t_ordered_unique_ids_.column2 as Id,\n\t_ordered_unique_ids_.column3 as lsid"); - sql.append("\nFROM _ordered_unique_ids_\n"); - sql.append("INNER JOIN exp.materials M ON _ordered_unique_ids_.column3 = M.lsid"); - sql.append("\n"); - } - if (!haveData) // no data to return but return data in the expected shape. - { - sql = new SQLFragment("SELECT\n"); - sql.append(orderedIdCols.stream() - .map(col -> { - int asIndex = col.indexOf("AS"); - if (asIndex > 0) - return "NULL AS " + col.substring(asIndex+ 3); - else - return "NULL AS " + col; - }) - .collect(Collectors.joining(",\t\n"))); - sql.append(",\t\n").append(StringUtils.join(sampleColumns, ",\t\n")); - sql.append("\nFROM ").append(samplesTable).append(" S WHERE 1 = 2"); - return sql; - } - else - { - sql.append(") OID"); - if (isFMEnabled) - sql.append("\nLEFT JOIN inventory.SampleItems S on S.RowId = OID.RowId"); - else - sql.append("\nINNER JOIN exp.materials S on S.RowId = OID.RowId"); - sql.append("\n\nORDER BY Ordinal"); - return sql; - } - } - } - - public static class FindByIdsForm extends FindSessionKeyForm - { - List _ids; - - public List getIds() - { - return _ids; - } - - public void setIds(List ids) - { - _ids = ids; - } - } - - - public static class FindSessionKeyForm - { - private String _sessionKey; - - public String getSessionKey() - { - return _sessionKey; - } - - public void setSessionKey(String sessionKey) - { - _sessionKey = sessionKey; - } - } - - static void validateEntitySequenceForm(EntitySequenceForm form, Errors errors) - { - String kindName = form.getKindName(); - if (StringUtils.isEmpty(kindName) || form.getSeqType() == null) - { - errors.reject(ERROR_REQUIRED, "KindName and SeqType must be provided"); - return; - } - - if (form.getSeqType() == NameGenerator.EntityCounter.genId) - { - if (form.getRowId() == null) - errors.reject(ERROR_REQUIRED, "Data type RowId must be provided for genId"); - } - else if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName)) - { - errors.reject(ERROR_MSG, form.getSeqType() + " is not supported for " + kindName); - } - - if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName) && !DataClassDomainKind.NAME.equalsIgnoreCase(kindName)) - errors.reject(ERROR_MSG, "Invalid KindName. Should be either " + SampleTypeDomainKind.NAME + " or " + DataClassDomainKind.NAME + "."); - - } - - @RequiresPermission(ReadPermission.class) - public static class GetEntitySequenceAction extends ReadOnlyApiAction - { - @Override - public void validateForm(EntitySequenceForm form, Errors errors) - { - validateEntitySequenceForm(form, errors); - } - - @Override - public Object execute(EntitySequenceForm form, BindException errors) throws Exception - { - long value = -1; - if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - if (form.getSeqType() == NameGenerator.EntityCounter.genId) - { - ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); - if (sampleType != null) - value = sampleType.getCurrentGenId(); - } - else - { - value = SampleTypeService.get().getCurrentCount(form.getSeqType(), getContainer()); - } - - } - else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); - if (dataClass != null) - value = dataClass.getCurrentGenId(); - } - - ApiSimpleResponse resp = new ApiSimpleResponse(); - resp.put("success", value > -1); - resp.put("value", value); - return resp; - } - } - - @RequiresPermission(ReadPermission.class) // actual permission checked later - public static class SetEntitySequenceAction extends MutatingApiAction - { - @Override - public void validateForm(EntitySequenceForm form, Errors errors) - { - validateEntitySequenceForm(form, errors); - - if (form.getNewValue() == null || form.getNewValue() < 0) - errors.reject(ERROR_MSG, "Invalid newValue."); - } - - @Override - public Object execute(EntitySequenceForm form, BindException errors) - { - ApiSimpleResponse resp = new ApiSimpleResponse(); - resp.put("success", true); - - try - { - Domain domain = null; - if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - if (form.getSeqType() == NameGenerator.EntityCounter.genId) - { - if (!getContainer().hasPermission(getUser(), DesignSampleTypePermission.class)) - throw new UnauthorizedException("Insufficient permissions."); - - ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); - if (sampleType != null) - { - sampleType.ensureMinGenId(form.getNewValue()); - domain = sampleType.getDomain(); - } - else - { - resp.put("success", false); - resp.put("error", "Sample type does not exist."); - } - } - else - { - if (!getContainer().hasPermission(getUser(), AdminPermission.class)) - throw new UnauthorizedException("Insufficient permissions."); - - SampleTypeService.get().ensureMinSampleCount(form.getNewValue(), form.getSeqType(), getContainer()); - } - } - else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - if (!getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) - throw new BadRequestException("Insufficient permissions."); - - ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); - if (dataClass != null) - { - dataClass.ensureMinGenId(form.getNewValue(), getContainer()); - domain = dataClass.getDomain(); - } - else - { - resp.put("success", false); - resp.put("error", "DataClass does not exist."); - } - } - - if (domain != null) - { - DomainAuditProvider.DomainAuditEvent event = new DomainAuditProvider.DomainAuditEvent(getContainer(), "The genId for domain " + domain.getName() + " has been updated to " + form.getNewValue() + "."); - event.setDomainUri(domain.getTypeURI()); - event.setDomainName(domain.getName()); - AuditLogService.get().addEvent(getUser(), event); - } - } - catch (ExperimentException e) - { - resp.put("success", false); - resp.put("error", e.getMessage()); - } - - return resp; - } - } - - public static class EntitySequenceForm - { - private String _kindName; - private NameGenerator.EntityCounter _seqType; - private Integer _rowId; - private Long _newValue; - - public Integer getRowId() - { - return _rowId; - } - - public void setRowId(Integer rowId) - { - _rowId = rowId; - } - - public String getKindName() - { - return _kindName; - } - - public void setKindName(String kindName) - { - _kindName = kindName; - } - - public Long getNewValue() - { - return _newValue; - } - - public void setNewValue(Long newValue) - { - this._newValue = newValue; - } - - public NameGenerator.EntityCounter getSeqType() - { - return _seqType; - } - - public void setSeqType(String seqType) - { - _seqType = NameGenerator.EntityCounter.valueOf(seqType); - } - - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetCrossFolderDataSelectionAction extends ReadOnlyApiAction - { - @Override - public void validateForm(CrossFolderSelectionForm form, Errors errors) - { - if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); - if (!"samples".equalsIgnoreCase(form.getDataType()) && !"exp.data".equalsIgnoreCase(form.getDataType())&& !"assay".equalsIgnoreCase(form.getDataType())) - errors.reject(ERROR_REQUIRED, "Data type (sample, data or assayrun) must be specified."); - } - - @Override - public Object execute(CrossFolderSelectionForm form, BindException errors) - { - Pair result = ExperimentServiceImpl.getCurrentAndCrossFolderDataCount(form.getIds(false), form.getDataType(), getContainer()); - - ApiSimpleResponse resp = new ApiSimpleResponse(); - resp.put("success", true); - resp.put("currentFolderSelectionCount", result.first); - resp.put("crossFolderSelectionCount", result.second); - - return success(resp); - } - } - - public static class CrossFolderSelectionForm extends DataViewSnapshotSelectionForm - { - private String _dataType; - private String _picklistName; - - public String getDataType() - { - return _dataType; - } - - public void setDataType(String dataType) - { - _dataType = dataType; - } - - public String getPicklistName() - { - return _picklistName; - } - - public void setPicklistName(String picklistName) - { - _picklistName = picklistName; - } - - @Override - public Set getIds(boolean clear) - { - Set selectedIds; - - if (_rowIds != null) - selectedIds = _rowIds; - else if (isUseSnapshotSelection()) - selectedIds = new HashSet<>(DataRegionSelection.getSnapshotSelectedIntegers(getViewContext(), getDataRegionSelectionKey())); - else - selectedIds = DataRegionSelection.getSelectedIntegers(getViewContext(), getDataRegionSelectionKey(), clear); - - if (_picklistName != null) - { - User user = getViewContext().getUser(); - Container container = getViewContext().getContainer(); - UserSchema schema = ListService.get().getUserSchema(user, container); - TableInfo tInfo = schema.getTable(_picklistName); - if (tInfo != null) - { - SimpleFilter filter = SimpleFilter.createContainerFilter(container); - filter.addInClause(FieldKey.fromParts("id"), selectedIds); - TableSelector selector = new TableSelector(tInfo, Collections.singleton("SampleID"), filter, null); - return new HashSet<>(selector.getArrayList(Long.class)); - } - } - return selectedIds; - } - } - - @RequiresPermission(AdminPermission.class) - public static class RecomputeAliquotRollup extends SimpleViewAction - { - @Override - public void addNavTrail(NavTree root) - { - } - - @Override - public ModelAndView getView(Object o, BindException errors) throws SQLException - { - try (var ignore = SpringActionController.ignoreSqlUpdates()) - { - Container container = getContainer(); - User user = getUser(); - - List sampleTypes = SampleTypeService.get() - .getSampleTypes(container, user, true); - - HtmlStringBuilder builder = HtmlStringBuilder.of(); - builder.unsafeAppend(""); - - SampleTypeService service = SampleTypeService.get(); - for (ExpSampleType sampleType : sampleTypes) - { - int updatedCount; - updatedCount = service.recomputeSampleTypeRollup(sampleType, container); - // we could check "if (0 < updatedCount) refresh(rollup)", but since this is a "manual" usage lets just always refresh - SampleTypeServiceImpl.get().refreshSampleTypeMaterializedView(sampleType, update); - builder.unsafeAppend(""); - } - - builder.unsafeAppend("
Sample Type#Recomputed
") - .append(sampleType.getName()) - .unsafeAppend("") - .append(updatedCount) - .unsafeAppend("
"); - return new HtmlView("Aliquot Rollup Recalculation Result", builder); - } - } - } - - /* Also see API CheckEdgesAction */ - @RequiresPermission(TroubleshooterPermission.class) - public static class CycleCheckAction extends FormViewAction - { - List cycleObjectIds = null; - - @Override - public void validateCommand(Object target, Errors errors) - { - - } - - @Override - public ModelAndView getView(Object o, boolean reshow, BindException errors) - { - if (!reshow) - { - return new HtmlView( - DIV("This operation can use a lot of memory.", - LK.FORM(at(method,"POST"), - PageFlowUtil.button("Continue").submit(true))) - ); - } - - if (null == cycleObjectIds) - return new HtmlView(HtmlString.of("No cycles found")); - - Map map = new LongHashMap<>(); - var cf = new ContainerFilter.AllFolders(getUser()); - var materials = ExperimentServiceImpl.get().getExpMaterialsByObjectId(cf, cycleObjectIds); - materials.forEach( (m) -> map.put(m.getObjectId(), m)); - var datas = ExperimentServiceImpl.get().getExpDatasByObjectId(cf, cycleObjectIds); - datas.forEach( (d) -> map.put(d.getObjectId(), d)); - var runs = ExperimentServiceImpl.get().getRunsByObjectId(cf, cycleObjectIds); - runs.forEach( (r) -> map.put(r.getObjectId(), r)); - - ExperimentUrls urls = ExperimentUrls.get(); - return new HtmlView( - DIV("Cycle found involving these objects.", - UL(cycleObjectIds.stream().map((objectid) -> - { - ExpObject exp = map.get(objectid); - if (exp instanceof ExpMaterial mat) - return LI(A(at(target, "_blank", href, urls.getMaterialDetailsURL(mat)), objectid + " : material - " + mat.getName())); - else if (exp instanceof ExpRun run) - return LI(A(at(target, "_blank", href, urls.getRunTextURL(run)), objectid + " : run - " + run.getName())); - else if (exp instanceof ExpData data) - return LI(A(at(target, "_blank", href, urls.getDataDetailsURL(data)), objectid + " : run - " + data.getName())); - else - return LI(String.valueOf(objectid)); - })) - ) - ); - } - - @Override - public boolean handlePost(Object o, BindException errors) - { - var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") - .resultSetStream() - .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) - .collect(toList()); - var cyclesEdges = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); - - var set = new LinkedHashSet(); - cyclesEdges.forEach( (edge) -> { - set.add(edge.first); - set.add(edge.second); - }); - cycleObjectIds = set.stream().toList(); - return false; - } - - @Override - public URLHelper getSuccessURL(Object o) - { - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - - } - } - - @RequiresPermission(AdminPermission.class) - public static class MissingFilesCheckAction extends ReadOnlyApiAction - { - @Override - public Object execute(Object o, BindException errors) throws Exception - { - Map> info = ExperimentServiceImpl.get().doMissingFilesCheck(getUser(), getContainer(), true); - JSONObject results = new JSONObject(); - for (String containerId : info.keySet()) - { - JSONObject containerResults = new JSONObject(); - for (String sourceName : info.get(containerId).keySet()) - containerResults.put(sourceName, info.get(containerId).get(sourceName).toJSON()); - results.put(containerId, containerResults); - } - - ApiSimpleResponse response = new ApiSimpleResponse(); - response.put("success", true); - response.put("result", results); - return response; - } - } - -} +/* + * Copyright (c) 2008-2019 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.labkey.experiment.controllers.exp; + +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import jakarta.servlet.http.HttpSession; +import org.apache.commons.collections4.MapUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.Strings; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.poi.ss.usermodel.Workbook; +import org.jetbrains.annotations.NotNull; +import org.jetbrains.annotations.Nullable; +import org.json.JSONArray; +import org.json.JSONException; +import org.json.JSONObject; +import org.labkey.api.action.ApiJsonWriter; +import org.labkey.api.action.ApiResponse; +import org.labkey.api.action.ApiSimpleResponse; +import org.labkey.api.action.ApiUsageException; +import org.labkey.api.action.ExportAction; +import org.labkey.api.action.FormHandlerAction; +import org.labkey.api.action.FormViewAction; +import org.labkey.api.action.HasViewContext; +import org.labkey.api.action.Marshal; +import org.labkey.api.action.Marshaller; +import org.labkey.api.action.MutatingApiAction; +import org.labkey.api.action.QueryViewAction; +import org.labkey.api.action.ReadOnlyApiAction; +import org.labkey.api.action.ReturnUrlForm; +import org.labkey.api.action.SimpleApiJsonForm; +import org.labkey.api.action.SimpleErrorView; +import org.labkey.api.action.SimpleResponse; +import org.labkey.api.action.SimpleViewAction; +import org.labkey.api.action.SpringActionController; +import org.labkey.api.assay.AssayFileWriter; +import org.labkey.api.assay.AssayProtocolSchema; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.actions.UploadWizardAction; +import org.labkey.api.assay.security.DesignAssayPermission; +import org.labkey.api.attachments.AttachmentParent; +import org.labkey.api.attachments.AttachmentService; +import org.labkey.api.attachments.BaseDownloadAction; +import org.labkey.api.audit.AbstractAuditTypeProvider; +import org.labkey.api.audit.AuditLogService; +import org.labkey.api.audit.DetailedAuditTypeEvent; +import org.labkey.api.audit.SampleTimelineAuditEvent; +import org.labkey.api.audit.TransactionAuditProvider; +import org.labkey.api.collections.CaseInsensitiveHashMap; +import org.labkey.api.collections.CaseInsensitiveHashSet; +import org.labkey.api.collections.LongHashMap; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.CompareType; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.ContainerManager; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.DataRegionSelection; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.DbScope; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.ExcelWriter; +import org.labkey.api.data.MenuButton; +import org.labkey.api.data.NameGenerator; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.ShowRows; +import org.labkey.api.data.SimpleDisplayColumn; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.SqlSelector; +import org.labkey.api.data.TSVJSONWriter; +import org.labkey.api.data.TSVWriter; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.TableSelector; +import org.labkey.api.dataiterator.DataIteratorContext; +import org.labkey.api.exp.AbstractParameter; +import org.labkey.api.exp.DeleteForm; +import org.labkey.api.exp.DuplicateMaterialException; +import org.labkey.api.exp.ExperimentDataHandler; +import org.labkey.api.exp.ExperimentException; +import org.labkey.api.exp.ExperimentRunForm; +import org.labkey.api.exp.ExperimentRunListView; +import org.labkey.api.exp.ExperimentRunType; +import org.labkey.api.exp.Identifiable; +import org.labkey.api.exp.Lsid; +import org.labkey.api.exp.LsidManager; +import org.labkey.api.exp.LsidType; +import org.labkey.api.exp.ObjectProperty; +import org.labkey.api.exp.OntologyManager; +import org.labkey.api.exp.ProtocolApplicationParameter; +import org.labkey.api.exp.XarContext; +import org.labkey.api.exp.api.DataClassDomainKindProperties; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExpDataClass; +import org.labkey.api.exp.api.ExpExperiment; +import org.labkey.api.exp.api.ExpLineageOptions; +import org.labkey.api.exp.api.ExpMaterial; +import org.labkey.api.exp.api.ExpMaterialRunInput; +import org.labkey.api.exp.api.ExpObject; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExpProtocolApplication; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExpRunAttachmentParent; +import org.labkey.api.exp.api.ExpRunEditor; +import org.labkey.api.exp.api.ExpRunItem; +import org.labkey.api.exp.api.ExpSampleType; +import org.labkey.api.exp.api.ExperimentJSONConverter; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.exp.api.ExperimentUrls; +import org.labkey.api.exp.api.NameExpressionOptionService; +import org.labkey.api.exp.api.ResolveLsidsForm; +import org.labkey.api.exp.api.SampleTypeDomainKind; +import org.labkey.api.exp.api.SampleTypeService; +import org.labkey.api.exp.list.ListService; +import org.labkey.api.exp.property.Domain; +import org.labkey.api.exp.property.DomainAuditProvider; +import org.labkey.api.exp.property.DomainKind; +import org.labkey.api.exp.property.DomainProperty; +import org.labkey.api.exp.property.DomainTemplate; +import org.labkey.api.exp.property.DomainTemplateGroup; +import org.labkey.api.exp.property.DomainUtil; +import org.labkey.api.exp.property.PropertyService; +import org.labkey.api.exp.query.ExpDataProtocolInputTable; +import org.labkey.api.exp.query.ExpInputTable; +import org.labkey.api.exp.query.ExpMaterialProtocolInputTable; +import org.labkey.api.exp.query.ExpSchema; +import org.labkey.api.exp.query.SamplesSchema; +import org.labkey.api.exp.xar.LSIDRelativizer; +import org.labkey.api.exp.xar.LsidUtils; +import org.labkey.api.files.FileContentService; +import org.labkey.api.gwt.client.AuditBehaviorType; +import org.labkey.api.inventory.InventoryService; +import org.labkey.api.module.ModuleHtmlView; +import org.labkey.api.module.ModuleLoader; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineService; +import org.labkey.api.pipeline.PipelineStatusFile; +import org.labkey.api.pipeline.PipelineUrls; +import org.labkey.api.pipeline.PipelineValidationException; +import org.labkey.api.qc.SampleStatusService; +import org.labkey.api.query.AbstractQueryImportAction; +import org.labkey.api.query.BatchValidationException; +import org.labkey.api.query.DetailsURL; +import org.labkey.api.query.DuplicateKeyException; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryAction; +import org.labkey.api.query.QueryDefinition; +import org.labkey.api.query.QueryException; +import org.labkey.api.query.QueryForm; +import org.labkey.api.query.QueryParam; +import org.labkey.api.query.QueryService; +import org.labkey.api.query.QuerySettings; +import org.labkey.api.query.QueryUpdateForm; +import org.labkey.api.query.QueryUpdateService; +import org.labkey.api.query.QueryUpdateServiceException; +import org.labkey.api.query.QueryView; +import org.labkey.api.query.SchemaKey; +import org.labkey.api.query.UserSchema; +import org.labkey.api.query.UserSchemaAction; +import org.labkey.api.reader.ColumnDescriptor; +import org.labkey.api.reader.DataLoader; +import org.labkey.api.reader.DataLoaderFactory; +import org.labkey.api.reader.ExcelFactory; +import org.labkey.api.search.SearchService; +import org.labkey.api.security.ActionNames; +import org.labkey.api.security.RequiresAnyOf; +import org.labkey.api.security.RequiresNoPermission; +import org.labkey.api.security.RequiresPermission; +import org.labkey.api.security.SecurableResource; +import org.labkey.api.security.User; +import org.labkey.api.security.permissions.AdminPermission; +import org.labkey.api.security.permissions.DeletePermission; +import org.labkey.api.security.permissions.DesignDataClassPermission; +import org.labkey.api.security.permissions.DesignSampleTypePermission; +import org.labkey.api.security.permissions.InsertPermission; +import org.labkey.api.security.permissions.Permission; +import org.labkey.api.security.permissions.ReadPermission; +import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; +import org.labkey.api.security.permissions.SiteAdminPermission; +import org.labkey.api.security.permissions.TroubleshooterPermission; +import org.labkey.api.security.permissions.UpdatePermission; +import org.labkey.api.settings.AppProps; +import org.labkey.api.settings.ConceptURIProperties; +import org.labkey.api.sql.LabKeySql; +import org.labkey.api.study.Dataset; +import org.labkey.api.study.StudyService; +import org.labkey.api.study.StudyUrls; +import org.labkey.api.study.publish.StudyPublishService; +import org.labkey.api.usageMetrics.SimpleMetricsService; +import org.labkey.api.util.DOM; +import org.labkey.api.util.DOM.LK; +import org.labkey.api.util.ErrorRenderer; +import org.labkey.api.util.ExceptionUtil; +import org.labkey.api.util.FileStream; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.HtmlString; +import org.labkey.api.util.HtmlStringBuilder; +import org.labkey.api.util.ImageUtil; +import org.labkey.api.util.JSoupUtil; +import org.labkey.api.util.LinkBuilder; +import org.labkey.api.util.NetworkDrive; +import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.util.Pair; +import org.labkey.api.util.ResponseHelper; +import org.labkey.api.util.SafeToRender; +import org.labkey.api.util.SessionHelper; +import org.labkey.api.util.StringExpression; +import org.labkey.api.util.StringUtilsLabKey; +import org.labkey.api.util.URLHelper; +import org.labkey.api.util.UniqueID; +import org.labkey.api.util.CsrfInput; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.BadRequestException; +import org.labkey.api.view.DataView; +import org.labkey.api.view.DataViewSnapshotSelectionForm; +import org.labkey.api.view.DetailsView; +import org.labkey.api.view.HBox; +import org.labkey.api.view.HtmlView; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.InsertView; +import org.labkey.api.view.JspView; +import org.labkey.api.view.NavTree; +import org.labkey.api.view.NotFoundException; +import org.labkey.api.view.RedirectException; +import org.labkey.api.view.UnauthorizedException; +import org.labkey.api.view.UpdateView; +import org.labkey.api.view.VBox; +import org.labkey.api.view.ViewBackgroundInfo; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.ViewServlet; +import org.labkey.api.view.WebPartView; +import org.labkey.api.view.template.ClientDependency; +import org.labkey.api.view.template.PageConfig; +import org.labkey.experiment.ChooseExperimentTypeBean; +import org.labkey.experiment.ConfirmDeleteView; +import org.labkey.experiment.CustomPropertiesView; +import org.labkey.experiment.DataClassWebPart; +import org.labkey.experiment.DerivedSamplePropertyHelper; +import org.labkey.experiment.DotGraph; +import org.labkey.experiment.ExpDataFileListener; +import org.labkey.experiment.ExperimentRunDisplayColumn; +import org.labkey.experiment.ExperimentRunGraph; +import org.labkey.experiment.LineageGraphDisplayColumn; +import org.labkey.experiment.MissingFilesCheckInfo; +import org.labkey.experiment.MoveRunsBean; +import org.labkey.experiment.ParentChildView; +import org.labkey.experiment.ProtocolApplicationDisplayColumn; +import org.labkey.experiment.ProtocolDisplayColumn; +import org.labkey.experiment.ProtocolWebPart; +import org.labkey.experiment.RunGroupWebPart; +import org.labkey.experiment.SampleTypeDisplayColumn; +import org.labkey.experiment.SampleTypeWebPart; +import org.labkey.experiment.StandardAndCustomPropertiesView; +import org.labkey.experiment.XarExportPipelineJob; +import org.labkey.experiment.XarExportType; +import org.labkey.experiment.XarExporter; +import org.labkey.experiment.api.ClosureQueryHelper; +import org.labkey.experiment.api.DataClass; +import org.labkey.experiment.api.DataClassDomainKind; +import org.labkey.experiment.api.ExpDataClassAttachmentParent; +import org.labkey.experiment.api.ExpDataClassImpl; +import org.labkey.experiment.api.ExpDataImpl; +import org.labkey.experiment.api.ExpExperimentImpl; +import org.labkey.experiment.api.ExpMaterialImpl; +import org.labkey.experiment.api.ExpProtocolApplicationImpl; +import org.labkey.experiment.api.ExpProtocolImpl; +import org.labkey.experiment.api.ExpRunImpl; +import org.labkey.experiment.api.ExpSampleTypeImpl; +import org.labkey.experiment.api.Experiment; +import org.labkey.experiment.api.ExperimentServiceImpl; +import org.labkey.experiment.api.GraphAlgorithms; +import org.labkey.experiment.api.ProtocolActionStepDetail; +import org.labkey.experiment.api.SampleTypeServiceImpl; +import org.labkey.experiment.api.SampleTypeUpdateServiceDI; +import org.labkey.experiment.controllers.property.PropertyController; +import org.labkey.experiment.lineage.ExpLineageServiceImpl; +import org.labkey.experiment.pipeline.ExperimentPipelineJob; +import org.labkey.experiment.types.TypesController; +import org.labkey.experiment.xar.XarExportSelection; +import org.labkey.vfs.FileLike; +import org.labkey.vfs.FileSystemLike; +import org.springframework.beans.PropertyValue; +import org.springframework.beans.PropertyValues; +import org.springframework.validation.BindException; +import org.springframework.validation.Errors; +import org.springframework.validation.ObjectError; +import org.springframework.web.multipart.MultipartFile; +import org.springframework.web.multipart.MultipartHttpServletRequest; +import org.springframework.web.servlet.ModelAndView; + +import javax.imageio.ImageIO; +import java.awt.*; +import java.awt.image.BufferedImage; +import java.io.BufferedOutputStream; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.net.URI; +import java.nio.file.Files; +import java.nio.file.Path; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Iterator; +import java.util.LinkedHashMap; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.Set; +import java.util.TreeSet; +import java.util.function.Function; +import java.util.stream.Collectors; + +import static java.util.stream.Collectors.toList; +import static org.labkey.api.data.DbScope.CommitTaskOption.POSTCOMMIT; +import static org.labkey.api.exp.query.ExpSchema.TableType.DataInputs; +import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM; +import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM; +import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_PROVIDER_PARAM; +import static org.labkey.api.util.DOM.A; +import static org.labkey.api.util.DOM.Attribute.action; +import static org.labkey.api.util.DOM.Attribute.href; +import static org.labkey.api.util.DOM.Attribute.id; +import static org.labkey.api.util.DOM.Attribute.method; +import static org.labkey.api.util.DOM.Attribute.name; +import static org.labkey.api.util.DOM.Attribute.size; +import static org.labkey.api.util.DOM.Attribute.src; +import static org.labkey.api.util.DOM.Attribute.target; +import static org.labkey.api.util.DOM.Attribute.type; +import static org.labkey.api.util.DOM.Attribute.value; +import static org.labkey.api.util.DOM.Attribute.width; +import static org.labkey.api.util.DOM.DIV; +import static org.labkey.api.util.DOM.IMG; +import static org.labkey.api.util.DOM.INPUT; +import static org.labkey.api.util.DOM.LI; +import static org.labkey.api.util.DOM.TABLE; +import static org.labkey.api.util.DOM.TD; +import static org.labkey.api.util.DOM.TR; +import static org.labkey.api.util.DOM.UL; +import static org.labkey.api.util.DOM.at; +import static org.labkey.api.util.DOM.cl; +import static org.labkey.experiment.ExpDataIterators.setContainerFilterForImport; +import static org.labkey.experiment.api.SampleTypeServiceImpl.SampleChangeType.update; + +public class ExperimentController extends SpringActionController +{ + private static final Logger _log = LogManager.getLogger(ExperimentController.class); + private static final DefaultActionResolver _actionResolver = new DefaultActionResolver( + ExperimentController.class + ); + private static final String GUEST_DIRECTORY_NAME = "guest"; + + public ExperimentController() + { + setActionResolver(_actionResolver); + } + + public static void ensureCorrectContainer(Container requestContainer, ExpObject object, ViewContext viewContext) + { + Container objectContainer = object.getContainer(); + if (!requestContainer.equals(objectContainer)) + { + ActionURL url = viewContext.cloneActionURL(); + url.setContainer(objectContainer); + throw new RedirectException(url); + } + } + + // Complete no-op, but leave in place in case we decide to adjust the base nav trail + private void addRootNavTrail(NavTree root) + { + // Intentionally don't add an "Experiment" node to the list because it's too overloaded. All content on the + // default action can be added to a portal page if desired. + } + + @Override + public PageConfig defaultPageConfig() + { + // set default help topic for controller + PageConfig config = super.defaultPageConfig(); + config.setHelpTopic("experiment"); + return config; + } + + @ActionNames("begin,gridView") + @RequiresPermission(ReadPermission.class) + public class BeginAction extends SimpleViewAction + { + @Override + public VBox getView(Object o, BindException errors) + { + VBox result = new VBox(); + + VBox runListView = createRunListView(20); + result.addView(runListView); + + RunGroupWebPart runGroups = new RunGroupWebPart(getViewContext(), false); + runGroups.showHeader(); + result.addView(runGroups); + + result.addView(new ProtocolWebPart(false, getViewContext())); + result.addView(new SampleTypeWebPart(false, getViewContext())); + result.addView(new DataClassWebPart(false, getViewContext(), null)); + + return result; + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Experiment"); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowRunsAction extends SimpleViewAction + { + @Override + public VBox getView(Object o, BindException errors) + { + return createRunListView(100); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Experiment Runs"); + } + } + + private VBox createRunListView(int defaultMaxRows) + { + Set types = ExperimentService.get().getExperimentRunTypes(getContainer()); + ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")), getViewContext().getActionURL().clone(), Collections.emptyList()); + JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean); + + ExperimentRunListView view = ExperimentService.get().createExperimentRunWebPart(getViewContext(), bean.getSelectedFilter()); + view.setFrame(WebPartView.FrameType.NONE); + + // When paginated and the user hasn't explicitly set a maxRows, use the default maxRows size. + QuerySettings settings = view.getSettings(); + if (!settings.isMaxRowsSet() && settings.getShowRows() == ShowRows.PAGINATED) + { + settings.setMaxRows(defaultMaxRows); + } + + VBox result = new VBox(chooserView, view); + result.setFrame(WebPartView.FrameType.PORTAL); + return result; + } + + @RequiresPermission(ReadPermission.class) + @ActionNames("showRunGroups, showExperiments") + public class ShowRunGroupsAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + RunGroupWebPart webPart = new RunGroupWebPart(getViewContext(), false); + webPart.setFrame(WebPartView.FrameType.NONE); + return webPart; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + addRootNavTrail(root); + root.addChild("Run Groups"); + } + } + + public record Field(String domainURI, String domainName, String name, Container container) {} + public record MiniExpObject(Object rowId, String name) {} + public record TimelineSummary(MiniExpObject miniExpObject, String mostRecentValue) {} + public record ProblemType(String tableName, String fieldName, String pkName) { + public Object toHtml(List summaries) + { + return DOM.DIV( + DOM.H4(tableName), + DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), + DOM.THEAD(DOM.TH(pkName), DOM.TH(fieldName)), + summaries.stream().map(summary -> + DOM.TR(DOM.TD(summary.miniExpObject.name), DOM.TD(summary.mostRecentValue))) + )); + } + } + + @RequiresPermission(SiteAdminPermission.class) + public static class ReportLostFieldValuesAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + // Find all the fields that could have lost data due to issue 52666 + TableInfo t = new ExpSchema(getUser(), ContainerManager.getRoot()).getTable(ExpSchema.TableType.Fields.name(), ContainerFilter.getUnsafeEverythingFilter()); + List fields = new TableSelector(t, + new SimpleFilter(FieldKey.fromParts("StorageColumnNameMatch"), false). + addCondition(FieldKey.fromParts("DomainURI"), ":AssayDomain-Data.", CompareType.DOES_NOT_CONTAIN), + null). + getArrayList(Field.class); + + // Prep audit table for querying + UserSchema auditSchema = AuditLogService.get().createSchema(getUser(), ContainerManager.getRoot()); + + Map> sampleTypeSummaries = new HashMap<>(); + Map> dataClassSummaries = new HashMap<>(); + Map> listSummaries = new HashMap<>(); + + Map> problematicFields = new LinkedHashMap<>(); + + for (Field field : fields) + { + String domainURI = field.domainURI; + String fieldName = field.name; + Container container = field.container; + Domain domain = PropertyService.get().getDomain(container, domainURI); + if (domain != null && domain.getDomainKind() != null) + { + TableInfo table = domain.getDomainKind().getTableInfo(getUser(), container, domain, ContainerFilter.getUnsafeEverythingFilter()); + + if (table != null) + { + // Drill into sample types + if (domain.getDomainKind().getClass().equals(SampleTypeDomainKind.class)) + { + // rows that currently have no value for the field with potential for data loss + List rowsWithNull = new TableSelector(table, + new HashSet<>(List.of("RowId", "Name")), + new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), + null). + getArrayList(MiniExpObject.class); + + List fixupsNeeded = checkData( + rowsWithNull, + fieldName, + obj -> new SimpleFilter(FieldKey.fromParts("SampleId"), obj.rowId), + auditSchema.getTable(SampleTimelineAuditEvent.EVENT_TYPE, ContainerFilter.getUnsafeEverythingFilter())); + if (!fixupsNeeded.isEmpty()) + { + sampleTypeSummaries.put(new ProblemType(table.getName(), fieldName, "SampleID"), fixupsNeeded); + } + } + // and data classes/sample sources + if (domain.getDomainKind().getClass().equals(DataClassDomainKind.class)) + { + // rows samples that current have no value for the field with potential for data loss + List rowsWithNull = new TableSelector(table, + new HashSet<>(List.of("RowId", "Name")), + new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), + null). + getArrayList(MiniExpObject.class); + + List fixupsNeeded = checkData( + rowsWithNull, + fieldName, + obj -> new SimpleFilter(FieldKey.fromParts("RowPk"), Objects.toString(obj.rowId)). + addCondition(FieldKey.fromParts("SchemaName"), "exp.data"). + addCondition(FieldKey.fromParts("QueryName"), domain.getName()), + auditSchema.getTable("QueryUpdateAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); + + if (!fixupsNeeded.isEmpty()) + { + dataClassSummaries.put(new ProblemType(table.getName(), fieldName, "SourceID"), fixupsNeeded); + } + } + // and lists + if ("lists".equals(table.getUserSchema().getName())) + { + // rows samples that current have no value for the field with potential for data loss + List rowsWithNull = new ArrayList<>(); + + ColumnInfo entityIdCol = table.getColumn("EntityId"); + ColumnInfo pkCol = table.getPkColumns().get(0); + + new TableSelector(table, + List.of(entityIdCol, pkCol), + new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), + null). + forEachResults(r -> + { + Object entityId = entityIdCol.getValue(r); + Object pk = pkCol.getValue(r); + rowsWithNull.add(new MiniExpObject(entityId, pk.toString())); + }); + + + List fixupsNeeded = checkData( + rowsWithNull, + fieldName, + obj -> new SimpleFilter(FieldKey.fromParts("ListItemEntityId"), obj.rowId), + auditSchema.getTable("ListAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); + + if (!fixupsNeeded.isEmpty()) + { + listSummaries.put(new ProblemType(table.getName(), fieldName, table.getPkColumnNames().get(0)), fixupsNeeded); + } + } + + long totalRows = new TableSelector(table).getRowCount(); + long emptyRows = new TableSelector(table, new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), null).getRowCount(); + problematicFields.put(field, Pair.of(totalRows, emptyRows)); + } + else + { + problematicFields.put(field, Pair.of(null, null)); + } + } + } + + return new HtmlView("Fixups Needed", + DOM.createHtmlFragment( + DOM.H2("Potentially Problematic Fields"), + problematicFields.isEmpty() ? "No problematic fields detected!" : + DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), + DOM.THEAD(DOM.TH("Domain Name"), DOM.TH("Domain URI"), DOM.TH("Field Name"), DOM.TH("Container"), DOM.TH("Total Rows"), DOM.TH("Rows with Nulls")), + problematicFields.entrySet().stream().map(e -> { + Field f = e.getKey(); + Pair counts = e.getValue(); + return DOM.TR( + DOM.TD(f.domainName), + DOM.TD(f.domainURI), + DOM.TD(f.name), + DOM.TD(f.container.getPath()), + DOM.TD(counts.first), + DOM.TD(counts.second) + ); + } + )), + + DOM.H2("Sample Types"), + sampleTypeSummaries.isEmpty() ? "No problems detected!" : + sampleTypeSummaries.entrySet().stream().map(e -> + e.getKey().toHtml(e.getValue())), + + DOM.H2("Data Classes"), + dataClassSummaries.isEmpty() ? "No problems detected!" : + dataClassSummaries.entrySet().stream().map(e -> + e.getKey().toHtml(e.getValue())), + + DOM.H2("Lists"), + listSummaries.isEmpty() ? "No problems detected!" : + listSummaries.entrySet().stream().map(e -> + e.getKey().toHtml(e.getValue())) + )); + } + + @NotNull + private List checkData(List rowsWithNull, String fieldName, Function filterGenerator, TableInfo auditTable) + { + List fixupsNeeded = new ArrayList<>(); + + // For each sample without a value today, check the audit history + for (MiniExpObject row : rowsWithNull) + { + // Order by RowId to get them in the sequence they happened in + var events = new TableSelector(auditTable, filterGenerator.apply(row), new Sort("RowId")).getArrayList(DetailedAuditTypeEvent.class); + // Remember the most recently set value + String mostRecentValue = null; + for (DetailedAuditTypeEvent event : events) + { + Map newValues = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(event.getNewRecordMap())); + if (newValues.containsKey(fieldName)) + { + // Will be the empty string if the value was intentionally set to blank + mostRecentValue = newValues.get(fieldName); + } + } + // If the value had been set before, and its most recent insert/update wasn't setting it blank, + // it's most likely a lost value + if (mostRecentValue != null && !mostRecentValue.isEmpty()) + { + fixupsNeeded.add(new TimelineSummary(row, mostRecentValue)); + } + } + return fixupsNeeded; + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Accidentally Nulled Field Report"); + } + } + + @RequiresPermission(ReadPermission.class) + public static class CreateHiddenRunGroupAction extends MutatingApiAction + { + @Override + public ApiResponse execute(SimpleApiJsonForm form, BindException errors) throws Exception + { + JSONObject json = form.getJsonObject(); + String selectionKey = json.optString("selectionKey", null); + List runs = new ArrayList<>(); + + // Accept either an explicit list of run IDs + if (json.has("runIds")) + { + JSONArray runIds = json.getJSONArray("runIds"); + for (int i = 0; i < runIds.length(); i++) + { + ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(runIds.getInt(i)); + if (run != null) + { + runs.add(run); + } + } + } + // Or a reference to a DataRegion selection key + else if (selectionKey != null) + { + Set ids = DataRegionSelection.getSelectedIntegers(getViewContext(), selectionKey, false); + for (Long id : ids) + { + ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(id); + if (run != null) + { + runs.add(run); + } + } + } + if (runs.isEmpty()) + { + throw new NotFoundException(); + } + + ExpExperiment group = ExperimentService.get().createHiddenRunGroup(getContainer(), getUser(), runs.toArray(new ExpRun[0])); + if (selectionKey != null) + DataRegionSelection.clearAll(getViewContext(), selectionKey); + + ApiSimpleResponse response = new ApiSimpleResponse(); + response.putBean(group, "rowId", "LSID", "name", "hidden"); + return response; + } + } + + + @RequiresPermission(ReadPermission.class) + public class DetailsAction extends QueryViewAction + { + private ExpExperimentImpl _experiment; + + public DetailsAction() + { + super(ExpObjectForm.class); + } + + private Pair> createViews(ExpObjectForm form, BindException errors) + { + _experiment = ExperimentServiceImpl.get().getExpExperiment(form.getRowId()); + if (_experiment == null) + { + throw new NotFoundException("Could not find an experiment with RowId " + form.getRowId()); + } + + if (!_experiment.getContainer().equals(getContainer())) + { + throw new RedirectException(getViewContext().cloneActionURL().setContainer(_experiment.getContainer())); + } + + List protocols = _experiment.getAllProtocols(); + + Set types = new TreeSet<>(ExperimentService.get().getExperimentRunTypes(getContainer())); + ExperimentRunType selectedType = ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")); + + ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, selectedType, getViewContext().getActionURL().clone(), protocols); + JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean, errors); + + ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), bean.getSelectedFilter(), true); + runListView.getRunTable().setExperiment(_experiment); + runListView.setShowRemoveFromExperimentButton(true); + runListView.setShowDeleteButton(true); + runListView.setShowAddToRunGroupButton(true); + runListView.setShowExportButtons(true); + runListView.setShowMoveRunsButton(true); + return new Pair<>(runListView, chooserView); + } + + @Override + protected ModelAndView getHtmlView(ExpObjectForm form, BindException errors) throws Exception + { + Pair> views = createViews(form, errors); + + CustomPropertiesView customPropertiesView = new CustomPropertiesView(_experiment.getLSID(), getContainer()); + + TableInfo runGroupsTable = new ExpSchema(getUser(), getContainer()).getTable(ExpSchema.TableType.RunGroups); + + DetailsView detailsView = new DetailsView(new DataRegion(), _experiment.getRowId()); + detailsView.getDataRegion().setTable(runGroupsTable); + detailsView.getDataRegion().addColumns(runGroupsTable, "RowId,Name,Created,Modified,Contact,ExperimentDescriptionURL,Hypothesis,Comments"); + detailsView.getDataRegion().getDisplayColumn(0).setVisible(false); + detailsView.getDataRegion().getDisplayColumn(2).setWidth("60%"); + + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + ActionButton b = new ActionButton(ExperimentUrlsImpl.get().getShowUpdateURL(_experiment), "Edit"); + b.setDisplayPermission(UpdatePermission.class); + bb.add(b); + detailsView.getDataRegion().setButtonBar(bb); + if (_experiment.getBatchProtocol() != null) + { + detailsView.setTitle("Batch Details"); + detailsView.getDataRegion().addColumns(runGroupsTable, "BatchProtocolId"); + } + else + { + detailsView.setTitle("Run Group Details"); + } + + VBox runsVBox = new VBox(views.second, createInitializedQueryView(form, errors, false, null)); + runsVBox.setTitle("Experiment Runs"); + runsVBox.setFrame(WebPartView.FrameType.PORTAL); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, customPropertiesView), runsVBox); + } + + @Override + protected ExperimentRunListView createQueryView(ExpObjectForm form, BindException errors, boolean forExport, String dataRegion) + { + return createViews(form, errors).first; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + addRootNavTrail(root); + root.addChild("Run Groups", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); + root.addChild(_experiment.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ListSampleTypesAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + SampleTypeWebPart view = new SampleTypeWebPart(false, getViewContext()); + view.setFrame(WebPartView.FrameType.NONE); + view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); + + return view; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types"); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowSampleTypeAction extends SimpleViewAction + { + private ExpSampleTypeImpl _sampleType; + + @Override + public ModelAndView getView(ExpObjectForm form, BindException errors) + { + _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getRowId()); + if (_sampleType == null && form.getLsid() != null) + { + if (form.getLsid().equalsIgnoreCase("Material") || form.getLsid().equalsIgnoreCase("Sample")) + { + // Not a real sample type - just show all the materials instead + throw new RedirectException(new ActionURL(ShowAllMaterialsAction.class, getContainer())); + } + // Check if the URL specifies the LSID, and stick the bean back into the form + _sampleType = SampleTypeServiceImpl.get().getSampleType(form.getLsid()); + } + + if (_sampleType == null) + { + throw new NotFoundException("No matching sample type found"); + } + + List allScopedSampleTypes = (List) SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true); + if (!allScopedSampleTypes.contains(_sampleType)) + { + ensureCorrectContainer(getContainer(), _sampleType, getViewContext()); + } + + SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); + QuerySettings settings = schema.getSettings(getViewContext(), "Material", _sampleType.getName()); + QueryView queryView = new SampleTypeContentsView(_sampleType, schema, settings, errors); + + DetailsView detailsView = new DetailsView(getSampleTypeRegion(getViewContext()), _sampleType.getRowId()); + detailsView.getDataRegion().getDisplayColumn("Name").setURL((ActionURL)null); + detailsView.getDataRegion().getDisplayColumn("LSID").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("MaterialLSIDPrefix").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("LabelColor").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("MetricUnit").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("Category").setVisible(false); + + detailsView.setTitle("Sample Type Properties"); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).setStyle(ButtonBar.Style.separateButtons); + + Container autoLinkContainer = _sampleType.getAutoLinkTargetContainer(); + if (null != autoLinkContainer) + { + DisplayColumn autoLinkTargetColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkTargetContainer"); + autoLinkTargetColumn.setVisible(false); + + SimpleDisplayColumn displayAutoLinkTargetColumn = new SimpleDisplayColumn(); + displayAutoLinkTargetColumn.setCaption("Auto Link Target Container:"); + String path = autoLinkContainer.getPath(); + displayAutoLinkTargetColumn.setDisplayHtml(path.equals("/") ? "" : path); + detailsView.getDataRegion().addDisplayColumn(displayAutoLinkTargetColumn); + } + + DisplayColumn autoLinkCategoryColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkCategory"); + autoLinkCategoryColumn.setVisible(false); + SimpleDisplayColumn displayAutoLinkCategoryColumn = new SimpleDisplayColumn(); + displayAutoLinkCategoryColumn.setCaption("Auto Link Category:"); + displayAutoLinkCategoryColumn.setDisplayHtml(_sampleType.getAutoLinkCategory()); + detailsView.getDataRegion().addDisplayColumn(displayAutoLinkCategoryColumn); + + if (_sampleType.hasNameAsIdCol()) + { + SimpleDisplayColumn nameIdCol = new SimpleDisplayColumn(); + nameIdCol.setCaption("Has Name Id Column:"); + nameIdCol.setDisplayHtml("true"); + detailsView.getDataRegion().addDisplayColumn(nameIdCol); + } + + if (_sampleType.hasIdColumns()) + { + SimpleDisplayColumn idCols = new SimpleDisplayColumn(); + idCols.setCaption("Id Column(s):"); + String names = _sampleType.getIdCols().stream() + .filter(Objects::nonNull) + .map(DomainProperty::getName) + .collect(Collectors.joining(", ")); + if (!names.isEmpty()) + { + idCols.setDisplayHtml(PageFlowUtil.filter(names)); + detailsView.getDataRegion().addDisplayColumn(idCols); + } + } + + if (_sampleType.getParentCol() != null) + { + SimpleDisplayColumn parentCol = new SimpleDisplayColumn(PageFlowUtil.filter(_sampleType.getParentCol().getName())); + parentCol.setCaption("Parent Column:"); + detailsView.getDataRegion().addDisplayColumn(parentCol); + } + + try + { + SimpleDisplayColumn importAliasCol = new SimpleDisplayColumn(); + importAliasCol.setCaption("Parent Import Alias(es):"); + if (!_sampleType.getImportAliases().isEmpty()) + importAliasCol.setDisplayHtml(PageFlowUtil.filter(StringUtils.join(_sampleType.getImportAliases().keySet(), ", "))); + detailsView.getDataRegion().addDisplayColumn(importAliasCol); + } + catch (IOException e) + { + // unable to parse import alias map from JSON + } + + if (!getContainer().equals(_sampleType.getContainer())) + { + ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowSampleTypeURL(_sampleType); + SimpleDisplayColumn definedInCol = new SimpleDisplayColumn("" + + PageFlowUtil.filter(_sampleType.getContainer().getPath()) + + ""); + definedInCol.setCaption("Defined In:"); + detailsView.getDataRegion().addDisplayColumn(definedInCol); + } + + // Not all sample types can be edited + DomainKind domainKind = _sampleType.getDomain().getDomainKind(); + if (domainKind != null && domainKind.canEditDefinition(getUser(), _sampleType.getDomain())) + { + if (domainKind instanceof SampleTypeDomainKind) + { + ActionURL updateURL = new ActionURL(EditSampleTypeAction.class, _sampleType.getContainer()); + updateURL.addParameter("RowId", _sampleType.getRowId()); + updateURL.addReturnUrl(getViewContext().getActionURL()); + + if (!getContainer().equals(_sampleType.getContainer())) + { + String editLink = updateURL.toString(); + ActionButton updateButton = new ActionButton("Edit Type"); + updateButton.setActionType(ActionButton.Action.SCRIPT); + updateButton.setScript("if (window.confirm('This sample type is defined in the " + _sampleType.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + editLink + "' }"); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); + } + else + { + ActionButton updateButton = new ActionButton(updateURL, "Edit Type", ActionButton.Action.LINK); + updateButton.setDisplayPermission(DesignSampleTypePermission.class); + updateButton.setPrimary(true); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); + } + + ActionURL deleteURL = new ActionURL(DeleteSampleTypesAction.class, _sampleType.getContainer()); + deleteURL.addParameter("singleObjectRowId", _sampleType.getRowId()); + deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ActionButton deleteButton = new ActionButton(deleteURL, "Delete Type", ActionButton.Action.LINK); + deleteButton.setDisplayPermission(DesignSampleTypePermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(deleteButton); + } + else + { + ActionURL editURL = domainKind.urlEditDefinition(_sampleType.getDomain(), new ViewBackgroundInfo(_sampleType.getContainer(), getUser(), getViewContext().getActionURL())); + if (editURL != null) + { + editURL.addReturnUrl(getViewContext().getActionURL()); + ActionButton editTypeButton = new ActionButton(editURL, "Edit Fields"); + editTypeButton.setDisplayPermission(UpdatePermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(editTypeButton); + } + } + } + + if (_sampleType.canImportMoreSamples()) + { + TableInfo table = queryView.getTable(); + if (table != null) + { + ActionURL importURL = table.getImportDataURL(getContainer()); + if (importURL != null) + { + importURL = importURL.clone(); + importURL.addReturnUrl(getViewContext().getActionURL()); + ActionButton uploadButton = new ActionButton(importURL, "Import More Samples", ActionButton.Action.LINK); + uploadButton.setDisplayPermission(UpdatePermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(uploadButton); + } + } + } + + var publish = StudyPublishService.get(); + if (AuditLogService.get().isViewable() && publish != null) + { + ContainerFilter cf = ContainerFilter.Type.CurrentAndSubfolders.create(getContainer(), getUser()); + ActionURL linkToStudyHistoryURL = publish.getPublishHistory(getContainer(), Dataset.PublishSource.SampleType, _sampleType.getRowId(), cf); + ActionButton linkToStudyHistoryButton = new ActionButton(linkToStudyHistoryURL, "Link to Study History", ActionButton.Action.LINK); + linkToStudyHistoryButton.setDisplayPermission(InsertPermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(linkToStudyHistoryButton); + } + + return new VBox(detailsView, queryView); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + ActionURL url = ExperimentUrls.get().getShowSampleTypeListURL(getContainer()); + addRootNavTrail(root); + root.addChild("Sample Types", url); + root.addChild("Sample Type " + _sampleType.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowAllMaterialsAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + ExpSchema schema = new ExpSchema(getUser(), getContainer()); + QuerySettings settings = schema.getSettings(getViewContext(), "Materials", ExpSchema.TableType.Materials.toString()); + QueryView view = new QueryView(schema, settings, errors) + { + @Override + protected void populateButtonBar(DataView view, ButtonBar bar) + { + super.populateButtonBar(view, bar); + bar.add(SampleTypeContentsView.getDeriveSamplesButton(getContainer(),null)); + } + }; + view.setShowDetailsColumn(false); + return view; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("All Materials"); + } + } + + /** + * Only shows standard and custom properties, not parent and child samples. Used for indexing + */ + @RequiresPermission(ReadPermission.class) + public class ShowMaterialSimpleAction extends SimpleViewAction + { + protected ExpMaterialImpl _material; + + @Override + public VBox getView(ExpObjectForm form, BindException errors) throws Exception + { + Container c = getContainer(); + _material = ExperimentServiceImpl.get().getExpMaterial(form.getRowId()); + if (_material == null && form.getLsid() != null) + { + _material = ExperimentServiceImpl.get().getExpMaterial(form.getLsid()); + } + if (_material == null) + { + throw new NotFoundException("Could not find a material with RowId " + form.getRowId()); + } + + ensureCorrectContainer(getContainer(), _material, getViewContext()); + + ExpRunImpl run = _material.getRun(); + ExpProtocol sourceProtocol = _material.getSourceProtocol(); + ExpProtocolApplication sourceProtocolApplication = _material.getSourceApplication(); + + DataRegion dr = new DataRegion(); + dr.addColumns(ExperimentServiceImpl.get().getTinfoMaterial().getUserEditableColumns()); + dr.removeColumns("RowId", "RunId", "LastIndexed", "LSID", "SourceApplicationId", "CpasType"); + + //dr.addColumns(extraProps); + dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); + dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); + dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); + dr.addDisplayColumn(new LineageGraphDisplayColumn(_material, run)); + dr.addDisplayColumn(new SampleTypeDisplayColumn(_material)); + + //TODO: Can't yet edit materials uploaded from a material source + dr.setButtonBar(new ButtonBar()); + DetailsView detailsView = new DetailsView(dr, _material.getRowId()); + detailsView.setTitle("Standard Properties"); + detailsView.setFrame(WebPartView.FrameType.PORTAL); + + CustomPropertiesView cpv = new CustomPropertiesView(_material, c, getUser()); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv)); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ExpSampleType sampleType = _material.getSampleType(); + if (sampleType != null) + { + root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); + } + root.addChild("Sample " + _material.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowMaterialAction extends ShowMaterialSimpleAction + { + @Override + public VBox getView(ExpObjectForm form, BindException errors) throws Exception + { + VBox vbox = super.getView(form, errors); + + List materialsToInvestigate = new ArrayList<>(); + final Set successorRuns = new HashSet<>(); + materialsToInvestigate.add(_material); + Set investigatedMaterials = new HashSet<>(); + do + { + // Query for all the next tier of materials at once - issue 45402 + List followupRuns = ExperimentService.get().getRunsUsingMaterials(materialsToInvestigate); + + // Mark this set as investigated and reset for the next cycle + investigatedMaterials.addAll(materialsToInvestigate); + materialsToInvestigate = new ArrayList<>(); + + for (ExpRun r : followupRuns) + { + // Only expand the material outputs of the run if it's our first time visiting it + if (successorRuns.add(r)) + { + materialsToInvestigate.addAll(r.getMaterialOutputs()); + } + } + + if (successorRuns.size() > 1000) + { + // Give up - there may be a cycle or other problematic data + break; + } + + // Cull the ones we've already looked up + materialsToInvestigate.removeAll(investigatedMaterials); + } + while (!materialsToInvestigate.isEmpty()); + + HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); + ExpSampleType st = _material.getSampleType(); + if (st != null && st.getContainer() != null && st.getContainer().hasPermission(getUser(), UpdatePermission.class)) + { + // XXX: ridiculous amount of work to get a update url expression for the sample type's table. + UserSchema samplesSchema = QueryService.get().getUserSchema(getUser(), st.getContainer(), "Samples"); + QueryDefinition queryDef = samplesSchema.getQueryDefForTable(st.getName()); + StringExpression expr = queryDef.urlExpr(QueryAction.updateQueryRow, null); + if (expr != null) + { + // Since we're building a detailsURL outside the context of a "row" need to set the correct + // container context on the generated expr. + ((DetailsURL) expr).setContainerContext(st.getContainer()); + String url = expr.eval(Collections.singletonMap(new FieldKey(null, "RowId"), _material.getRowId())); + updateLinks.append(LinkBuilder.labkeyLink("edit", url)).append(" "); + } + } + + if (getContainer().hasPermission(getUser(), InsertPermission.class)) + { + ActionURL deriveURL = new ActionURL(DeriveSamplesChooseTargetAction.class, getContainer()); + deriveURL.addParameter("rowIds", _material.getRowId()); + if (st != null) + deriveURL.addParameter("targetSampleTypeId", st.getRowId()); + + updateLinks.append(LinkBuilder.labkeyLink("derive samples from this sample", deriveURL)).append(" "); + } + + vbox.addView(new HtmlView(updateLinks)); + + ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); + runListView.setShowRecordSelectors(false); + runListView.getRunTable().setRuns(successorRuns); + runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); + runListView.setAllowableContainerFilterTypes(ContainerFilter.Type.Current, ContainerFilter.Type.CurrentAndSubfolders, ContainerFilter.Type.AllFolders); + runListView.setTitle("Runs associated with this material or a derived material"); + + ParentChildView pv = new ParentChildView(_material, getViewContext()); + vbox.addView(pv); + vbox.addView(runListView); + + return vbox; + } + } + + + // + // DataClass + // + + @RequiresPermission(ReadPermission.class) + public class ListDataClassAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + DataClassWebPart view = new DataClassWebPart(false, getViewContext(), null); + view.setFrame(WebPartView.FrameType.NONE); + view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); + + return view; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + addRootNavTrail(root); + root.addChild("Data Classes"); + } + } + + public static class DataClassForm extends ExpObjectForm + { + private String _name; + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + public ExpDataClassImpl getDataClass(@Nullable Container container) + { + ExpDataClassImpl dataClass = null; + + if (getName() != null) + { + dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getName()); + if (dataClass == null) + throw new NotFoundException("No data class found for name '" + getName() + "'."); + } + else if (getRowId() > 0) + { + dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getRowId()); + } + + if (dataClass == null) + throw new NotFoundException("No data class found."); + else if (container != null && !container.equals(dataClass.getContainer())) + throw new NotFoundException("Data class is not defined in the given container."); + + return dataClass; + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowDataClassAction extends SimpleViewAction + { + private ExpDataClassImpl _dataClass; + + @Override + public ModelAndView getView(DataClassForm form, BindException errors) + { + _dataClass = form.getDataClass(null); + return new VBox(getDataClassPropertiesView(), getDataClassContentsView(errors)); + } + + private DetailsView getDataClassPropertiesView() + { + ExpSchema expSchema = new ExpSchema(getUser(), _dataClass.getContainer()); + + TableInfo table = ExpSchema.TableType.DataClasses.createTable(expSchema, null, null); + QueryUpdateForm tvf = new QueryUpdateForm(table, getViewContext(), null); + tvf.setPkVal(_dataClass.getRowId()); + DetailsView detailsView = new DetailsView(tvf); + detailsView.setTitle("Data Class Properties"); + + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + boolean inDefinitionContainer = getContainer().equals(_dataClass.getContainer()); + + DomainKind domainKind = _dataClass.getDomain().getDomainKind(); + if (domainKind != null && domainKind.canEditDefinition(getUser(), _dataClass.getDomain())) + { + ActionURL updateURL = new ActionURL(EditDataClassAction.class, _dataClass.getContainer()); + updateURL.addParameter("rowId", _dataClass.getRowId()); + updateURL.addReturnUrl(urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId())); + + if (inDefinitionContainer) + { + ActionButton updateButton = new ActionButton(updateURL, "Edit Data Class", ActionButton.Action.LINK); + updateButton.setDisplayPermission(DesignDataClassPermission.class); + updateButton.setPrimary(true); + bb.add(updateButton); + } + else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) + { + ActionButton updateButton = new ActionButton("Edit Data Class"); + updateButton.setActionType(ActionButton.Action.SCRIPT); + updateButton.setScript("if (window.confirm('This data class is defined in the " + _dataClass.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + updateURL + "' }"); + updateButton.setPrimary(true); + bb.add(updateButton); + } + + ActionURL deleteURL = new ActionURL(DeleteDataClassAction.class, _dataClass.getContainer()); + deleteURL.addParameter("singleObjectRowId", _dataClass.getRowId()); + deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + ActionButton deleteButton = new ActionButton(deleteURL, "Delete Data Class", ActionButton.Action.LINK); + + if (inDefinitionContainer) + { + deleteButton.setDisplayPermission(DesignDataClassPermission.class); + bb.add(deleteButton); + } + else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) + { + bb.add(deleteButton); + } + } + detailsView.getDataRegion().setButtonBar(bb); + + if (!inDefinitionContainer) + { + ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId()); + LinkBuilder link = LinkBuilder.simpleLink(_dataClass.getContainer().getPath(), definitionURL); + SimpleDisplayColumn definedInCol = new SimpleDisplayColumn(link.toString()); + definedInCol.setCaption("Defined In:"); + detailsView.getDataRegion().addDisplayColumn(definedInCol); + } + + return detailsView; + } + + private QueryView getDataClassContentsView(BindException errors) + { + UserSchema dataClassSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_EXP_DATA); + QuerySettings settings = dataClassSchema.getSettings(getViewContext(), QueryView.DATAREGIONNAME_DEFAULT, _dataClass.getName()); + + return new QueryView(dataClassSchema, settings, errors) + { + @Override + public @NotNull LinkedHashSet getClientDependencies() + { + LinkedHashSet resources = super.getClientDependencies(); + resources.add(ClientDependency.fromPath("Ext4")); + resources.add(ClientDependency.fromPath("dataregion/confirmDelete.js")); + return resources; + } + + @Override + public ActionButton createDeleteButton() + { + ActionButton button = super.createDeleteButton(); + if (button != null) + { + String dependencyText = ExperimentService.get() + .getObjectReferencers() + .stream() + .map(referencer -> referencer.getObjectReferenceDescription(ExpData.class)) + .collect(Collectors.joining(" or ")); + + button.setScript("LABKEY.dataregion.confirmDelete(" + + PageFlowUtil.jsString(getDataRegionName()) + ", " + + PageFlowUtil.jsString(ExpSchema.SCHEMA_EXP_DATA.toString()) + ", " + + PageFlowUtil.jsString(getQueryDef().getName()) + ", " + + "'experiment', 'getDataOperationConfirmationData.api', " + + PageFlowUtil.jsString(getSelectionKey()) + ", " + + "'data object', 'data objects', '" + dependencyText + "', {dataOperation: 'Delete'})"); + button.setRequiresSelection(true); + } + return button; + } + }; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + addRootNavTrail(root); + root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + root.addChild(_dataClass.getName()); + } + } + + @RequiresPermission(DesignDataClassPermission.class) + public class DeleteDataClassAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + super.addNavTrail(root); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + List dataClasses = getDataClasses(deleteForm); + if (!ensureCorrectContainer(dataClasses)) + { + throw new UnauthorizedException(); + } + for (ExpRun run : getRuns(dataClasses)) + { + if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new UnauthorizedException(); + } + } + for (ExpDataClass dataClass : dataClasses) + { + dataClass.delete(getUser(), deleteForm.getUserComment()); + } + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List dataClasses = getDataClasses(deleteForm); + + if (!ensureCorrectContainer(dataClasses)) + { + throw new RedirectException(ExperimentUrlsImpl.get().getDataClassListURL(getContainer(), "To delete a data class, you must be in its folder or project.")); + } + + return new ConfirmDeleteView("Data Class", ShowDataClassAction.class, dataClasses, deleteForm, getRuns(dataClasses)); + } + + private List getDataClasses(DeleteForm deleteForm) + { + List dataClasses = new ArrayList<>(); + for (long rowId : deleteForm.getIds(false)) + { + ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), rowId); + if (dataClass != null) + { + dataClasses.add(dataClass); + } + } + return dataClasses; + } + + private boolean ensureCorrectContainer(List dataClasses) + { + for (ExpDataClass dataClass : dataClasses) + { + Container sourceContainer = dataClass.getContainer(); + if (!sourceContainer.equals(getContainer())) + { + return false; + } + } + return true; + } + + private List getRuns(List dataClasses) + { + if (!dataClasses.isEmpty()) + { + List runArray = ExperimentService.get().getRunsUsingDataClasses(dataClasses); + return ExperimentService.get().runsDeletedWithInput(runArray); + } + else + { + return Collections.emptyList(); + } + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetDataClassPropertiesAction extends ReadOnlyApiAction + { + @Override + public Object execute(DataClassForm form, BindException errors) throws Exception + { + ExpDataClass dataClass = form.getDataClass(getContainer()); + if (dataClass != null) + return new DataClassDomainKindProperties(dataClass); + else + throw new NotFoundException("Data class does not exist in this container for rowId " + form.getRowId() + "."); + } + } + + @RequiresPermission(DesignDataClassPermission.class) + public static class EditDataClassAction extends SimpleViewAction + { + private ExpDataClassImpl _dataClass; + + @Override + public ModelAndView getView(DataClassForm form, BindException errors) + { + boolean create = form.getLSID() == null && form.getRowId() == 0 && form.getName() == null; + if (!create) + _dataClass = form.getDataClass(getContainer()); + + return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("dataClassDesigner")); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + + root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + if (_dataClass == null) + { + root.addChild("Create Data Class"); + } + else + { + root.addChild(_dataClass.getName(), ExperimentUrlsImpl.get().getShowDataClassURL(getContainer(), _dataClass.getRowId())); + root.addChild("Update Data Class"); + } + } + } + + @RequiresPermission(DesignDataClassPermission.class) + public static class CreateDataClassFromTemplateAction extends FormViewAction + { + private ActionURL _successUrl; + private Map _domainTemplates; + + @Override + public void validateCommand(CreateDataClassFromTemplateForm form, Errors errors) + { + String name = null; + _domainTemplates = DomainTemplateGroup.getAllTemplates(getContainer()); + + if (!_domainTemplates.containsKey(form.getDomainTemplate())) + { + errors.reject(ERROR_MSG, "Unknown template selected: " + form.getDomainTemplate()); + } + else + { + DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); + name = template.getTemplateName(); + + // Issue 40230: if template includes sample type option, verify that it exists + if (template.getOptions().containsKey("sampleSet")) + { + String sampleTypeName = template.getOptions().get("sampleSet").toString(); + ExpSampleType sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), sampleTypeName); + if (sampleType == null) + errors.reject(ERROR_MSG, "Unable to find a sample type in this container with name: " + sampleTypeName + "."); + } + } + + if (StringUtils.isBlank(name)) + errors.reject(ERROR_MSG, "DataClass template selection is required."); + else if (ExperimentService.get().getDataClass(getContainer(), getUser(), name) != null) + errors.reject(ERROR_MSG, "DataClass '" + name + "' already exists."); + + } + + @Override + public ModelAndView getView(CreateDataClassFromTemplateForm form, boolean reshow, BindException errors) + { + Set templates = DomainTemplateGroup.getTemplatesForDomainKind(getContainer(), DataClassDomainKind.NAME); + form.setAvailableDomainTemplateNames(templates); + + Set messages = new HashSet<>(); + Map groups = DomainTemplateGroup.getAllGroups(getContainer()); + for (DomainTemplateGroup g : groups.values()) + messages.addAll(g.getErrors()); + form.setXmlParseErrors(messages); + + return new JspView<>("/org/labkey/experiment/createDataClassFromTemplate.jsp", form, errors); + } + + @Override + public boolean handlePost(CreateDataClassFromTemplateForm form, BindException errors) throws Exception + { + DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); + Domain domain = DomainUtil.createDomain(template, getContainer(), getUser(), form.getName()); + + _successUrl = domain.getDomainKind().urlEditDefinition(domain, getViewContext()); + return true; + } + + @Override + public URLHelper getSuccessURL(CreateDataClassFromTemplateForm form) + { + return _successUrl; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + root.addChild("Create Data Class from Template"); + } + } + + public static class CreateDataClassFromTemplateForm extends DataClass + { + private String _domainTemplate; + private Set _availableDomainTemplateNames; + private Set _xmlParseErrors; + private final ReturnUrlForm _returnUrlForm = new ReturnUrlForm(); + + public String getDomainTemplate() + { + return _domainTemplate; + } + + public void setDomainTemplate(String domainTemplate) + { + _domainTemplate = domainTemplate; + } + + public Set getAvailableDomainTemplateNames() + { + return _availableDomainTemplateNames; + } + + public void setAvailableDomainTemplateNames(Set availableDomainTemplateNames) + { + _availableDomainTemplateNames = availableDomainTemplateNames; + } + + public Set getXmlParseErrors() + { + return _xmlParseErrors; + } + + public void setXmlParseErrors(Set xmlParseErrors) + { + _xmlParseErrors = xmlParseErrors; + } + + @Nullable + public String getReturnUrl() + { + return _returnUrlForm.getReturnUrl(); + } + + public void setReturnUrl(String s) + { + _returnUrlForm.setReturnUrl(s); + } + } + + public static class ConceptURIForm + { + private String _conceptURI; + + public String getConceptURI() + { + return _conceptURI; + } + + public void setConceptURI(String conceptURI) + { + _conceptURI = conceptURI; + } + } + + @RequiresPermission(AdminPermission.class) + public static class RemoveConceptMappingAction extends MutatingApiAction + { + @Override + public void validateForm(ConceptURIForm form, Errors errors) + { + if (form.getConceptURI() == null || ConceptURIProperties.getLookup(getContainer(), form.getConceptURI()) == null) + errors.reject(ERROR_MSG, "Concept URI not found: " + form.getConceptURI()); + } + + @Override + public Object execute(ConceptURIForm form, BindException errors) + { + ConceptURIProperties.removeLookup(getContainer(), form.getConceptURI()); + return new ApiSimpleResponse("success", true); + } + } + + @RequiresPermission(ReadPermission.class) + public static class RunAttachmentDownloadAction extends BaseDownloadAction + { + @Nullable + @Override + public Pair getAttachment(AttachmentForm form) + { + if (form.getLsid() == null || form.getName() == null) + throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); + + ExpRun run = ExperimentService.get().getExpRun(form.getLsid()); + if (run == null) + throw new NotFoundException("Run not found: " + form.getLsid()); + + if (!run.getContainer().equals(getContainer())) + { + if (run.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new RedirectException(getViewContext().cloneActionURL().setContainer(run.getContainer())); + else + throw new NotFoundException("Run not found"); + } + + AttachmentParent parent = new ExpRunAttachmentParent(run); + return new Pair<>(parent, form.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public static class DataClassAttachmentDownloadAction extends BaseDownloadAction + { + @Nullable + @Override + public Pair getAttachment(AttachmentForm form) + { + if (form.getLsid() == null || form.getName() == null) + throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); + + Lsid lsid = new Lsid(form.getLsid()); + ExpData data = ExperimentServiceImpl.get().getExpData(lsid.toString()); + if (data == null) + throw new NotFoundException("Error: Data object not found for the given LSID: " + lsid); + AttachmentParent parent = new ExpDataClassAttachmentParent(data.getContainer(), lsid); + + return new Pair<>(parent, form.getName()); + } + } + + public static class AttachmentForm extends LsidForm implements BaseDownloadAction.InlineDownloader + { + private String _name; + private boolean _inline = true; + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + @Override + public boolean isInline() + { + return _inline; + } + + public void setInline(boolean inline) + { + _inline = inline; + } + } + + // + // END DataClass actions + // + + public static ActionURL getRunGraphURL(Container c, long runId) + { + return new ActionURL(ShowRunGraphAction.class, c).addParameter("rowId", runId); + } + + + @RequiresPermission(ReadPermission.class) + public class ShowRunGraphAction extends AbstractShowRunAction + { + @Override + protected VBox createLowerView(ExpRunImpl experimentRun, BindException errors) + { + return new VBox( + createRunViewTabs(experimentRun, false, true, true), + new ExperimentRunGraphView(experimentRun, false)); + } + } + + + @RequiresPermission(ReadPermission.class) + public static class DownloadGraphAction extends SimpleViewAction + { + @Override + public ModelAndView getView(ExperimentRunForm form, BindException errors) throws Exception + { + boolean detail = form.isDetail(); + String focus = form.getFocus(); + String focusType = form.getFocusType(); + + ExpRunImpl experimentRun = (ExpRunImpl) form.lookupRun(); + ensureCorrectContainer(getContainer(), experimentRun, getViewContext()); + + ExperimentRunGraph.RunGraphFiles files; + try + { + files = ExperimentRunGraph.generateRunGraph(getViewContext(), experimentRun, detail, focus, focusType); + } + catch (ExperimentException e) + { + PageFlowUtil.streamTextAsImage(getViewContext().getResponse(), "ERROR: " + e.getMessage(), 600, 150, Color.RED); + return null; + } + + try + { + PageFlowUtil.streamFile(getViewContext().getResponse(), new File(files.getImageFile().getAbsolutePath()), false); + } + catch (FileNotFoundException e) + { + getViewContext().getResponse().sendRedirect(getViewContext().getRequest().getContextPath() + "/experiment/ExperimentRunNotFound.gif"); + } + finally + { + files.release(); + } + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + throw new UnsupportedOperationException(); + } + } + + private abstract class AbstractShowRunAction extends SimpleViewAction + { + private ExpRunImpl _experimentRun; + + @Override + public ModelAndView getView(ExperimentRunForm form, BindException errors) + { + _experimentRun = (ExpRunImpl) form.lookupRun(); + ensureCorrectContainer(getContainer(), _experimentRun, getViewContext()); + + VBox vbox = new VBox(); + + JspView detailsView = new JspView<>("/org/labkey/experiment/ExperimentRunDetails.jsp", _experimentRun); + detailsView.setTitle("Standard Properties"); + + var attachmentParent = new ExpRunAttachmentParent(_experimentRun); + var attachments = AttachmentService.get().getAttachments(attachmentParent) + .stream() + .map(att -> Pair.of(att.getName(), new ActionURL(RunAttachmentDownloadAction.class, _experimentRun.getContainer()).addParameter("name", att.getName()).addParameter("lsid", _experimentRun.getLSID()))) + .collect(toList()); + CustomPropertiesView cpv = new CustomPropertiesView(_experimentRun.getLSID(), getContainer(), attachments); + + vbox.addView(new StandardAndCustomPropertiesView(detailsView, cpv)); + + HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); + List runEditors = ExperimentService.get().getRunEditors(); + for (ExpRunEditor editor : runEditors) + { + if (editor.isProtocolEditor(form.lookupRun().getProtocol())) + { + updateLinks.append(LinkBuilder.labkeyLink("edit " + editor.getDisplayName() + " run", editor.getEditUrl(getContainer()).addParameter("rowId", form.getRowId()))); + } + } + + if (!updateLinks.isEmpty()) + { + HtmlView view = new HtmlView(updateLinks); + vbox.addView(view); + } + + VBox lowerView = createLowerView(_experimentRun, errors); + lowerView.setFrame(WebPartView.FrameType.PORTAL); + lowerView.setTitle("Run Details"); + NavTree tree = new NavTree(""); + File runRoot = _experimentRun.getFilePathRoot(); + if (NetworkDrive.exists(runRoot)) + { + if (!runRoot.isDirectory()) + { + runRoot = runRoot.getParentFile(); + } + PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(_experimentRun.getContainer()); + if (pipelineRoot != null) + { + if (pipelineRoot.isUnderRoot(runRoot)) + { + String path = pipelineRoot.relativePath(runRoot); + tree.addChild("View Files", urlProvider(PipelineUrls.class).urlBrowse(_experimentRun.getContainer(), null, path)); + } + } + } + + final String exportFilesFormId = "exportFilesForm"; + NavTree downloadFiles = new NavTree("Download all files"); + downloadFiles.setScript("document.getElementById('" + exportFilesFormId + "').submit();"); + tree.addChild(downloadFiles); + + // CONSIDER: Show modal dialog using ExperimentService.get().createRunExportView() + NavTree exportXarFiles = new NavTree("Export XAR"); + exportXarFiles.setScript("LABKEY.Experiment.exportRuns({runIds: [" + _experimentRun.getRowId() + "] });"); + tree.addChild(exportXarFiles); + + lowerView.setNavMenu(tree); + lowerView.setIsWebPart(false); + + vbox.addView(lowerView); + vbox.addView(new ExperimentRunGroupsView(getUser(), getContainer(), _experimentRun, getViewContext().getActionURL(), errors)); + + DOM.Renderable exportFilesForm = LK.FORM(at( + id, exportFilesFormId, + method, "POST", + action, new ActionURL(ExportRunFilesAction.class, _experimentRun.getContainer())), + INPUT(at(type, "hidden", + name, DataRegionSelection.DATA_REGION_SELECTION_KEY, + value, "ExportSingleRun")), + INPUT(at(type, "hidden", + name, DataRegion.SELECT_CHECKBOX_NAME, + value, _experimentRun.getRowId())), + INPUT(at(type, "hidden", + name, "zipFileName", + value, _experimentRun.getName() + ".zip"))); + + HtmlView hiddenFormView = new HtmlView(exportFilesForm); + vbox.addView(hiddenFormView); + + return vbox; + } + + protected abstract VBox createLowerView(ExpRunImpl experimentRun, BindException errors); + + @Override + public void addNavTrail(NavTree root) + { + root.addChild(_experimentRun.getName()); + } + } + + public static class ToggleRunExperimentMembershipForm + { + private int _runId; + private int _experimentId; + private boolean _included; + + public int getRunId() + { + return _runId; + } + + public void setRunId(int runId) + { + _runId = runId; + } + + public int getExperimentId() + { + return _experimentId; + } + + public void setExperimentId(int experimentId) + { + _experimentId = experimentId; + } + + public boolean isIncluded() + { + return _included; + } + + public void setIncluded(boolean included) + { + _included = included; + } + } + + @RequiresPermission(UpdatePermission.class) + public static class ToggleRunExperimentMembershipAction extends FormHandlerAction + { + @Override + public boolean handlePost(ToggleRunExperimentMembershipForm form, BindException errors) + { + ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); + // Check if the user has permission to update this run + if (run == null || !run.getContainer().hasPermission(getUser(), UpdatePermission.class)) + { + throw new NotFoundException(); + } + + ExpExperiment exp = ExperimentService.get().getExpExperiment(form.getExperimentId()); + if (exp == null) + { + throw new NotFoundException(); + } + // Check if this + if (!ExperimentService.get().getExperiments(run.getContainer(), getUser(), true, false).contains(exp)) + { + throw new NotFoundException(); + } + // Users must have permission to view, but not necessarily update, the container the holds the run group + if (!exp.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new UnauthorizedException(); + } + + if (form.isIncluded()) + { + exp.addRuns(getUser(), run); + } + else + { + exp.removeRun(getUser(), run); + } + + return true; + } + + @Override + public URLHelper getSuccessURL(ToggleRunExperimentMembershipForm form) + { + return null; + } + + @Override + public void validateCommand(ToggleRunExperimentMembershipForm target, Errors errors) + { + } + } + + private HtmlView createRunViewTabs(ExpRun expRun, boolean showGraphSummary, boolean showGraphDetail, boolean showText) + { + return new HtmlView( + TABLE(cl("labkey-tab-strip"), + TR( + createTabSpacer(false), + createTab("Graph Summary View", ExperimentUrlsImpl.get().getRunGraphURL(expRun), !showGraphSummary), + createTabSpacer(false), + createTab("Graph Detail View", ExperimentUrlsImpl.get().getRunGraphDetailURL(expRun), !showGraphDetail), + createTabSpacer(false), + createTab("Text View", ExperimentUrlsImpl.get().getRunTextURL(expRun), !showText), + createTabSpacer(true)))); + } + + private DOM.Renderable createTab(String text, ActionURL url, boolean selected) + { + return TD(cl(selected,"labkey-tab-selected", "labkey-tab"), + A(at(href, url), text)); + } + + private DOM.Renderable createTabSpacer(boolean fullWidth) + { + return TD(cl("labkey-tab-space").at(fullWidth, width, "100%"), + IMG(at(src, AppProps.getInstance().getContextPath() + "/_.gif", width, "5"))); + } + + @RequiresPermission(ReadPermission.class) + public class ShowRunTextAction extends AbstractShowRunAction + { + @Override + protected VBox createLowerView(ExpRunImpl expRun, BindException errors) + { + JspView applicationsView = new JspView<>("/org/labkey/experiment/ProtocolApplications.jsp", expRun); + applicationsView.setFrame(WebPartView.FrameType.TITLE); + applicationsView.setTitle("Protocol Applications"); + + HtmlView toggleView = createRunViewTabs(expRun, true, true, false); + + QuerySettings runDataInputsSettings = new QuerySettings(getViewContext(), "RunDataInputs", DataInputs.name()); + UsageQueryView runDataInputsView = new UsageQueryView("Data Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runDataInputsSettings, errors); + runDataInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); + + QuerySettings runDataOutputsSettings = new QuerySettings(getViewContext(), "RunDataOutputs", DataInputs.name()); + UsageQueryView runDataOutputsView = new UsageQueryView("Data Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runDataOutputsSettings, errors); + runDataOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); + + QuerySettings runMaterialInputsSetting = new QuerySettings(getViewContext(), "RunMaterialInputs", ExpSchema.TableType.MaterialInputs.name()); + UsageQueryView runMaterialInputsView = new UsageQueryView("Material Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runMaterialInputsSetting, errors); + runMaterialInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); + + QuerySettings runMaterialOutputsSettings = new QuerySettings(getViewContext(), "RunMaterialOutputs", ExpSchema.TableType.MaterialInputs.name()); + UsageQueryView runMaterialOutputsView = new UsageQueryView("Material Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runMaterialOutputsSettings, errors); + runMaterialOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); + + HBox inputsView = new HBox(runDataInputsView, runMaterialInputsView); + HBox registeredInputsView = new HBox(); + + var expService = ExperimentService.get(); + expService.getRunInputsViewProviders().forEach(provider -> + { + var queryView = provider.createView(getViewContext(), expRun, errors); + if (queryView != null) + { + registeredInputsView.addView(queryView); + } + }); + HBox outputsView = new HBox(runDataOutputsView, runMaterialOutputsView); + HBox registeredOutputsView = new HBox(); + expService.getRunOutputsViewProviders().forEach(provider -> + { + var queryView = provider.createView(getViewContext(), expRun, errors); + if (queryView != null) + { + registeredOutputsView.addView(queryView); + } + }); + + var vBox = new VBox(); + vBox.addView(toggleView); + vBox.addView(inputsView); + if (!registeredInputsView.isEmpty()) + vBox.addView(registeredInputsView); + vBox.addView(outputsView); + if (!registeredOutputsView.isEmpty()) + vBox.addView(registeredOutputsView); + vBox.addView(applicationsView); + + return vBox; + } + } + + private static class UsageQueryView extends QueryView + { + private final ExpRun _run; + private final ExpProtocol.ApplicationType _type; + + public UsageQueryView(String title, ViewContext context, ExpRun run, ExpProtocol.ApplicationType type, + QuerySettings settings, BindException errors) + { + super(new ExpSchema(context.getUser(), context.getContainer()), settings, errors); + setTitle(title); + setFrame(FrameType.TITLE); + _run = run; + _type = type; + setShowBorders(true); + setShadeAlternatingRows(true); + setShowExportButtons(false); + setShowPagination(false); + disableContainerFilterSelection(); + } + + @Override + protected TableInfo createTable() + { + String tableName = getSettings().getQueryName(); + ExpInputTable tableInfo = (ExpInputTable) getSchema().getTable(tableName, new ContainerFilter.AllFolders(getUser()), true, true); + tableInfo.setRun(_run, _type); + tableInfo.setLocked(true); + return tableInfo; + } + } + + + public static ActionURL getShowRunGraphDetailURL(Container c, long rowId) + { + ActionURL url = new ActionURL(ShowRunGraphDetailAction.class, c); + url.addParameter("rowId", rowId); + return url; + } + + + @RequiresPermission(ReadPermission.class) + public class ShowRunGraphDetailAction extends AbstractShowRunAction + { + @Override + protected VBox createLowerView(ExpRunImpl run, BindException errors) + { + ExperimentRunGraphView gw = new ExperimentRunGraphView(run, true); + if (null != getViewContext().getActionURL().getParameter("focus")) + gw.setFocus(getViewContext().getActionURL().getParameter("focus")); + if (null != getViewContext().getActionURL().getParameter("focusType")) + gw.setFocusType(getViewContext().getActionURL().getParameter("focusType")); + return new VBox(createRunViewTabs(run, true, false, true), gw); + } + } + + private abstract class AbstractDataAction extends SimpleViewAction + { + protected ExpDataImpl _data; + + @Override + public final ModelAndView getView(DataForm form, BindException errors) throws Exception + { + _data = form.lookupData(); + if (_data == null) + { + throw new NotFoundException("Could not find a data with RowId " + form.getRowId()); + } + + ensureCorrectContainer(getContainer(), _data, getViewContext()); + return getDataView(form, errors); + } + + protected abstract ModelAndView getDataView(DataForm form, BindException errors) throws Exception; + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Data " + _data.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowDataAction extends AbstractDataAction + { + @Override + public ModelAndView getDataView(DataForm form, BindException errors) + { + ExpRun run = _data.getRun(); + ExpProtocol sourceProtocol = _data.getSourceProtocol(); + ExpProtocolApplication sourceProtocolApplication = _data.getSourceApplication(); + ExpDataClass dataClass = _data.getDataClass(getUser()); + + ExpSchema schema = new ExpSchema(getUser(), getContainer()); + TableInfo table; + long pk; + if (dataClass == null) + { + table = schema.getDatasTable(); + pk = _data.getRowId(); + } + else + { + table = schema.getSchema(ExpSchema.NestedSchemas.data).getTable(dataClass.getName()); + pk = new TableSelector(table, Collections.singleton("rowId"), new SimpleFilter(FieldKey.fromParts("lsid"), _data.getLSID()), null).getObject(Integer.class); + } + + DataRegion dr = new DataRegion(); + dr.setTable(table); + List cols = table.getColumns().stream().filter(ColumnInfo::isShownInDetailsView).collect(toList()); + dr.addColumns(cols); + dr.removeColumns("RowId", "Created", "CreatedBy", "Modified", "ModifiedBy", "DataFileUrl", "Run", "LSID", "CpasType", "SourceApplicationId", "Folder", "Generated"); + dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); + dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); + dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); + dr.addDisplayColumn(new LineageGraphDisplayColumn(_data, run)); + DetailsView detailsView = new DetailsView(dr, pk); + detailsView.setTitle("Standard Properties"); + detailsView.setFrame(WebPartView.FrameType.PORTAL); + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + + ExperimentDataHandler handler = _data.findDataHandler(); + ActionURL viewDataURL = handler == null ? null : handler.getContentURL(_data); + if (viewDataURL != null) + { + bb.add(new ActionButton("View data", viewDataURL)); + } + + if (_data.isPathAccessible()) + { + bb.add(new ActionButton("View file", ExperimentUrlsImpl.get().getShowFileURL(_data, true))); + bb.add(new ActionButton("Download file", ExperimentUrlsImpl.get().getShowFileURL(_data, false))); + + if (getContainer().hasPermission(getUser(), InsertPermission.class)) + { + String relativePath = null; + PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); + if (root != null) + { + Path rootFile = root.getRootNioPath(); + Path dataFile = _data.getFilePath(); + if (dataFile != null) + { + Path pathRelative; + try + { + pathRelative = rootFile.relativize(dataFile); + if (null != pathRelative) + relativePath = pathRelative.toString(); + } + catch (IllegalArgumentException e) + { + // dataFile not relative to root + } + } + } + ActionURL browseURL = urlProvider(PipelineUrls.class).urlBrowse(getContainer(), getViewContext().getActionURL(), relativePath); + bb.add(new ActionButton("Browse in pipeline", browseURL)); + } + } + + // add links to any other exp.data that share the same dataFileUrl path + var altDataList = ExperimentService.get().getAllExpDataByURL(_data.getDataFileUrl(), getContainer()); + altDataList.removeIf(_data::equals); + if (!altDataList.isEmpty()) + { + MenuButton menu = new MenuButton("Alternate Data"); + for (ExpData altData : altDataList) + { + ExpRun altDataRun = altData.getRun(); + StringBuilder sb = new StringBuilder(altData.getName()); + if (altDataRun != null) + sb.append(" created by run '").append(altDataRun.getName()).append("' (").append(altDataRun.getProtocol().getName()).append(")"); + menu.addMenuItem(sb.toString(), altData.detailsURL()); + } + bb.add(menu); + } + + dr.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); + dr.setButtonBar(bb); + + CustomPropertiesView cpv = new CustomPropertiesView(_data.getLSID(), getContainer()); + HBox hbox = new StandardAndCustomPropertiesView(detailsView, cpv); + + VBox vbox = new VBox(hbox); + + ParentChildView pv = new ParentChildView(_data, getViewContext()); + vbox.addView(pv); + + ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); + runListView.getRunTable().setInputData(_data); + runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); + runListView.getRunTable().setLocked(true); + runListView.setTitle("Runs using this data as an input"); + vbox.addView(runListView); + + if (_data.isInlineImage() && _data.isFileOnDisk()) + { + ActionURL showFileURL = new ActionURL(ShowFileAction.class, getContainer()).addParameter("rowId", _data.getRowId()); + HtmlView imageView = new HtmlView(IMG(at(src, showFileURL))); + return new VBox(vbox, imageView); + } + return vbox; + } + } + + @RequiresPermission(AdminPermission.class) + public static class CheckDataFileAction extends MutatingApiAction + { + private ExpDataImpl _data; + + @Override + public void validateForm(DataFileForm form, Errors errors) + { + _data = form.lookupData(); + if (_data == null) + { + errors.reject(ERROR_MSG, "No ExpData found for id: " + form.getRowId()); + } + } + + @Override + public ApiResponse execute(DataFileForm form, BindException errors) + { + File dataFile = _data.getFile(); + Container dataContainer = _data.getContainer(); + boolean fileExists = _data.isFileOnDisk(); + boolean fileExistsAtCurrent = false; + File newDataFile = null; + + ApiSimpleResponse response = new ApiSimpleResponse(); + response.put("dataFileUrl", _data.getDataFileUrl()); + response.put("fileExists", fileExists); + response.put("containerPath", dataContainer.getPath()); + + if (!fileExists) + { + PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(dataContainer); + if (pipelineRoot != null && pipelineRoot.isValid() && dataFile != null) + { + newDataFile = pipelineRoot.resolvePath("/" + AssayFileWriter.DIR_NAME + "/" + dataFile.getName()); + fileExistsAtCurrent = NetworkDrive.exists(newDataFile); + response.put("fileExistsAtCurrent", fileExistsAtCurrent); + } + } + + // if the current dataFileUrl does not exist on disk and we have the file at the current + // pipeline root /assaydata dir, fix the dataFileUrl value + if (form.isAttemptFilePathFix()) + { + if (fileExistsAtCurrent) + { + ExpDataFileListener fileListener = new ExpDataFileListener(); + fileListener.fileMoved(dataFile, newDataFile, getUser(), dataContainer); + response.put("filePathFixed", true); + + // update the ExpData object so that we can get the new dataFileUrl + _data = form.lookupData(); + response.put("newDataFileUrl", _data.getDataFileUrl()); + } + else + { + response.put("filePathFixed", false); + } + } + + response.put("success", true); + return response; + } + } + + public static class DataFileForm extends DataForm + { + private boolean _attemptFilePathFix; + + public boolean isAttemptFilePathFix() + { + return _attemptFilePathFix; + } + + public void setAttemptFilePathFix(boolean attemptFilePathFix) + { + _attemptFilePathFix = attemptFilePathFix; + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowFileAction extends AbstractDataAction + { + @Override + protected ModelAndView getDataView(DataForm form, BindException errors) throws IOException + { + if (!_data.isPathAccessible()) + { + throw new NotFoundException("Data file " + _data.getDataFileUrl() + " does not exist on disk"); + } + + PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); + if (root != null && !root.isUnderRoot(_data.getFilePath())) + { + // Issue 35649: ImmPort module "publish" creates exp.data object in this container for paths that originate in a different container + FileContentService fileSvc = FileContentService.get(); + if (fileSvc == null) + throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); + + List containers = fileSvc.getContainersForFilePath(_data.getFilePath()); + if (containers.isEmpty() || containers.stream().noneMatch(c -> c.hasPermission(getUser(), ReadPermission.class))) + throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); + } + + //Issues 25667 and 31152 + if (form.isInline()) + { + ExperimentDataHandler h = _data.findDataHandler(); + if (h != null) + { + URLHelper url = h.getShowFileURL(_data); + if (url != null) + { + throw new RedirectException(url, false); + } + } + } + + try + { + Path realContent = _data.getFilePath(); + if (null == realContent) + throw new IllegalStateException("Path not found."); + + boolean inline = _data.isInlineImage() || form.isInline() || "inlineImage".equalsIgnoreCase(form.getFormat()); + if (_data.isInlineImage() && form.getMaxDimension() != null) + { + try (InputStream inputStream = Files.newInputStream(realContent)) + { + BufferedImage image = ImageIO.read(inputStream); + // If image, create a thumbnail, otherwise fall through as a regular download attempt + if (image != null) + { + int imageMax = Math.max(image.getHeight(), image.getWidth()); + if (imageMax > form.getMaxDimension().intValue()) + { + double scale = (double) form.getMaxDimension().intValue() / (double) imageMax; + ByteArrayOutputStream bOut = new ByteArrayOutputStream(); + ImageUtil.resizeImage(image, bOut, scale, 1); + PageFlowUtil.streamFileBytes(getViewContext().getResponse(), FileUtil.getFileName(realContent) + ".png", bOut.toByteArray(), !inline); + return null; + } + } + } + } + + boolean extended = "jsonTSVExtended".equalsIgnoreCase(form.getFormat()); + boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(form.getFormat()); + if ("jsonTSV".equalsIgnoreCase(form.getFormat()) || extended || ignoreTypes) + { + if (!FileUtil.hasCloudScheme(realContent)) // TODO: handle streaming from S3 to JSON + streamToJSON(FileSystemLike.wrapFile(realContent), form.getFormat(), -1, null); + return null; + } + + try (InputStream inputStream = Files.newInputStream(realContent)) + { + PageFlowUtil.streamFile(getViewContext().getResponse(), Collections.emptyMap(), FileUtil.getFileName(realContent), inputStream, !inline); + } + } + catch (IOException e) + { + try + { + // Try to write the exception back to the caller if we haven't already flushed the buffer + ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse()); + writer.writeResponse(e); + } + catch (IllegalStateException ise) + { + // Most likely that a disconnected client caused the IOException writing back the response + } + } + + return null; + } + } + + + public static class ParseForm + { + String format = "jsonTSV"; + int maxRows = -1; + + public String getFormat() + { + return format; + } + + public void setFormat(String format) + { + this.format = format; + } + + public int getMaxRows() + { + return maxRows; + } + + public void setMaxRows(int maxRow) + { + this.maxRows = maxRow; + } + } + + @RequiresNoPermission + public class ParseFileAction extends MutatingApiAction + { + @Override + public Object execute(ParseForm form, BindException errors) throws Exception + { + if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) + throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); + + MultipartFile formFile = getFileMap().get("file"); + if (formFile == null) + { + return true; + } + + FileLike tempFile = null; + try + { + tempFile = FileUtil.createTempFileLike("parse", formFile.getOriginalFilename()); + FileUtil.copyData(formFile.getInputStream(), tempFile.openOutputStream()); + streamToJSON(tempFile, form.getFormat(), form.getMaxRows(), formFile.getOriginalFilename()); + } + finally + { + if (null != tempFile) + tempFile.delete(); + } + return null; + } + } + + + // SampleTypeTest + private void streamToJSON(FileLike realContent, String format, int maxRow, String originalFileName) throws IOException + { + String lowerCaseFileName = realContent.getName().toLowerCase(); + boolean extended = "jsonTSVExtended".equalsIgnoreCase(format); + boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(format); + + JSONArray sheetsArray; + if (lowerCaseFileName.endsWith(".xls") || lowerCaseFileName.endsWith(".xlsx")) + { + try (InputStream in = realContent.openInputStream()) + { + sheetsArray = ExcelFactory.convertExcelToJSON(in, extended, maxRow); + } + } + else + { + DataLoaderFactory dlf = DataLoader.get().findFactory(realContent, null); + if (null == dlf) + { + throw new ApiUsageException("Unable to parse file " + realContent + ", it is likely of an unsupported file type"); + } + + try (InputStream in = realContent.openInputStream(); + DataLoader tabLoader = dlf.createLoader(in, true)) + { + tabLoader.setScanAheadLineCount(5000); + ColumnDescriptor[] cols = tabLoader.getColumns(); + + if (ignoreTypes) + for (ColumnDescriptor col : cols) + col.clazz = String.class; + + JSONArray rowsArray = new JSONArray(); + JSONArray headerArray = new JSONArray(); + for (ColumnDescriptor col : cols) + { + if (extended) + { + JSONObject valueObject = new JSONObject(); + valueObject.put("value", col.name); + headerArray.put(valueObject); + } + else + { + headerArray.put(col.name); + } + } + rowsArray.put(headerArray); + for (Map rowMap : tabLoader) + { + // headers count as a row to be consistent + if (maxRow > -1 && maxRow <= rowsArray.length() + 1) + break; + + JSONArray rowArray = new JSONArray(); + for (ColumnDescriptor col : cols) + { + Object value = rowMap.get(col.name); + if (extended) + { + JSONObject valueObject = new JSONObject(); + valueObject.put("value", value); + rowArray.put(valueObject); + } + else + { + rowArray.put(value); + } + } + rowsArray.put(rowArray); + } + + JSONObject sheetJSON = new JSONObject(); + sheetJSON.put("name", "flat"); + sheetJSON.put("data", rowsArray); + sheetsArray = new JSONArray(); + sheetsArray.put(sheetJSON); + } + } + + try (ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse())) + { + JSONObject workbookJSON = new JSONObject(); + workbookJSON.put("fileName", realContent.getName()); + workbookJSON.put("sheets", sheetsArray); + if (originalFileName != null) + workbookJSON.put("originalFileName", originalFileName); + writer.writeResponse(new ApiSimpleResponse(workbookJSON)); + } + } + + + public static class ConvertArraysToExcelForm + { + private String _json; + + public String getJson() + { + return _json; + } + + public void setJson(String json) + { + _json = json; + } + } + + @RequiresPermission(ReadPermission.class) + public static class ConvertArraysToExcelAction extends ExportAction + { + @Override + public void validate(ConvertArraysToExcelForm form, BindException errors) + { + if (form.getJson() == null) + { + errors.reject(ERROR_MSG, "Unable to convert to Excel - no spreadsheet data given"); + } + } + + @Override + public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception + { + try + { + JSONObject rootObject; + JSONArray sheetsArray; + if (form.getJson() == null || form.getJson().trim().isEmpty()) + { + // Create JSON so that we return an empty file + rootObject = new JSONObject(); + sheetsArray = new JSONArray(); + JSONObject sheetObject = new JSONObject(); + sheetsArray.put(sheetObject); + } + else + { + rootObject = new JSONObject(form.getJson()); + sheetsArray = rootObject.getJSONArray("sheets"); + } + String filename = rootObject.has("fileName") ? rootObject.getString("fileName") : "ExcelExport.xls"; + ExcelWriter.ExcelDocumentType docType = filename.toLowerCase().endsWith(".xlsx") ? ExcelWriter.ExcelDocumentType.xlsx : ExcelWriter.ExcelDocumentType.xls; + + try (Workbook workbook = ExcelFactory.createFromArray(sheetsArray, docType)) + { + response.setContentType(docType.getMimeType()); + ResponseHelper.setContentDisposition(response, ResponseHelper.ContentDispositionType.attachment, filename); + ResponseHelper.setPrivate(response); + workbook.write(response.getOutputStream()); + + JSONObject qInfo = rootObject.has("queryinfo") ? rootObject.getJSONObject("queryinfo") : null; + if (qInfo != null) + { + QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), + qInfo.getString("query"), getViewContext().getActionURL(), + rootObject.getString("auditMessage") + filename, + null); + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asExcel"); + } + } + } + catch (JSONException | ClassCastException e) + { + // We can get a ClassCastException if we expect an array and get a simple String, for example + ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to Excel - invalid input", e, false, false); + } + } + } + + @RequiresPermission(ReadPermission.class) + public static class ConvertArraysToTableAction extends ExportAction + { + @Override + public void validate(ConvertArraysToExcelForm form, BindException errors) + { + if (form.getJson() == null) + { + errors.reject(ERROR_MSG, "Unable to convert to table - no data given"); + } + } + + @Override + public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception + { + try + { + JSONObject rootObject; + JSONArray rowsArray; + if (form.getJson() == null || form.getJson().trim().isEmpty()) + { + // Create JSON so that we return an empty file + rootObject = new JSONObject(); + rowsArray = new JSONArray(); + } + else + { + rootObject = new JSONObject(form.getJson()); + rowsArray = rootObject.getJSONArray("rows"); + } + + TSVWriter.DELIM delimType = (!rootObject.isNull("delim") ? TSVWriter.DELIM.valueOf(rootObject.getString("delim")) : TSVWriter.DELIM.TAB); + TSVWriter.QUOTE quoteType = (!rootObject.isNull("quoteChar") ? TSVWriter.QUOTE.valueOf(rootObject.getString("quoteChar")) : TSVWriter.QUOTE.NONE); + String filenamePrefix = (!rootObject.isNull("fileNamePrefix") ? rootObject.getString("fileNamePrefix") : "Export"); + String filename = filenamePrefix + "." + delimType.extension; + String newlineChar = !rootObject.isNull("newlineChar") ? rootObject.getString("newlineChar") : "\n"; + + response.setCharacterEncoding(StringUtilsLabKey.DEFAULT_CHARSET.name()); + + try(var tsvWriter = new TSVJSONWriter(filenamePrefix, rowsArray)) + { + tsvWriter.setRowSeparator(newlineChar); + tsvWriter.setDelimiterCharacter(delimType); + tsvWriter.setQuoteCharacter(quoteType); + tsvWriter.write(response); + } + + JSONObject qInfo = rootObject.optJSONObject("queryinfo"); + if (qInfo != null) + { + QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), qInfo.getString("query"), + getViewContext().getActionURL(), + rootObject.getString("auditMessage") + filename, + rowsArray.length()); + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asDelimited"); + } + } + catch (JSONException e) + { + ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to table - invalid input", e, false, false); + } + } + } + + + public static class ConvertHtmlToExcelForm + { + private String _baseUrl; + private String _htmlFragment; + private String _name = "workbook.xls"; + + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + public String getBaseUrl() + { + return _baseUrl; + } + + public void setBaseUrl(String baseUrl) + { + _baseUrl = baseUrl; + } + + public String getHtmlFragment() + { + return _htmlFragment; + } + + public void setHtmlFragment(String htmlFragment) + { + _htmlFragment = htmlFragment; + } + } + + + @RequiresPermission(ReadPermission.class) + public static class ConvertHtmlToExcelAction extends FormViewAction + { + String _responseHtml = null; + + @Override + public void validateCommand(ConvertHtmlToExcelForm target, Errors errors) + { + } + + @Override + public ModelAndView getView(ConvertHtmlToExcelForm form, boolean reshow, BindException errors) + { + String html = + "

" + + "" + + new CsrfInput(getViewContext()) + + "
"; + return HtmlView.unsafe(html); + } + + @Override + public boolean handlePost(ConvertHtmlToExcelForm form, BindException errors) + { + ActionURL url = getViewContext().getActionURL(); + String base = url.getBaseServerURI(); + if (!base.endsWith("/")) base += "/"; + + String baseTag = ""; + SafeToRender css = PageFlowUtil.getStylesheetIncludes(getContainer()); + String htmlFragment = StringUtils.trimToEmpty(form.getHtmlFragment()); + String html = "" + baseTag + css + "" + htmlFragment + ""; + + // UNDONE: strip script + List tidyErrors = new ArrayList<>(); + String tidy = JSoupUtil.tidyHTML(html, false, tidyErrors); + + if (!tidyErrors.isEmpty()) + { + for (String err : tidyErrors) + { + errors.reject(ERROR_MSG, err); + } + return false; + } + + _responseHtml = tidy; + return true; + } + + @Override + public ModelAndView getSuccessView(ConvertHtmlToExcelForm form) + { + ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, form.getName()); + getPageConfig().setTemplate(PageConfig.Template.None); + HtmlView v = HtmlView.unsafe(_responseHtml); + v.setContentType("application/vnd.ms-excel"); + v.setFrame(WebPartView.FrameType.NONE); + return v; + } + + @Override + public URLHelper getSuccessURL(ConvertHtmlToExcelForm convertHtmlToExcelForm) + { + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + } + } + + + public static ActionURL getShowApplicationURL(Container c, long rowId) + { + ActionURL url = new ActionURL(ShowApplicationAction.class, c); + url.addParameter("rowId", rowId); + + return url; + } + + + @RequiresPermission(ReadPermission.class) + public class ShowApplicationAction extends SimpleViewAction + { + private ExpProtocolApplicationImpl _app; + private ExpRun _run; + + @Override + public ModelAndView getView(ExpObjectForm form, BindException errors) + { + _app = ExperimentServiceImpl.get().getExpProtocolApplication(form.getRowId()); + if (_app == null) + { + throw new NotFoundException("Could not find Protocol Application"); + } + _run = _app.getRun(); + if (_run == null) + { + throw new NotFoundException("No experiment run associated with Protocol Application"); + } + ensureCorrectContainer(getContainer(), _app, getViewContext()); + + ExpProtocol protocol = _app.getProtocol(); + + DataRegion dr = new DataRegion(); + dr.addColumns(ExperimentServiceImpl.get().getTinfoProtocolApplication().getUserEditableColumns()); + DetailsView detailsView = new DetailsView(dr, form.getRowId()); + dr.removeColumns("RunId", "ProtocolLSID", "RowId", "LSID"); + dr.addDisplayColumn(new ExperimentRunDisplayColumn(_run)); + dr.addDisplayColumn(new ProtocolDisplayColumn(protocol)); + dr.addDisplayColumn(new LineageGraphDisplayColumn(_app, _run)); + detailsView.setTitle("Protocol Application"); + + Container c = getContainer(); + ApplicationOutputGrid outMGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoMaterial()); + ApplicationOutputGrid outDGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoData()); + Map map = new HashMap<>(); + for (ProtocolApplicationParameter param : ExperimentService.get().getProtocolApplicationParameters(_app.getRowId())) + { + map.put(param.getOntologyEntryURI(), param); + } + + JspView> paramsView = new JspView<>("/org/labkey/experiment/Parameters.jsp", map); + paramsView.setTitle("Protocol Application Parameters"); + CustomPropertiesView cpv = new CustomPropertiesView(_app.getLSID(), c); + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), paramsView, outMGrid, outDGrid); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Experiment Run", ExperimentUrlsImpl.get().getRunGraphDetailURL(_run)); + root.addChild("Protocol Application " + _app.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowProtocolGridAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + return new ProtocolWebPart(false, getViewContext()); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Protocols"); + } + } + + @RequiresPermission(ReadPermission.class) + public class ProtocolDetailsAction extends SimpleViewAction + { + private ExpProtocolImpl _protocol; + + @Override + public ModelAndView getView(ExpObjectForm form, BindException errors) + { + _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getRowId()); + if (_protocol == null) + { + _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getLSID()); + } + + if (_protocol == null) + { + throw new NotFoundException("Unable to find a matching protocol"); + } + ensureCorrectContainer(getContainer(), _protocol, getViewContext()); + + JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", _protocol); + detailsView.setTitle("Standard Properties"); + + CustomPropertiesView cpv = new CustomPropertiesView(_protocol.getLSID(), getContainer()); + ProtocolParametersView parametersView = new ProtocolParametersView(_protocol); + + VBox protocolDetails = new VBox(); + protocolDetails.setFrame(WebPartView.FrameType.PORTAL); + protocolDetails.setTitle("Protocol Details"); + protocolDetails.addView(new ProtocolInputOutputsView(_protocol, errors)); + + JspView stepsView = new JspView<>("/org/labkey/experiment/ProtocolSteps.jsp", _protocol); + stepsView.setTitle("Protocol Steps"); + stepsView.setFrame(WebPartView.FrameType.TITLE); + protocolDetails.addView(stepsView); + + ExpSchema schema = new ExpSchema(getUser(), getContainer()); + ExperimentRunListView runView = new ExperimentRunListView(schema, ExperimentRunListView.getRunListQuerySettings(schema, getViewContext(), ExpSchema.TableType.Runs.name(), true), ExperimentRunType.ALL_RUNS_TYPE) + { + @Override + public DataView createDataView() + { + DataView result = super.createDataView(); + result.getRenderContext().setBaseFilter(new SimpleFilter(FieldKey.fromParts("Protocol", "LSID"), _protocol.getLSID())); + return result; + } + }; + + runView.setTitle("Runs Using This Protocol"); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails, runView); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); + root.addChild("Protocol: " + _protocol.getName()); + } + } + + public class ProtocolInputOutputsView extends VBox + { + ProtocolInputOutputsView(ExpProtocol protocol, Errors errors) + { + HBox inputsView = new HBox(); + addView(inputsView); + + HBox outputsView = new HBox(); + addView(outputsView); + + UserSchema expSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_NAME); + + class ProtocolInputGrid extends QueryView + { + public ProtocolInputGrid(String title, QuerySettings settings, @Nullable Errors errors) + { + super(expSchema, settings, errors); + + setFrame(FrameType.TITLE); + setTitle(title); + setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); + setShowBorders(true); + setShadeAlternatingRows(true); + setShowExportButtons(false); + setShowPagination(false); + disableContainerFilterSelection(); + } + } + + // INPUTS + + QuerySettings materialInputsSettings = expSchema.getSettings("mpi", ExpSchema.TableType.MaterialProtocolInputs.toString()); + materialInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + materialInputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) + )); + QueryView materialInputsView = new ProtocolInputGrid("Material Inputs", materialInputsSettings, errors); + inputsView.addView(materialInputsView); + + QuerySettings dataInputsSettings = expSchema.getSettings("dpi", ExpSchema.TableType.DataProtocolInputs.toString()); + dataInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + dataInputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) + )); + QueryView dataInputsView = new ProtocolInputGrid("Data Inputs", dataInputsSettings, errors); + inputsView.addView(dataInputsView); + + // OUTPUTS + + QuerySettings materialOutputsSettings = expSchema.getSettings("mpo", ExpSchema.TableType.MaterialProtocolInputs.toString()); + materialOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + materialOutputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) + )); + QueryView materialOutputsView = new ProtocolInputGrid("Material Outputs", materialOutputsSettings, errors); + outputsView.addView(materialOutputsView); + + QuerySettings dataOutputsSettings = expSchema.getSettings("dpo", ExpSchema.TableType.DataProtocolInputs.toString()); + dataOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + dataOutputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) + )); + QueryView dataOutputsView = new ProtocolInputGrid("Data Outputs", dataOutputsSettings, errors); + outputsView.addView(dataOutputsView); + } + } + + + @RequiresPermission(ReadPermission.class) + public class ProtocolPredecessorsAction extends SimpleViewAction + { + private ExpProtocol _parentProtocol; + private ProtocolActionStepDetail _actionStep; + + @Override + public ModelAndView getView(Object o, BindException errors) + { + ActionURL url = getViewContext().getActionURL(); + + String parentProtocolLSID = url.getParameter("ParentLSID"); + int actionSequence; + try + { + actionSequence = Integer.parseInt(url.getParameter("Sequence")); + } + catch (NumberFormatException e) + { + throw new NotFoundException("Could not find SequenceId " + url.getParameter("Sequence")); + } + + _parentProtocol = ExperimentService.get().getExpProtocol(parentProtocolLSID); + if (_parentProtocol == null) + { + throw new NotFoundException("Unable to find a matching protocol"); + } + + ensureCorrectContainer(getContainer(), _parentProtocol, getViewContext()); + + _actionStep = ExperimentServiceImpl.get().getProtocolActionStepDetail(parentProtocolLSID, actionSequence); + + if (_actionStep == null) + { + throw new NotFoundException("Unable to find a matching protocol action step"); + } + + ExpProtocol childProtocol = ExperimentService.get().getExpProtocol(_actionStep.getChildProtocolLSID()); + + JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", childProtocol); + detailsView.setTitle("Standard Properties"); + + CustomPropertiesView cpv = new CustomPropertiesView(childProtocol.getLSID(), getContainer()); + + ProtocolParametersView parametersView = new ProtocolParametersView(childProtocol); + + VBox protocolDetails = new VBox(); + protocolDetails.setFrame(WebPartView.FrameType.PORTAL); + protocolDetails.setTitle("Protocol Details"); + protocolDetails.addView(new ProtocolInputOutputsView(childProtocol, errors)); + protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "PredecessorChildLSID", "PredecessorSequence", "ActionSequence", "Protocol Predecessors")); + protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "ChildProtocolLSID", "ActionSequence", "PredecessorSequence", "Protocol Successors")); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); + root.addChild("Parent Protocol '" + _parentProtocol.getName() + "'", ExperimentUrlsImpl.get().getProtocolDetailsURL(_parentProtocol)); + root.addChild("Protocol Step: " + _actionStep.getName()); + } + } + + public static class DataForm + { + private boolean _inline; + private long _rowId; + private String _lsid; + private Integer _maxDimension; + private String _format; + + public boolean isInline() + { + return _inline; + } + + public void setInline(boolean inline) + { + _inline = inline; + } + + public long getRowId() + { + return _rowId; + } + + public void setRowId(long rowId) + { + _rowId = rowId; + } + + public String getLsid() + { + return _lsid; + } + + public void setLsid(String lsid) + { + _lsid = lsid; + } + + public ExpDataImpl lookupData() + { + ExpDataImpl result = ExperimentServiceImpl.get().getExpData(getRowId()); + if (result == null && getLsid() != null) + { + result = ExperimentServiceImpl.get().getExpData(getLsid()); + } + return result; + } + + public Integer getMaxDimension() + { + return _maxDimension; + } + + public void setMaxDimension(Integer maxDimension) + { + _maxDimension = maxDimension; + } + + public String getFormat() + { + return _format; + } + + public void setFormat(String format) + { + _format = format; + } + } + + public static class ExpObjectForm extends QueryViewAction.QueryExportForm + { + private long _rowId; + private String _lsid; + + public String getLsid() + { + return _lsid; + } + + public void setLsid(String lsid) + { + _lsid = lsid; + } + + public String getLSID() + { + return getLsid(); + } + + public void setLSID(String lsid) + { + setLsid(lsid); + } + + public long getRowId() + { + return _rowId; + } + + public void setRowId(long rowId) + { + _rowId = rowId; + } + } + + @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) + public class DeleteSelectedExpRunsAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + // UNDONE: Need help topic on Runs + setHelpTopic("experiment"); + super.addNavTrail(root); + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List runs = new ArrayList<>(); + + Map idToRunMap = new LongHashMap<>(); + for (long runId : deleteForm.getIds(false)) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run != null) + { + if (!run.canDelete(getUser())) + throw new UnauthorizedException("You do not have permission to delete " + + (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") + + " in " + run.getContainer()); + + runs.add(run); + idToRunMap.put(run.getRowId(), run); + } + } + + Map referencedItems = new LongHashMap<>(); + List referenceDescriptions = new ArrayList<>(); + AssayService assayService = AssayService.get(); + if (!idToRunMap.isEmpty() && assayService != null ) + { + // using the first run as a representative, since all interactions here are (I believe) using the same protocol. + ExpProtocol protocol = runs.get(0).getProtocol(); + AssayProvider provider = assayService.getProvider(protocol); + if (provider != null) + { + SchemaKey key = AssayProtocolSchema.schemaName(provider, protocol); + ExperimentService.get().getObjectReferencers() + .forEach(referencer -> { + Collection referenced = referencer.getItemsWithReferences( + idToRunMap.keySet(), + key.toString(), + "Runs" + ); + referenced.forEach(id -> referencedItems.put(id, idToRunMap.get(id))); + referenceDescriptions.add(referencer.getObjectReferenceDescription(ExpRun.class)); + } + ); + } + + } + + List> permissionDatasetRows = new ArrayList<>(); + List> noPermissionDatasetRows = new ArrayList<>(); + if (StudyPublishService.get() != null) + { + for (Dataset dataset : StudyPublishService.get().getDatasetsForAssayRuns(runs, getUser())) + { + ActionURL url = urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId()); + TableInfo t = dataset.getTableInfo(getUser()); + if (null != t && t.hasPermission(getUser(),DeletePermission.class)) + { + permissionDatasetRows.add(new Pair<>(dataset, url)); + } + else + { + noPermissionDatasetRows.add(new Pair<>(dataset, url)); + } + } + } + + return new ConfirmDeleteView( + "run", + ShowRunGraphAction.class, + runs.stream().filter(run -> !referencedItems.containsKey(run.getRowId())).toList(), + deleteForm, + Collections.emptyList(), + "dataset(s) have one or more rows which", + permissionDatasetRows, + noPermissionDatasetRows, + referencedItems.values().stream().toList(), + referenceDescriptions.stream().filter(Objects::nonNull).collect(Collectors.joining(", or "))); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + ExperimentServiceImpl.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), deleteForm.getUserComment(), deleteForm.getIds(false), getTransactionAuditDetails()); + } + } + + public static class DeleteRunForm + { + private int _runId; + + public int getRunId() + { + return _runId; + } + + public void setRunId(int runId) + { + _runId = runId; + } + } + + /** + * Separate delete action from the client API + */ + @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) + public static class DeleteRunAction extends MutatingApiAction + { + @Override + public ApiResponse execute(DeleteRunForm form, BindException errors) + { + ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); + if (run == null) + { + throw new NotFoundException("Could not find run with ID " + form.getRunId()); + } + if (!run.canDelete(getUser())) + throw new UnauthorizedException("You do not have permission to delete " + + (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") + " in this container."); + + run.delete(getUser()); + return new ApiSimpleResponse("success", true); + } + } + + + @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) + public static class DeleteRunsAction extends AbstractDeleteAPIAction + { + @Override + protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) + { + Set runIdsToDelete = new HashSet<>(form.getIds(true)); + Set runIdsCascadeDeleted = new HashSet<>(); + + if (form.isCascade()) + { + for (long runId : runIdsToDelete) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run != null) + addReplacesRuns(run, runIdsCascadeDeleted); + } + + if (!runIdsCascadeDeleted.isEmpty()) + runIdsToDelete.addAll(runIdsCascadeDeleted); + } + + Map transactionAuditDetails = getTransactionAuditDetails(); + if (form.getRequestSource() != null) + transactionAuditDetails.put(TransactionAuditProvider.TransactionDetail.RequestSource, form.getRequestSource()); + if (form.getEditMethod() != null) + transactionAuditDetails.put(TransactionAuditProvider.TransactionDetail.EditMethod, form.getEditMethod()); + ExperimentService.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), form.getUserComment(), runIdsToDelete, transactionAuditDetails); + + ApiSimpleResponse response = new ApiSimpleResponse("success", true); + response.put("runIdsDeleted", runIdsToDelete); + if (!runIdsCascadeDeleted.isEmpty()) + response.put("runIdsCascadeDeleted", runIdsCascadeDeleted); + return response; + } + + private void addReplacesRuns(ExpRun run, Set runIds) + { + for (ExpRun replacedRun : run.getReplacesRuns()) + { + runIds.add(replacedRun.getRowId()); + addReplacesRuns(replacedRun, runIds); + } + } + } + + private abstract static class AbstractDeleteAPIAction extends MutatingApiAction + { + @Override + public void validateForm(CascadeDeleteForm form, Errors errors) + { + if (form.getSingleObjectRowId() == null && form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "Either singleObjectRowId, dataRegionSelectionKey, or rowIds is required"); + } + + @Override + public ApiResponse execute(CascadeDeleteForm form, BindException errors) throws Exception + { + ApiSimpleResponse response; + + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + tx.addCommitTask(form::clearSelected, POSTCOMMIT); + + response = deleteObjects(form); + tx.commit(); + } + + if (null != response.get("success")) + response.put("success", !errors.hasErrors()); + + return response; + } + + protected abstract ApiSimpleResponse deleteObjects(CascadeDeleteForm form) throws Exception; + } + + public static class CascadeDeleteForm extends DeleteForm + { + private boolean _cascade; + + public boolean isCascade() + { + return _cascade; + } + + public void setCascade(boolean cascade) + { + _cascade = cascade; + } + } + + private abstract static class AbstractDeleteAction extends FormViewAction + { + @Override + public void validateCommand(DeleteForm target, Errors errors) + { + } + + @Override + public boolean handlePost(DeleteForm deleteForm, BindException errors) throws Exception + { + if (!deleteForm.isForceDelete()) + { + return false; + } + else + { + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + tx.addCommitTask(deleteForm::clearSelected, POSTCOMMIT); + + deleteObjects(deleteForm); + tx.commit(); + } + catch (BatchValidationException v) + { + v.addToErrors(errors); + } + + return !errors.hasErrors(); + } + } + + @Override + public ActionURL getSuccessURL(DeleteForm form) + { + return form.getSuccessActionURL(ExperimentUrlsImpl.get().getOverviewURL(getContainer())); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Confirm Deletion"); + } + + protected abstract void deleteObjects(DeleteForm form) throws Exception; + } + + @RequiresPermission(DesignAssayPermission.class) + public static class DeleteProtocolByRowIdsAPIAction extends AbstractDeleteAPIAction + { + @Override + protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) + { + for (ExpProtocol protocol : getProtocolsForDeletion(form)) + { + if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) + throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); + + protocol.delete(getUser(), form.getUserComment()); + } + + return new ApiSimpleResponse(); + } + } + + public static List getProtocolsForDeletion(DeleteForm form) + { + List protocols = new ArrayList<>(); + for (long protocolId : form.getIds(false)) + { + ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); + if (protocol != null) + { + protocols.add(protocol); + } + } + return protocols; + } + + @RequiresPermission(DesignAssayPermission.class) + public class DeleteProtocolByRowIdsAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + // UNDONE: Need help topic on protocols + setHelpTopic("experiment"); + super.addNavTrail(root); + } + + @Override + public ModelAndView getView(DeleteForm form, boolean reshow, BindException errors) + { + List runs = ExperimentService.get().getExpRunsForProtocolIds(false, form.getIds(false)); + List protocols = getProtocolsForDeletion(form); + String noun = "Assay Design"; + List> deleteableDatasets = new ArrayList<>(); + List> noPermissionDatasets = new ArrayList<>(); + if (AssayService.get() != null && StudyService.get() != null) + { + for (ExpProtocol protocol : protocols) + { + if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) + throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); + + if (AssayService.get().getProvider(protocol) == null) + { + noun = "Protocol"; + } + for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(protocol.getRowId(), Dataset.PublishSource.Assay)) + { + Pair entry = new Pair<>(dataset, urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId())); + if (dataset.canDeleteDefinition(getUser())) + { + deleteableDatasets.add(entry); + } + else + { + noPermissionDatasets.add(entry); + } + } + } + } + + return new ConfirmDeleteView(noun, ProtocolDetailsAction.class, protocols, form, runs, "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); + } + + @Override + protected void deleteObjects(DeleteForm form) + { + for (ExpProtocol protocol : getProtocolsForDeletion(form)) + { + protocol.delete(getUser(), form.getUserComment()); + } + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetDataOperationConfirmationDataAction extends ReadOnlyApiAction + { + @Override + public void validateForm(DataOperationConfirmationForm form, Errors errors) + { + if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey"); + if (form.getDataOperation() == null) + errors.reject(ERROR_REQUIRED, "An operation type must be provided."); + } + + @Override + public Object execute(DataOperationConfirmationForm form, BindException errors) + { + Collection requestIds = form.getIds(false); + ExperimentServiceImpl service = ExperimentServiceImpl.get(); + List allData = service.getExpDatas(requestIds); + + Set notAllowedIds = new HashSet<>(); + if (form.getDataOperation() == ExpDataImpl.DataOperations.Delete) + service.getObjectReferencers().forEach(referencer -> + notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "exp.data"))); + + Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allData); + + Collection containers = new HashSet<>(); + Collection notPermittedIds = new ArrayList<>(); + Class permClass = form.getDataOperation().getPermissionClass(); + for (ExpDataImpl expData : allData) + { + Container c = expData.getContainer(); + if (c.hasPermission(getUser(), ReadPermission.class)) + containers.add(c); + if (permClass != null && !c.hasPermission(getUser(), permClass)) + notPermittedIds.add(expData.getRowId()); + } + + NameExpressionOptionService svc = NameExpressionOptionService.get(); + response.put("containers", containers.stream().map(c -> Map.of( + "id", c.getEntityId(), + "path", (Object) c.getPath(), + "permitted", permClass == null || c.hasPermission(getUser(), permClass), + "canEditName", svc.getAllowUserSpecificNamesValue(c) + )).toList()); + + response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); + + return success(response); + } + } + + + public static class DataOperationConfirmationForm extends DataViewSnapshotSelectionForm + { + private ExpDataImpl.DataOperations _dataOperation; + + public ExpDataImpl.DataOperations getDataOperation() + { + return _dataOperation; + } + + public void setDataOperation(ExpDataImpl.DataOperations dataOperation) + { + _dataOperation = dataOperation; + } + + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetMaterialOperationConfirmationDataAction extends ReadOnlyApiAction + { + @Override + public void validateForm(MaterialOperationConfirmationForm form, Errors errors) + { + if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); + if (form.getSampleOperation() == null) + errors.reject(ERROR_REQUIRED, "An operation type must be provided."); + } + + @Override + public Object execute(MaterialOperationConfirmationForm form, BindException errors) + { + Set requestIds = form.getIds(false); + ExperimentServiceImpl service = ExperimentServiceImpl.get(); + List allMaterials = service.getExpMaterials(requestIds); + + Set notAllowedIds = new HashSet<>(); + // We prevent deletion if a sample is used as a parent, has assay data, is used in a job, etc. + if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) + service.getObjectReferencers().forEach(referencer -> + notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "samples"))); + + if (SampleStatusService.get().supportsSampleStatus()) + notAllowedIds.addAll(service.findIdsNotPermittedForOperation(allMaterials, form.getSampleOperation())); + + Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allMaterials); + + Collection containers = new HashSet<>(); + Collection notPermittedIds = new ArrayList<>(); + Class permClass = form.getSampleOperation().getPermissionClass(); + for (ExpMaterial material : allMaterials) + { + Container c = material.getContainer(); + if (c.hasPermission(getUser(), ReadPermission.class)) + containers.add(c); + if (permClass != null && !c.hasPermission(getUser(), permClass)) + notPermittedIds.add(material.getRowId()); + } + + NameExpressionOptionService svc = NameExpressionOptionService.get(); + + response.put("containers", containers.stream().map(c -> Map.of( + "id", c.getEntityId(), + "path", (Object) c.getPath(), + "permitted", permClass == null || c.hasPermission(getUser(), permClass), + "canEditName", svc.getAllowUserSpecificNamesValue(c) + )).toList()); + + response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); + + if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) + // String 'associatedDatasets' must be synced to its handling in confirmDelete.js, confirmDelete() + response.put("associatedDatasets", ExperimentServiceImpl.includeLinkedToStudyText(allMaterials, requestIds, getUser(), getContainer())); + + return success(response); + } + } + + public static class MaterialOperationConfirmationForm extends DataViewSnapshotSelectionForm + { + private SampleTypeService.SampleOperations _sampleOperation; + + public SampleTypeService.SampleOperations getSampleOperation() + { + return _sampleOperation; + } + + public void setSampleOperation(SampleTypeService.SampleOperations sampleOperation) + { + _sampleOperation = sampleOperation; + } + } + + @RequiresPermission(DeletePermission.class) + public class DeleteSelectedDataAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + // UNDONE: Need help topic on Datas + setHelpTopic("experiment"); + super.addNavTrail(root); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) throws Exception + { + List datas = getDatas(deleteForm, false); + + for (ExpRun run : getRuns(datas)) + { + if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) + throw new UnauthorizedException(); + } + + // Issue 32076: Delete the exp.Data objects using QueryUpdateService so trigger scripts will be executed + Map, List> byDataClass = datas.stream().collect(Collectors.groupingBy(d -> Optional.ofNullable(d.getDataClass(null)))); + for (Optional opt : byDataClass.keySet()) + { + SchemaKey schemaKey; + String queryName; + ExpDataClass dc = opt.orElse(null); + List ds = byDataClass.get(opt); + if (dc == null) + { + // Reference to exp.Data table + schemaKey = ExpSchema.SCHEMA_EXP; + queryName = ExpSchema.TableType.Data.name(); + } + else + { + // Reference to exp.data. table + schemaKey = ExpSchema.SCHEMA_EXP_DATA; + queryName = dc.getName(); + } + + UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), schemaKey); + if (schema == null) + throw new IllegalStateException("Failed to get schema '" + schemaKey + "'"); + + TableInfo table = schema.getTable(queryName); + if (table == null) + throw new IllegalStateException("Failed to get table '" + queryName + "' in schema '" + schemaKey + "'"); + + QueryUpdateService qus = table.getUpdateService(); + if (qus == null) + throw new IllegalStateException(); + + qus.deleteRows(getUser(), getContainer(), toKeys(ds), null, null); + } + } + + protected List> toKeys(List datas) + { + return datas.stream().map(d -> CaseInsensitiveHashMap.of("rowId", d.getRowId())).collect(toList()); + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + if (errors.hasErrors()) + return new SimpleErrorView(errors, false); + + List datas = getDatas(deleteForm, false); + List runs = getRuns(datas); + + return new ConfirmDeleteView("Data", ShowDataAction.class, datas, deleteForm, runs); + } + + private List getRuns(List datas) + { + List runArray = ExperimentService.get().getRunsUsingDatas(datas); + return new ArrayList<>(ExperimentService.get().runsDeletedWithInput(runArray)); + } + + private List getDatas(DeleteForm deleteForm, boolean clear) + { + List datas = new ArrayList<>(); + for (long dataId : deleteForm.getIds(clear)) + { + ExpData data = ExperimentService.get().getExpData(dataId); + if (data != null) + { + datas.add(data); + } + } + return datas; + } + } + + @RequiresPermission(DeletePermission.class) + public class DeleteSelectedExperimentsAction extends AbstractDeleteAction + { + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + for (ExpExperiment exp : lookupExperiments(deleteForm)) + { + exp.delete(getUser()); + } + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List experiments = lookupExperiments(deleteForm); + + List runs = new ArrayList<>(); + boolean allBatches = true; + for (ExpExperiment experiment : experiments) + { + // Deleting a batch also deletes all of its runs + if (experiment.getBatchProtocol() != null) + { + runs.addAll(experiment.getRuns()); + } + else + { + allBatches = false; + } + } + + return new ConfirmDeleteView(allBatches ? "batch" : "run group", DetailsAction.class, experiments, deleteForm, runs); + } + + private List lookupExperiments(DeleteForm deleteForm) + { + List experiments = new ArrayList<>(); + for (long experimentId : deleteForm.getIds(false)) + { + ExpExperiment experiment = ExperimentService.get().getExpExperiment(experimentId); + if (experiment != null) + { + experiments.add(experiment); + } + } + return experiments; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + super.addNavTrail(root); + } + } + + @RequiresPermission(DesignSampleTypePermission.class) + public class DeleteSampleTypesAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + super.addNavTrail(root); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + List sampleTypes = getSampleTypes(deleteForm); + if (sampleTypes.isEmpty()) + { + throw new NotFoundException("No sample types found for ids provided."); + } + if (!ensureCorrectContainer(sampleTypes)) + { + throw new UnauthorizedException(); + } + + for (ExpRun run : getRuns(sampleTypes)) + { + if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new UnauthorizedException(); + } + } + + for (ExpSampleType source : sampleTypes) + { + Domain domain = source.getDomain(); + if (!domain.getDomainKind().canDeleteDefinition(getUser(), domain)) + { + throw new UnauthorizedException(); + } + + source.delete(getUser(), deleteForm.getUserComment()); + } + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List sampleTypes = getSampleTypes(deleteForm); + if (!ensureCorrectContainer(sampleTypes)) + { + throw new RedirectException(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer(), "To delete a sample type, you must be in its folder or project.")); + } + + List> deleteableDatasets = new ArrayList<>(); + List> noPermissionDatasets = new ArrayList<>(); + if (StudyService.get() != null && StudyPublishService.get() != null) + { + for (ExpSampleType sampleType: sampleTypes) + { + for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(sampleType.getRowId(), Dataset.PublishSource.SampleType)) + { + ActionURL datasetURL = StudyService.get().getDatasetURL(getContainer(), dataset.getDatasetId()); + Pair entry = new Pair<>(dataset, datasetURL); + if (dataset.canDeleteDefinition(getUser())) + { + deleteableDatasets.add(entry); + } + else + { + noPermissionDatasets.add(entry); + } + } + } + } + return new ConfirmDeleteView("Sample Type", ShowSampleTypeAction.class, sampleTypes, deleteForm, getRuns(sampleTypes), "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); + } + + private List getSampleTypes(DeleteForm deleteForm) + { + List sources = new ArrayList<>(); + for (long rowId : deleteForm.getIds(false)) + { + ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId); + if (sampleType != null) + { + sources.add(sampleType); + } + } + return sources; + } + + private boolean ensureCorrectContainer(List sampleTypes) + { + for (ExpSampleType source : sampleTypes) + { + Container sourceContainer = source.getContainer(); + if (!sourceContainer.equals(getContainer())) + { + return false; + } + } + return true; + } + + private List getRuns(List sampleTypes) + { + if (!sampleTypes.isEmpty()) + { + List runArray = ExperimentService.get().getRunsUsingSampleTypes(sampleTypes.toArray(new ExpSampleType[0])); + return ExperimentService.get().runsDeletedWithInput(runArray); + } + else + { + return Collections.emptyList(); + } + } + } + + private DataRegion getSampleTypeRegion(ViewContext model) + { + TableInfo tableInfo = ExperimentServiceImpl.get().getTinfoSampleType(); + + QuerySettings settings = new QuerySettings(model, "SampleType"); + settings.setSelectionKey(DataRegionSelection.getSelectionKey(tableInfo.getSchema().getName(), tableInfo.getName(), "SampleType", settings.getDataRegionName())); + + DataRegion dr = new DataRegion(); + dr.setSettings(settings); + dr.addColumns(tableInfo.getUserEditableColumns()); + dr.removeColumns("lastindexed"); + dr.getDisplayColumn(0).setVisible(false); + + dr.getDisplayColumn("idcol1").setVisible(false); + dr.getDisplayColumn("idcol2").setVisible(false); + dr.getDisplayColumn("idcol3").setVisible(false); + dr.getDisplayColumn("lsid").setVisible(false); + dr.getDisplayColumn("materiallsidprefix").setVisible(false); + dr.getDisplayColumn("parentcol").setVisible(false); + + ActionURL url = new ActionURL(ShowSampleTypeAction.class, model.getContainer()); + dr.getDisplayColumn(1).setURL(url.addParameter("rowId", "${RowId}")); + dr.setShowRecordSelectors(getContainer().hasOneOf(getUser(), DeletePermission.class, UpdatePermission.class)); + + return dr; + } + + @RequiresPermission(ReadPermission.class) + @ActionNames("getSampleType,getSampleTypeApi") // Referenced in labkey-ui-components components/samples/actions.ts TODO: migrate getSampleTypeApi -> getSampleType + public static class GetSampleTypeAction extends ReadOnlyApiAction + { + @Override + public void validateForm(SampleTypeForm form, Errors errors) + { + if (form.getRowId() == null && form.getLSID() == null) + errors.reject(ERROR_REQUIRED, "RowId or LSID must be provided"); + } + + @Override + public Object execute(SampleTypeForm form, BindException errors) throws Exception + { + ExpSampleTypeImpl st = form.getSampleType(getContainer()); + + return getSampleTypeResponse(st); + } + } + + @NotNull + private static ApiSimpleResponse getSampleTypeResponse(ExpSampleType st) throws IOException + { + Map sampleType = new HashMap<>(); + sampleType.put("name", st.getName()); + sampleType.put("nameExpression", st.getNameExpression()); + sampleType.put("labelColor", st.getLabelColor()); + sampleType.put("metricUnit", st.getMetricUnit()); + sampleType.put("description", st.getDescription()); + sampleType.put("importAliases", st.getImportAliasMap()); + sampleType.put("lsid", st.getLSID()); + sampleType.put("rowId", st.getRowId()); + sampleType.put("domainId", st.getDomain().getTypeId()); + sampleType.put("category", st.getCategory()); + + return new ApiSimpleResponse(Map.of("sampleSet", sampleType, "success", true)); + } + + public static class DataTypesWithRequiredLineageForm + { + private Integer _parentDataTypeRowId; + private boolean _sampleParent; + + public Integer getParentDataTypeRowId() + { + return _parentDataTypeRowId; + } + + public void setParentDataTypeRowId(Integer parentDataTypeRowId) + { + this._parentDataTypeRowId = parentDataTypeRowId; + } + + public boolean isSampleParent() + { + return _sampleParent; + } + + public void setSampleParent(boolean sampleParent) + { + _sampleParent = sampleParent; + } + } + + @RequiresPermission(ReadPermission.class) + public static class GetDataTypesWithRequiredLineageAction extends ReadOnlyApiAction + { + @Override + public void validateForm(DataTypesWithRequiredLineageForm form, Errors errors) + { + if (form.getParentDataTypeRowId() == null) + errors.reject(ERROR_REQUIRED, "ParentDataTypeRowId must be provided"); + } + + @Override + public Object execute(DataTypesWithRequiredLineageForm form, BindException errors) throws Exception + { + return getDataTypesWithRequiredLineageResponse(form.getParentDataTypeRowId(), form.isSampleParent(), getContainer(), getUser()); + } + } + @NotNull + private static ApiSimpleResponse getDataTypesWithRequiredLineageResponse(Integer parentDataType, boolean isSampleParent, Container container, User user) + { + Pair, Set> requiredLineages = ExperimentServiceImpl.get().getDataTypesWithRequiredLineage(parentDataType, isSampleParent, container, user); + return new ApiSimpleResponse(Map.of("sampleTypes", requiredLineages.first, "dataClasses", requiredLineages.second,"success", true)); + } + + @RequiresPermission(DesignSampleTypePermission.class) + public static class EditSampleTypeAction extends SimpleViewAction + { + private ExpSampleTypeImpl _sampleType; + + @Override + public ModelAndView getView(SampleTypeForm form, BindException errors) + { + boolean create = form.getLSID() == null && form.getRowId() == null; + if (!create) + _sampleType = form.getSampleType(getContainer()); + + return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("sampleTypeDesigner")); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + if (_sampleType == null) + { + root.addChild("Create Sample Type"); + } + else + { + root.addChild(_sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(_sampleType)); + root.addChild("Update Sample Type"); + } + } + } + + public static class SampleTypeForm extends ReturnUrlForm + { + private Integer rowId; + private String lsid; + + public Integer getRowId() + { + return rowId; + } + + public void setRowId(Integer rowId) + { + this.rowId = rowId; + } + + public String getLSID() + { + return this.lsid; + } + + public void setLSID(String lsid) + { + this.lsid = lsid; + } + + public ExpSampleTypeImpl getSampleType(Container container) throws NotFoundException + { + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getLSID()); + if (sampleType == null) + sampleType = SampleTypeServiceImpl.get().getSampleType(getRowId()); + + if (sampleType == null) + { + throw new NotFoundException("Sample type not found: " + (getLSID() != null ? getLSID() : getRowId())); + } + + if (!container.equals(sampleType.getContainer())) + { + throw new NotFoundException("Sample type is not defined in the given container."); + } + + return sampleType; + } + } + + @RequiresPermission(InsertPermission.class) + public static class ImportSamplesAction extends AbstractExpDataImportAction + { + ExpSampleTypeImpl _sampleType; + boolean _isCrossTypeImport = false; + + @Override + public void validateForm(QueryForm queryForm, Errors errors) + { + _form = queryForm; + _insertOption = queryForm.getInsertOption(); + _isCrossTypeImport = getOptionParamValue(Params.crossTypeImport); + _form.setSchemaName(getTargetSchemaName()); + if (_isCrossTypeImport) + { + _form.setQueryName(getPipelineTargetQueryName()); + } + super.validateForm(queryForm, errors); + if (queryForm.getQueryName() == null) + errors.reject(ERROR_REQUIRED, "Sample type name is required"); + else + { + if (!_isCrossTypeImport) + { + _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), queryForm.getQueryName()); + if (_sampleType == null) + { + errors.reject(ERROR_GENERIC, "Sample type '" + queryForm.getQueryName() + " not found."); + } + } + } + } + + private String getTargetSchemaName() + { + return getOptionParamValue(Params.crossTypeImport) ? ExpSchema.SCHEMA_NAME : "samples"; + } + + @Override + protected UserSchema getTargetSchema() + { + return getOptionParamValue(Params.crossTypeImport) ? QueryService.get().getUserSchema(getUser(), getContainer(), getTargetSchemaName()) : super.getTargetSchema(); + } + + @Override + protected String getPipelineTargetQueryName() + { + return getOptionParamValue(Params.crossTypeImport) ? "materials" : super.getPipelineTargetQueryName(); + } + + @Override + protected Map getRenamedColumns() + { + Map renamedColumns = super.getRenamedColumns(); + renamedColumns.putAll(SampleTypeUpdateServiceDI.SAMPLE_ALT_IMPORT_NAME_COLS); + return renamedColumns; + } + + @Override + protected @Nullable Set getLineageImportAliases() throws IOException + { + Set aliases = new CaseInsensitiveHashSet(); + // Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import + aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT); + aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL); + boolean crossTypeImport = getOptionParamValue(AbstractQueryImportAction.Params.crossTypeImport); + // Issue 51894: We need to stop conversion to numbers for alias fields for all type + // If there are aliases defined for one type that are number fields in another type, this will prevent + // conversion to numbers during the initial partitioning, but the conversion will happen when the partition + // file is loaded. + if (crossTypeImport) + { + List sampleTypes = SampleTypeServiceImpl.get().getSampleTypes(getContainer(), true); + for (ExpSampleTypeImpl sampleType : sampleTypes) + aliases.addAll(sampleType.getImportAliases().keySet()); + } + else + { + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), _form.getQueryName()); + aliases.addAll(sampleType.getImportAliases().keySet()); + } + return aliases; + } + + @Override + protected int importData( + DataLoader dl, + FileStream file, + String originalName, + BatchValidationException errors, + @Nullable AuditBehaviorType auditBehaviorType, + TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, + @Nullable String auditUserComment + ) throws IOException + { + initContext(dl, errors, auditBehaviorType, auditUserComment); + + TableInfo tInfo = _target; + QueryUpdateService updateService = _updateService; + if (getOptionParamValue(Params.crossTypeImport)) + { + tInfo = ExperimentService.get().createMaterialTable(new SamplesSchema(getUser(), getContainer()), ContainerFilter.current(this), null); + updateService = tInfo.getUpdateService(); + } + + int count = importData(dl, tInfo, updateService, _context, auditEvent, getUser(), getContainer()); + + if (getOptionParamValue(Params.crossTypeImport)) + { + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeImport"); + if (_context.getInsertOption() == QueryUpdateService.InsertOption.UPDATE) + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeUpdate"); + else if (_context.getInsertOption() == QueryUpdateService.InsertOption.MERGE) + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeMerge"); + } + + return count; + } + + @Override + public ModelAndView getView(QueryForm form, BindException errors) throws Exception + { + initRequest(form); + setHelpTopic("importSampleSets"); // page-wide help topic + setImportHelpTopic("importSampleSets"); // importOptions help topic + setTypeName("samples"); + return getDefaultImportView(form, errors); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ActionURL url = _form.urlFor(QueryAction.executeQuery); + if (_form.getQueryName() != null && url != null) + root.addChild(_form.getQueryName(), url); + root.addChild("Import Data"); + } + + @Override + protected JSONObject createSuccessResponse(int rowCount) + { + JSONObject json = super.createSuccessResponse(rowCount); + if (!_context.getResponseInfo().isEmpty()) + { + for (String key : _context.getResponseInfo().keySet()) + json.put(key, _context.getResponseInfo().get(key)); + } + return json; + } + + } + + public abstract static class AbstractExpDataImportAction extends AbstractQueryImportAction + { + protected QueryForm _form; + protected DataIteratorContext _context; + + @Override + public void validateForm(QueryForm form, Errors errors) + { + QueryDefinition query = form.getQueryDef(); + if (query.getContainerFilter() != null && query.getContainerFilter().getType() != null) + { + // cross folder import not supported + if (query.getContainerFilter().getType() != ContainerFilter.Type.Current) + errors.reject(ERROR_GENERIC, "ContainerFilter is not supported for import actions."); + } + } + + @Override + protected void initRequest(QueryForm form) throws ServletException + { + QueryDefinition query = form.getQueryDef(); + setContainerFilterForImport(query, getContainer(), getUser()); + List qpe = new ArrayList<>(); + TableInfo t = query.getTable(form.getSchema(), qpe, true); + + if (!qpe.isEmpty()) + throw qpe.get(0); + if (!getOptionParamValue(Params.crossTypeImport) && null != t) + { + setTarget(t); + setShowMergeOption(t.supportsInsertOption(QueryUpdateService.InsertOption.MERGE)); + setShowUpdateOption(t.supportsInsertOption(QueryUpdateService.InsertOption.UPDATE)); + } + + _auditBehaviorType = form.getAuditBehavior(); + _auditUserComment = form.getAuditUserComment(); + } + + @Override + protected Map getRenamedColumns() + { + final String renameParamPrefix = "importAlias."; + Map renameColumns = new CaseInsensitiveHashMap<>(); + PropertyValue[] pvs = _form.getInitParameters().getPropertyValues(); + for (PropertyValue pv : pvs) + { + String paramName = pv.getName(); + if (!paramName.startsWith(renameParamPrefix) || pv.getValue() == null) + continue; + + renameColumns.put(paramName.substring(renameParamPrefix.length()), (String) pv.getValue()); + } + return renameColumns; + } + + @Override + protected Set getLineageImportAliases() throws IOException + { + ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), _form.getQueryName()); + return new CaseInsensitiveHashSet(dataClass.getImportAliases().keySet()); + } + + protected void initContext(DataLoader dl, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, @Nullable String auditUserComment) + { + _context = createDataIteratorContext(_insertOption, getOptionParamsMap(), getLookupResolutionType(), auditBehaviorType, auditUserComment, errors, null, getContainer()); + + if (_context.isCrossFolderImport() && !getContainer().hasProductFolders()) + _context.setCrossFolderImport(false); + } + + @Override + protected int importData(DataLoader dl, FileStream file, String originalName, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, @Nullable String auditUserComment) throws IOException + { + initContext(dl, errors, auditBehaviorType, auditUserComment); + return importData(dl, _target, _updateService, _context, auditEvent, getUser(), getContainer()); + } + + @Override + protected String getQueryImportProviderName() + { + PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_PROVIDER_PARAM); + return pv == null ? null : (String) pv.getValue(); + } + + @Override + protected String getQueryImportDescription() + { + PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM); + return pv == null ? null : (String) pv.getValue(); + } + + @Override + protected String getQueryImportJobNotificationProviderName() + { + PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM); + return pv == null ? null : (String) pv.getValue(); + } + + @Override + protected boolean isBackgroundImportSupported() + { + return true; + } + + @Override + protected boolean allowLineageColumns() + { + return true; + } + + } + + @RequiresPermission(InsertPermission.class) + public static class ImportDataAction extends AbstractExpDataImportAction + { + @Override + public void validateForm(QueryForm queryForm, Errors errors) + { + _form = queryForm; + _form.setSchemaName("exp.data"); + _insertOption = queryForm.getInsertOption(); + super.validateForm(queryForm, errors); + if (queryForm.getQueryName() == null) + errors.reject(ERROR_REQUIRED, "Data class name is required"); + else + { + ExpDataClass dataClass = ExperimentService.get().getDataClass(getContainer(), getUser(), queryForm.getQueryName()); + if (dataClass == null) + { + errors.reject(ERROR_GENERIC, "Data class '" + queryForm.getQueryName() + " not found."); + } + } + } + + @Override + public ModelAndView getView(QueryForm form, BindException errors) throws Exception + { + initRequest(form); + setHelpTopic("dataClass"); // page wide help topic + setImportHelpTopic("dataClass#ui"); // importOptions help topic + setTypeName("data"); + return getDefaultImportView(form, errors); + } + + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + ActionURL url = _form.urlFor(QueryAction.executeQuery); + if (_form.getQueryName() != null && url != null) + root.addChild(_form.getQueryName(), url); + root.addChild("Import Data"); + } + + } + + @RequiresPermission(UpdatePermission.class) + public class ShowUpdateAction extends SimpleViewAction + { + @Override + public ModelAndView getView(ExperimentForm form, BindException errors) + { + form.refreshFromDb(); + Experiment exp = form.getBean(); + if (exp == null) + { + throw new NotFoundException(); + } + ensureCorrectContainer(getContainer(), ExperimentService.get().getExpExperiment(exp.getRowId()), getViewContext()); + + return new ExperimentUpdateView(new DataRegion(), form, errors); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + addRootNavTrail(root); + root.addChild("Update Run Group"); + } + } + + @RequiresPermission(UpdatePermission.class) + public static class UpdateAction extends FormHandlerAction + { + private Experiment _exp; + + @Override + public void validateCommand(ExperimentForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ExperimentForm form, BindException errors) throws Exception + { + form.doUpdate(); + form.refreshFromDb(); + _exp = form.getBean(); + return true; + } + + @Override + public ActionURL getSuccessURL(ExperimentForm experimentForm) + { + return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), ExperimentService.get().getExpExperiment(_exp.getRowId())); + } + } + + public static class ExportBean + { + private final LSIDRelativizer _selectedRelativizer; + private final XarExportType _selectedExportType; + private final String _fileName; + private final String _dataRegionSelectionKey; + private final String _error; + private final Long _expRowId; + private final Long _protocolId; + private final ActionURL _postURL; + private final Set _roles; + + public ExportBean(LSIDRelativizer selectedRelativizer, XarExportType selectedExportType, String fileName, ExportOptionsForm form, Set roles, ActionURL postURL) + { + _selectedRelativizer = selectedRelativizer; + _selectedExportType = selectedExportType; + _fileName = fileName; + _dataRegionSelectionKey = form.getDataRegionSelectionKey(); + _error = form.getError(); + _expRowId = form.getExpRowId(); + _postURL = postURL; + _roles = roles; + _protocolId = form.getProtocolId(); + } + + public LSIDRelativizer getSelectedRelativizer() + { + return _selectedRelativizer; + } + + public XarExportType getSelectedExportType() + { + return _selectedExportType; + } + + public String getError() + { + return _error; + } + + public String getFileName() + { + return _fileName; + } + + public Set getRoles() + { + return _roles; + } + + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + public ActionURL getPostURL() + { + return _postURL; + } + + public Long getProtocolId() + { + return _protocolId; + } + + public Long getExpRowId() + { + return _expRowId; + } + } + + + private String fixupExportName(String runName) + { + runName = runName.replace('/', '-'); + runName = runName.replace('\\', '-'); + return runName; + } + + public static class ExportOptionsForm extends ExperimentRunListForm + { + private String _error; + private XarExportType _exportType; + private LSIDRelativizer _lsidOutputType; + private String _xarFileName; + private String _zipFileName; + private String _fileExportType; + private Long _protocolId; + private Integer _sampleTypeId; + private long[] _dataIds; + private String[] _roles = new String[0]; + + public String getError() + { + return _error; + } + + public void setError(String error) + { + _error = error; + } + + public XarExportType getExportType() + { + return _exportType; + } + + public LSIDRelativizer getLsidOutputType() + { + return _lsidOutputType; + } + + public String getFileExportType() + { + return _fileExportType; + } + + public void setFileExportType(String fileExportType) + { + _fileExportType = fileExportType; + } + + public String getXarFileName() + { + return _xarFileName; + } + + public void setXarFileName(String xarFileName) + { + _xarFileName = xarFileName; + } + + public String getZipFileName() + { + return _zipFileName; + } + + public void setZipFileName(String zipFileName) + { + _zipFileName = zipFileName; + } + + public void setExportType(XarExportType exportType) + { + _exportType = exportType; + } + + public void setLsidOutputType(LSIDRelativizer lsidOutputType) + { + _lsidOutputType = lsidOutputType; + } + + public Long getProtocolId() + { + return _protocolId; + } + + public void setProtocolId(Long protocolId) + { + _protocolId = protocolId; + } + + public String[] getRoles() + { + return _roles; + } + + public void setRoles(String[] roles) + { + _roles = roles; + } + + public Integer getSampleTypeId() + { + return _sampleTypeId; + } + + public void setSampleTypeId(Integer sampleTypeId) + { + _sampleTypeId = sampleTypeId; + } + + public long[] getDataIds() + { + return _dataIds; + } + + public void setDataIds(long[] dataIds) + { + _dataIds = dataIds; + } + + public List lookupProtocols(ViewContext context, boolean clearSelection) + { + List protocols = new ArrayList<>(); + + if (_protocolId != null) + { + ExpProtocol protocol = ExperimentService.get().getExpProtocol(_protocolId.intValue()); + if (protocol == null || !protocol.getContainer().equals(context.getContainer())) + { + throw new NotFoundException(); + } + protocols.add(protocol); + return protocols; + } + + for (Long protocolId : DataRegionSelection.getSelectedIntegers(context, clearSelection)) + { + try + { + ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); + if (protocol == null || !protocol.getContainer().equals(context.getContainer())) + { + throw new NotFoundException(); + } + protocols.add(protocol); + } + catch (NumberFormatException e) + { + throw new NotFoundException("Invalid protocol id: " + protocolId); + } + } + if (protocols.isEmpty()) + { + throw new NotFoundException("No protocols selected"); + } + return protocols; + } + } + + private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable String fileName) + throws ExperimentException, IOException, PipelineValidationException + { + return exportXAR(selection, null, null, fileName); + } + + private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable LSIDRelativizer lsidRelativizer, @Nullable XarExportType exportType, @Nullable String fileName) + throws ExperimentException, IOException, PipelineValidationException + { + if (lsidRelativizer == null) + lsidRelativizer = LSIDRelativizer.FOLDER_RELATIVE; + + if (exportType == null) + exportType = XarExportType.BROWSER_DOWNLOAD; + + if (fileName == null || fileName.isEmpty()) + fileName = "export.xar"; + + fileName = fixupExportName(fileName); + String xarXmlFileName = null; + if (Strings.CI.endsWith(fileName, ".xar")) + xarXmlFileName = fileName + ".xml"; + + switch (exportType) + { + case BROWSER_DOWNLOAD: + XarExporter exporter = new XarExporter(lsidRelativizer, selection, getUser(), xarXmlFileName, null, getContainer()); + + getViewContext().getResponse().setContentType("application/zip"); + ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, fileName); + ResponseHelper.setPrivate(getViewContext().getResponse()); + + exporter.writeAsArchive(getViewContext().getResponse().getOutputStream()); + return null; + case PIPELINE_FILE: + if (!PipelineService.get().hasValidPipelineRoot(getContainer())) + { + throw new IllegalStateException("You must set a valid pipeline root before you can export a XAR to it."); + } + PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); + XarExportPipelineJob job = new XarExportPipelineJob(getViewBackgroundInfo(), pipeRoot, fileName, lsidRelativizer, selection, xarXmlFileName); + PipelineService.get().queueJob(job); + PipelineStatusFile status = PipelineService.get().getStatusFile(job.getJobGUID()); + return PageFlowUtil.urlProvider(PipelineUrls.class).statusDetails(getContainer(), status.getRowId()); + default: + throw new IllegalArgumentException("Unknown export type: " + exportType); + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportProtocolsAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + List protocols = form.lookupProtocols(getViewContext(), false); + + long[] ids = new long[protocols.size()]; + for (int i = 0; i < ids.length; i++) + { + ids[i] = protocols.get(i).getRowId(); + } + XarExportSelection selection = new XarExportSelection(); + selection.addProtocolIds(ids); + + exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); + + if (form.getDataRegionSelectionKey() != null) + { + // Clear the selection + form.lookupProtocols(getViewContext(), true); + } + return true; + } + } + + public abstract static class AbstractExportAction extends FormViewAction + { + protected ActionURL _resultURL; + + @Override + public void validateCommand(ExportOptionsForm target, Errors errors) + { + } + + @Override + public ActionURL getSuccessURL(ExportOptionsForm exportOptionsForm) + { + return _resultURL; + } + + @Override + public ModelAndView getSuccessView(ExportOptionsForm exportOptionsForm) + { + return null; + } + + @Override + public ModelAndView getView(ExportOptionsForm form, boolean reshow, BindException errors) throws Exception + { + // FormViewAction can reinvoke getView() in response to a POST if we're not redirecting the browser, + // so avoid double-creating the export + if ("get".equalsIgnoreCase(getViewContext().getRequest().getMethod())) + handlePost(form, errors); + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + } + + public List lookupRuns(ExportOptionsForm form) + { + Set runIds; + if (form.getRunIds() != null && form.getRunIds().length > 0) + runIds = new HashSet<>(Arrays.asList(form.getRunIds())); + else + runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); + + if (runIds.isEmpty()) + { + throw new NotFoundException(); + } + List result = new ArrayList<>(); + + for (long id : runIds) + { + ExpRun run = ExperimentService.get().getExpRun(id); + if (run == null || !run.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new NotFoundException("Could not find run " + id); + } + result.add(run); + } + return result; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportRunsAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + XarExportSelection selection = new XarExportSelection(); + if (form.getExpRowId() != null) + { + ExpExperiment experiment = ExperimentService.get().getExpExperiment(form.getExpRowId()); + if (experiment != null && !experiment.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new NotFoundException("Run group " + form.getExpRowId()); + } + selection.addExperimentIds(experiment.getRowId()); + } + selection.addRuns(lookupRuns(form)); + + _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + return true; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportSampleTypeAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + Integer rowId = form.getSampleTypeId(); + if (rowId == null) + { + throw new NotFoundException("No sampleTypeId parameter specified"); + } + ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId.intValue()); + if (sampleType == null) + { + throw new NotFoundException("No such sample type with RowId " + rowId); + } + if (!sampleType.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new UnauthorizedException(); + } + + XarExportSelection selection = new XarExportSelection(); + selection.addSampleType(sampleType); + + _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), FileUtil.makeLegalName(sampleType.getName() + ".xar")); + return true; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportRunFilesAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + XarExportSelection selection = new XarExportSelection(); + selection.setIncludeXarXml(false); + if ("role".equalsIgnoreCase(form.getFileExportType())) + { + selection.addRoles(form.getRoles()); + } + selection.addRuns(lookupRuns(form)); + + _resultURL = exportXAR(selection, form.getZipFileName()); + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + return true; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportFilesAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + long[] dataIds = form.getDataIds(); + if (dataIds == null || dataIds.length == 0) + { + throw new NotFoundException(); + } + + try + { + for (long id : dataIds) + { + ExpData data = ExperimentService.get().getExpData(id); + if (data == null || !data.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new NotFoundException("Could not find file " + id); + } + } + + XarExportSelection selection = new XarExportSelection(); + selection.setIncludeXarXml(false); + selection.addDataIds(dataIds); + + _resultURL = exportXAR(selection, form.getZipFileName()); + return true; + } + catch (NumberFormatException e) + { + throw new NotFoundException(Arrays.toString(dataIds)); + } + } + } + + public static class ExperimentRunListForm implements DataRegionSelection.DataSelectionKeyForm + { + private String _dataRegionSelectionKey; + private Long _expRowId; + private Long[] _runIds; + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String key) + { + _dataRegionSelectionKey = key; + } + + public Long getExpRowId() + { + return _expRowId; + } + + public void setExpRowId(Long expRowId) + { + _expRowId = expRowId; + } + + public Long[] getRunIds() + { + return _runIds; + } + + public void setRunIds(Long[] runIds) + { + _runIds = runIds; + } + + public ExpExperiment lookupExperiment() + { + return getExpRowId() == null ? null : ExperimentService.get().getExpExperiment(getExpRowId().intValue()); + } + } + + private void addSelectedRunsToExperiment(ExpExperiment exp, String dataRegionSelectionKey) + { + Collection runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), dataRegionSelectionKey, true); + List runs = new ArrayList<>(); + for (long runId : runIds) + { + ExpRun run = ExperimentServiceImpl.get().getExpRun(runId); + if (run != null) + { + runs.add(run); + } + } + exp.addRuns(getUser(), runs.toArray(new ExpRun[0])); + } + + + @RequiresPermission(InsertPermission.class) + public class AddRunsToExperimentAction extends FormHandlerAction + { + @Override + public void validateCommand(ExperimentRunListForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ExperimentRunListForm form, BindException errors) + { + addSelectedRunsToExperiment(form.lookupExperiment(), form.getDataRegionSelectionKey()); + return true; + } + + @Override + public ActionURL getSuccessURL(ExperimentRunListForm form) + { + return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); + } + } + + @RequiresPermission(DeletePermission.class) + public static class RemoveSelectedExpRunsAction extends FormHandlerAction + { + @Override + public void validateCommand(ExperimentRunListForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ExperimentRunListForm form, BindException errors) + { + ExpExperiment exp = form.lookupExperiment(); + if (exp == null || !exp.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new NotFoundException("Could not find run group with RowId " + form.getExpRowId()); + } + + for (long runId : DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false)) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run == null || !run.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new NotFoundException("Could not find run with RowId " + runId); + } + exp.removeRun(getUser(), run); + } + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + return true; + } + + @Override + public ActionURL getSuccessURL(ExperimentRunListForm form) + { + return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); + } + } + + public static ActionURL getResolveLsidURL(Container c, @NotNull String type, @NotNull String lsid) + { + ActionURL url = new ActionURL(ResolveLSIDAction.class, c); + url.addParameter("type", type); + url.addParameter("lsid", lsid); + + return url; + } + + + @RequiresPermission(ReadPermission.class) + public static class ResolveLSIDAction extends SimpleViewAction + { + @Override + public ModelAndView getView(LsidForm form, BindException errors) + { + String message = ""; + if (!PageFlowUtil.empty(form.getLsid())) + { + try + { + String lsid = Lsid.canonical(form.getLsid().trim()); + ActionURL url = LsidManager.get().getDisplayURL(lsid); + if (url == null && form.getType() != null) + { + url = switch (form.getType().toLowerCase()) + { + case "data" -> LsidType.Data.getDisplayURL(new Lsid(lsid)); + case "material" -> LsidType.Material.getDisplayURL(new Lsid(lsid)); + default -> url; + }; + } + if (null != url) + { + throw new RedirectException(url); + } + message = "Could not map LSID to URL"; + } + catch (IllegalArgumentException e) + { + message = "Invalid LSID"; + } + } + + return new HtmlView("Enter LSID", + DOM.createHtmlFragment( + message, + DOM.FORM(at(action, getViewContext().cloneActionURL().setAction(ResolveLSIDAction.class)), + "LSID: ", + DOM.INPUT(at(type, "text", name, "lsid", size, "80", value, form.getLsid())), + PageFlowUtil.button("Go").submit(true)))); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Resolve LSID"); + } + } + + public static class LsidForm + { + private String _lsid; + + public String getType() + { + return _type; + } + + public void setType(String type) + { + _type = type; + } + + private String _type; + + public void setLsid(String lsid) + { + _lsid = lsid; + } + + public String getLsid() + { + return _lsid; + } + } + + public static class SetFlagForm extends LsidForm + { + private String _comment; + private boolean _redirect = true; + + public String getComment() + { + return _comment; + } + + public void setComment(String comment) + { + _comment = comment; + } + + public boolean isRedirect() + { + return _redirect; + } + + public void setRedirect(boolean redirect) + { + _redirect = redirect; + } + } + + /** + * Check for update on the object itself + */ + @RequiresNoPermission + public static class SetFlagAction extends FormHandlerAction + { + @Override + public void validateCommand(SetFlagForm target, Errors errors) + { + } + + @Override + public boolean handlePost(SetFlagForm form, BindException errors) throws Exception + { + String lsid = form.getLsid(); + if (lsid == null) + throw new NotFoundException(); + ExpObject obj = ExperimentService.get().findObjectFromLSID(lsid); + if (obj == null) + throw new NotFoundException(); + Container container = obj.getContainer(); + if (!container.hasPermission(getUser(), UpdatePermission.class)) + { + throw new UnauthorizedException(); + } + + obj.setComment(getUser(), form.getComment()); + return true; + } + + @Override + public URLHelper getSuccessURL(SetFlagForm form) + { + return null; + } + } + + @RequiresPermission(InsertPermission.class) + public class DeriveSamplesChooseTargetAction extends SimpleViewAction + { + private List _materials; + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; + if (sampleType != null) + { + root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); + } + root.addChild("Derive Samples"); + } + + @Override + public void validate(DeriveMaterialForm form, BindException errors) + { + _materials = form.lookupMaterials(); + if (_materials.isEmpty()) + { + throw new NotFoundException("Could not find any matching materials"); + } + } + + @Override + public ModelAndView getView(DeriveMaterialForm form, BindException errors) + { + Container c = getContainer(); + PipeRoot root = PipelineService.get().findPipelineRoot(c); + + if (root == null || !root.isValid()) + { + ActionURL pipelineURL = urlProvider(PipelineUrls.class).urlSetup(c); + return new HtmlView(DIV("You must ", + DOM.A(DOM.at(href, pipelineURL), "configure a valid pipeline root for this folder"), + " before deriving samples.")); + } + else + { + Set materialInputRoles = new TreeSet<>(ExperimentService.get().getMaterialInputRoles(getContainer(), getUser())); + Map materialsWithRoles = new LinkedHashMap<>(); + for (ExpMaterial material : _materials) + { + materialsWithRoles.put(material, null); + } + + List sampleTypes = getUploadableSampleTypes(); + + DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), sampleTypes, materialsWithRoles, form.getOutputCount(), materialInputRoles, null); + return new JspView<>("/org/labkey/experiment/deriveSamplesChooseTarget.jsp", bean); + } + } + } + + public static class DeriveSamplesChooseTargetBean implements DataRegionSelection.DataSelectionKeyForm + { + private String _dataRegionSelectionKey; + + private final Integer _targetSampleTypeId; + private final List _sampleTypes; + private final Map _sourceMaterials; + private final int _sampleCount; + private final Collection _inputRoles; + private final DerivedSamplePropertyHelper _propertyHelper; + + public static final String CUSTOM_ROLE = "--CUSTOM--"; + + public DeriveSamplesChooseTargetBean(String dataRegionSelectionKey, Integer targetSampleTypeId, List sampleTypes, Map sourceMaterials, int sampleCount, Collection inputRoles, DerivedSamplePropertyHelper helper) + { + _dataRegionSelectionKey = dataRegionSelectionKey; + _targetSampleTypeId = targetSampleTypeId; + _sampleTypes = sampleTypes; + _sourceMaterials = sourceMaterials; + _sampleCount = sampleCount; + _inputRoles = inputRoles; + _propertyHelper = helper; + } + + public Integer getTargetSampleTypeId() + { + return _targetSampleTypeId; + } + + public DerivedSamplePropertyHelper getPropertyHelper() + { + return _propertyHelper; + } + + public int getSampleCount() + { + return _sampleCount; + } + + public Map getSourceMaterials() + { + return _sourceMaterials; + } + + public List getSampleTypes() + { + return _sampleTypes; + } + + public Collection getInputRoles() + { + return _inputRoles; + } + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String key) + { + _dataRegionSelectionKey = key; + } + } + + private List getUploadableSampleTypes() + { + // Make a copy so we can modify it + List sampleTypes = new ArrayList<>(SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true)); + sampleTypes.removeIf(sampleType -> !sampleType.canImportMoreSamples()); + return sampleTypes; + } + + @RequiresPermission(InsertPermission.class) + public class DeriveSamplesAction extends FormViewAction + { + private List _materials; + private ActionURL _successUrl; + private final Map _inputMaterials = new LinkedHashMap<>(); + + @Override + public ModelAndView getView(DeriveMaterialForm form, boolean reshow, BindException errors) + { + _materials = form.lookupMaterials(); + if (_materials.isEmpty()) + { + throw new NotFoundException("Could not find any matching materials"); + } + + Container c = getContainer(); + + if (form.getOutputCount() <= 0) + { + form.setOutputCount(1); + } + + if (form.getTargetSampleTypeId() == 0) + throw new NotFoundException("Target sample type required for the derived samples"); + + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); + if (sampleType == null) + throw new NotFoundException("Could not find sample type with rowId " + form.getTargetSampleTypeId()); + + InsertView insertView = new InsertView(new DataRegion(), errors); + + DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), c, getUser()); + helper.addSampleColumns(insertView, getUser()); + + int[] rowIds = form.getRowIds(); + for (int i = 0; i < rowIds.length; i++) + { + insertView.getDataRegion().addHiddenFormField("rowIds", Integer.toString(rowIds[i])); + insertView.getDataRegion().addHiddenFormField("inputRole" + i, form.getInputRole(i) == null ? "" : form.getInputRole(i)); + insertView.getDataRegion().addHiddenFormField("customRole" + i, form.getCustomRole(i) == null ? "" : form.getCustomRole(i)); + } + + insertView.getDataRegion().addHiddenFormField("targetSampleTypeId", Integer.toString(form.getTargetSampleTypeId())); + insertView.getDataRegion().addHiddenFormField("outputCount", Integer.toString(form.getOutputCount())); + if (form.getDataRegionSelectionKey() != null) + insertView.getDataRegion().addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, form.getDataRegionSelectionKey()); + insertView.setInitialValues(ViewServlet.adaptParameterMap(getViewContext().getRequest().getParameterMap())); + ButtonBar bar = new ButtonBar(); + bar.setStyle(ButtonBar.Style.separateButtons); + ActionButton submitButton = new ActionButton(DeriveSamplesAction.class, "Submit"); + submitButton.setActionType(ActionButton.Action.POST); + bar.add(submitButton); + insertView.getDataRegion().setButtonBar(bar); + insertView.setTitle("Output Samples"); + + Map materialsWithRoles = new LinkedHashMap<>(); + List materials = form.lookupMaterials(); + for (int i = 0; i < materials.size(); i++) + { + materialsWithRoles.put(materials.get(i), form.determineLabel(i)); + } + + DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), getUploadableSampleTypes(), materialsWithRoles, form.getOutputCount(), Collections.emptyList(), helper); + JspView view = new JspView<>("/org/labkey/experiment/summarizeMaterialInputs.jsp", bean); + view.setTitle("Input Samples"); + + return new VBox(view, insertView); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; + if (sampleType != null) + { + root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); + } + root.addChild("Derive Samples"); + } + + @Override + public void validateCommand(DeriveMaterialForm form, Errors errors) + { + List materials = form.lookupMaterials(); + + List lockedSamples = new ArrayList<>(); + for (int i = 0; i < materials.size(); i++) + { + ExpMaterial m = materials.get(i); + if (!m.isOperationPermitted(SampleTypeService.SampleOperations.EditLineage)) + { + lockedSamples.add(m); + } + String inputRole = form.determineLabel(i); + if (inputRole == null || inputRole.isEmpty()) + { + ExpSampleType st = m.getSampleType(); + inputRole = st != null ? st.getName() : ExpMaterialRunInput.DEFAULT_ROLE; + } + _inputMaterials.put(materials.get(i), inputRole); + } + + if (!lockedSamples.isEmpty()) + { + errors.reject(ERROR_MSG, SampleTypeService.get().getOperationNotPermittedMessage(lockedSamples, SampleTypeService.SampleOperations.EditLineage)); + } + } + + @Override + public boolean handlePost(DeriveMaterialForm form, BindException errors) + { + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); + + DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), getContainer(), getUser()); + + Map, Map> allProperties; + try + { + boolean valid = true; + for (Map.Entry> entry : helper.getPostedPropertyValues(getViewContext().getRequest()).entrySet()) + valid = UploadWizardAction.validatePostedProperties(getViewContext(), entry.getValue(), errors) && valid; + if (!valid) + return false; + + allProperties = helper.getSampleProperties(getViewContext().getRequest(), _inputMaterials.keySet()); + } + catch (DuplicateMaterialException e) + { + errors.addError(new ObjectError(e.getColName(), null, null, e.getMessage())); + return false; + } + catch (ExperimentException e) + { + errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); + return false; + } + + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + Map outputMaterials = new HashMap<>(); + int i = 0; + for (Map.Entry, Map> entry : allProperties.entrySet()) + { + Lsid lsid = entry.getKey().first; + String name = entry.getKey().second; + assert name != null; + + ExpMaterialImpl outputMaterial = ExperimentServiceImpl.get().createExpMaterial(getContainer(), lsid.toString(), name); + if (sampleType != null) + { + outputMaterial.setCpasType(sampleType.getLSID()); + } + outputMaterial.save(getUser()); + + if (sampleType != null) + { + Map pvs = new HashMap<>(); + for (Map.Entry propertyEntry : entry.getValue().entrySet()) + pvs.put(propertyEntry.getKey().getName(), propertyEntry.getValue()); + outputMaterial.setProperties(getUser(), pvs, false); + } + + outputMaterials.put(outputMaterial, helper.getSampleNames().get(i++)); + } + + ExperimentService.get().deriveSamples(_inputMaterials, outputMaterials, getViewBackgroundInfo(), _log); + + tx.commit(); + + // automatically link samples to study, if configured + StudyPublishService.get().autoLinkDerivedSamples(sampleType, outputMaterials.keySet().stream().map(ExpObject::getRowId).collect(toList()), getContainer(), getUser()); + + _successUrl = ExperimentUrlsImpl.get().getShowSampleURL(getContainer(), outputMaterials.keySet().iterator().next()); + + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + } + catch (Exception e) + { + errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); + return false; + } + + return true; + } + + @Override + public URLHelper getSuccessURL(DeriveMaterialForm deriveMaterialForm) + { + return _successUrl; + } + } + + public static class DeriveMaterialForm implements HasViewContext, DataRegionSelection.DataSelectionKeyForm + { + private String _dataRegionSelectionKey; + private int _outputCount = 1; + private int _targetSampleTypeId; + private int[] _rowIds; + private String _name; + + private ViewContext _context; + + @Override + public void setViewContext(ViewContext context) + { + _context = context; + } + + @Override + public ViewContext getViewContext() + { + return _context; + } + + public List lookupMaterials() + { + List result = new ArrayList<>(); + for (int rowId : getRowIds()) + { + ExpMaterial material = ExperimentService.get().getExpMaterial(rowId); + if (material != null) + { + if (material.getContainer().hasPermission(_context.getUser(), ReadPermission.class)) + { + result.add(material); + } + else + { + throw new UnauthorizedException(); + } + } + else + { + throw new NotFoundException("No material with RowId " + rowId); + } + } + result.sort(Comparator.comparing(Identifiable::getName)); + return result; + } + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String dataRegionSelectionKey) + { + _dataRegionSelectionKey = dataRegionSelectionKey; + } + + public int[] getRowIds() + { + if (_rowIds == null) + { + _rowIds = PageFlowUtil.toInts(DataRegionSelection.getSelected(getViewContext(), getDataRegionSelectionKey(), false)); + } + return _rowIds; + } + + public void setRowIds(int[] rowIds) + { + _rowIds = rowIds; + } + + public int getOutputCount() + { + return _outputCount; + } + + public void setOutputCount(int outputCount) + { + _outputCount = outputCount; + } + + public int getTargetSampleTypeId() + { + return _targetSampleTypeId; + } + + public void setTargetSampleTypeId(int targetSampleTypeId) + { + _targetSampleTypeId = targetSampleTypeId; + } + + public String getInputRole(int i) + { + return _context.getRequest().getParameter("inputRole" + i); + } + + public String getCustomRole(int i) + { + return _context.getRequest().getParameter("customRole" + i); + } + + public String determineLabel(int index) + { + String result = getInputRole(index); + if (DeriveSamplesChooseTargetBean.CUSTOM_ROLE.equals(result)) + { + result = getCustomRole(index); + } + if (result != null) + { + result = result.trim(); + } + return result; + } + } + + + public static class ExpInput + { + public String role; + public int rowId; + public Lsid lsid; + } + + public static class DerivationSpec + { + public String role; + public Map values; + } + + public static class DerivationForm + { + public List dataInputs; + public List materialInputs; + + public int dataOutputCount; + public Lsid targetDataClass; + public Map dataDefault; + public List dataOutputs; + + public int materialOutputCount; + public Lsid targetSampleType; + public Map materialDefault; + public List materialOutputs; + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(InsertPermission.class) + public static class DeriveAction extends MutatingApiAction + { + @Override + public void validateForm(DerivationForm form, Errors errors) + { + if (errors.hasErrors()) + return; + + if (form.materialOutputCount > 0 && form.materialOutputs != null && !form.materialOutputs.isEmpty()) + errors.reject(ERROR_MSG, "Either 'materialOutputCount' or 'materialOutputs' property can be specified, but not both."); + + if (form.dataOutputCount > 0 && form.dataOutputs != null && !form.dataOutputs.isEmpty()) + errors.reject(ERROR_MSG, "Either 'dataOutputCount' or 'dataOutputs' property can be specified, but not both."); + + boolean hasMaterialOutputs = form.materialOutputCount > 0 || form.materialOutputs != null && !form.materialOutputs.isEmpty(); + boolean hasDataOutputs = form.dataOutputCount > 0 || form.dataOutputs != null && !form.dataOutputs.isEmpty(); + + if (!hasMaterialOutputs && !hasDataOutputs) + errors.reject(ERROR_MSG, "At least one data output or material output is required"); + + if (hasMaterialOutputs && form.targetSampleType == null) + errors.reject(ERROR_MSG, "targetSampleType lsid required for material outputs"); + + if (hasDataOutputs && form.targetDataClass == null) + errors.reject(ERROR_MSG, "targetDataClass lsid required for data outputs"); + } + + @Override + public Object execute(DerivationForm form, BindException errors) throws Exception + { + // Find material inputs + Map materialInputs = new LinkedHashMap<>(); + if (form.materialInputs != null) + { + for (ExpInput in : form.materialInputs) + { + ExpMaterial m = null; + if (in.lsid != null) + { + m = ExperimentService.get().getExpMaterial(in.lsid.toString()); + if (m == null) + errors.reject(ERROR_MSG, "Can't resolve sample '" + in.lsid + "'"); + } + else if (in.rowId > 0) + { + m = ExperimentService.get().getExpMaterial(in.rowId); + if (m == null) + errors.reject(ERROR_MSG, "Can't resolve sample '" + in.rowId + "'"); + } + + if (m == null) + { + errors.reject(ERROR_MSG, "Material input lsid or rowId required"); + continue; + } + + ExpSampleType st = m.getSampleType(); + if (st == null) + { + errors.reject(ERROR_MSG, "Material input is not a member of a SampleType"); + continue; + } + + String role = in.role; + if (role == null || role.isEmpty()) + { + role = st.getName(); + } + materialInputs.put(m, role); + } + } + + // Find input data + Map dataInputs = new LinkedHashMap<>(); + if (form.dataInputs != null) + { + for (ExpInput in : form.dataInputs) + { + ExpData d = null; + if (in.lsid != null) + { + d = ExperimentService.get().getExpData(in.lsid.toString()); + if (d == null) + errors.reject(ERROR_MSG, "Can't resolve data '" + in.lsid + "'"); + } + else if (in.rowId > 0) + { + d = ExperimentService.get().getExpData(in.rowId); + if (d == null) + errors.reject(ERROR_MSG, "Can't resolve data '" + in.rowId + "'"); + } + + if (d == null) + { + errors.reject(ERROR_MSG, "Data input lsid or rowId required"); + continue; + } + + ExpDataClass dc = d.getDataClass(getUser()); + if (dc == null) + { + errors.reject(ERROR_MSG, "Data input is not a member of a DataClass"); + continue; + } + + String role = in.role; + if (role == null || role.isEmpty()) + { + role = dc.getName(); + } + dataInputs.put(d, role); + } + } + + ExpSampleType outSampleType; + if (form.targetSampleType != null) + { + // TODO: check in scope and has permission + outSampleType = SampleTypeService.get().getSampleType(form.targetSampleType.toString()); + if (outSampleType == null) + errors.reject(ERROR_MSG, "Sample type not found: " + form.targetSampleType.toString()); + } + else + { + outSampleType = null; + } + + ExpDataClass outDataClass; + if (form.targetDataClass != null) + { + // TODO: check in scope and has permission + outDataClass = ExperimentServiceImpl.get().getDataClass(form.targetDataClass.toString()); + if (outDataClass == null) + errors.reject(ERROR_MSG, "DataClass not found: " + form.targetDataClass.toString()); + } + else + { + outDataClass = null; + } + + if (errors.hasErrors()) + return null; + + // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names + // Create "MaterialInputs/" columns with a value containing a comma-separated list of Material names + final Map> parentInputNames = new HashMap<>(); + Set inputTypes = new CaseInsensitiveHashSet(); + for (ExpMaterial material : materialInputs.keySet()) + { + ExpSampleType st = material.getSampleType(); + String keyName = ExpMaterial.MATERIAL_INPUT_PARENT + "/" + st.getName(); + inputTypes.add(keyName); + parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(material.getName()); + } + + // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names + // Create "DataInputs/" columns with a value containing a comma-separated list of ExpData names + for (ExpData d : dataInputs.keySet()) + { + ExpDataClass dc = d.getDataClass(getUser()); + String keyName = ExpData.DATA_INPUT_PARENT + "/" + dc.getName(); + inputTypes.add(keyName); + parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(d.getName()); + } + + + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + Set requiredParentTypes = new CaseInsensitiveHashSet(); + + // output materials + Map outputMaterials = new HashMap<>(); + int materialOutputCount = Math.max(form.materialOutputCount, form.materialOutputs != null ? form.materialOutputs.size() : 0); + if (materialOutputCount > 0 && outSampleType != null) + { + requiredParentTypes.addAll(outSampleType.getRequiredImportAliases().values()); + DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.materialDefault, form.materialOutputs, materialOutputCount, ExpMaterial.DEFAULT_CPAS_TYPE) + { + @Override + protected TableInfo createTable() + { + SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); + return schema.getTable(outSampleType.getName()); + } + + @Override + protected List getExpObject(List> insertedRows) + { + List rowIds = insertedRows.stream().map(r -> MapUtils.getLong(r,"rowid")).collect(toList()); + return ExperimentService.get().getExpMaterials(rowIds); + } + }; + + outputMaterials = derived.createOutputs(); + } + + + // create output data + Map outputData = new HashMap<>(); + int dataOutputCount = Math.max(form.dataOutputCount, form.dataOutputs != null ? form.dataOutputs.size() : 0); + if (dataOutputCount > 0 && outDataClass != null) + { + requiredParentTypes.addAll(outDataClass.getRequiredImportAliases().values()); + DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.dataDefault, form.dataOutputs, dataOutputCount, ExpData.DEFAULT_CPAS_TYPE) + { + @Override + protected TableInfo createTable() + { + ExpSchema expSchema = new ExpSchema(getUser(), getContainer()); + UserSchema dataSchema = expSchema.getUserSchema(ExpSchema.NestedSchemas.data.name()); + return dataSchema.getTable(outDataClass.getName()); + } + + @Override + protected List getExpObject(List> insertedRows) + { + List lsids = insertedRows.stream().map(r -> (String) r.get("lsid")).collect(toList()); + return ExperimentService.get().getExpDatasByLSID(lsids); + } + }; + + outputData = derived.createOutputs(); + } + + if (outputMaterials.isEmpty() && outputData.isEmpty()) + throw new IllegalStateException("Expected to create " + materialOutputCount + " materials and " + dataOutputCount + " datas"); + + boolean hasMissingRequiredParent = false; + for (String required : requiredParentTypes) + { + if (!inputTypes.contains(required)) + { + hasMissingRequiredParent = true; + break; + } + } + if (hasMissingRequiredParent) + throw new IllegalStateException("Inputs are required: " + String.join(",", requiredParentTypes)); + + // finally, create the derived run if there are any parents + ExpRun run = null; + if (!materialInputs.isEmpty() || !dataInputs.isEmpty()) + run = ExperimentService.get().derive(materialInputs, dataInputs, outputMaterials, outputData, new ViewBackgroundInfo(getContainer(), getUser(), null), _log); + tx.commit(); + + StringBuilder successMessage = new StringBuilder("Created "); + if (!outputMaterials.isEmpty()) + successMessage.append(outputMaterials.size()).append(" materials"); + if (!outputData.isEmpty()) + successMessage.append(outputData.size()).append(" data"); + + JSONObject ret; + if (run != null) + ret = ExperimentJSONConverter.serializeRun(run, null, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); + else + ret = ExperimentJSONConverter.serializeRunOutputs(outputData.keySet(), outputMaterials.keySet(), getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); + + return success(successMessage.toString(), ret); + } + } + + // Helper class that prepares and executes the QueryUpdateService.insertRows() on the data or material table. + private abstract class DerivedOutputs + { + private final @NotNull Map> _parentInputNames; + private final @Nullable Map _defaultValues; + private final @Nullable List _values; + private final int _outputCount; + private final String _rolePrefix; + + + public DerivedOutputs(@NotNull Map> parentInputNames, @Nullable Map defaultValues, @Nullable List values, int outputCount, String rolePrefix) + { + _parentInputNames = parentInputNames; + _defaultValues = defaultValues; + _values = values; + _outputCount = outputCount; + _rolePrefix = rolePrefix; + } + + public Pair>, List> prepareRows() + { + List> rows = new ArrayList<>(); + List roles = new ArrayList<>(); + int unknownOutputDataCount = 0; + + for (int i = 0; i < _outputCount; i++) + { + Map row = new CaseInsensitiveHashMap<>(); + if (_defaultValues != null) + row.putAll(_defaultValues); + DerivationSpec spec = _values != null && i < _values.size() ? _values.get(i) : null; + String role = null; + if (spec != null) + { + row.putAll(spec.values); + role = spec.role; + } + + // NOTE: Input parents are added to each row, but are only used for name generation and not for derivation. + // NOTE: We will derive the inserted samples in a single derivation run after the sample/date have been inserted. + row.putAll(_parentInputNames); + + rows.add(row); + + if (StringUtils.trimToNull(role) == null) + { + role = _rolePrefix + (unknownOutputDataCount == 0 ? "" : Integer.toString(unknownOutputDataCount + 1)); + unknownOutputDataCount++; + } + roles.add(role); + } + return Pair.of(rows, roles); + } + + protected abstract TableInfo createTable(); + + protected abstract List getExpObject(List> insertedRows); + + public Map createOutputs() throws BatchValidationException, DuplicateKeyException, SQLException, QueryUpdateServiceException + { + Pair>, List> pair = prepareRows(); + List> rows = pair.first; + List roles = pair.second; + + TableInfo table = createTable(); + QueryUpdateService qus = table.getUpdateService(); + if (qus == null) + throw new IllegalStateException(); + + Map configParams = new HashMap<>(); + // Skip derivation during insert -- DeriveAction will call ExperimentService.get().derive() after samples are inserted + configParams.put(SampleTypeUpdateServiceDI.Options.SkipDerivation, true); + + BatchValidationException qusErrors = new BatchValidationException(); + List> insertedRows = qus.insertRows(getUser(), getContainer(), rows, qusErrors, configParams, null); + if (qusErrors.hasErrors()) + throw qusErrors; + + if (insertedRows.size() != roles.size()) + throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); + + List outputs = getExpObject(insertedRows); + if (outputs.size() != roles.size()) + throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); + + Map outputMap = new HashMap<>(); + for (int i = 0; i < outputs.size(); i++) + { + String role = roles.get(i); + T data = outputs.get(i); + outputMap.put(data, role); + } + + return outputMap; + } + } + } + + public static class CreateExperimentForm extends ExperimentForm implements DataRegionSelection.DataSelectionKeyForm + { + private boolean _addSelectedRuns; + private String _dataRegionSelectionKey; + + public boolean isAddSelectedRuns() + { + return _addSelectedRuns; + } + + public void setAddSelectedRuns(boolean addSelectedRuns) + { + _addSelectedRuns = addSelectedRuns; + } + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String dataRegionSelectionKey) + { + _dataRegionSelectionKey = dataRegionSelectionKey; + } + } + + @RequiresPermission(InsertPermission.class) + @ActionNames("createRunGroup, createExperiment") + public class CreateRunGroupAction extends FormViewAction + { + @Override + public ModelAndView getView(CreateExperimentForm form, boolean reshow, BindException errors) + { + // HACK - convert ExperimentForm to not be a BeanViewForm + form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); + form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + + DataRegion drg = new DataRegion(); + + drg.addHiddenFormField(ActionURL.Param.returnUrl, getViewContext().getRequest().getParameter(ActionURL.Param.returnUrl.name())); + drg.addHiddenFormField("addSelectedRuns", Boolean.toString("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns")))); + form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + // Fix issue 27562 - include session-stored selection + if (form.getDataRegionSelectionKey() != null) + { + for (String rowId : DataRegionSelection.getSelected(getViewContext(), form.getDataRegionSelectionKey(), false)) + { + drg.addHiddenFormField(DataRegion.SELECT_CHECKBOX_NAME, rowId); + } + } + drg.addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + + drg.addColumns(ExperimentServiceImpl.get().getTinfoExperiment(), "RowId,Name,LSID,ContactId,ExperimentDescriptionURL,Hypothesis,Comments,Created"); + + DisplayColumn col = drg.getDisplayColumn("RowId"); + col.setVisible(false); + drg.getDisplayColumn("LSID").setVisible(false); + drg.getDisplayColumn("Created").setVisible(false); + + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + ActionButton insertButton = new ActionButton(new ActionURL(CreateRunGroupAction.class, getContainer()), "Submit", ActionButton.Action.POST); + bb.add(insertButton); + + drg.setButtonBar(bb); + + return new InsertView(drg, errors); + } + + + @Override + public boolean handlePost(CreateExperimentForm form, BindException errors) throws Exception + { + // This is strange... but the "Create new run group..." menu item on the run grid always POSTs, probably to + // allow for long lists of run IDs. This "noPost" parameter on the initial POST is used to inform the action + // that it wants to display the form, not try to save anything yet. + if (!"true".equals(getViewContext().getRequest().getParameter("noPost"))) + { + form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); + form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + + Experiment exp = form.getBean(); + if (exp.getName() == null || exp.getName().trim().isEmpty()) + { + errors.reject(ERROR_MSG, "You must specify a name for the experiment"); + } + else + { + int maxNameLength = ExperimentService.get().getTinfoExperimentRun().getColumn("Name").getScale(); + if (exp.getName().length() > maxNameLength) + { + errors.reject(ERROR_MSG, "Name of the experiment must be " + maxNameLength + " characters or less."); + } + } + + String lsid; + int suffix = 1; + do + { + String template = "urn:lsid:" + XarContext.LSID_AUTHORITY_SUBSTITUTION + ":Experiment.Folder-" + XarContext.CONTAINER_ID_SUBSTITUTION + ":" + exp.getName(); + if (suffix > 1) + { + template = template + suffix; + } + suffix++; + lsid = LsidUtils.resolveLsidFromTemplate(template, new XarContext("Experiment Creation", getContainer(), getUser()), ExpExperiment.DEFAULT_CPAS_TYPE); + } + while (ExperimentService.get().getExpExperiment(lsid) != null); + exp.setLSID(lsid); + exp.setContainer(getContainer()); + + if (errors.getErrorCount() == 0) + { + ExpExperimentImpl wrapper = new ExpExperimentImpl(exp); + wrapper.save(getUser()); + + if (form.isAddSelectedRuns()) + { + addSelectedRunsToExperiment(wrapper, form.getDataRegionSelectionKey()); + } + + if (form.getReturnUrl() != null) + { + throw new RedirectException(form.getReturnUrl()); + } + throw new RedirectException(ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); + } + } + return true; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + root.addChild("Create Run Group"); + } + + @Override + public URLHelper getSuccessURL(CreateExperimentForm createExperimentForm) + { + return null; // null is used to show the form in the case where IDs are POSTed from the grid + } + + @Override + public void validateCommand(CreateExperimentForm target, Errors errors) { } + } + + public static class MoveRunsForm implements DataRegionSelection.DataSelectionKeyForm + { + private String _targetContainerId; + private String _dataRegionSelectionKey; + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String key) + { + _dataRegionSelectionKey = key; + } + + public String getTargetContainerId() + { + return _targetContainerId; + } + + public void setTargetContainerId(String targetContainerId) + { + _targetContainerId = targetContainerId; + } + } + + @RequiresPermission(DeletePermission.class) + public class MoveRunsLocationAction extends SimpleViewAction + { + @Override + public ModelAndView getView(MoveRunsForm form, BindException errors) + { + ActionURL moveURL = new ActionURL(MoveRunsAction.class, getContainer()); + PipelineRootContainerTree ct = new PipelineRootContainerTree(getUser(), moveURL) + { + private boolean _clickHandlerRegistered = false; + + @Override + protected void renderCellContents(StringBuilder html, Container c, ActionURL url, boolean hasRoot) + { + boolean renderLink = hasRoot && !c.equals(getContainer()); + + if (renderLink) + { + html.append(""); + } + html.append(PageFlowUtil.filter(c.getName())); + if (renderLink) + { + html.append(""); + } + + if (!_clickHandlerRegistered) + { + HttpView.currentPageConfig().addHandlerForQuerySelector("a.move-target-container", "click", "moveTo(this.attributes.getNamedItem('data-objectid').value);" ); + _clickHandlerRegistered = true; + } + } + }; + ct.setInitialLevel(1); + + MoveRunsBean bean = new MoveRunsBean(ct, form.getDataRegionSelectionKey()); + JspView result = new JspView<>("/org/labkey/experiment/moveRunsLocation.jsp", bean); + result.setTitle("Choose Destination Folder"); + result.setFrame(WebPartView.FrameType.PORTAL); + return result; + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Move Runs"); + } + } + + + @RequiresPermission(DeletePermission.class) + public class MoveRunsAction extends FormHandlerAction + { + private Container _targetContainer; + + @Override + public void validateCommand(MoveRunsForm target, Errors errors) + { + } + + @Override + public boolean handlePost(MoveRunsForm form, BindException errors) + { + _targetContainer = ContainerManager.getForId(form.getTargetContainerId()); + if (_targetContainer == null || !_targetContainer.hasPermission(getUser(), InsertPermission.class)) + { + throw new UnauthorizedException(); + } + + Set runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); + List runs = new ArrayList<>(); + for (Long runId : runIds) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run != null) + { + runs.add(run); + } + } + + ViewBackgroundInfo info = getViewBackgroundInfo(); + info.setContainer(_targetContainer); + + try + { + ExperimentService.get().moveRuns(info, getContainer(), runs); + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + } + catch (IOException e) + { + throw new NotFoundException("Failed to initialize move. Check that the pipeline root is configured correctly. " + e); + } + return true; + } + + @Override + public ActionURL getSuccessURL(MoveRunsForm form) + { + return urlProvider(PipelineUrls.class).urlBegin(_targetContainer); + } + } + + public static class ShowExternalDocsForm + { + private String _objectURI; + private String _propertyURI; + + public String getObjectURI() + { + return _objectURI; + } + + public void setObjectURI(String objectURI) + { + _objectURI = objectURI; + } + + public String getPropertyURI() + { + return _propertyURI; + } + + public void setPropertyURI(String propertyURI) + { + _propertyURI = propertyURI; + } + } + + @RequiresPermission(ReadPermission.class) + public static class ShowExternalDocsAction extends SimpleViewAction + { + @Override + public ModelAndView getView(ShowExternalDocsForm form, BindException errors) throws Exception + { + Map props = OntologyManager.getPropertyObjects(getContainer(), form.getObjectURI()); + ObjectProperty prop = props.get(form.getPropertyURI()); + if (prop == null || !getContainer().equals(prop.getContainer())) + { + throw new NotFoundException(); + } + URI uri = new URI(prop.getStringValue()); + File f = new File(uri); + if (!f.exists()) + { + throw new NotFoundException(); + } + + PageFlowUtil.streamFile(getViewContext().getResponse(), new File(f.getAbsolutePath()), false); + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + } + } + + + // TODO: DotGraph has been adding a "runId" parameter, but ShowGraphMoreListAction + public static ActionURL getShowGraphMoreListURL(Container c, @Nullable Long runId, @NotNull String objtype) + { + ActionURL url = new ActionURL(ShowGraphMoreListAction.class, c); + + if (null != runId) + url.addParameter("runId", runId); + + url.addParameter("objtype", objtype); + + return url; + } + + + @RequiresPermission(ReadPermission.class) + public static class ShowGraphMoreListAction extends SimpleViewAction + { + private ExperimentRunForm _form; + + @Override + public ModelAndView getView(ExperimentRunForm form, BindException errors) + { + _form = form; + return new GraphMoreGrid(getContainer(), errors, getViewContext().getActionURL()); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild(new NavTree("Experiments", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer()))); + ExpRun run = ExperimentService.get().getExpRun(_form.getRowId()); + if (run != null) + { + root.addChild(new NavTree("Experiment Run", ExperimentUrlsImpl.get().getRunGraphURL(_form.lookupRun()))); + } + root.addChild(new NavTree("Selected Protocol Applications")); + } + } + + @RequiresPermission(DesignAssayPermission.class) + public class AssayXarFileAction extends MutatingApiAction + { + + @Override + public Object execute(Object o, BindException errors) throws Exception + { + ApiSimpleResponse response = new ApiSimpleResponse(); + + if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) + throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); + + if (!PipelineService.get().hasValidPipelineRoot(getContainer())) + { + return false; + } + + MultipartFile formFile = getFileMap().get("file"); + if (formFile == null) + { + errors.reject(ERROR_MSG, "No file was posted by the browser."); + return false; + } + + byte[] bytes = formFile.getBytes(); + if (bytes.length == 0) + { + errors.reject(ERROR_MSG, "No file was posted by the browser."); + return false; + } + + PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); + FileLike systemDir = pipeRoot.ensureSystemDirectory(); + FileLike uploadDir = systemDir.resolveChild("UploadedXARs"); + FileUtil.createDirectories(uploadDir); + if (!uploadDir.isDirectory()) + { + errors.reject(ERROR_MSG, "Unable to create a 'system/UploadedXARs' directory under the pipeline root"); + return false; + } + String userDirName = getUser().getEmail(); + if (userDirName == null || userDirName.isEmpty()) + { + userDirName = GUEST_DIRECTORY_NAME; + } + FileLike userDir = uploadDir.resolveChild(userDirName); + FileUtil.createDirectories(userDir); + if (!userDir.isDirectory()) + { + errors.reject(ERROR_MSG, "Unable to create an 'UploadedXARs/" + userDirName + "' directory under the pipeline root"); + return false; + } + + FileLike xarFile = userDir.resolveChild(formFile.getOriginalFilename()); + + // As this is multi-part will need to use finally to close, to prevent a stream closure exception + try (OutputStream out = new BufferedOutputStream(xarFile.openOutputStream())) + { + out.write(bytes); + } + catch (IOException e) + { + errors.reject(ERROR_MSG, "Unable to write uploaded XAR file to " + xarFile); + return false; + } + //noinspection EmptyCatchBlock + + ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), xarFile, + "Uploaded file", true, pipeRoot); + PipelineService.get().queueJob(job); + + response.put("success", true); + return response; + } + } + + @RequiresPermission(InsertPermission.class) + public class ImportXarFileAction extends FormHandlerAction + { + @Override + public void validateCommand(ImportXarForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ImportXarForm form, BindException errors) throws Exception + { + for (FileLike f : form.getValidatedFiles(getContainer())) + { + if (f.isFile()) + { + ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); + + // TODO: Configure module resources with the appropriate log location per container + if (form.getModule() != null) + { + FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); + job.setLogFile(logFile); + } + + PipelineService.get().queueJob(job); + } + else + { + throw new NotFoundException("Expected a file but found a directory: " + f.getName()); + } + } + + return true; + } + + @Override + public URLHelper getSuccessURL(ImportXarForm importXarForm) + { + return getContainer().getStartURL(getUser()); + } + } + + + @RequiresPermission(InsertPermission.class) + public class ImportXarAction extends MutatingApiAction + { + @Override + public Object execute(ImportXarForm form, BindException errors) throws Exception + { + ApiSimpleResponse response = new ApiSimpleResponse(); + + List> archives = new ArrayList<>(); + for (FileLike f : form.getValidatedFiles(getContainer())) + { + Map archive = new HashMap<>(); + ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); + + // TODO: Configure module resources with the appropriate log location per container + if (form.getModule() != null) + { + FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); + job.setLogFile(logFile); + } + + PipelineService.get().queueJob(job); + + archive.put("file", f.getName()); + archive.put("job", job.getJobGUID()); + archive.put("path", form.getPath()); // echo back the public path + + archives.add(archive); + } + + response.put("success", true); + response.put("archives", archives); + + return response; + } + } + + + /** + * User: jeckels + * Date: Jan 27, 2008 + */ + public static class ExperimentUrlsImpl implements ExperimentUrls + { + public ActionURL getOverviewURL(Container c) + { + return new ActionURL(BeginAction.class, c); + } + + @Override + public ActionURL getExperimentDetailsURL(Container c, ExpExperiment expExperiment) + { + return new ActionURL(DetailsAction.class, c).addParameter("rowId", expExperiment.getRowId()); + } + + public ActionURL getShowSampleURL(Container c, ExpMaterial material) + { + return getMaterialDetailsBaseURL(c, null).addParameter("rowId", material.getRowId()); + } + + @Override + public ActionURL getExportProtocolURL(Container container, ExpProtocol protocol) + { + return new ActionURL(ExperimentController.ExportProtocolsAction.class, container). + addParameter("protocolId", protocol.getRowId()). + addParameter("xarFileName", protocol.getName() + ".xar"); + } + + @Override + public ActionURL getMoveRunsLocationURL(Container container) + { + return new ActionURL(ExperimentController.MoveRunsLocationAction.class, container); + } + + @Override + public ActionURL getProtocolDetailsURL(ExpProtocol protocol) + { + return new ActionURL(ProtocolDetailsAction.class, protocol.getContainer()).addParameter("rowId", protocol.getRowId()); + } + + @Override + public ActionURL getProtocolApplicationDetailsURL(ExpProtocolApplication app) + { + return getShowApplicationURL(app.getContainer(), app.getRowId()); + } + + public ActionURL getProtocolGridURL(Container c) + { + return new ActionURL(ShowProtocolGridAction.class, c); + } + + public ActionURL getRunGraphDetailURL(ExpRun run) + { + return getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpData focus) + { + return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_DATA); + } + + public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpMaterial focus) + { + return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_MATERIAL); + } + + public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpProtocolApplication focus) + { + return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_PROT_APP); + } + + private ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpObject focus, String typeCode) + { + ActionURL result = getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); + result.addParameter("detail", "true"); + if (focus != null) + { + result.addParameter("focus", typeCode + focus.getRowId()); + } + return result; + } + + @Override + public ActionURL getRunGraphURL(Container container, long runId) + { + return ExperimentController.getRunGraphURL(container, runId); + } + + @Override + public ActionURL getRunGraphURL(ExpRun run) + { + return getRunGraphURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getRunTextURL(Container c, long runId) + { + return new ActionURL(ShowRunTextAction.class, c).addParameter("rowId", runId); + } + + @Override + public ActionURL getRunTextURL(ExpRun run) + { + return getRunTextURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getDeleteExperimentsURL(Container container, URLHelper returnUrl) + { + return new ActionURL(DeleteSelectedExperimentsAction.class, container).addReturnUrl(returnUrl); + } + + @Override + public ActionURL getDeleteProtocolURL(@NotNull ExpProtocol protocol, URLHelper returnUrl) + { + ActionURL result = new ActionURL(DeleteProtocolByRowIdsAction.class, protocol.getContainer()); + result.addParameter("singleObjectRowId", protocol.getRowId()); + if (returnUrl != null) + { + result.addReturnUrl(returnUrl); + } + return result; + } + + @Override + public ActionURL getAddRunsToExperimentURL(Container c, ExpExperiment exp) + { + return new ActionURL(AddRunsToExperimentAction.class, c).addParameter("expRowId", exp.getRowId()); + } + + @Override + public ActionURL getShowRunsURL(Container c, ExperimentRunType type) + { + ActionURL result = new ActionURL(ShowRunsAction.class, c); + result.addParameter("experimentRunFilter", type.getDescription()); + return result; + } + + public ActionURL getShowExperimentsURL(Container c) + { + return new ActionURL(ShowRunGroupsAction.class, c); + } + + @Override + public ActionURL getShowSampleTypeListURL(Container c) + { + return getShowSampleTypeListURL(c, null); + } + + @Override + public ActionURL getShowSampleTypeURL(ExpSampleType sampleType) + { + return getShowSampleTypeURL(sampleType, sampleType.getContainer()); + } + + @Override + public ActionURL getShowSampleTypeURL(ExpSampleType sampleType, Container container) + { + return new ActionURL(ShowSampleTypeAction.class, container).addParameter("rowId", sampleType.getRowId()); + } + + public ActionURL getExperimentListURL(Container container) + { + return new ActionURL(ShowRunGroupsAction.class, container); + } + + public ActionURL getShowSampleTypeListURL(Container c, String errorMessage) + { + ActionURL url = new ActionURL(ListSampleTypesAction.class, c); + if (errorMessage != null) + { + url.addParameter("errorMessage", errorMessage); + } + return url; + } + + @Override + public ActionURL getDataClassListURL(Container c) + { + return getDataClassListURL(c, null); + } + + public ActionURL getDataClassListURL(Container c, String errorMessage) + { + ActionURL url = new ActionURL(ListDataClassAction.class, c); + if (errorMessage != null) + { + url.addParameter("errorMessage", errorMessage); + } + return url; + } + + @Override + public ActionURL getDeleteDatasURL(Container c, URLHelper returnUrl) + { + ActionURL url = new ActionURL(DeleteSelectedDataAction.class, c); + if (returnUrl != null) + url.addReturnUrl(returnUrl); + return url; + } + + public ActionURL getDeleteSelectedExperimentsURL(Container c, URLHelper returnUrl) + { + ActionURL result = new ActionURL(DeleteSelectedExperimentsAction.class, c); + if (returnUrl != null) + result.addReturnUrl(returnUrl); + return result; + } + + @Override + public ActionURL getDeleteSelectedExpRunsURL(Container container, URLHelper returnUrl) + { + return new ActionURL(DeleteSelectedExpRunsAction.class, container).addReturnUrl(returnUrl); + } + + public ActionURL getShowUpdateURL(ExpExperiment experiment) + { + return new ActionURL(ShowUpdateAction.class, experiment.getContainer()).addParameter("rowId", experiment.getRowId()); + } + + @Override + public ActionURL getRemoveSelectedExpRunsURL(Container container, URLHelper returnUrl, ExpExperiment exp) + { + return new ActionURL(RemoveSelectedExpRunsAction.class, container).addReturnUrl(returnUrl).addParameter("expRowId", exp.getRowId()); + } + + @Override + public ActionURL getCreateRunGroupURL(Container container, URLHelper returnUrl, boolean addSelectedRuns) + { + ActionURL result = new ActionURL(CreateRunGroupAction.class, container); + if (returnUrl != null) + { + result.addReturnUrl(returnUrl); + } + if (addSelectedRuns) + { + result.addParameter("addSelectedRuns", "true"); + } + return result; + } + + + public static ExperimentUrlsImpl get() + { + return (ExperimentUrlsImpl) urlProvider(ExperimentUrls.class); + } + + public ActionURL getDownloadGraphURL(ExpRun run, boolean detail, String focus, String focusType) + { + ActionURL result = new ActionURL(DownloadGraphAction.class, run.getContainer()); + result.addParameter("rowId", run.getRowId()).addParameter("detail", detail); + if (focus != null) + { + result.addParameter("focus", focus); + } + if (focusType != null) + { + result.addParameter("focusType", focusType); + } + return result; + } + + public ActionURL getBeginURL(Container container) + { + return new ActionURL(BeginAction.class, container); + } + + @Override + public ActionURL getDomainEditorURL(Container container, String domainURI, boolean createOrEdit) + { + Domain domain = PropertyService.get().getDomain(container, domainURI); + if (domain != null) + return getDomainEditorURL(container, domain); + + ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); + url.addParameter("domainURI", domainURI); + if (createOrEdit) + url.addParameter("createOrEdit", true); + return url; + } + + @Override + public ActionURL getDomainEditorURL(Container container, Domain domain) + { + ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); + url.addParameter("domainId", domain.getTypeId()); + return url; + } + + @Override + public ActionURL getCreateDataClassURL(Container container) + { + return new ActionURL(EditDataClassAction.class, container); + } + + @Override + public ActionURL getShowDataClassURL(Container container, long rowId) + { + ActionURL url = new ActionURL(ShowDataClassAction.class, container); + url.addParameter("rowId", rowId); + return url; + } + + @Override + public ActionURL getShowFileURL(ExpData data, boolean inline) + { + ActionURL result = getShowFileURL(data.getContainer()).addParameter("rowId", data.getRowId()); + if (inline) + { + result.addParameter("inline", inline); + } + return result; + } + + @Override + public ActionURL getMaterialDetailsURL(ExpMaterial material) + { + return getMaterialDetailsURL(material.getContainer(), material.getRowId()); + } + + @Override + public ActionURL getMaterialDetailsURL(Container c, long materialRowId) + { + return getMaterialDetailsBaseURL(c, null).addParameter("rowId", materialRowId); + } + + @Override + public ActionURL getMaterialDetailsBaseURL(Container c, @Nullable String materialIdFieldKey) + { + return new ActionURL(ShowMaterialAction.class, c); + } + + @Override + public ActionURL getCreateSampleTypeURL(Container container) + { + return new ActionURL(EditSampleTypeAction.class, container); + } + + @Override + public ActionURL getImportSamplesURL(Container container, String sampleTypeName) + { + ActionURL url = new ActionURL(ImportSamplesAction.class, container); + url.addParameter("query.queryName", sampleTypeName); + url.addParameter("schemaName", "exp.materials"); + return url; + } + + @Override + public ActionURL getImportDataURL(Container container, String dataClassName) + { + ActionURL url = new ActionURL(ImportDataAction.class, container); + url.addParameter("query.queryName", dataClassName); + url.addParameter("schemaName", "exp.data"); + return url; + } + + @Override + public ActionURL getDataDetailsURL(ExpData data) + { + return new ActionURL(ShowDataAction.class, data.getContainer()).addParameter("rowId", data.getRowId()); + } + + @Override + public ActionURL getShowFileURL(Container c) + { + return new ActionURL(ShowFileAction.class, c); + } + + @Override + public ActionURL getSetFlagURL(Container container) + { + return new ActionURL(SetFlagAction.class, container); + } + + @Override + public ActionURL getShowRunGraphURL(ExpRun run) + { + return ExperimentController.getRunGraphURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getRepairTypeURL(Container container) + { + return new ActionURL(TypesController.RepairAction.class, container); + } + + @Override + public ActionURL getUpdateMaterialQueryRowAction(Container c, TableInfo table) + { + ActionURL url = new ActionURL(UpdateMaterialQueryRowAction.class, c); + url.addParameter("schemaName", "samples"); + url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); + + return url; + } + + @Override + public ActionURL getInsertMaterialQueryRowAction(Container c, TableInfo table) + { + ActionURL url = new ActionURL(InsertMaterialQueryRowAction.class, c); + url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); + + return url; + } + + @Override + public ActionURL getDataClassAttachmentDownloadAction(Container c) + { + return new ActionURL(ExperimentController.DataClassAttachmentDownloadAction.class, c); + } + + } + + private static abstract class BaseResolveLsidApiAction extends ReadOnlyApiAction + { + protected Set _seeds; + + @Override + public void validateForm(F form, Errors errors) + { + if (null != form.getLsids()) + { + _seeds = new LinkedHashSet<>(form.getLsids().size()); + for (String lsid : form.getLsids()) + { + Identifiable id = LsidManager.get().getObject(lsid); + if (id == null) + throw new NotFoundException("Unable to resolve object: " + lsid); + + // ensure the user has read permission in the seed container + if (!getContainer().equals(id.getContainer())) + { + if (!id.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new UnauthorizedException("User does not have permission to read object: " + lsid); + } + + _seeds.add(id); + } + } + else + { + throw new ApiUsageException("Starting lsids required"); + } + } + } + + @RequiresPermission(ReadPermission.class) + public static class ResolveAction extends BaseResolveLsidApiAction + { + @Override + public Object execute(ResolveLsidsForm form, BindException errors) + { + var settings = new ExperimentJSONConverter.Settings(form.isIncludeProperties(), form.isIncludeInputsAndOutputs(), form.isIncludeRunSteps()); + var data = _seeds.stream().map(n -> ExperimentJSONConverter.serialize(n, getUser(), settings)).collect(toList()); + return new ApiSimpleResponse("data", data); + } + } + + @RequiresPermission(ReadPermission.class) + public static class LineageAction extends BaseResolveLsidApiAction + { + @Override + public Object execute(ExpLineageOptions options, BindException errors) throws Exception + { + ExpLineageServiceImpl.get().streamLineage(getContainer(), getUser(), getViewContext().getResponse(), _seeds, options); + return null; + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class RebuildEdgesAction extends MutatingApiAction + { + @Override + public Object execute(ExperimentRunForm form, BindException errors) + { + if (form.getRowId() != 0 || form.getLsid() != null) + { + ExpRun run = form.lookupRun(); + if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new UnauthorizedException("Not permitted"); + + ExperimentServiceImpl.get().syncRunEdges(run); + } + else + { + // should this require site admin permissions? + ExperimentServiceImpl.get().rebuildAllRunEdges(); + } + return success(); + } + } + + private static class VerifyEdgesForm extends ExperimentRunForm + { + private Integer _limit; + + public Integer getLimit() + { + return _limit; + } + + public void setLimit(Integer limit) + { + _limit = limit; + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class VerifyEdgesAction extends ReadOnlyApiAction + { + @Override + public Object execute(VerifyEdgesForm form, BindException errors) + { + if (form.getRowId() != 0 || form.getLsid() != null) + { + ExpRun run = form.lookupRun(); + if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new UnauthorizedException("Not permitted"); + + ExperimentServiceImpl.get().verifyRunEdges(run); + } + else + { + ExperimentServiceImpl.get().verifyAllEdges(getContainer(), form.getLimit()); + } + return success(); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class RebuildAncestorsAction extends MutatingApiAction + { + @Override + public Object execute(Object form, BindException errors) + { + ClosureQueryHelper.truncateAndRecreate(); + return success(); + } + } + + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class CheckDataClassesIndexedAction extends ReadOnlyApiAction + { + @Override + public Object execute(Object o, BindException errors) throws Exception + { + List> notInIndex = new ArrayList<>(100); + + List list = ExperimentService.get().getDataClasses(getContainer(), getUser(), false); + for (ExpDataClass dc : list) + { + for (ExpData d : dc.getDatas()) + { + String docId = d.getDocumentId(); + if (docId != null) + { + SearchService.SearchHit hit = SearchService.get().find(docId); + if (hit == null) + { + JSONObject props = ExperimentJSONConverter.serializeData(d, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); + props.put("docid", docId); + notInIndex.add(props.toMap()); + } + } + } + } + + return success(notInIndex); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class CheckEdgesAction extends ReadOnlyApiAction + { + @Override + public Object execute(Object o, BindException errors) throws Exception + { + List result; + DbSchema schema = ExperimentService.get().getSchema(); + TableInfo edgeTable = schema.getTable("Edge"); + + if (null != edgeTable.getColumn("fromObjectId")) + { + var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") + .resultSetStream() + .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) + .collect(toList()); + var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); + result = cycles.stream().map(e -> new Integer[]{e.first, e.second}).collect(toList()); + } + else + { + var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromLsid, toLsid FROM exp.Edge") + .resultSetStream() + .map(r -> { try { return new Pair<>(r.getString(1), r.getString(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) + .collect(toList()); + var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); + result = cycles.stream().map(e -> new String[]{e.first, e.second}).collect(toList()); + } + + JSONObject ret = new JSONObject(); + ret.put("result", result); + ret.put("success", true); + return ret; + } + } + + @RequiresPermission(UpdatePermission.class) + public static class UpdateMaterialQueryRowAction extends UserSchemaAction + { + @Override + protected QueryForm createQueryForm(ViewContext context) + { + QueryForm form = new QueryForm("samples", null); + form.setViewContext(getViewContext()); + form.bindParameters(getViewContext().getBindPropertyValues()); + return form; + } + + @Override + public BindException bindParameters(PropertyValues m) throws Exception + { + BindException bind = super.bindParameters(m); + + QueryUpdateForm tableForm = (QueryUpdateForm)bind.getTarget(); + + int sampleId; + try + { + sampleId = Integer.parseInt((String) tableForm.getPkVal()); + } + catch (NumberFormatException e) + { + throw new NotFoundException("Invalid RowId: " + tableForm.getPkVal()); + } + + ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); + if (material == null) + throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); + + return bind; + } + + @Override + public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) + { + int sampleId = Integer.parseInt((String) tableForm.getPkVal()); + + ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); + if (material == null) + throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); + + boolean isAliquot = !StringUtils.isEmpty(material.getAliquotedFromLSID()); + + TableInfo tableInfo = tableForm.getTable(); + Map scopedFields = new CaseInsensitiveHashMap<>(); + for (DomainProperty dp : tableInfo.getDomain().getProperties()) + { + if (!ExpSchema.DerivationDataScopeType.All.name().equalsIgnoreCase(dp.getDerivationDataScope())) + scopedFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); + } + + for (var column : tableInfo.getColumns()) + { + String columnName = column.getName(); + if (scopedFields.containsKey(columnName)) + { + boolean isAliquotField = scopedFields.get(columnName); + boolean show = (isAliquot && isAliquotField) || (!isAliquot && !isAliquotField); + ((BaseColumnInfo)column).setUserEditable(show); + ((BaseColumnInfo)column).setHidden(!show); + } + } + + ButtonBar bb = createSubmitCancelButtonBar(tableForm); + UpdateView view = new UpdateView(tableForm, errors); + view.getDataRegion().setButtonBar(bb); + return view; + } + + @Override + public boolean handlePost(QueryUpdateForm tableForm, BindException errors) + { + doInsertUpdate(tableForm, errors, false); + return 0 == errors.getErrorCount(); + } + + @Override + public void addNavTrail(NavTree root) + { + super.addNavTrail(root); + root.addChild("Edit " + _form.getQueryName()); + } + } + + @RequiresPermission(InsertPermission.class) + public static class InsertMaterialQueryRowAction extends UserSchemaAction + { + @Override + protected QueryForm createQueryForm(ViewContext context) + { + QueryForm form = new QueryForm("samples", null); + form.setViewContext(getViewContext()); + form.bindParameters(getViewContext().getBindPropertyValues()); + + return form; + } + + @Override + public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) + { + TableInfo tableInfo = tableForm.getTable(); + Map propertyFields = new CaseInsensitiveHashMap<>(); + for (DomainProperty dp : tableInfo.getDomain().getProperties()) + { + propertyFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); + } + + for (var column : tableInfo.getColumns()) + { + String columnName = column.getName(); + if (propertyFields.containsKey(columnName)) + { + boolean isAliquotField = propertyFields.get(columnName); + ((BaseColumnInfo)column).setUserEditable(!isAliquotField); + ((BaseColumnInfo)column).setHidden(isAliquotField); + } + } + + InsertView view = new InsertView(tableForm, errors); + view.getDataRegion().setButtonBar(createSubmitCancelButtonBar(tableForm)); + return view; + } + + @Override + public boolean handlePost(QueryUpdateForm tableForm, BindException errors) + { + doInsertUpdate(tableForm, errors, true); + return 0 == errors.getErrorCount(); + } + + @Override + public void addNavTrail(NavTree root) + { + super.addNavTrail(root); + root.addChild("Insert " + _form.getQueryName()); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class SaveFindIdsAction extends ReadOnlyApiAction + { + + public static final String FIND_BY_IDS_SESSION_KEY_PREFIX = "findByIds"; + + @Override + public Object execute(FindByIdsForm form, BindException errors) throws Exception + { + HttpServletRequest request = getViewContext().getRequest(); + String key = form.getSessionKey(); + boolean removePrevious = false; + + if (key == null) + { + removePrevious = true; + key = FIND_BY_IDS_SESSION_KEY_PREFIX + "_" + UniqueID.getServerSessionScopedUID(); + } + + if (request != null) + { + if (removePrevious) + SessionHelper.clearAttributesWithPrefix(request, FIND_BY_IDS_SESSION_KEY_PREFIX); + HttpSession session = request.getSession(false); + if (session != null) + { + @SuppressWarnings("unchecked") + List existingIds = (List) session.getAttribute(key); + + // deduplicate from existing ids + if (existingIds != null && form.getSessionKey() != null) + { + existingIds.addAll(form.getIds().stream().filter(id -> !existingIds.contains(id)).toList()); + session.setAttribute(key, existingIds); + } + else + { + session.setAttribute(key, form.getIds()); + } + return success("Saved ids to session key", key); + } + } + + return new SimpleResponse<>(false, "Unable to save to session. Session or request may be null."); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class SaveOrderedSamplesQueryAction extends ReadOnlyApiAction + { + private static final String SAMPLE_ID_PREFIX = "s:"; + private static final String UNIQUE_ID_PREFIX = "u:"; + + private List _ids; + private Map> _uniqueIdLsids; + + @Override + public void validateForm(FindByIdsForm form, Errors errors) + { + if (form.getSessionKey() == null) + errors.reject(ERROR_REQUIRED, "sessionKey must be provided"); + else + { + _ids = getFindIdsFromSession(form.getSessionKey()); + if (_ids == null || _ids.isEmpty()) + errors.reject(ERROR_REQUIRED, "No ids found corresponding to session key " + form.getSessionKey()); + } + } + + private void ensureUniqueIdLsids() + { + boolean hasUniqueId = _ids.stream().anyMatch(s -> s.startsWith(UNIQUE_ID_PREFIX)); + if (hasUniqueId && _uniqueIdLsids == null) + { + List uniqueIds = _ids.stream().map(s -> s.substring(UNIQUE_ID_PREFIX.length())).toList(); + _uniqueIdLsids = ExperimentService.get().getUniqueIdLsids(uniqueIds, getUser(), getContainer()); + } + } + + @Override + public Object execute(FindByIdsForm form, BindException errors) throws Exception + { + ensureUniqueIdLsids(); + + SQLFragment select = getOrderedRowsSql(); + // need to set the key field so selections are possible + // need the SampleTypeUnits so we will display using that unit + String metadata = + """ + + + + + true + true + + + true + + + true + + +
+ """; + QueryDefinition def = QueryService.get().saveSessionQuery(getViewContext(), getContainer(), ExperimentServiceImpl.getExpSchema().getName(), select.getSQL(), metadata); + return success("Session query created", Map.of("queryName", def.getName(), "ids", _ids)); + } + + + private List getFindIdsFromSession(String sessionKey) + { + HttpServletRequest request = getViewContext().getRequest(); + List ids = new ArrayList<>(); + if (request != null) + { + HttpSession session = request.getSession(false); + if (session != null) + { + ids = (List) session.getAttribute(sessionKey); + } + } + return ids; + } + + private SQLFragment getOrderedRowsSql() + { + boolean isFMEnabled = InventoryService.isFreezerManagementEnabled(getContainer()); + String samplesTable = isFMEnabled ? "inventory.SampleItems" : "exp.materials"; + List orderedIdCols = new ArrayList<>(Arrays.asList("Id AS ProvidedID", "RowId", "Ordinal")); + List sampleColumns = new ArrayList<>(); + if (!isFMEnabled) + { + sampleColumns.addAll(Arrays.asList( + "S.Name AS SampleID", + "S.MaterialExpDate AS ExpirationDate", + "S.SampleSet as SampleType", + "S.SampleState", + "S.isAliquot", + "S.Created", + "S.CreatedBy" + )); + } + else + { + sampleColumns.addAll(Arrays.asList( + "S.Name AS SampleID", + "S.MaterialExpDate AS ExpirationDate", + "S.LabelColor", + "S.SampleSet", + "S.SampleState", + "S.StoredAmount", + "S.Units", + "S.SampleTypeUnits", + "S.FreezeThawCount", + "S.StorageStatus", + "S.CheckedOutBy", + "S.StorageLocation", + "S.StorageRow", + "S.StorageCol", + "S.StoragePositionNumber", + "S.IsAliquot", + "S.Created", + "S.CreatedBy" + )); + } + + + String sampleIdComma = ""; + String uniqueIdComma = ""; + int index = 1; + SQLFragment sampleIdValuesSql = new SQLFragment(); + SQLFragment uniqueIdValuesSql = new SQLFragment(); + for (String id : _ids) + { + if (id.startsWith(SAMPLE_ID_PREFIX)) + { + sampleIdValuesSql.append(sampleIdComma).append("\t(").appendValue(index); + sampleIdValuesSql.append(", "); + sampleIdValuesSql.append(LabKeySql.quoteString(id.substring(SAMPLE_ID_PREFIX.length()))); + sampleIdValuesSql.append(", "); + sampleIdValuesSql.append(LabKeySql.quoteString("null")); + sampleIdValuesSql.append(")"); + sampleIdComma = "\n,"; + } + else if (id.startsWith(UNIQUE_ID_PREFIX)) + { + String idClean = id.substring(UNIQUE_ID_PREFIX.length()); + + List lsids = _uniqueIdLsids.get(idClean); + if (lsids != null) + { + for (String lsid : lsids) + { + uniqueIdValuesSql.append(uniqueIdComma).append("\t(").appendValue(index); + uniqueIdValuesSql.append(", "); + uniqueIdValuesSql.append(LabKeySql.quoteString(idClean)); + uniqueIdValuesSql.append(", "); + uniqueIdValuesSql.append(LabKeySql.quoteString(lsid)); + uniqueIdValuesSql.append(")"); + uniqueIdComma = "\n,"; + } + } + } + index++; + } + + boolean haveData = !sampleIdValuesSql.isEmpty() || !_uniqueIdLsids.isEmpty(); + SQLFragment sql = new SQLFragment(); + if (!sampleIdValuesSql.isEmpty()) + { + sql.append("WITH _ordered_ids_ AS (\nSELECT * FROM (VALUES\n"); + sql.append(sampleIdValuesSql); + sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter + } + if (!uniqueIdValuesSql.isEmpty()) + { + if (!sampleIdValuesSql.isEmpty()) + sql.append(",\n"); + else + sql.append("WITH "); + + sql.append("_ordered_unique_ids_ AS (\nSELECT * FROM (VALUES\n"); + sql.append(uniqueIdValuesSql); + sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter + } + + sql.append("SELECT "); + sql.append("\n\tOID.").append(StringUtils.join(orderedIdCols, ",\n\tOID.")); + sql.append(",\n\t").append(StringUtils.join( sampleColumns, ",\n\t")); + sql.append("\nFROM\n("); + if (!sampleIdValuesSql.isEmpty()) + { + sql.append("SELECT\n\tM.RowId,\n\t_ordered_ids_.column1 as Ordinal,\n\t_ordered_ids_.column2 as Id,\n\t_ordered_ids_.column2 as lsid"); + sql.append("\nFROM _ordered_ids_\n"); + sql.append("INNER JOIN exp.materials M ON _ordered_ids_.column2 = M.Name"); + sql.append("\n"); + } + if (!uniqueIdValuesSql.isEmpty()) + { + if (!sampleIdValuesSql.isEmpty()) + sql.append("\nUNION ALL\n\n"); + + sql.append("SELECT\n\tM.RowId,\n\t_ordered_unique_ids_.column1 as Ordinal,\n\t_ordered_unique_ids_.column2 as Id,\n\t_ordered_unique_ids_.column3 as lsid"); + sql.append("\nFROM _ordered_unique_ids_\n"); + sql.append("INNER JOIN exp.materials M ON _ordered_unique_ids_.column3 = M.lsid"); + sql.append("\n"); + } + if (!haveData) // no data to return but return data in the expected shape. + { + sql = new SQLFragment("SELECT\n"); + sql.append(orderedIdCols.stream() + .map(col -> { + int asIndex = col.indexOf("AS"); + if (asIndex > 0) + return "NULL AS " + col.substring(asIndex+ 3); + else + return "NULL AS " + col; + }) + .collect(Collectors.joining(",\t\n"))); + sql.append(",\t\n").append(StringUtils.join(sampleColumns, ",\t\n")); + sql.append("\nFROM ").append(samplesTable).append(" S WHERE 1 = 2"); + return sql; + } + else + { + sql.append(") OID"); + if (isFMEnabled) + sql.append("\nLEFT JOIN inventory.SampleItems S on S.RowId = OID.RowId"); + else + sql.append("\nINNER JOIN exp.materials S on S.RowId = OID.RowId"); + sql.append("\n\nORDER BY Ordinal"); + return sql; + } + } + } + + public static class FindByIdsForm extends FindSessionKeyForm + { + List _ids; + + public List getIds() + { + return _ids; + } + + public void setIds(List ids) + { + _ids = ids; + } + } + + + public static class FindSessionKeyForm + { + private String _sessionKey; + + public String getSessionKey() + { + return _sessionKey; + } + + public void setSessionKey(String sessionKey) + { + _sessionKey = sessionKey; + } + } + + static void validateEntitySequenceForm(EntitySequenceForm form, Errors errors) + { + String kindName = form.getKindName(); + if (StringUtils.isEmpty(kindName) || form.getSeqType() == null) + { + errors.reject(ERROR_REQUIRED, "KindName and SeqType must be provided"); + return; + } + + if (form.getSeqType() == NameGenerator.EntityCounter.genId) + { + if (form.getRowId() == null) + errors.reject(ERROR_REQUIRED, "Data type RowId must be provided for genId"); + } + else if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName)) + { + errors.reject(ERROR_MSG, form.getSeqType() + " is not supported for " + kindName); + } + + if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName) && !DataClassDomainKind.NAME.equalsIgnoreCase(kindName)) + errors.reject(ERROR_MSG, "Invalid KindName. Should be either " + SampleTypeDomainKind.NAME + " or " + DataClassDomainKind.NAME + "."); + + } + + @RequiresPermission(ReadPermission.class) + public static class GetEntitySequenceAction extends ReadOnlyApiAction + { + @Override + public void validateForm(EntitySequenceForm form, Errors errors) + { + validateEntitySequenceForm(form, errors); + } + + @Override + public Object execute(EntitySequenceForm form, BindException errors) throws Exception + { + long value = -1; + if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + if (form.getSeqType() == NameGenerator.EntityCounter.genId) + { + ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); + if (sampleType != null) + value = sampleType.getCurrentGenId(); + } + else + { + value = SampleTypeService.get().getCurrentCount(form.getSeqType(), getContainer()); + } + + } + else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); + if (dataClass != null) + value = dataClass.getCurrentGenId(); + } + + ApiSimpleResponse resp = new ApiSimpleResponse(); + resp.put("success", value > -1); + resp.put("value", value); + return resp; + } + } + + @RequiresPermission(ReadPermission.class) // actual permission checked later + public static class SetEntitySequenceAction extends MutatingApiAction + { + @Override + public void validateForm(EntitySequenceForm form, Errors errors) + { + validateEntitySequenceForm(form, errors); + + if (form.getNewValue() == null || form.getNewValue() < 0) + errors.reject(ERROR_MSG, "Invalid newValue."); + } + + @Override + public Object execute(EntitySequenceForm form, BindException errors) + { + ApiSimpleResponse resp = new ApiSimpleResponse(); + resp.put("success", true); + + try + { + Domain domain = null; + if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + if (form.getSeqType() == NameGenerator.EntityCounter.genId) + { + if (!getContainer().hasPermission(getUser(), DesignSampleTypePermission.class)) + throw new UnauthorizedException("Insufficient permissions."); + + ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); + if (sampleType != null) + { + sampleType.ensureMinGenId(form.getNewValue()); + domain = sampleType.getDomain(); + } + else + { + resp.put("success", false); + resp.put("error", "Sample type does not exist."); + } + } + else + { + if (!getContainer().hasPermission(getUser(), AdminPermission.class)) + throw new UnauthorizedException("Insufficient permissions."); + + SampleTypeService.get().ensureMinSampleCount(form.getNewValue(), form.getSeqType(), getContainer()); + } + } + else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + if (!getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) + throw new BadRequestException("Insufficient permissions."); + + ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); + if (dataClass != null) + { + dataClass.ensureMinGenId(form.getNewValue(), getContainer()); + domain = dataClass.getDomain(); + } + else + { + resp.put("success", false); + resp.put("error", "DataClass does not exist."); + } + } + + if (domain != null) + { + DomainAuditProvider.DomainAuditEvent event = new DomainAuditProvider.DomainAuditEvent(getContainer(), "The genId for domain " + domain.getName() + " has been updated to " + form.getNewValue() + "."); + event.setDomainUri(domain.getTypeURI()); + event.setDomainName(domain.getName()); + AuditLogService.get().addEvent(getUser(), event); + } + } + catch (ExperimentException e) + { + resp.put("success", false); + resp.put("error", e.getMessage()); + } + + return resp; + } + } + + public static class EntitySequenceForm + { + private String _kindName; + private NameGenerator.EntityCounter _seqType; + private Integer _rowId; + private Long _newValue; + + public Integer getRowId() + { + return _rowId; + } + + public void setRowId(Integer rowId) + { + _rowId = rowId; + } + + public String getKindName() + { + return _kindName; + } + + public void setKindName(String kindName) + { + _kindName = kindName; + } + + public Long getNewValue() + { + return _newValue; + } + + public void setNewValue(Long newValue) + { + this._newValue = newValue; + } + + public NameGenerator.EntityCounter getSeqType() + { + return _seqType; + } + + public void setSeqType(String seqType) + { + _seqType = NameGenerator.EntityCounter.valueOf(seqType); + } + + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetCrossFolderDataSelectionAction extends ReadOnlyApiAction + { + @Override + public void validateForm(CrossFolderSelectionForm form, Errors errors) + { + if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); + if (!"samples".equalsIgnoreCase(form.getDataType()) && !"exp.data".equalsIgnoreCase(form.getDataType())&& !"assay".equalsIgnoreCase(form.getDataType())) + errors.reject(ERROR_REQUIRED, "Data type (sample, data or assayrun) must be specified."); + } + + @Override + public Object execute(CrossFolderSelectionForm form, BindException errors) + { + Pair result = ExperimentServiceImpl.getCurrentAndCrossFolderDataCount(form.getIds(false), form.getDataType(), getContainer()); + + ApiSimpleResponse resp = new ApiSimpleResponse(); + resp.put("success", true); + resp.put("currentFolderSelectionCount", result.first); + resp.put("crossFolderSelectionCount", result.second); + + return success(resp); + } + } + + public static class CrossFolderSelectionForm extends DataViewSnapshotSelectionForm + { + private String _dataType; + private String _picklistName; + + public String getDataType() + { + return _dataType; + } + + public void setDataType(String dataType) + { + _dataType = dataType; + } + + public String getPicklistName() + { + return _picklistName; + } + + public void setPicklistName(String picklistName) + { + _picklistName = picklistName; + } + + @Override + public Set getIds(boolean clear) + { + Set selectedIds; + + if (_rowIds != null) + selectedIds = _rowIds; + else if (isUseSnapshotSelection()) + selectedIds = new HashSet<>(DataRegionSelection.getSnapshotSelectedIntegers(getViewContext(), getDataRegionSelectionKey())); + else + selectedIds = DataRegionSelection.getSelectedIntegers(getViewContext(), getDataRegionSelectionKey(), clear); + + if (_picklistName != null) + { + User user = getViewContext().getUser(); + Container container = getViewContext().getContainer(); + UserSchema schema = ListService.get().getUserSchema(user, container); + TableInfo tInfo = schema.getTable(_picklistName); + if (tInfo != null) + { + SimpleFilter filter = SimpleFilter.createContainerFilter(container); + filter.addInClause(FieldKey.fromParts("id"), selectedIds); + TableSelector selector = new TableSelector(tInfo, Collections.singleton("SampleID"), filter, null); + return new HashSet<>(selector.getArrayList(Long.class)); + } + } + return selectedIds; + } + } + + @RequiresPermission(AdminPermission.class) + public static class RecomputeAliquotRollup extends SimpleViewAction + { + @Override + public void addNavTrail(NavTree root) + { + } + + @Override + public ModelAndView getView(Object o, BindException errors) throws SQLException + { + try (var ignore = SpringActionController.ignoreSqlUpdates()) + { + Container container = getContainer(); + User user = getUser(); + + List sampleTypes = SampleTypeService.get() + .getSampleTypes(container, user, true); + + HtmlStringBuilder builder = HtmlStringBuilder.of(); + builder.unsafeAppend(""); + + SampleTypeService service = SampleTypeService.get(); + for (ExpSampleType sampleType : sampleTypes) + { + int updatedCount; + updatedCount = service.recomputeSampleTypeRollup(sampleType, container); + // we could check "if (0 < updatedCount) refresh(rollup)", but since this is a "manual" usage lets just always refresh + SampleTypeServiceImpl.get().refreshSampleTypeMaterializedView(sampleType, update); + builder.unsafeAppend(""); + } + + builder.unsafeAppend("
Sample Type#Recomputed
") + .append(sampleType.getName()) + .unsafeAppend("") + .append(updatedCount) + .unsafeAppend("
"); + return new HtmlView("Aliquot Rollup Recalculation Result", builder); + } + } + } + + /* Also see API CheckEdgesAction */ + @RequiresPermission(TroubleshooterPermission.class) + public static class CycleCheckAction extends FormViewAction + { + List cycleObjectIds = null; + + @Override + public void validateCommand(Object target, Errors errors) + { + + } + + @Override + public ModelAndView getView(Object o, boolean reshow, BindException errors) + { + if (!reshow) + { + return new HtmlView( + DIV("This operation can use a lot of memory.", + LK.FORM(at(method,"POST"), + PageFlowUtil.button("Continue").submit(true))) + ); + } + + if (null == cycleObjectIds) + return new HtmlView(HtmlString.of("No cycles found")); + + Map map = new LongHashMap<>(); + var cf = new ContainerFilter.AllFolders(getUser()); + var materials = ExperimentServiceImpl.get().getExpMaterialsByObjectId(cf, cycleObjectIds); + materials.forEach( (m) -> map.put(m.getObjectId(), m)); + var datas = ExperimentServiceImpl.get().getExpDatasByObjectId(cf, cycleObjectIds); + datas.forEach( (d) -> map.put(d.getObjectId(), d)); + var runs = ExperimentServiceImpl.get().getRunsByObjectId(cf, cycleObjectIds); + runs.forEach( (r) -> map.put(r.getObjectId(), r)); + + ExperimentUrls urls = ExperimentUrls.get(); + return new HtmlView( + DIV("Cycle found involving these objects.", + UL(cycleObjectIds.stream().map((objectid) -> + { + ExpObject exp = map.get(objectid); + if (exp instanceof ExpMaterial mat) + return LI(A(at(target, "_blank", href, urls.getMaterialDetailsURL(mat)), objectid + " : material - " + mat.getName())); + else if (exp instanceof ExpRun run) + return LI(A(at(target, "_blank", href, urls.getRunTextURL(run)), objectid + " : run - " + run.getName())); + else if (exp instanceof ExpData data) + return LI(A(at(target, "_blank", href, urls.getDataDetailsURL(data)), objectid + " : run - " + data.getName())); + else + return LI(String.valueOf(objectid)); + })) + ) + ); + } + + @Override + public boolean handlePost(Object o, BindException errors) + { + var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") + .resultSetStream() + .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) + .collect(toList()); + var cyclesEdges = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); + + var set = new LinkedHashSet(); + cyclesEdges.forEach( (edge) -> { + set.add(edge.first); + set.add(edge.second); + }); + cycleObjectIds = set.stream().toList(); + return false; + } + + @Override + public URLHelper getSuccessURL(Object o) + { + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + + } + } + + @RequiresPermission(AdminPermission.class) + public static class MissingFilesCheckAction extends ReadOnlyApiAction + { + @Override + public Object execute(Object o, BindException errors) throws Exception + { + Map> info = ExperimentServiceImpl.get().doMissingFilesCheck(getUser(), getContainer(), true); + JSONObject results = new JSONObject(); + for (String containerId : info.keySet()) + { + JSONObject containerResults = new JSONObject(); + for (String sourceName : info.get(containerId).keySet()) + containerResults.put(sourceName, info.get(containerId).get(sourceName).toJSON()); + results.put(containerId, containerResults); + } + + ApiSimpleResponse response = new ApiSimpleResponse(); + response.put("success", true); + response.put("result", results); + return response; + } + } + +} From b9743c6516edb5448c50f859b5bd5970ab3bcb8c Mon Sep 17 00:00:00 2001 From: XingY Date: Tue, 11 Nov 2025 20:33:05 -0800 Subject: [PATCH 2/3] crlf --- .../org/labkey/experiment/api/ExpRunImpl.java | 2152 ++++++++--------- 1 file changed, 1076 insertions(+), 1076 deletions(-) diff --git a/experiment/src/org/labkey/experiment/api/ExpRunImpl.java b/experiment/src/org/labkey/experiment/api/ExpRunImpl.java index dbb3747b312..73ac80aecae 100644 --- a/experiment/src/org/labkey/experiment/api/ExpRunImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpRunImpl.java @@ -1,1076 +1,1076 @@ -/* - * Copyright (c) 2008-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.labkey.experiment.api; - -import org.apache.commons.io.FileUtils; -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.cloud.CloudStoreService; -import org.labkey.api.data.Container; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; -import org.labkey.api.data.SqlExecutor; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.Table; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; -import org.labkey.api.data.dialect.SqlDialect; -import org.labkey.api.exp.ExperimentException; -import org.labkey.api.exp.ExperimentRunType; -import org.labkey.api.exp.OntologyManager; -import org.labkey.api.exp.api.DataType; -import org.labkey.api.exp.api.ExpData; -import org.labkey.api.exp.api.ExpMaterial; -import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.exp.api.ExpProtocolAction; -import org.labkey.api.exp.api.ExpProtocolApplication; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ProtocolImplementation; -import org.labkey.api.exp.api.ProvenanceService; -import org.labkey.api.exp.query.ExpRunTable; -import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.query.BatchValidationException; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryRowReference; -import org.labkey.api.security.User; -import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; -import org.labkey.api.security.permissions.UpdatePermission; -import org.labkey.api.util.FileUtil; -import org.labkey.api.util.NetworkDrive; -import org.labkey.api.view.ActionURL; -import org.labkey.api.view.UnauthorizedException; -import org.labkey.experiment.DotGraph; -import org.labkey.experiment.ExperimentRunGraph; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.Date; -import java.util.HashMap; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Map; -import java.util.Set; - -import static org.labkey.experiment.api.ExperimentServiceImpl.getExpSchema; - -public class ExpRunImpl extends ExpIdentifiableEntityImpl implements ExpRun -{ - public static final String NAMESPACE_PREFIX = "Run"; - - private boolean _populated; - private List _protocolSteps; - private Map _materialInputs = new HashMap<>(); - private Map _dataInputs = new HashMap<>(); - private List _materialOutputs = new ArrayList<>(); - private List _dataOutputs = new ArrayList<>(); - private ExpRunImpl _replacedByRun; - private Integer _maxOutputActionSequence = null; - private static final Logger LOG = LogManager.getLogger(ExpRunImpl.class); - private ExpProtocolApplication _workflowTask; - - static public List fromRuns(List runs) - { - List ret = new ArrayList<>(runs.size()); - for (ExperimentRun run : runs) - { - ret.add(new ExpRunImpl(run)); - } - return ret; - } - - // For serialization - protected ExpRunImpl() {} - - public ExpRunImpl(ExperimentRun run) - { - super(run); - if (null != run && null != run.getObjectId()) - _objectId = run.getObjectId(); - } - - @Override - public ActionURL detailsURL() - { - return _object.detailsURL(); - } - - @Override - public @Nullable QueryRowReference getQueryRowReference() - { - ExpProtocol protocol = getProtocol(); - if (protocol != null) - { - ProtocolImplementation impl = protocol.getImplementation(); - if (impl != null) - { - QueryRowReference ref = impl.getQueryRowReference(protocol, this); - if (ref != null) - return ref; - } - - ExperimentRunType type = ExperimentService.get().getExperimentRunType(protocol); - if (type != null) - { - QueryRowReference ref = type.getQueryRowReference(protocol, this); - if (ref != null) - return ref; - } - } - - return new QueryRowReference(getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Runs.name(), FieldKey.fromParts(ExpRunTable.Column.RowId), getRowId()); - } - - @Override - public Container getContainer() - { - return _object.getContainer(); - } - - @Override - public long getRowId() - { - return _object.getRowId(); - } - - @Override - public List getExperiments() - { - final String sql= " SELECT E.* FROM " + ExperimentServiceImpl.get().getTinfoExperiment() + " E " - + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoRunList() + " RL ON (E.RowId = RL.ExperimentId) " - + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoExperimentRun() + " ER ON (ER.RowId = RL.ExperimentRunId) " - + " WHERE ER.LSID = ? AND E.Hidden = ?"; - - return ExpExperimentImpl.fromExperiments(new SqlSelector(getExpSchema(), sql, _object.getLSID(), Boolean.FALSE).getArray(Experiment.class)); - } - - @Override - public @Nullable ExpExperimentImpl getBatch() - { - if (_object.getBatchId() == null) - return null; - - ExpExperimentImpl batch = ExperimentServiceImpl.get().getExpExperiment(_object.getBatchId()); - if (batch == null) - return null; - - assert checkBatch(batch); - return batch; - } - - private boolean checkBatch(ExpExperimentImpl batch) - { - List exps = getExperiments(); - if (!exps.contains(batch)) - { - LOG.warn("Expected batch '" + batch.getRowId() + "' to be in list of experiments: " + exps); - return false; - } - - if (!getProtocol().equals(batch.getBatchProtocol())) - { - LOG.warn("Expected batch '" + batch.getRowId() + "' to have same protocol as run. Expected protocol '" + getProtocol() + "', but found '" + batch.getBatchProtocol() + "'"); - return false; - } - - return true; - } - - protected void setBatchId(Long batchId) - { - assert batchId == null || checkBatch(ExperimentServiceImpl.get().getExpExperiment(batchId)); - _object.setBatchId(batchId); - } - - @Override - public ExpProtocolImpl getProtocol() - { - return ExperimentServiceImpl.get().getExpProtocol(_object.getProtocolLSID()); - } - - @Override - public boolean isFinalOutput(ExpData data) - { - ExpProtocolApplication sourceApplication = data.getSourceApplication(); - return sourceApplication != null && sourceApplication.getActionSequence() == getMaxOutputActionSequence(); - } - - private int getMaxOutputActionSequence() - { - if (_maxOutputActionSequence == null) - { - _maxOutputActionSequence = 0; - for (ExpProtocolApplication app : getProtocolApplications()) - if (!app.getDataOutputs().isEmpty() && app.getActionSequence() > _maxOutputActionSequence) - _maxOutputActionSequence = app.getActionSequence(); - } - return _maxOutputActionSequence; - } - - @Override - public List getOutputDatas(@Nullable DataType type) - { - return ExperimentServiceImpl.get().getOutputDatas(getRowId(), type); - } - - @Override - public List getInputDatas(@Nullable String inputRole, @Nullable ExpProtocol.ApplicationType applicationType) - { - SQLFragment sql = new SQLFragment(); - sql.append("SELECT exp.Data.* FROM exp.Data WHERE exp.Data.RowId IN "); - sql.append("\n(SELECT exp.DataInput.DataId FROM exp.DataInput "); - sql.append("\nINNER JOIN exp.ProtocolApplication ON exp.DataInput.TargetApplicationId = exp.ProtocolApplication.RowId"); - sql.append("\nWHERE exp.ProtocolApplication.RunId = ?"); - sql.add(getRowId()); - if (inputRole != null) - { - sql.append("\nAND exp.DataInput.Role = ? "); - sql.add(inputRole); - } - if (applicationType != null) - { - sql.append("\nAND exp.ProtocolApplication.CpasType = "); - sql.appendValue(applicationType.toString()); - } - sql.append(")"); - return ExpDataImpl.fromDatas(new SqlSelector(ExperimentService.get().getSchema(), sql).getArrayList(Data.class)); - } - - @Override - public File getFilePathRoot() - { - if (_object.getFilePathRoot() == null || FileUtil.hasCloudScheme(_object.getFilePathRoot())) - return null; - else - return new File(FileUtil.createUri(_object.getFilePathRoot(), false)); - } - - @Override - public void setFilePathRoot(File file) - { - ensureUnlocked(); - // We want "/Users/..." for local file system - _object.setFilePathRoot(file == null ? null : file.toPath().toString()); - } - - @Override - public Path getFilePathRootPath() - { - if (_object.getFilePathRoot() == null) - return null; - else if (FileUtil.hasCloudScheme(_object.getFilePathRoot())) - return CloudStoreService.get().getPathFromUrl(getContainer(), _object.getFilePathRoot()); - else - return new File(FileUtil.createUri(_object.getFilePathRoot(), false)).toPath(); - } - - @Override - public void setFilePathRootPath(Path filePathRoot) - { - ensureUnlocked(); - _object.setFilePathRoot(filePathRoot == null ? null : - FileUtil.hasCloudScheme(filePathRoot) ? - FileUtil.pathToString(filePathRoot) : - filePathRoot.toString()); - } - - @Override - public void save(User user) throws BatchValidationException - { - ExperimentServiceImpl expService = ExperimentServiceImpl.get(); - try (DbScope.Transaction t = getExpSchema().getScope().ensureTransaction()) - { - boolean newRun = getRowId() == 0; - expService.onBeforeRunSaved(getProtocol(), this, getContainer(), user); - save(user, expService.getTinfoExperimentRun(), true); - if (newRun) - expService.auditRunEvent(user, this.getProtocol(), this, null, this.getProtocol().getName() + " run loaded"); - t.addCommitTask(() -> expService.onAfterRunSaved(getProtocol(), this, getContainer(), user), DbScope.CommitTaskOption.POSTCOMMIT); - t.commit(); - } - } - - @Override - protected void save(User user, TableInfo table, boolean ensureObject) - { - assert ensureObject; - super.save(user, table, true); - ExperimentServiceImpl.get().invalidateExperimentRun(getLSID()); - } - - @Override - public void delete(User user) - { - delete(user, null); - } - - @Override - public void delete(User user, @Nullable final String auditUserComment) - { - if (!canDelete(user)) - { - throw new UnauthorizedException(); - } - ExperimentServiceImpl.get().deleteExperimentRuns(getContainer(), user, auditUserComment, Arrays.asList(this), null); - } - - @Override - public void setProtocol(ExpProtocol protocol) - { - _object.setProtocolLSID(protocol.getLSID()); - } - - @Override - public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name) - { - return addProtocolApplication(user, action, appType, name, null, null, null); - } - - public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name, java.util.Date startTime, java.util.Date endTime, Integer recordCount) - { - ensureUnlocked(); - ProtocolApplication pa = new ProtocolApplication(); - if (action == null) - { - if (appType != ExpProtocol.ApplicationType.ExperimentRun) - { - throw new IllegalArgumentException("Only the ExperimentRun protocol application type is allowed to have a null protocol action."); - } - pa.setProtocolLSID(getProtocol().getLSID()); - } - else - { - pa.setProtocolLSID(action.getChildProtocol().getLSID()); - pa.setActionSequence(action.getActionSequence()); - } - pa.setName(name); - pa.setLSID(ExperimentService.get().generateGuidLSID(getContainer(), ExpProtocolApplication.class)); - pa.setCpasType(appType.toString()); - pa.setRunId(getRowId()); - pa.setStartTime(startTime); - pa.setEndTime(endTime); - pa.setRecordCount(recordCount); - - pa = Table.insert(user, ExperimentServiceImpl.get().getTinfoProtocolApplication(), pa); - return new ExpProtocolApplicationImpl(pa); - } - - @Override - public String getComments() - { - return _object.getComments(); - } - - @Override - public void setComments(String comments) - { - ensureUnlocked(); - _object.setComments(comments); - } - - @Override - public void setEntityId(String entityId) - { - ensureUnlocked(); - _object.setEntityId(entityId); - } - - @Override - public String getEntityId() - { - return _object.getEntityId(); - } - - - @Override - public void setContainer(Container container) - { - _object.setContainer(container); - } - - @Override - public void setJobId(Long jobId) - { - ensureUnlocked(); - _object.setJobId(jobId); - } - - @Override - public Long getJobId() - { - return _object.getJobId(); - } - - public void setProtocolApplications(List protocolSteps) - { - ensureUnlocked(); - _protocolSteps = protocolSteps; - } - - @Override - public @NotNull Map getMaterialInputs() - { - ensureFullyPopulated(); - return _materialInputs; - } - - @Override - public @NotNull Map getDataInputs() - { - ensureFullyPopulated(); - return _dataInputs; - } - - @Override - public List getMaterialOutputs() - { - ensureFullyPopulated(); - return _materialOutputs; - } - - @Override - public List getDataOutputs() - { - ensureFullyPopulated(); - return _dataOutputs; - } - - @Override - public List getProtocolApplications() - { - ensureFullyPopulated(); - return _protocolSteps; - } - - @Override - public @Nullable ExpProtocolApplication getProtocolApplication() - { - return findProtocolApplication(ExpProtocol.ApplicationType.ProtocolApplication); - } - - @Override - public @Nullable ExpProtocolApplication getInputProtocolApplication() - { - return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRun); - } - - private @Nullable ExpProtocolApplication findProtocolApplication(ExpProtocol.ApplicationType type) - { - for (ExpProtocolApplicationImpl expProtocolApplication : getProtocolApplications()) - { - if (type.equals(expProtocolApplication.getApplicationType())) - { - return expProtocolApplication; - } - } - return null; - } - - @Override - public @Nullable ExpProtocolApplication getOutputProtocolApplication() - { - return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRunOutput); - } - - @Override - public void deleteProtocolApplications(User user) - { - ensureUnlocked(); - deleteProtocolApplications(getOutputDatas(null), user); - } - - @Override - public void setReplacedByRun(ExpRun run) - { - ensureUnlocked(); - if (run != null && run.getRowId() < 1) - { - throw new IllegalArgumentException("Run must have already been saved to the database"); - } - _object.setReplacedByRunId(run == null ? null : run.getRowId()); - } - - @Override - public ExpRun getReplacedByRun() - { - Long id = _object.getReplacedByRunId(); - if (id == null) - { - return null; - } - if (_replacedByRun == null || _replacedByRun.getRowId() != id.intValue()) - { - _replacedByRun = ExperimentServiceImpl.get().getExpRun(id.intValue()); - } - return _replacedByRun; - } - - @Override - public List getReplacesRuns() - { - return fromRuns(new TableSelector(ExperimentServiceImpl.get().getTinfoExperimentRun(), new SimpleFilter(FieldKey.fromParts("ReplacedByRunId"), getRowId()), new Sort("Name")).getArrayList(ExperimentRun.class)); - } - - public void deleteProtocolApplications(List datasToDelete, User user) - { - if (user == null || !canDelete(user)) - { - throw new UnauthorizedException("Attempting to delete an ExperimentRun without having delete permissions for its container"); - } - final ExperimentServiceImpl svc = ExperimentServiceImpl.get(); - final SqlDialect dialect = svc.getSchema().getSqlDialect(); - - svc.invalidateExperimentRun(getLSID()); - - deleteProtocolApplicationProvenance(); - - svc.beforeDeleteData(user, getContainer(), datasToDelete); - - deleteInputObjects(svc, dialect); - - deleteAppParametersAndInputs(); - - deleteRunMaterials(user); - - deleteRunProtocolApps(); - - clearCache(); - - // Clear the cache in a commit task, which allows us to do a single clear (which is semi-expensive) if multiple - // runs are being deleted in the same transaction, like deleting a container - svc.getSchema().getScope().addCommitTask(ExperimentRunGraph.getCacheClearingCommitTask(getContainer()), DbScope.CommitTaskOption.POSTCOMMIT); - } - - @Override - public boolean canDelete(User user) - { - ExpProtocolImpl protocol = getProtocol(); - boolean isWorkflow = ExpProtocol.isSampleWorkflowProtocol(protocol.getLSID()); - if (isWorkflow && getContainer().hasPermission(user, SampleWorkflowDeletePermission.class)) - return true; - - // Issue 50776: To update lineage we need to delete existing runs - if ((ExperimentServiceImpl.get().isSampleAliquot(protocol) || ExperimentServiceImpl.get().isSampleDerivation(protocol)) && getContainer().hasPermission(user, UpdatePermission.class)) - return true; - - return !isWorkflow && getContainer().hasPermission(user, DeletePermission.class); - } - - // Clean up DataInput and MaterialInput exp.object and properties - private void deleteInputObjects(ExperimentServiceImpl svc, SqlDialect dialect) - { - SQLFragment materialSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + DataInput.lsidPrefix() + "'", - "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoDataInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", getRowId()); - - SQLFragment materialInputSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", - "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoMaterialInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", + getRowId()); - - SQLFragment dataSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + DataInput.lsidPrefix() + "'", - "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoDataInput() + " WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)", getRowId()); - - SQLFragment dataInputSQL = new SQLFragment("SELECT " + - dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", - "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + - " FROM " + svc.getTinfoMaterialInput() + " WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)", getRowId()); - - // Build a single UNION to help reduce DB round trips - SQLFragment unionSQL = new SQLFragment("(") - .append(materialSQL) - .append("\n UNION \n") - .append(materialInputSQL) - .append("\n UNION \n") - .append(dataSQL) - .append("\n UNION \n") - .append(dataInputSQL) - .append(")"); - - OntologyManager.deleteOntologyObjects(svc.getSchema(), unionSQL, getContainer()); - } - - private void deleteProtocolApplicationProvenance() - { - ProvenanceService pvs = ProvenanceService.get(); - pvs.deleteRunProvenance(getRowId()); - } - - private void deleteAppParametersAndInputs() - { - SQLFragment sql = new SQLFragment(); - sql.append("DELETE FROM exp.ProtocolApplicationParameter WHERE ProtocolApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); - - //per Josh: break relation between all datas with this run id and don't delete them - sql.append("UPDATE exp.Data SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); - sql.append("UPDATE exp.Material SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); - - sql.append("DELETE FROM exp.DataInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); - sql.append("DELETE FROM exp.MaterialInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); - sql.append("DELETE FROM exp.DataInput WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)").add(getRowId()).appendEOS(); - sql.append("DELETE FROM exp.MaterialInput WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)").add(getRowId()).appendEOS(); - - new SqlExecutor(getExpSchema()).execute(sql); - } - - private void deleteRunMaterials(User user) - { - for (ExpMaterial expMaterial : ExperimentServiceImpl.get().getExpMaterialsForRun(getRowId())) - { - expMaterial.delete(user); - } - } - - private void deleteRunProtocolApps() - { - new SqlExecutor(getExpSchema()).execute("DELETE FROM exp.ProtocolApplication WHERE RunId = ?", getRowId()); - } - - private synchronized void ensureFullyPopulated() - { - if (!_populated) - { - _populated = true; - ExperimentServiceImpl.get().populateRun(this); - Collections.sort(_materialOutputs); - Collections.sort(_dataOutputs); - - for (ExpProtocolApplicationImpl step : _protocolSteps) - { - Collections.sort(step.getInputDatas()); - Collections.sort(step.getOutputDatas()); - Collections.sort(step.getInputMaterials()); - Collections.sort(step.getOutputMaterials()); - } - } - } - - public void trimRunTree(Integer id, String type) throws ExperimentException - { - ensureUnlocked(); - List listPA = new ArrayList<>(); - List listM = new ArrayList<>(); - List listD = new ArrayList<>(); - Set ancestorPAStack = new LinkedHashSet<>(); - Set descendantPAStack = new LinkedHashSet<>(); - List apps = getProtocolApplications(); - - boolean found = false; - - // support focus on a starting material that is not part of the run - if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) - { - for (ExpMaterialImpl m : getMaterialInputs().keySet()) - if (m.getRowId() == id.intValue()) - { - found = true; - listM.add(m); - listPA.addAll(m.getSuccessorApps()); - descendantPAStack.addAll(m.getSuccessorApps()); - break; - } - } - if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) - { - for (ExpDataImpl d : getDataInputs().keySet()) - if (d.getRowId() == id.intValue()) - { - found = true; - listD.add(d); - listPA.addAll(d.getSuccessorApps()); - descendantPAStack.addAll(d.getSuccessorApps()); - break; - } - } - if (!found) - { - for (ExpProtocolApplicationImpl app : apps) - { - if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) - { - for (ExpMaterialImpl m : app.getOutputMaterials()) - if (m.getRowId() == id.intValue()) - { - found = true; - listM.add(m); - listPA.addAll(m.getSuccessorApps()); - descendantPAStack.addAll(m.getSuccessorApps()); - if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) - { - listPA.add(m.getSourceApplication()); - ancestorPAStack.add(m.getSourceApplication()); - } - break; - } - } - if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) - { - for (ExpDataImpl d : app.getOutputDatas()) - { - if (d.getRowId() == id.intValue()) - { - found = true; - listD.add(d); - listPA.addAll(d.getSuccessorApps()); - descendantPAStack.addAll(d.getSuccessorApps()); - if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) - { - listPA.add(d.getSourceApplication()); - ancestorPAStack.add(d.getSourceApplication()); - } - break; - } - } - } - if (type == null || DotGraph.TYPECODE_PROT_APP.equalsIgnoreCase(type)) - { - if (app.getRowId() == id.intValue()) - { - found = true; - listPA.add(app); - ancestorPAStack.add(app); - descendantPAStack.add(app); - break; - } - } - if (found) - break; - } - } - if (!found) - throw new ExperimentException("Specified node not found in Experiment Run"); - - int loopCount = 0; - while (!descendantPAStack.isEmpty()) - { - if (loopCount++ > 10000) - { - throw new IllegalStateException("Infinite loop detected for run " + getRowId()); - } - - ExpProtocolApplicationImpl pa = descendantPAStack.iterator().next(); - for (ExpMaterialImpl m : pa.getOutputMaterials()) - { - listM.add(m); - descendantPAStack.addAll(m.getSuccessorApps()); - } - for (ExpDataImpl d : pa.getOutputDatas()) - { - listD.add(d); - descendantPAStack.addAll(d.getSuccessorApps()); - } - descendantPAStack.remove(pa); - listPA.add(pa); - if (loopCount++ > 10000) - { - throw new IllegalStateException("Infinite loop detected for run " + getRowId()); - } - } - - loopCount = 0; - while (!ancestorPAStack.isEmpty()) - { - if (loopCount++ > 10000) - { - throw new IllegalStateException("Infinite loop detected for run " + getRowId()); - } - - ExpProtocolApplicationImpl pa = ancestorPAStack.iterator().next(); - if (pa.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun) - break; - for (ExpMaterialImpl m : pa.getInputMaterials()) - { - listM.add(m); - if (getMaterialInputs().containsKey(m)) - { - ExpProtocolApplication runNode = getProtocolApplications().get(0); - assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; - listPA.add(runNode); - continue; - } - if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) - ancestorPAStack.add(m.getSourceApplication()); - } - for (ExpDataImpl d : pa.getInputDatas()) - { - listD.add(d); - if (getDataInputs().containsKey(d)) - { - ExpProtocolApplication runNode = getProtocolApplications().get(0); - assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; - listPA.add(runNode); - continue; - } - if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) - ancestorPAStack.add(d.getSourceApplication()); - } - ancestorPAStack.remove(pa); - listPA.add(pa); - } - - List allPA = new ArrayList<>(); - List deletePA; - List deleteM; - List deleteD; - - setProtocolApplications(null); - - for (ExpProtocolApplicationImpl app : apps) - { - if (listPA.contains(app)) - { - allPA.add(app); - deleteM = new ArrayList<>(); - for (ExpMaterialImpl m : app.getInputMaterials()) - { - if (listM.contains(m)) - { - deletePA = new ArrayList<>(); - for (ExpProtocolApplicationImpl p : m.getSuccessorApps()) - if (!listPA.contains(p)) - deletePA.add(p); - for (ExpProtocolApplicationImpl p : deletePA) - m.getSuccessorApps().remove(p); - } - else - deleteM.add(m); - } - for (ExpMaterialImpl m : deleteM) - { - app.getInputMaterials().remove(m); - getMaterialInputs().remove(m); - } - - deleteD = new ArrayList<>(); - for (ExpDataImpl d : app.getInputDatas()) - { - if (listD.contains(d)) - { - deletePA = new ArrayList<>(); - for (ExpProtocolApplicationImpl p : d.getSuccessorApps()) - if (!listPA.contains(p)) - deletePA.add(p); - for (ExpProtocolApplicationImpl p : deletePA) - d.getSuccessorApps().remove(p); - } - else - deleteD.add(d); - } - for (ExpDataImpl d : deleteD) - { - app.getInputDatas().remove(d); - getDataInputs().remove(d); - } - - deleteM = new ArrayList<>(); - for (ExpMaterialImpl m : app.getOutputMaterials()) - { - if (!listM.contains(m)) - deleteM.add(m); - } - for (ExpMaterialImpl m : deleteM) - app.getOutputMaterials().remove(m); - - - deleteD = new ArrayList<>(); - for (ExpDataImpl d : app.getOutputDatas()) - { - if (!listD.contains(d)) - deleteD.add(d); - } - for (ExpDataImpl d : deleteD) - app.getOutputDatas().remove(d); - } - } - setProtocolApplications(allPA); - } - - @Override - public List getAllDataUsedByRun() - { - SQLFragment sql = new SQLFragment(); - sql.append("select d.* from "); - sql.append(ExperimentServiceImpl.get().getTinfoDataInput(), "di"); - sql.append(", "); - sql.append(ExperimentServiceImpl.get().getTinfoData(), "d"); - sql.append(", "); - sql.append(ExperimentServiceImpl.get().getTinfoProtocolApplication(), "pa"); - sql.append(" where di.targetapplicationid=pa.rowid and pa.runid=? and di.dataid=d.rowid"); - sql.add(getRowId()); - return ExpDataImpl.fromDatas(new SqlSelector(ExperimentServiceImpl.get().getSchema(), sql).getArrayList(Data.class)); - } - - public void clearCache() - { - _populated = false; - _dataInputs = new HashMap<>(); - _materialInputs = new HashMap<>(); - _materialOutputs = new ArrayList<>(); - _dataOutputs = new ArrayList<>(); - _protocolSteps = null; - } - - @Override - public void archiveDataFiles(User user) - { - try - { - PipeRoot pipeRoot = PipelineService.get().getPipelineRootSetting(getContainer()); - if (pipeRoot != null && pipeRoot.isValid()) - { - for (ExpData expData : getAllDataUsedByRun()) - { - File file = expData.getFile(); - // If we can find the file on disk, and it's in the assaydata directory or was created by this run, - // and there aren't any other usages, move it into an archived subdirectory. - if (NetworkDrive.exists(file) && file.isFile() && - (inAssayData(file) || isGeneratedByRun(expData)) && - !hasOtherRunUsing(expData, this)) - { - File archivedDir; - try - { - archivedDir = AssayFileWriter.ensureSubdirectory(getContainer(), AssayFileWriter.ARCHIVED_DIR_NAME).toNioPathForWrite().toFile(); - } - catch (ExperimentException e) - { - // In this case, the archived directory was not created correctly perhaps due to file permission or - // some other problem. This exception has been observed on production servers. The error is being - // ignored and the file is not archived. Archiving is a best attempt action. - LOG.warn("Unable to create an archive directory - discontinue archive and delete."); - return; - } - File targetFile = FileUtil.findUniqueFileName(file.getName(), archivedDir); - targetFile = FileUtil.getAbsoluteCaseSensitiveFile(targetFile); - FileUtils.moveFile(file, targetFile); - expData.setDataFileURI(targetFile.toURI()); - expData.save(user); - } - } - } - } - // Warn if the move fails for some reason (file is open / file deleted during archive) - catch (IOException e) - { - LOG.warn("Unable to archive file: " + e.getMessage()); - } - // Fail silently if the parent directory does not exist - archiving is a best effort action - catch (ExperimentException e) - { - LOG.warn("Unable to read parent directory: " + e.getMessage()); - } - } - - private boolean inAssayData(File file) throws ExperimentException - { - var uploadDir = AssayFileWriter.ensureUploadDirectory(getContainer()).toNioPathForWrite().toFile(); - return file.getParentFile().equals(uploadDir); - } - - /** - * Returns true if the ExpData is flagged as being generated by a run - * and the ExpData's source protocol application references this run. - */ - private boolean isGeneratedByRun(ExpData data) - { - // TODO: is using data.getRun() sufficient or must we check sourceApp.getRun() to see if the data was created by this run? - ExpProtocolApplication sourceApp = data.getSourceApplication(); - if (data.isGenerated() && sourceApp != null && this.equals(sourceApp.getRun())) - return true; - - return false; - } - - @Override - public void setCreated(Date created) - { - _object.setCreated(created); - } - - @Override - public void setCreatedBy(User user) - { - _object.setCreatedBy(user == null ? 0 : user.getUserId()); - } - - private boolean hasOtherRunUsing(ExpData originalData, ExpRun originalRun) - { - if (originalData.getDataFileUrl() != null) - { - for (ExpData data : ExperimentService.get().getAllExpDataByURL(originalData.getDataFileUrl(), null)) - { - for (ExpRun run : data.getTargetRuns()) - { - if (!run.equals(originalRun)) - { - return true; - } - } - } - } - return false; - } - - @Override - public void setWorkflowTaskId(@Nullable Long workflowTaskId) - { - _object.setWorkflowTask(workflowTaskId); - } - - @Override - public ExpProtocolApplication getWorkflowTask() - { - Long id = _object.getWorkflowTask(); - - if (id == null) { - return null; - } - - if (_workflowTask == null || _workflowTask.getRowId() != id.intValue()) - { - _workflowTask = ExperimentServiceImpl.get().getExpProtocolApplication(id); - } - - return _workflowTask; - } - - @Override - public void setWorkflowTask(ExpProtocolApplication workflowTask) - { - ensureUnlocked(); - - if (workflowTask == null) - _object.setWorkflowTask(null); - else - _object.setWorkflowTask(workflowTask.getRowId()); - } -} +/* + * Copyright (c) 2008-2019 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.labkey.experiment.api; + +import org.apache.commons.io.FileUtils; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.NotNull; +import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayFileWriter; +import org.labkey.api.cloud.CloudStoreService; +import org.labkey.api.data.Container; +import org.labkey.api.data.DbScope; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.SqlExecutor; +import org.labkey.api.data.SqlSelector; +import org.labkey.api.data.Table; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.TableSelector; +import org.labkey.api.data.dialect.SqlDialect; +import org.labkey.api.exp.ExperimentException; +import org.labkey.api.exp.ExperimentRunType; +import org.labkey.api.exp.OntologyManager; +import org.labkey.api.exp.api.DataType; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExpMaterial; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExpProtocolAction; +import org.labkey.api.exp.api.ExpProtocolApplication; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.exp.api.ProtocolImplementation; +import org.labkey.api.exp.api.ProvenanceService; +import org.labkey.api.exp.query.ExpRunTable; +import org.labkey.api.exp.query.ExpSchema; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineService; +import org.labkey.api.query.BatchValidationException; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryRowReference; +import org.labkey.api.security.User; +import org.labkey.api.security.permissions.DeletePermission; +import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; +import org.labkey.api.security.permissions.UpdatePermission; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.NetworkDrive; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.UnauthorizedException; +import org.labkey.experiment.DotGraph; +import org.labkey.experiment.ExperimentRunGraph; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Date; +import java.util.HashMap; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.labkey.experiment.api.ExperimentServiceImpl.getExpSchema; + +public class ExpRunImpl extends ExpIdentifiableEntityImpl implements ExpRun +{ + public static final String NAMESPACE_PREFIX = "Run"; + + private boolean _populated; + private List _protocolSteps; + private Map _materialInputs = new HashMap<>(); + private Map _dataInputs = new HashMap<>(); + private List _materialOutputs = new ArrayList<>(); + private List _dataOutputs = new ArrayList<>(); + private ExpRunImpl _replacedByRun; + private Integer _maxOutputActionSequence = null; + private static final Logger LOG = LogManager.getLogger(ExpRunImpl.class); + private ExpProtocolApplication _workflowTask; + + static public List fromRuns(List runs) + { + List ret = new ArrayList<>(runs.size()); + for (ExperimentRun run : runs) + { + ret.add(new ExpRunImpl(run)); + } + return ret; + } + + // For serialization + protected ExpRunImpl() {} + + public ExpRunImpl(ExperimentRun run) + { + super(run); + if (null != run && null != run.getObjectId()) + _objectId = run.getObjectId(); + } + + @Override + public ActionURL detailsURL() + { + return _object.detailsURL(); + } + + @Override + public @Nullable QueryRowReference getQueryRowReference() + { + ExpProtocol protocol = getProtocol(); + if (protocol != null) + { + ProtocolImplementation impl = protocol.getImplementation(); + if (impl != null) + { + QueryRowReference ref = impl.getQueryRowReference(protocol, this); + if (ref != null) + return ref; + } + + ExperimentRunType type = ExperimentService.get().getExperimentRunType(protocol); + if (type != null) + { + QueryRowReference ref = type.getQueryRowReference(protocol, this); + if (ref != null) + return ref; + } + } + + return new QueryRowReference(getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Runs.name(), FieldKey.fromParts(ExpRunTable.Column.RowId), getRowId()); + } + + @Override + public Container getContainer() + { + return _object.getContainer(); + } + + @Override + public long getRowId() + { + return _object.getRowId(); + } + + @Override + public List getExperiments() + { + final String sql= " SELECT E.* FROM " + ExperimentServiceImpl.get().getTinfoExperiment() + " E " + + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoRunList() + " RL ON (E.RowId = RL.ExperimentId) " + + " INNER JOIN " + ExperimentServiceImpl.get().getTinfoExperimentRun() + " ER ON (ER.RowId = RL.ExperimentRunId) " + + " WHERE ER.LSID = ? AND E.Hidden = ?"; + + return ExpExperimentImpl.fromExperiments(new SqlSelector(getExpSchema(), sql, _object.getLSID(), Boolean.FALSE).getArray(Experiment.class)); + } + + @Override + public @Nullable ExpExperimentImpl getBatch() + { + if (_object.getBatchId() == null) + return null; + + ExpExperimentImpl batch = ExperimentServiceImpl.get().getExpExperiment(_object.getBatchId()); + if (batch == null) + return null; + + assert checkBatch(batch); + return batch; + } + + private boolean checkBatch(ExpExperimentImpl batch) + { + List exps = getExperiments(); + if (!exps.contains(batch)) + { + LOG.warn("Expected batch '" + batch.getRowId() + "' to be in list of experiments: " + exps); + return false; + } + + if (!getProtocol().equals(batch.getBatchProtocol())) + { + LOG.warn("Expected batch '" + batch.getRowId() + "' to have same protocol as run. Expected protocol '" + getProtocol() + "', but found '" + batch.getBatchProtocol() + "'"); + return false; + } + + return true; + } + + protected void setBatchId(Long batchId) + { + assert batchId == null || checkBatch(ExperimentServiceImpl.get().getExpExperiment(batchId)); + _object.setBatchId(batchId); + } + + @Override + public ExpProtocolImpl getProtocol() + { + return ExperimentServiceImpl.get().getExpProtocol(_object.getProtocolLSID()); + } + + @Override + public boolean isFinalOutput(ExpData data) + { + ExpProtocolApplication sourceApplication = data.getSourceApplication(); + return sourceApplication != null && sourceApplication.getActionSequence() == getMaxOutputActionSequence(); + } + + private int getMaxOutputActionSequence() + { + if (_maxOutputActionSequence == null) + { + _maxOutputActionSequence = 0; + for (ExpProtocolApplication app : getProtocolApplications()) + if (!app.getDataOutputs().isEmpty() && app.getActionSequence() > _maxOutputActionSequence) + _maxOutputActionSequence = app.getActionSequence(); + } + return _maxOutputActionSequence; + } + + @Override + public List getOutputDatas(@Nullable DataType type) + { + return ExperimentServiceImpl.get().getOutputDatas(getRowId(), type); + } + + @Override + public List getInputDatas(@Nullable String inputRole, @Nullable ExpProtocol.ApplicationType applicationType) + { + SQLFragment sql = new SQLFragment(); + sql.append("SELECT exp.Data.* FROM exp.Data WHERE exp.Data.RowId IN "); + sql.append("\n(SELECT exp.DataInput.DataId FROM exp.DataInput "); + sql.append("\nINNER JOIN exp.ProtocolApplication ON exp.DataInput.TargetApplicationId = exp.ProtocolApplication.RowId"); + sql.append("\nWHERE exp.ProtocolApplication.RunId = ?"); + sql.add(getRowId()); + if (inputRole != null) + { + sql.append("\nAND exp.DataInput.Role = ? "); + sql.add(inputRole); + } + if (applicationType != null) + { + sql.append("\nAND exp.ProtocolApplication.CpasType = "); + sql.appendValue(applicationType.toString()); + } + sql.append(")"); + return ExpDataImpl.fromDatas(new SqlSelector(ExperimentService.get().getSchema(), sql).getArrayList(Data.class)); + } + + @Override + public File getFilePathRoot() + { + if (_object.getFilePathRoot() == null || FileUtil.hasCloudScheme(_object.getFilePathRoot())) + return null; + else + return new File(FileUtil.createUri(_object.getFilePathRoot(), false)); + } + + @Override + public void setFilePathRoot(File file) + { + ensureUnlocked(); + // We want "/Users/..." for local file system + _object.setFilePathRoot(file == null ? null : file.toPath().toString()); + } + + @Override + public Path getFilePathRootPath() + { + if (_object.getFilePathRoot() == null) + return null; + else if (FileUtil.hasCloudScheme(_object.getFilePathRoot())) + return CloudStoreService.get().getPathFromUrl(getContainer(), _object.getFilePathRoot()); + else + return new File(FileUtil.createUri(_object.getFilePathRoot(), false)).toPath(); + } + + @Override + public void setFilePathRootPath(Path filePathRoot) + { + ensureUnlocked(); + _object.setFilePathRoot(filePathRoot == null ? null : + FileUtil.hasCloudScheme(filePathRoot) ? + FileUtil.pathToString(filePathRoot) : + filePathRoot.toString()); + } + + @Override + public void save(User user) throws BatchValidationException + { + ExperimentServiceImpl expService = ExperimentServiceImpl.get(); + try (DbScope.Transaction t = getExpSchema().getScope().ensureTransaction()) + { + boolean newRun = getRowId() == 0; + expService.onBeforeRunSaved(getProtocol(), this, getContainer(), user); + save(user, expService.getTinfoExperimentRun(), true); + if (newRun) + expService.auditRunEvent(user, this.getProtocol(), this, null, this.getProtocol().getName() + " run loaded"); + t.addCommitTask(() -> expService.onAfterRunSaved(getProtocol(), this, getContainer(), user), DbScope.CommitTaskOption.POSTCOMMIT); + t.commit(); + } + } + + @Override + protected void save(User user, TableInfo table, boolean ensureObject) + { + assert ensureObject; + super.save(user, table, true); + ExperimentServiceImpl.get().invalidateExperimentRun(getLSID()); + } + + @Override + public void delete(User user) + { + delete(user, null); + } + + @Override + public void delete(User user, @Nullable final String auditUserComment) + { + if (!canDelete(user)) + { + throw new UnauthorizedException(); + } + ExperimentServiceImpl.get().deleteExperimentRuns(getContainer(), user, auditUserComment, Arrays.asList(this), null); + } + + @Override + public void setProtocol(ExpProtocol protocol) + { + _object.setProtocolLSID(protocol.getLSID()); + } + + @Override + public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name) + { + return addProtocolApplication(user, action, appType, name, null, null, null); + } + + public ExpProtocolApplicationImpl addProtocolApplication(User user, ExpProtocolAction action, ExpProtocol.ApplicationType appType, String name, java.util.Date startTime, java.util.Date endTime, Integer recordCount) + { + ensureUnlocked(); + ProtocolApplication pa = new ProtocolApplication(); + if (action == null) + { + if (appType != ExpProtocol.ApplicationType.ExperimentRun) + { + throw new IllegalArgumentException("Only the ExperimentRun protocol application type is allowed to have a null protocol action."); + } + pa.setProtocolLSID(getProtocol().getLSID()); + } + else + { + pa.setProtocolLSID(action.getChildProtocol().getLSID()); + pa.setActionSequence(action.getActionSequence()); + } + pa.setName(name); + pa.setLSID(ExperimentService.get().generateGuidLSID(getContainer(), ExpProtocolApplication.class)); + pa.setCpasType(appType.toString()); + pa.setRunId(getRowId()); + pa.setStartTime(startTime); + pa.setEndTime(endTime); + pa.setRecordCount(recordCount); + + pa = Table.insert(user, ExperimentServiceImpl.get().getTinfoProtocolApplication(), pa); + return new ExpProtocolApplicationImpl(pa); + } + + @Override + public String getComments() + { + return _object.getComments(); + } + + @Override + public void setComments(String comments) + { + ensureUnlocked(); + _object.setComments(comments); + } + + @Override + public void setEntityId(String entityId) + { + ensureUnlocked(); + _object.setEntityId(entityId); + } + + @Override + public String getEntityId() + { + return _object.getEntityId(); + } + + + @Override + public void setContainer(Container container) + { + _object.setContainer(container); + } + + @Override + public void setJobId(Long jobId) + { + ensureUnlocked(); + _object.setJobId(jobId); + } + + @Override + public Long getJobId() + { + return _object.getJobId(); + } + + public void setProtocolApplications(List protocolSteps) + { + ensureUnlocked(); + _protocolSteps = protocolSteps; + } + + @Override + public @NotNull Map getMaterialInputs() + { + ensureFullyPopulated(); + return _materialInputs; + } + + @Override + public @NotNull Map getDataInputs() + { + ensureFullyPopulated(); + return _dataInputs; + } + + @Override + public List getMaterialOutputs() + { + ensureFullyPopulated(); + return _materialOutputs; + } + + @Override + public List getDataOutputs() + { + ensureFullyPopulated(); + return _dataOutputs; + } + + @Override + public List getProtocolApplications() + { + ensureFullyPopulated(); + return _protocolSteps; + } + + @Override + public @Nullable ExpProtocolApplication getProtocolApplication() + { + return findProtocolApplication(ExpProtocol.ApplicationType.ProtocolApplication); + } + + @Override + public @Nullable ExpProtocolApplication getInputProtocolApplication() + { + return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRun); + } + + private @Nullable ExpProtocolApplication findProtocolApplication(ExpProtocol.ApplicationType type) + { + for (ExpProtocolApplicationImpl expProtocolApplication : getProtocolApplications()) + { + if (type.equals(expProtocolApplication.getApplicationType())) + { + return expProtocolApplication; + } + } + return null; + } + + @Override + public @Nullable ExpProtocolApplication getOutputProtocolApplication() + { + return findProtocolApplication(ExpProtocol.ApplicationType.ExperimentRunOutput); + } + + @Override + public void deleteProtocolApplications(User user) + { + ensureUnlocked(); + deleteProtocolApplications(getOutputDatas(null), user); + } + + @Override + public void setReplacedByRun(ExpRun run) + { + ensureUnlocked(); + if (run != null && run.getRowId() < 1) + { + throw new IllegalArgumentException("Run must have already been saved to the database"); + } + _object.setReplacedByRunId(run == null ? null : run.getRowId()); + } + + @Override + public ExpRun getReplacedByRun() + { + Long id = _object.getReplacedByRunId(); + if (id == null) + { + return null; + } + if (_replacedByRun == null || _replacedByRun.getRowId() != id.intValue()) + { + _replacedByRun = ExperimentServiceImpl.get().getExpRun(id.intValue()); + } + return _replacedByRun; + } + + @Override + public List getReplacesRuns() + { + return fromRuns(new TableSelector(ExperimentServiceImpl.get().getTinfoExperimentRun(), new SimpleFilter(FieldKey.fromParts("ReplacedByRunId"), getRowId()), new Sort("Name")).getArrayList(ExperimentRun.class)); + } + + public void deleteProtocolApplications(List datasToDelete, User user) + { + if (user == null || !canDelete(user)) + { + throw new UnauthorizedException("Attempting to delete an ExperimentRun without having delete permissions for its container"); + } + final ExperimentServiceImpl svc = ExperimentServiceImpl.get(); + final SqlDialect dialect = svc.getSchema().getSqlDialect(); + + svc.invalidateExperimentRun(getLSID()); + + deleteProtocolApplicationProvenance(); + + svc.beforeDeleteData(user, getContainer(), datasToDelete); + + deleteInputObjects(svc, dialect); + + deleteAppParametersAndInputs(); + + deleteRunMaterials(user); + + deleteRunProtocolApps(); + + clearCache(); + + // Clear the cache in a commit task, which allows us to do a single clear (which is semi-expensive) if multiple + // runs are being deleted in the same transaction, like deleting a container + svc.getSchema().getScope().addCommitTask(ExperimentRunGraph.getCacheClearingCommitTask(getContainer()), DbScope.CommitTaskOption.POSTCOMMIT); + } + + @Override + public boolean canDelete(User user) + { + ExpProtocolImpl protocol = getProtocol(); + boolean isWorkflow = ExpProtocol.isSampleWorkflowProtocol(protocol.getLSID()); + if (isWorkflow && getContainer().hasPermission(user, SampleWorkflowDeletePermission.class)) + return true; + + // Issue 50776: To update lineage we need to delete existing runs + if ((ExperimentServiceImpl.get().isSampleAliquot(protocol) || ExperimentServiceImpl.get().isSampleDerivation(protocol)) && getContainer().hasPermission(user, UpdatePermission.class)) + return true; + + return !isWorkflow && getContainer().hasPermission(user, DeletePermission.class); + } + + // Clean up DataInput and MaterialInput exp.object and properties + private void deleteInputObjects(ExperimentServiceImpl svc, SqlDialect dialect) + { + SQLFragment materialSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + DataInput.lsidPrefix() + "'", + "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoDataInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", getRowId()); + + SQLFragment materialInputSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", + "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoMaterialInput() + " WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)", + getRowId()); + + SQLFragment dataSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + DataInput.lsidPrefix() + "'", + "CAST(dataId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoDataInput() + " WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)", getRowId()); + + SQLFragment dataInputSQL = new SQLFragment("SELECT " + + dialect.concatenate("'" + MaterialInput.lsidPrefix() + "'", + "CAST(materialId AS VARCHAR)", "'.'", "CAST(targetApplicationId AS VARCHAR)") + + " FROM " + svc.getTinfoMaterialInput() + " WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)", getRowId()); + + // Build a single UNION to help reduce DB round trips + SQLFragment unionSQL = new SQLFragment("(") + .append(materialSQL) + .append("\n UNION \n") + .append(materialInputSQL) + .append("\n UNION \n") + .append(dataSQL) + .append("\n UNION \n") + .append(dataInputSQL) + .append(")"); + + OntologyManager.deleteOntologyObjects(svc.getSchema(), unionSQL, getContainer()); + } + + private void deleteProtocolApplicationProvenance() + { + ProvenanceService pvs = ProvenanceService.get(); + pvs.deleteRunProvenance(getRowId()); + } + + private void deleteAppParametersAndInputs() + { + SQLFragment sql = new SQLFragment(); + sql.append("DELETE FROM exp.ProtocolApplicationParameter WHERE ProtocolApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); + + //per Josh: break relation between all datas with this run id and don't delete them + sql.append("UPDATE exp.Data SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); + sql.append("UPDATE exp.Material SET SourceApplicationId = NULL, RunId = NULL WHERE RunId = ?").add(getRowId()).appendEOS(); + + sql.append("DELETE FROM exp.DataInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); + sql.append("DELETE FROM exp.MaterialInput WHERE TargetApplicationId IN (SELECT RowId FROM exp.ProtocolApplication WHERE RunId = ?)").add(getRowId()).appendEOS(); + sql.append("DELETE FROM exp.DataInput WHERE DataId IN (SELECT RowId FROM exp.Data WHERE RunId = ?)").add(getRowId()).appendEOS(); + sql.append("DELETE FROM exp.MaterialInput WHERE MaterialId IN (SELECT RowId FROM exp.Material WHERE RunId = ?)").add(getRowId()).appendEOS(); + + new SqlExecutor(getExpSchema()).execute(sql); + } + + private void deleteRunMaterials(User user) + { + for (ExpMaterial expMaterial : ExperimentServiceImpl.get().getExpMaterialsForRun(getRowId())) + { + expMaterial.delete(user); + } + } + + private void deleteRunProtocolApps() + { + new SqlExecutor(getExpSchema()).execute("DELETE FROM exp.ProtocolApplication WHERE RunId = ?", getRowId()); + } + + private synchronized void ensureFullyPopulated() + { + if (!_populated) + { + _populated = true; + ExperimentServiceImpl.get().populateRun(this); + Collections.sort(_materialOutputs); + Collections.sort(_dataOutputs); + + for (ExpProtocolApplicationImpl step : _protocolSteps) + { + Collections.sort(step.getInputDatas()); + Collections.sort(step.getOutputDatas()); + Collections.sort(step.getInputMaterials()); + Collections.sort(step.getOutputMaterials()); + } + } + } + + public void trimRunTree(Integer id, String type) throws ExperimentException + { + ensureUnlocked(); + List listPA = new ArrayList<>(); + List listM = new ArrayList<>(); + List listD = new ArrayList<>(); + Set ancestorPAStack = new LinkedHashSet<>(); + Set descendantPAStack = new LinkedHashSet<>(); + List apps = getProtocolApplications(); + + boolean found = false; + + // support focus on a starting material that is not part of the run + if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) + { + for (ExpMaterialImpl m : getMaterialInputs().keySet()) + if (m.getRowId() == id.intValue()) + { + found = true; + listM.add(m); + listPA.addAll(m.getSuccessorApps()); + descendantPAStack.addAll(m.getSuccessorApps()); + break; + } + } + if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) + { + for (ExpDataImpl d : getDataInputs().keySet()) + if (d.getRowId() == id.intValue()) + { + found = true; + listD.add(d); + listPA.addAll(d.getSuccessorApps()); + descendantPAStack.addAll(d.getSuccessorApps()); + break; + } + } + if (!found) + { + for (ExpProtocolApplicationImpl app : apps) + { + if (type == null || DotGraph.TYPECODE_MATERIAL.equalsIgnoreCase(type)) + { + for (ExpMaterialImpl m : app.getOutputMaterials()) + if (m.getRowId() == id.intValue()) + { + found = true; + listM.add(m); + listPA.addAll(m.getSuccessorApps()); + descendantPAStack.addAll(m.getSuccessorApps()); + if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) + { + listPA.add(m.getSourceApplication()); + ancestorPAStack.add(m.getSourceApplication()); + } + break; + } + } + if (type == null || DotGraph.TYPECODE_DATA.equalsIgnoreCase(type)) + { + for (ExpDataImpl d : app.getOutputDatas()) + { + if (d.getRowId() == id.intValue()) + { + found = true; + listD.add(d); + listPA.addAll(d.getSuccessorApps()); + descendantPAStack.addAll(d.getSuccessorApps()); + if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) + { + listPA.add(d.getSourceApplication()); + ancestorPAStack.add(d.getSourceApplication()); + } + break; + } + } + } + if (type == null || DotGraph.TYPECODE_PROT_APP.equalsIgnoreCase(type)) + { + if (app.getRowId() == id.intValue()) + { + found = true; + listPA.add(app); + ancestorPAStack.add(app); + descendantPAStack.add(app); + break; + } + } + if (found) + break; + } + } + if (!found) + throw new ExperimentException("Specified node not found in Experiment Run"); + + int loopCount = 0; + while (!descendantPAStack.isEmpty()) + { + if (loopCount++ > 10000) + { + throw new IllegalStateException("Infinite loop detected for run " + getRowId()); + } + + ExpProtocolApplicationImpl pa = descendantPAStack.iterator().next(); + for (ExpMaterialImpl m : pa.getOutputMaterials()) + { + listM.add(m); + descendantPAStack.addAll(m.getSuccessorApps()); + } + for (ExpDataImpl d : pa.getOutputDatas()) + { + listD.add(d); + descendantPAStack.addAll(d.getSuccessorApps()); + } + descendantPAStack.remove(pa); + listPA.add(pa); + if (loopCount++ > 10000) + { + throw new IllegalStateException("Infinite loop detected for run " + getRowId()); + } + } + + loopCount = 0; + while (!ancestorPAStack.isEmpty()) + { + if (loopCount++ > 10000) + { + throw new IllegalStateException("Infinite loop detected for run " + getRowId()); + } + + ExpProtocolApplicationImpl pa = ancestorPAStack.iterator().next(); + if (pa.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun) + break; + for (ExpMaterialImpl m : pa.getInputMaterials()) + { + listM.add(m); + if (getMaterialInputs().containsKey(m)) + { + ExpProtocolApplication runNode = getProtocolApplications().get(0); + assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; + listPA.add(runNode); + continue; + } + if (null != m.getSourceApplication() && m.getRun() != null && getRowId() == m.getRun().getRowId()) + ancestorPAStack.add(m.getSourceApplication()); + } + for (ExpDataImpl d : pa.getInputDatas()) + { + listD.add(d); + if (getDataInputs().containsKey(d)) + { + ExpProtocolApplication runNode = getProtocolApplications().get(0); + assert runNode.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun; + listPA.add(runNode); + continue; + } + if (null != d.getSourceApplication() && d.getRun() != null && getRowId() == d.getRun().getRowId()) + ancestorPAStack.add(d.getSourceApplication()); + } + ancestorPAStack.remove(pa); + listPA.add(pa); + } + + List allPA = new ArrayList<>(); + List deletePA; + List deleteM; + List deleteD; + + setProtocolApplications(null); + + for (ExpProtocolApplicationImpl app : apps) + { + if (listPA.contains(app)) + { + allPA.add(app); + deleteM = new ArrayList<>(); + for (ExpMaterialImpl m : app.getInputMaterials()) + { + if (listM.contains(m)) + { + deletePA = new ArrayList<>(); + for (ExpProtocolApplicationImpl p : m.getSuccessorApps()) + if (!listPA.contains(p)) + deletePA.add(p); + for (ExpProtocolApplicationImpl p : deletePA) + m.getSuccessorApps().remove(p); + } + else + deleteM.add(m); + } + for (ExpMaterialImpl m : deleteM) + { + app.getInputMaterials().remove(m); + getMaterialInputs().remove(m); + } + + deleteD = new ArrayList<>(); + for (ExpDataImpl d : app.getInputDatas()) + { + if (listD.contains(d)) + { + deletePA = new ArrayList<>(); + for (ExpProtocolApplicationImpl p : d.getSuccessorApps()) + if (!listPA.contains(p)) + deletePA.add(p); + for (ExpProtocolApplicationImpl p : deletePA) + d.getSuccessorApps().remove(p); + } + else + deleteD.add(d); + } + for (ExpDataImpl d : deleteD) + { + app.getInputDatas().remove(d); + getDataInputs().remove(d); + } + + deleteM = new ArrayList<>(); + for (ExpMaterialImpl m : app.getOutputMaterials()) + { + if (!listM.contains(m)) + deleteM.add(m); + } + for (ExpMaterialImpl m : deleteM) + app.getOutputMaterials().remove(m); + + + deleteD = new ArrayList<>(); + for (ExpDataImpl d : app.getOutputDatas()) + { + if (!listD.contains(d)) + deleteD.add(d); + } + for (ExpDataImpl d : deleteD) + app.getOutputDatas().remove(d); + } + } + setProtocolApplications(allPA); + } + + @Override + public List getAllDataUsedByRun() + { + SQLFragment sql = new SQLFragment(); + sql.append("select d.* from "); + sql.append(ExperimentServiceImpl.get().getTinfoDataInput(), "di"); + sql.append(", "); + sql.append(ExperimentServiceImpl.get().getTinfoData(), "d"); + sql.append(", "); + sql.append(ExperimentServiceImpl.get().getTinfoProtocolApplication(), "pa"); + sql.append(" where di.targetapplicationid=pa.rowid and pa.runid=? and di.dataid=d.rowid"); + sql.add(getRowId()); + return ExpDataImpl.fromDatas(new SqlSelector(ExperimentServiceImpl.get().getSchema(), sql).getArrayList(Data.class)); + } + + public void clearCache() + { + _populated = false; + _dataInputs = new HashMap<>(); + _materialInputs = new HashMap<>(); + _materialOutputs = new ArrayList<>(); + _dataOutputs = new ArrayList<>(); + _protocolSteps = null; + } + + @Override + public void archiveDataFiles(User user) + { + try + { + PipeRoot pipeRoot = PipelineService.get().getPipelineRootSetting(getContainer()); + if (pipeRoot != null && pipeRoot.isValid()) + { + for (ExpData expData : getAllDataUsedByRun()) + { + File file = expData.getFile(); + // If we can find the file on disk, and it's in the assaydata directory or was created by this run, + // and there aren't any other usages, move it into an archived subdirectory. + if (NetworkDrive.exists(file) && file.isFile() && + (inAssayData(file) || isGeneratedByRun(expData)) && + !hasOtherRunUsing(expData, this)) + { + File archivedDir; + try + { + archivedDir = AssayFileWriter.ensureSubdirectory(getContainer(), AssayFileWriter.ARCHIVED_DIR_NAME).toNioPathForWrite().toFile(); + } + catch (ExperimentException e) + { + // In this case, the archived directory was not created correctly perhaps due to file permission or + // some other problem. This exception has been observed on production servers. The error is being + // ignored and the file is not archived. Archiving is a best attempt action. + LOG.warn("Unable to create an archive directory - discontinue archive and delete."); + return; + } + File targetFile = FileUtil.findUniqueFileName(file.getName(), archivedDir); + targetFile = FileUtil.getAbsoluteCaseSensitiveFile(targetFile); + FileUtils.moveFile(file, targetFile); + expData.setDataFileURI(targetFile.toURI()); + expData.save(user); + } + } + } + } + // Warn if the move fails for some reason (file is open / file deleted during archive) + catch (IOException e) + { + LOG.warn("Unable to archive file: " + e.getMessage()); + } + // Fail silently if the parent directory does not exist - archiving is a best effort action + catch (ExperimentException e) + { + LOG.warn("Unable to read parent directory: " + e.getMessage()); + } + } + + private boolean inAssayData(File file) throws ExperimentException + { + var uploadDir = AssayFileWriter.ensureUploadDirectory(getContainer()).toNioPathForWrite().toFile(); + return file.getParentFile().equals(uploadDir); + } + + /** + * Returns true if the ExpData is flagged as being generated by a run + * and the ExpData's source protocol application references this run. + */ + private boolean isGeneratedByRun(ExpData data) + { + // TODO: is using data.getRun() sufficient or must we check sourceApp.getRun() to see if the data was created by this run? + ExpProtocolApplication sourceApp = data.getSourceApplication(); + if (data.isGenerated() && sourceApp != null && this.equals(sourceApp.getRun())) + return true; + + return false; + } + + @Override + public void setCreated(Date created) + { + _object.setCreated(created); + } + + @Override + public void setCreatedBy(User user) + { + _object.setCreatedBy(user == null ? 0 : user.getUserId()); + } + + private boolean hasOtherRunUsing(ExpData originalData, ExpRun originalRun) + { + if (originalData.getDataFileUrl() != null) + { + for (ExpData data : ExperimentService.get().getAllExpDataByURL(originalData.getDataFileUrl(), null)) + { + for (ExpRun run : data.getTargetRuns()) + { + if (!run.equals(originalRun)) + { + return true; + } + } + } + } + return false; + } + + @Override + public void setWorkflowTaskId(@Nullable Long workflowTaskId) + { + _object.setWorkflowTask(workflowTaskId); + } + + @Override + public ExpProtocolApplication getWorkflowTask() + { + Long id = _object.getWorkflowTask(); + + if (id == null) { + return null; + } + + if (_workflowTask == null || _workflowTask.getRowId() != id.intValue()) + { + _workflowTask = ExperimentServiceImpl.get().getExpProtocolApplication(id); + } + + return _workflowTask; + } + + @Override + public void setWorkflowTask(ExpProtocolApplication workflowTask) + { + ensureUnlocked(); + + if (workflowTask == null) + _object.setWorkflowTask(null); + else + _object.setWorkflowTask(workflowTask.getRowId()); + } +} From dcafd9251973f0adb6db0d8718e294387e7f2095 Mon Sep 17 00:00:00 2001 From: XingY Date: Tue, 11 Nov 2025 20:33:29 -0800 Subject: [PATCH 3/3] crlf --- .../controllers/exp/ExperimentController.java | 16698 ++++++++-------- 1 file changed, 8349 insertions(+), 8349 deletions(-) diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java index 8bb65850ca3..09ab704bce0 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java @@ -1,8349 +1,8349 @@ -/* - * Copyright (c) 2008-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.labkey.experiment.controllers.exp; - -import jakarta.servlet.ServletException; -import jakarta.servlet.http.HttpServletRequest; -import jakarta.servlet.http.HttpServletResponse; -import jakarta.servlet.http.HttpSession; -import org.apache.commons.collections4.MapUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.lang3.Strings; -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; -import org.apache.poi.ss.usermodel.Workbook; -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.json.JSONArray; -import org.json.JSONException; -import org.json.JSONObject; -import org.labkey.api.action.ApiJsonWriter; -import org.labkey.api.action.ApiResponse; -import org.labkey.api.action.ApiSimpleResponse; -import org.labkey.api.action.ApiUsageException; -import org.labkey.api.action.ExportAction; -import org.labkey.api.action.FormHandlerAction; -import org.labkey.api.action.FormViewAction; -import org.labkey.api.action.HasViewContext; -import org.labkey.api.action.Marshal; -import org.labkey.api.action.Marshaller; -import org.labkey.api.action.MutatingApiAction; -import org.labkey.api.action.QueryViewAction; -import org.labkey.api.action.ReadOnlyApiAction; -import org.labkey.api.action.ReturnUrlForm; -import org.labkey.api.action.SimpleApiJsonForm; -import org.labkey.api.action.SimpleErrorView; -import org.labkey.api.action.SimpleResponse; -import org.labkey.api.action.SimpleViewAction; -import org.labkey.api.action.SpringActionController; -import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.actions.UploadWizardAction; -import org.labkey.api.assay.security.DesignAssayPermission; -import org.labkey.api.attachments.AttachmentParent; -import org.labkey.api.attachments.AttachmentService; -import org.labkey.api.attachments.BaseDownloadAction; -import org.labkey.api.audit.AbstractAuditTypeProvider; -import org.labkey.api.audit.AuditLogService; -import org.labkey.api.audit.DetailedAuditTypeEvent; -import org.labkey.api.audit.SampleTimelineAuditEvent; -import org.labkey.api.audit.TransactionAuditProvider; -import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.labkey.api.collections.CaseInsensitiveHashSet; -import org.labkey.api.collections.LongHashMap; -import org.labkey.api.data.ActionButton; -import org.labkey.api.data.BaseColumnInfo; -import org.labkey.api.data.ButtonBar; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.DataRegion; -import org.labkey.api.data.DataRegionSelection; -import org.labkey.api.data.DbSchema; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.DisplayColumn; -import org.labkey.api.data.ExcelWriter; -import org.labkey.api.data.MenuButton; -import org.labkey.api.data.NameGenerator; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.ShowRows; -import org.labkey.api.data.SimpleDisplayColumn; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.TSVJSONWriter; -import org.labkey.api.data.TSVWriter; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; -import org.labkey.api.dataiterator.DataIteratorContext; -import org.labkey.api.exp.AbstractParameter; -import org.labkey.api.exp.DeleteForm; -import org.labkey.api.exp.DuplicateMaterialException; -import org.labkey.api.exp.ExperimentDataHandler; -import org.labkey.api.exp.ExperimentException; -import org.labkey.api.exp.ExperimentRunForm; -import org.labkey.api.exp.ExperimentRunListView; -import org.labkey.api.exp.ExperimentRunType; -import org.labkey.api.exp.Identifiable; -import org.labkey.api.exp.Lsid; -import org.labkey.api.exp.LsidManager; -import org.labkey.api.exp.LsidType; -import org.labkey.api.exp.ObjectProperty; -import org.labkey.api.exp.OntologyManager; -import org.labkey.api.exp.ProtocolApplicationParameter; -import org.labkey.api.exp.XarContext; -import org.labkey.api.exp.api.DataClassDomainKindProperties; -import org.labkey.api.exp.api.ExpData; -import org.labkey.api.exp.api.ExpDataClass; -import org.labkey.api.exp.api.ExpExperiment; -import org.labkey.api.exp.api.ExpLineageOptions; -import org.labkey.api.exp.api.ExpMaterial; -import org.labkey.api.exp.api.ExpMaterialRunInput; -import org.labkey.api.exp.api.ExpObject; -import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.exp.api.ExpProtocolApplication; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.api.ExpRunAttachmentParent; -import org.labkey.api.exp.api.ExpRunEditor; -import org.labkey.api.exp.api.ExpRunItem; -import org.labkey.api.exp.api.ExpSampleType; -import org.labkey.api.exp.api.ExperimentJSONConverter; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ExperimentUrls; -import org.labkey.api.exp.api.NameExpressionOptionService; -import org.labkey.api.exp.api.ResolveLsidsForm; -import org.labkey.api.exp.api.SampleTypeDomainKind; -import org.labkey.api.exp.api.SampleTypeService; -import org.labkey.api.exp.list.ListService; -import org.labkey.api.exp.property.Domain; -import org.labkey.api.exp.property.DomainAuditProvider; -import org.labkey.api.exp.property.DomainKind; -import org.labkey.api.exp.property.DomainProperty; -import org.labkey.api.exp.property.DomainTemplate; -import org.labkey.api.exp.property.DomainTemplateGroup; -import org.labkey.api.exp.property.DomainUtil; -import org.labkey.api.exp.property.PropertyService; -import org.labkey.api.exp.query.ExpDataProtocolInputTable; -import org.labkey.api.exp.query.ExpInputTable; -import org.labkey.api.exp.query.ExpMaterialProtocolInputTable; -import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.exp.query.SamplesSchema; -import org.labkey.api.exp.xar.LSIDRelativizer; -import org.labkey.api.exp.xar.LsidUtils; -import org.labkey.api.files.FileContentService; -import org.labkey.api.gwt.client.AuditBehaviorType; -import org.labkey.api.inventory.InventoryService; -import org.labkey.api.module.ModuleHtmlView; -import org.labkey.api.module.ModuleLoader; -import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.pipeline.PipelineStatusFile; -import org.labkey.api.pipeline.PipelineUrls; -import org.labkey.api.pipeline.PipelineValidationException; -import org.labkey.api.qc.SampleStatusService; -import org.labkey.api.query.AbstractQueryImportAction; -import org.labkey.api.query.BatchValidationException; -import org.labkey.api.query.DetailsURL; -import org.labkey.api.query.DuplicateKeyException; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryAction; -import org.labkey.api.query.QueryDefinition; -import org.labkey.api.query.QueryException; -import org.labkey.api.query.QueryForm; -import org.labkey.api.query.QueryParam; -import org.labkey.api.query.QueryService; -import org.labkey.api.query.QuerySettings; -import org.labkey.api.query.QueryUpdateForm; -import org.labkey.api.query.QueryUpdateService; -import org.labkey.api.query.QueryUpdateServiceException; -import org.labkey.api.query.QueryView; -import org.labkey.api.query.SchemaKey; -import org.labkey.api.query.UserSchema; -import org.labkey.api.query.UserSchemaAction; -import org.labkey.api.reader.ColumnDescriptor; -import org.labkey.api.reader.DataLoader; -import org.labkey.api.reader.DataLoaderFactory; -import org.labkey.api.reader.ExcelFactory; -import org.labkey.api.search.SearchService; -import org.labkey.api.security.ActionNames; -import org.labkey.api.security.RequiresAnyOf; -import org.labkey.api.security.RequiresNoPermission; -import org.labkey.api.security.RequiresPermission; -import org.labkey.api.security.SecurableResource; -import org.labkey.api.security.User; -import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.security.permissions.DesignDataClassPermission; -import org.labkey.api.security.permissions.DesignSampleTypePermission; -import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.security.permissions.Permission; -import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; -import org.labkey.api.security.permissions.SiteAdminPermission; -import org.labkey.api.security.permissions.TroubleshooterPermission; -import org.labkey.api.security.permissions.UpdatePermission; -import org.labkey.api.settings.AppProps; -import org.labkey.api.settings.ConceptURIProperties; -import org.labkey.api.sql.LabKeySql; -import org.labkey.api.study.Dataset; -import org.labkey.api.study.StudyService; -import org.labkey.api.study.StudyUrls; -import org.labkey.api.study.publish.StudyPublishService; -import org.labkey.api.usageMetrics.SimpleMetricsService; -import org.labkey.api.util.DOM; -import org.labkey.api.util.DOM.LK; -import org.labkey.api.util.ErrorRenderer; -import org.labkey.api.util.ExceptionUtil; -import org.labkey.api.util.FileStream; -import org.labkey.api.util.FileUtil; -import org.labkey.api.util.HtmlString; -import org.labkey.api.util.HtmlStringBuilder; -import org.labkey.api.util.ImageUtil; -import org.labkey.api.util.JSoupUtil; -import org.labkey.api.util.LinkBuilder; -import org.labkey.api.util.NetworkDrive; -import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.util.Pair; -import org.labkey.api.util.ResponseHelper; -import org.labkey.api.util.SafeToRender; -import org.labkey.api.util.SessionHelper; -import org.labkey.api.util.StringExpression; -import org.labkey.api.util.StringUtilsLabKey; -import org.labkey.api.util.URLHelper; -import org.labkey.api.util.UniqueID; -import org.labkey.api.util.CsrfInput; -import org.labkey.api.view.ActionURL; -import org.labkey.api.view.BadRequestException; -import org.labkey.api.view.DataView; -import org.labkey.api.view.DataViewSnapshotSelectionForm; -import org.labkey.api.view.DetailsView; -import org.labkey.api.view.HBox; -import org.labkey.api.view.HtmlView; -import org.labkey.api.view.HttpView; -import org.labkey.api.view.InsertView; -import org.labkey.api.view.JspView; -import org.labkey.api.view.NavTree; -import org.labkey.api.view.NotFoundException; -import org.labkey.api.view.RedirectException; -import org.labkey.api.view.UnauthorizedException; -import org.labkey.api.view.UpdateView; -import org.labkey.api.view.VBox; -import org.labkey.api.view.ViewBackgroundInfo; -import org.labkey.api.view.ViewContext; -import org.labkey.api.view.ViewServlet; -import org.labkey.api.view.WebPartView; -import org.labkey.api.view.template.ClientDependency; -import org.labkey.api.view.template.PageConfig; -import org.labkey.experiment.ChooseExperimentTypeBean; -import org.labkey.experiment.ConfirmDeleteView; -import org.labkey.experiment.CustomPropertiesView; -import org.labkey.experiment.DataClassWebPart; -import org.labkey.experiment.DerivedSamplePropertyHelper; -import org.labkey.experiment.DotGraph; -import org.labkey.experiment.ExpDataFileListener; -import org.labkey.experiment.ExperimentRunDisplayColumn; -import org.labkey.experiment.ExperimentRunGraph; -import org.labkey.experiment.LineageGraphDisplayColumn; -import org.labkey.experiment.MissingFilesCheckInfo; -import org.labkey.experiment.MoveRunsBean; -import org.labkey.experiment.ParentChildView; -import org.labkey.experiment.ProtocolApplicationDisplayColumn; -import org.labkey.experiment.ProtocolDisplayColumn; -import org.labkey.experiment.ProtocolWebPart; -import org.labkey.experiment.RunGroupWebPart; -import org.labkey.experiment.SampleTypeDisplayColumn; -import org.labkey.experiment.SampleTypeWebPart; -import org.labkey.experiment.StandardAndCustomPropertiesView; -import org.labkey.experiment.XarExportPipelineJob; -import org.labkey.experiment.XarExportType; -import org.labkey.experiment.XarExporter; -import org.labkey.experiment.api.ClosureQueryHelper; -import org.labkey.experiment.api.DataClass; -import org.labkey.experiment.api.DataClassDomainKind; -import org.labkey.experiment.api.ExpDataClassAttachmentParent; -import org.labkey.experiment.api.ExpDataClassImpl; -import org.labkey.experiment.api.ExpDataImpl; -import org.labkey.experiment.api.ExpExperimentImpl; -import org.labkey.experiment.api.ExpMaterialImpl; -import org.labkey.experiment.api.ExpProtocolApplicationImpl; -import org.labkey.experiment.api.ExpProtocolImpl; -import org.labkey.experiment.api.ExpRunImpl; -import org.labkey.experiment.api.ExpSampleTypeImpl; -import org.labkey.experiment.api.Experiment; -import org.labkey.experiment.api.ExperimentServiceImpl; -import org.labkey.experiment.api.GraphAlgorithms; -import org.labkey.experiment.api.ProtocolActionStepDetail; -import org.labkey.experiment.api.SampleTypeServiceImpl; -import org.labkey.experiment.api.SampleTypeUpdateServiceDI; -import org.labkey.experiment.controllers.property.PropertyController; -import org.labkey.experiment.lineage.ExpLineageServiceImpl; -import org.labkey.experiment.pipeline.ExperimentPipelineJob; -import org.labkey.experiment.types.TypesController; -import org.labkey.experiment.xar.XarExportSelection; -import org.labkey.vfs.FileLike; -import org.labkey.vfs.FileSystemLike; -import org.springframework.beans.PropertyValue; -import org.springframework.beans.PropertyValues; -import org.springframework.validation.BindException; -import org.springframework.validation.Errors; -import org.springframework.validation.ObjectError; -import org.springframework.web.multipart.MultipartFile; -import org.springframework.web.multipart.MultipartHttpServletRequest; -import org.springframework.web.servlet.ModelAndView; - -import javax.imageio.ImageIO; -import java.awt.*; -import java.awt.image.BufferedImage; -import java.io.BufferedOutputStream; -import java.io.ByteArrayOutputStream; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; -import java.net.URI; -import java.nio.file.Files; -import java.nio.file.Path; -import java.sql.SQLException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.Collections; -import java.util.Comparator; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Map; -import java.util.Objects; -import java.util.Optional; -import java.util.Set; -import java.util.TreeSet; -import java.util.function.Function; -import java.util.stream.Collectors; - -import static java.util.stream.Collectors.toList; -import static org.labkey.api.data.DbScope.CommitTaskOption.POSTCOMMIT; -import static org.labkey.api.exp.query.ExpSchema.TableType.DataInputs; -import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM; -import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM; -import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_PROVIDER_PARAM; -import static org.labkey.api.util.DOM.A; -import static org.labkey.api.util.DOM.Attribute.action; -import static org.labkey.api.util.DOM.Attribute.href; -import static org.labkey.api.util.DOM.Attribute.id; -import static org.labkey.api.util.DOM.Attribute.method; -import static org.labkey.api.util.DOM.Attribute.name; -import static org.labkey.api.util.DOM.Attribute.size; -import static org.labkey.api.util.DOM.Attribute.src; -import static org.labkey.api.util.DOM.Attribute.target; -import static org.labkey.api.util.DOM.Attribute.type; -import static org.labkey.api.util.DOM.Attribute.value; -import static org.labkey.api.util.DOM.Attribute.width; -import static org.labkey.api.util.DOM.DIV; -import static org.labkey.api.util.DOM.IMG; -import static org.labkey.api.util.DOM.INPUT; -import static org.labkey.api.util.DOM.LI; -import static org.labkey.api.util.DOM.TABLE; -import static org.labkey.api.util.DOM.TD; -import static org.labkey.api.util.DOM.TR; -import static org.labkey.api.util.DOM.UL; -import static org.labkey.api.util.DOM.at; -import static org.labkey.api.util.DOM.cl; -import static org.labkey.experiment.ExpDataIterators.setContainerFilterForImport; -import static org.labkey.experiment.api.SampleTypeServiceImpl.SampleChangeType.update; - -public class ExperimentController extends SpringActionController -{ - private static final Logger _log = LogManager.getLogger(ExperimentController.class); - private static final DefaultActionResolver _actionResolver = new DefaultActionResolver( - ExperimentController.class - ); - private static final String GUEST_DIRECTORY_NAME = "guest"; - - public ExperimentController() - { - setActionResolver(_actionResolver); - } - - public static void ensureCorrectContainer(Container requestContainer, ExpObject object, ViewContext viewContext) - { - Container objectContainer = object.getContainer(); - if (!requestContainer.equals(objectContainer)) - { - ActionURL url = viewContext.cloneActionURL(); - url.setContainer(objectContainer); - throw new RedirectException(url); - } - } - - // Complete no-op, but leave in place in case we decide to adjust the base nav trail - private void addRootNavTrail(NavTree root) - { - // Intentionally don't add an "Experiment" node to the list because it's too overloaded. All content on the - // default action can be added to a portal page if desired. - } - - @Override - public PageConfig defaultPageConfig() - { - // set default help topic for controller - PageConfig config = super.defaultPageConfig(); - config.setHelpTopic("experiment"); - return config; - } - - @ActionNames("begin,gridView") - @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction - { - @Override - public VBox getView(Object o, BindException errors) - { - VBox result = new VBox(); - - VBox runListView = createRunListView(20); - result.addView(runListView); - - RunGroupWebPart runGroups = new RunGroupWebPart(getViewContext(), false); - runGroups.showHeader(); - result.addView(runGroups); - - result.addView(new ProtocolWebPart(false, getViewContext())); - result.addView(new SampleTypeWebPart(false, getViewContext())); - result.addView(new DataClassWebPart(false, getViewContext(), null)); - - return result; - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Experiment"); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowRunsAction extends SimpleViewAction - { - @Override - public VBox getView(Object o, BindException errors) - { - return createRunListView(100); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Experiment Runs"); - } - } - - private VBox createRunListView(int defaultMaxRows) - { - Set types = ExperimentService.get().getExperimentRunTypes(getContainer()); - ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")), getViewContext().getActionURL().clone(), Collections.emptyList()); - JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean); - - ExperimentRunListView view = ExperimentService.get().createExperimentRunWebPart(getViewContext(), bean.getSelectedFilter()); - view.setFrame(WebPartView.FrameType.NONE); - - // When paginated and the user hasn't explicitly set a maxRows, use the default maxRows size. - QuerySettings settings = view.getSettings(); - if (!settings.isMaxRowsSet() && settings.getShowRows() == ShowRows.PAGINATED) - { - settings.setMaxRows(defaultMaxRows); - } - - VBox result = new VBox(chooserView, view); - result.setFrame(WebPartView.FrameType.PORTAL); - return result; - } - - @RequiresPermission(ReadPermission.class) - @ActionNames("showRunGroups, showExperiments") - public class ShowRunGroupsAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - RunGroupWebPart webPart = new RunGroupWebPart(getViewContext(), false); - webPart.setFrame(WebPartView.FrameType.NONE); - return webPart; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - addRootNavTrail(root); - root.addChild("Run Groups"); - } - } - - public record Field(String domainURI, String domainName, String name, Container container) {} - public record MiniExpObject(Object rowId, String name) {} - public record TimelineSummary(MiniExpObject miniExpObject, String mostRecentValue) {} - public record ProblemType(String tableName, String fieldName, String pkName) { - public Object toHtml(List summaries) - { - return DOM.DIV( - DOM.H4(tableName), - DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), - DOM.THEAD(DOM.TH(pkName), DOM.TH(fieldName)), - summaries.stream().map(summary -> - DOM.TR(DOM.TD(summary.miniExpObject.name), DOM.TD(summary.mostRecentValue))) - )); - } - } - - @RequiresPermission(SiteAdminPermission.class) - public static class ReportLostFieldValuesAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - // Find all the fields that could have lost data due to issue 52666 - TableInfo t = new ExpSchema(getUser(), ContainerManager.getRoot()).getTable(ExpSchema.TableType.Fields.name(), ContainerFilter.getUnsafeEverythingFilter()); - List fields = new TableSelector(t, - new SimpleFilter(FieldKey.fromParts("StorageColumnNameMatch"), false). - addCondition(FieldKey.fromParts("DomainURI"), ":AssayDomain-Data.", CompareType.DOES_NOT_CONTAIN), - null). - getArrayList(Field.class); - - // Prep audit table for querying - UserSchema auditSchema = AuditLogService.get().createSchema(getUser(), ContainerManager.getRoot()); - - Map> sampleTypeSummaries = new HashMap<>(); - Map> dataClassSummaries = new HashMap<>(); - Map> listSummaries = new HashMap<>(); - - Map> problematicFields = new LinkedHashMap<>(); - - for (Field field : fields) - { - String domainURI = field.domainURI; - String fieldName = field.name; - Container container = field.container; - Domain domain = PropertyService.get().getDomain(container, domainURI); - if (domain != null && domain.getDomainKind() != null) - { - TableInfo table = domain.getDomainKind().getTableInfo(getUser(), container, domain, ContainerFilter.getUnsafeEverythingFilter()); - - if (table != null) - { - // Drill into sample types - if (domain.getDomainKind().getClass().equals(SampleTypeDomainKind.class)) - { - // rows that currently have no value for the field with potential for data loss - List rowsWithNull = new TableSelector(table, - new HashSet<>(List.of("RowId", "Name")), - new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), - null). - getArrayList(MiniExpObject.class); - - List fixupsNeeded = checkData( - rowsWithNull, - fieldName, - obj -> new SimpleFilter(FieldKey.fromParts("SampleId"), obj.rowId), - auditSchema.getTable(SampleTimelineAuditEvent.EVENT_TYPE, ContainerFilter.getUnsafeEverythingFilter())); - if (!fixupsNeeded.isEmpty()) - { - sampleTypeSummaries.put(new ProblemType(table.getName(), fieldName, "SampleID"), fixupsNeeded); - } - } - // and data classes/sample sources - if (domain.getDomainKind().getClass().equals(DataClassDomainKind.class)) - { - // rows samples that current have no value for the field with potential for data loss - List rowsWithNull = new TableSelector(table, - new HashSet<>(List.of("RowId", "Name")), - new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), - null). - getArrayList(MiniExpObject.class); - - List fixupsNeeded = checkData( - rowsWithNull, - fieldName, - obj -> new SimpleFilter(FieldKey.fromParts("RowPk"), Objects.toString(obj.rowId)). - addCondition(FieldKey.fromParts("SchemaName"), "exp.data"). - addCondition(FieldKey.fromParts("QueryName"), domain.getName()), - auditSchema.getTable("QueryUpdateAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); - - if (!fixupsNeeded.isEmpty()) - { - dataClassSummaries.put(new ProblemType(table.getName(), fieldName, "SourceID"), fixupsNeeded); - } - } - // and lists - if ("lists".equals(table.getUserSchema().getName())) - { - // rows samples that current have no value for the field with potential for data loss - List rowsWithNull = new ArrayList<>(); - - ColumnInfo entityIdCol = table.getColumn("EntityId"); - ColumnInfo pkCol = table.getPkColumns().get(0); - - new TableSelector(table, - List.of(entityIdCol, pkCol), - new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), - null). - forEachResults(r -> - { - Object entityId = entityIdCol.getValue(r); - Object pk = pkCol.getValue(r); - rowsWithNull.add(new MiniExpObject(entityId, pk.toString())); - }); - - - List fixupsNeeded = checkData( - rowsWithNull, - fieldName, - obj -> new SimpleFilter(FieldKey.fromParts("ListItemEntityId"), obj.rowId), - auditSchema.getTable("ListAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); - - if (!fixupsNeeded.isEmpty()) - { - listSummaries.put(new ProblemType(table.getName(), fieldName, table.getPkColumnNames().get(0)), fixupsNeeded); - } - } - - long totalRows = new TableSelector(table).getRowCount(); - long emptyRows = new TableSelector(table, new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), null).getRowCount(); - problematicFields.put(field, Pair.of(totalRows, emptyRows)); - } - else - { - problematicFields.put(field, Pair.of(null, null)); - } - } - } - - return new HtmlView("Fixups Needed", - DOM.createHtmlFragment( - DOM.H2("Potentially Problematic Fields"), - problematicFields.isEmpty() ? "No problematic fields detected!" : - DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), - DOM.THEAD(DOM.TH("Domain Name"), DOM.TH("Domain URI"), DOM.TH("Field Name"), DOM.TH("Container"), DOM.TH("Total Rows"), DOM.TH("Rows with Nulls")), - problematicFields.entrySet().stream().map(e -> { - Field f = e.getKey(); - Pair counts = e.getValue(); - return DOM.TR( - DOM.TD(f.domainName), - DOM.TD(f.domainURI), - DOM.TD(f.name), - DOM.TD(f.container.getPath()), - DOM.TD(counts.first), - DOM.TD(counts.second) - ); - } - )), - - DOM.H2("Sample Types"), - sampleTypeSummaries.isEmpty() ? "No problems detected!" : - sampleTypeSummaries.entrySet().stream().map(e -> - e.getKey().toHtml(e.getValue())), - - DOM.H2("Data Classes"), - dataClassSummaries.isEmpty() ? "No problems detected!" : - dataClassSummaries.entrySet().stream().map(e -> - e.getKey().toHtml(e.getValue())), - - DOM.H2("Lists"), - listSummaries.isEmpty() ? "No problems detected!" : - listSummaries.entrySet().stream().map(e -> - e.getKey().toHtml(e.getValue())) - )); - } - - @NotNull - private List checkData(List rowsWithNull, String fieldName, Function filterGenerator, TableInfo auditTable) - { - List fixupsNeeded = new ArrayList<>(); - - // For each sample without a value today, check the audit history - for (MiniExpObject row : rowsWithNull) - { - // Order by RowId to get them in the sequence they happened in - var events = new TableSelector(auditTable, filterGenerator.apply(row), new Sort("RowId")).getArrayList(DetailedAuditTypeEvent.class); - // Remember the most recently set value - String mostRecentValue = null; - for (DetailedAuditTypeEvent event : events) - { - Map newValues = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(event.getNewRecordMap())); - if (newValues.containsKey(fieldName)) - { - // Will be the empty string if the value was intentionally set to blank - mostRecentValue = newValues.get(fieldName); - } - } - // If the value had been set before, and its most recent insert/update wasn't setting it blank, - // it's most likely a lost value - if (mostRecentValue != null && !mostRecentValue.isEmpty()) - { - fixupsNeeded.add(new TimelineSummary(row, mostRecentValue)); - } - } - return fixupsNeeded; - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Accidentally Nulled Field Report"); - } - } - - @RequiresPermission(ReadPermission.class) - public static class CreateHiddenRunGroupAction extends MutatingApiAction - { - @Override - public ApiResponse execute(SimpleApiJsonForm form, BindException errors) throws Exception - { - JSONObject json = form.getJsonObject(); - String selectionKey = json.optString("selectionKey", null); - List runs = new ArrayList<>(); - - // Accept either an explicit list of run IDs - if (json.has("runIds")) - { - JSONArray runIds = json.getJSONArray("runIds"); - for (int i = 0; i < runIds.length(); i++) - { - ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(runIds.getInt(i)); - if (run != null) - { - runs.add(run); - } - } - } - // Or a reference to a DataRegion selection key - else if (selectionKey != null) - { - Set ids = DataRegionSelection.getSelectedIntegers(getViewContext(), selectionKey, false); - for (Long id : ids) - { - ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(id); - if (run != null) - { - runs.add(run); - } - } - } - if (runs.isEmpty()) - { - throw new NotFoundException(); - } - - ExpExperiment group = ExperimentService.get().createHiddenRunGroup(getContainer(), getUser(), runs.toArray(new ExpRun[0])); - if (selectionKey != null) - DataRegionSelection.clearAll(getViewContext(), selectionKey); - - ApiSimpleResponse response = new ApiSimpleResponse(); - response.putBean(group, "rowId", "LSID", "name", "hidden"); - return response; - } - } - - - @RequiresPermission(ReadPermission.class) - public class DetailsAction extends QueryViewAction - { - private ExpExperimentImpl _experiment; - - public DetailsAction() - { - super(ExpObjectForm.class); - } - - private Pair> createViews(ExpObjectForm form, BindException errors) - { - _experiment = ExperimentServiceImpl.get().getExpExperiment(form.getRowId()); - if (_experiment == null) - { - throw new NotFoundException("Could not find an experiment with RowId " + form.getRowId()); - } - - if (!_experiment.getContainer().equals(getContainer())) - { - throw new RedirectException(getViewContext().cloneActionURL().setContainer(_experiment.getContainer())); - } - - List protocols = _experiment.getAllProtocols(); - - Set types = new TreeSet<>(ExperimentService.get().getExperimentRunTypes(getContainer())); - ExperimentRunType selectedType = ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")); - - ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, selectedType, getViewContext().getActionURL().clone(), protocols); - JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean, errors); - - ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), bean.getSelectedFilter(), true); - runListView.getRunTable().setExperiment(_experiment); - runListView.setShowRemoveFromExperimentButton(true); - runListView.setShowDeleteButton(true); - runListView.setShowAddToRunGroupButton(true); - runListView.setShowExportButtons(true); - runListView.setShowMoveRunsButton(true); - return new Pair<>(runListView, chooserView); - } - - @Override - protected ModelAndView getHtmlView(ExpObjectForm form, BindException errors) throws Exception - { - Pair> views = createViews(form, errors); - - CustomPropertiesView customPropertiesView = new CustomPropertiesView(_experiment.getLSID(), getContainer()); - - TableInfo runGroupsTable = new ExpSchema(getUser(), getContainer()).getTable(ExpSchema.TableType.RunGroups); - - DetailsView detailsView = new DetailsView(new DataRegion(), _experiment.getRowId()); - detailsView.getDataRegion().setTable(runGroupsTable); - detailsView.getDataRegion().addColumns(runGroupsTable, "RowId,Name,Created,Modified,Contact,ExperimentDescriptionURL,Hypothesis,Comments"); - detailsView.getDataRegion().getDisplayColumn(0).setVisible(false); - detailsView.getDataRegion().getDisplayColumn(2).setWidth("60%"); - - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - ActionButton b = new ActionButton(ExperimentUrlsImpl.get().getShowUpdateURL(_experiment), "Edit"); - b.setDisplayPermission(UpdatePermission.class); - bb.add(b); - detailsView.getDataRegion().setButtonBar(bb); - if (_experiment.getBatchProtocol() != null) - { - detailsView.setTitle("Batch Details"); - detailsView.getDataRegion().addColumns(runGroupsTable, "BatchProtocolId"); - } - else - { - detailsView.setTitle("Run Group Details"); - } - - VBox runsVBox = new VBox(views.second, createInitializedQueryView(form, errors, false, null)); - runsVBox.setTitle("Experiment Runs"); - runsVBox.setFrame(WebPartView.FrameType.PORTAL); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, customPropertiesView), runsVBox); - } - - @Override - protected ExperimentRunListView createQueryView(ExpObjectForm form, BindException errors, boolean forExport, String dataRegion) - { - return createViews(form, errors).first; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - addRootNavTrail(root); - root.addChild("Run Groups", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); - root.addChild(_experiment.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ListSampleTypesAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - SampleTypeWebPart view = new SampleTypeWebPart(false, getViewContext()); - view.setFrame(WebPartView.FrameType.NONE); - view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); - - return view; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types"); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowSampleTypeAction extends SimpleViewAction - { - private ExpSampleTypeImpl _sampleType; - - @Override - public ModelAndView getView(ExpObjectForm form, BindException errors) - { - _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getRowId()); - if (_sampleType == null && form.getLsid() != null) - { - if (form.getLsid().equalsIgnoreCase("Material") || form.getLsid().equalsIgnoreCase("Sample")) - { - // Not a real sample type - just show all the materials instead - throw new RedirectException(new ActionURL(ShowAllMaterialsAction.class, getContainer())); - } - // Check if the URL specifies the LSID, and stick the bean back into the form - _sampleType = SampleTypeServiceImpl.get().getSampleType(form.getLsid()); - } - - if (_sampleType == null) - { - throw new NotFoundException("No matching sample type found"); - } - - List allScopedSampleTypes = (List) SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true); - if (!allScopedSampleTypes.contains(_sampleType)) - { - ensureCorrectContainer(getContainer(), _sampleType, getViewContext()); - } - - SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); - QuerySettings settings = schema.getSettings(getViewContext(), "Material", _sampleType.getName()); - QueryView queryView = new SampleTypeContentsView(_sampleType, schema, settings, errors); - - DetailsView detailsView = new DetailsView(getSampleTypeRegion(getViewContext()), _sampleType.getRowId()); - detailsView.getDataRegion().getDisplayColumn("Name").setURL((ActionURL)null); - detailsView.getDataRegion().getDisplayColumn("LSID").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("MaterialLSIDPrefix").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("LabelColor").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("MetricUnit").setVisible(false); - detailsView.getDataRegion().getDisplayColumn("Category").setVisible(false); - - detailsView.setTitle("Sample Type Properties"); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).setStyle(ButtonBar.Style.separateButtons); - - Container autoLinkContainer = _sampleType.getAutoLinkTargetContainer(); - if (null != autoLinkContainer) - { - DisplayColumn autoLinkTargetColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkTargetContainer"); - autoLinkTargetColumn.setVisible(false); - - SimpleDisplayColumn displayAutoLinkTargetColumn = new SimpleDisplayColumn(); - displayAutoLinkTargetColumn.setCaption("Auto Link Target Container:"); - String path = autoLinkContainer.getPath(); - displayAutoLinkTargetColumn.setDisplayHtml(path.equals("/") ? "" : path); - detailsView.getDataRegion().addDisplayColumn(displayAutoLinkTargetColumn); - } - - DisplayColumn autoLinkCategoryColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkCategory"); - autoLinkCategoryColumn.setVisible(false); - SimpleDisplayColumn displayAutoLinkCategoryColumn = new SimpleDisplayColumn(); - displayAutoLinkCategoryColumn.setCaption("Auto Link Category:"); - displayAutoLinkCategoryColumn.setDisplayHtml(_sampleType.getAutoLinkCategory()); - detailsView.getDataRegion().addDisplayColumn(displayAutoLinkCategoryColumn); - - if (_sampleType.hasNameAsIdCol()) - { - SimpleDisplayColumn nameIdCol = new SimpleDisplayColumn(); - nameIdCol.setCaption("Has Name Id Column:"); - nameIdCol.setDisplayHtml("true"); - detailsView.getDataRegion().addDisplayColumn(nameIdCol); - } - - if (_sampleType.hasIdColumns()) - { - SimpleDisplayColumn idCols = new SimpleDisplayColumn(); - idCols.setCaption("Id Column(s):"); - String names = _sampleType.getIdCols().stream() - .filter(Objects::nonNull) - .map(DomainProperty::getName) - .collect(Collectors.joining(", ")); - if (!names.isEmpty()) - { - idCols.setDisplayHtml(PageFlowUtil.filter(names)); - detailsView.getDataRegion().addDisplayColumn(idCols); - } - } - - if (_sampleType.getParentCol() != null) - { - SimpleDisplayColumn parentCol = new SimpleDisplayColumn(PageFlowUtil.filter(_sampleType.getParentCol().getName())); - parentCol.setCaption("Parent Column:"); - detailsView.getDataRegion().addDisplayColumn(parentCol); - } - - try - { - SimpleDisplayColumn importAliasCol = new SimpleDisplayColumn(); - importAliasCol.setCaption("Parent Import Alias(es):"); - if (!_sampleType.getImportAliases().isEmpty()) - importAliasCol.setDisplayHtml(PageFlowUtil.filter(StringUtils.join(_sampleType.getImportAliases().keySet(), ", "))); - detailsView.getDataRegion().addDisplayColumn(importAliasCol); - } - catch (IOException e) - { - // unable to parse import alias map from JSON - } - - if (!getContainer().equals(_sampleType.getContainer())) - { - ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowSampleTypeURL(_sampleType); - SimpleDisplayColumn definedInCol = new SimpleDisplayColumn("" + - PageFlowUtil.filter(_sampleType.getContainer().getPath()) + - ""); - definedInCol.setCaption("Defined In:"); - detailsView.getDataRegion().addDisplayColumn(definedInCol); - } - - // Not all sample types can be edited - DomainKind domainKind = _sampleType.getDomain().getDomainKind(); - if (domainKind != null && domainKind.canEditDefinition(getUser(), _sampleType.getDomain())) - { - if (domainKind instanceof SampleTypeDomainKind) - { - ActionURL updateURL = new ActionURL(EditSampleTypeAction.class, _sampleType.getContainer()); - updateURL.addParameter("RowId", _sampleType.getRowId()); - updateURL.addReturnUrl(getViewContext().getActionURL()); - - if (!getContainer().equals(_sampleType.getContainer())) - { - String editLink = updateURL.toString(); - ActionButton updateButton = new ActionButton("Edit Type"); - updateButton.setActionType(ActionButton.Action.SCRIPT); - updateButton.setScript("if (window.confirm('This sample type is defined in the " + _sampleType.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + editLink + "' }"); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); - } - else - { - ActionButton updateButton = new ActionButton(updateURL, "Edit Type", ActionButton.Action.LINK); - updateButton.setDisplayPermission(DesignSampleTypePermission.class); - updateButton.setPrimary(true); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); - } - - ActionURL deleteURL = new ActionURL(DeleteSampleTypesAction.class, _sampleType.getContainer()); - deleteURL.addParameter("singleObjectRowId", _sampleType.getRowId()); - deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ActionButton deleteButton = new ActionButton(deleteURL, "Delete Type", ActionButton.Action.LINK); - deleteButton.setDisplayPermission(DesignSampleTypePermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(deleteButton); - } - else - { - ActionURL editURL = domainKind.urlEditDefinition(_sampleType.getDomain(), new ViewBackgroundInfo(_sampleType.getContainer(), getUser(), getViewContext().getActionURL())); - if (editURL != null) - { - editURL.addReturnUrl(getViewContext().getActionURL()); - ActionButton editTypeButton = new ActionButton(editURL, "Edit Fields"); - editTypeButton.setDisplayPermission(UpdatePermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(editTypeButton); - } - } - } - - if (_sampleType.canImportMoreSamples()) - { - TableInfo table = queryView.getTable(); - if (table != null) - { - ActionURL importURL = table.getImportDataURL(getContainer()); - if (importURL != null) - { - importURL = importURL.clone(); - importURL.addReturnUrl(getViewContext().getActionURL()); - ActionButton uploadButton = new ActionButton(importURL, "Import More Samples", ActionButton.Action.LINK); - uploadButton.setDisplayPermission(UpdatePermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(uploadButton); - } - } - } - - var publish = StudyPublishService.get(); - if (AuditLogService.get().isViewable() && publish != null) - { - ContainerFilter cf = ContainerFilter.Type.CurrentAndSubfolders.create(getContainer(), getUser()); - ActionURL linkToStudyHistoryURL = publish.getPublishHistory(getContainer(), Dataset.PublishSource.SampleType, _sampleType.getRowId(), cf); - ActionButton linkToStudyHistoryButton = new ActionButton(linkToStudyHistoryURL, "Link to Study History", ActionButton.Action.LINK); - linkToStudyHistoryButton.setDisplayPermission(InsertPermission.class); - detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(linkToStudyHistoryButton); - } - - return new VBox(detailsView, queryView); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - ActionURL url = ExperimentUrls.get().getShowSampleTypeListURL(getContainer()); - addRootNavTrail(root); - root.addChild("Sample Types", url); - root.addChild("Sample Type " + _sampleType.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowAllMaterialsAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - ExpSchema schema = new ExpSchema(getUser(), getContainer()); - QuerySettings settings = schema.getSettings(getViewContext(), "Materials", ExpSchema.TableType.Materials.toString()); - QueryView view = new QueryView(schema, settings, errors) - { - @Override - protected void populateButtonBar(DataView view, ButtonBar bar) - { - super.populateButtonBar(view, bar); - bar.add(SampleTypeContentsView.getDeriveSamplesButton(getContainer(),null)); - } - }; - view.setShowDetailsColumn(false); - return view; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("All Materials"); - } - } - - /** - * Only shows standard and custom properties, not parent and child samples. Used for indexing - */ - @RequiresPermission(ReadPermission.class) - public class ShowMaterialSimpleAction extends SimpleViewAction - { - protected ExpMaterialImpl _material; - - @Override - public VBox getView(ExpObjectForm form, BindException errors) throws Exception - { - Container c = getContainer(); - _material = ExperimentServiceImpl.get().getExpMaterial(form.getRowId()); - if (_material == null && form.getLsid() != null) - { - _material = ExperimentServiceImpl.get().getExpMaterial(form.getLsid()); - } - if (_material == null) - { - throw new NotFoundException("Could not find a material with RowId " + form.getRowId()); - } - - ensureCorrectContainer(getContainer(), _material, getViewContext()); - - ExpRunImpl run = _material.getRun(); - ExpProtocol sourceProtocol = _material.getSourceProtocol(); - ExpProtocolApplication sourceProtocolApplication = _material.getSourceApplication(); - - DataRegion dr = new DataRegion(); - dr.addColumns(ExperimentServiceImpl.get().getTinfoMaterial().getUserEditableColumns()); - dr.removeColumns("RowId", "RunId", "LastIndexed", "LSID", "SourceApplicationId", "CpasType"); - - //dr.addColumns(extraProps); - dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); - dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); - dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); - dr.addDisplayColumn(new LineageGraphDisplayColumn(_material, run)); - dr.addDisplayColumn(new SampleTypeDisplayColumn(_material)); - - //TODO: Can't yet edit materials uploaded from a material source - dr.setButtonBar(new ButtonBar()); - DetailsView detailsView = new DetailsView(dr, _material.getRowId()); - detailsView.setTitle("Standard Properties"); - detailsView.setFrame(WebPartView.FrameType.PORTAL); - - CustomPropertiesView cpv = new CustomPropertiesView(_material, c, getUser()); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv)); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ExpSampleType sampleType = _material.getSampleType(); - if (sampleType != null) - { - root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); - } - root.addChild("Sample " + _material.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowMaterialAction extends ShowMaterialSimpleAction - { - @Override - public VBox getView(ExpObjectForm form, BindException errors) throws Exception - { - VBox vbox = super.getView(form, errors); - - List materialsToInvestigate = new ArrayList<>(); - final Set successorRuns = new HashSet<>(); - materialsToInvestigate.add(_material); - Set investigatedMaterials = new HashSet<>(); - do - { - // Query for all the next tier of materials at once - issue 45402 - List followupRuns = ExperimentService.get().getRunsUsingMaterials(materialsToInvestigate); - - // Mark this set as investigated and reset for the next cycle - investigatedMaterials.addAll(materialsToInvestigate); - materialsToInvestigate = new ArrayList<>(); - - for (ExpRun r : followupRuns) - { - // Only expand the material outputs of the run if it's our first time visiting it - if (successorRuns.add(r)) - { - materialsToInvestigate.addAll(r.getMaterialOutputs()); - } - } - - if (successorRuns.size() > 1000) - { - // Give up - there may be a cycle or other problematic data - break; - } - - // Cull the ones we've already looked up - materialsToInvestigate.removeAll(investigatedMaterials); - } - while (!materialsToInvestigate.isEmpty()); - - HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); - ExpSampleType st = _material.getSampleType(); - if (st != null && st.getContainer() != null && st.getContainer().hasPermission(getUser(), UpdatePermission.class)) - { - // XXX: ridiculous amount of work to get a update url expression for the sample type's table. - UserSchema samplesSchema = QueryService.get().getUserSchema(getUser(), st.getContainer(), "Samples"); - QueryDefinition queryDef = samplesSchema.getQueryDefForTable(st.getName()); - StringExpression expr = queryDef.urlExpr(QueryAction.updateQueryRow, null); - if (expr != null) - { - // Since we're building a detailsURL outside the context of a "row" need to set the correct - // container context on the generated expr. - ((DetailsURL) expr).setContainerContext(st.getContainer()); - String url = expr.eval(Collections.singletonMap(new FieldKey(null, "RowId"), _material.getRowId())); - updateLinks.append(LinkBuilder.labkeyLink("edit", url)).append(" "); - } - } - - if (getContainer().hasPermission(getUser(), InsertPermission.class)) - { - ActionURL deriveURL = new ActionURL(DeriveSamplesChooseTargetAction.class, getContainer()); - deriveURL.addParameter("rowIds", _material.getRowId()); - if (st != null) - deriveURL.addParameter("targetSampleTypeId", st.getRowId()); - - updateLinks.append(LinkBuilder.labkeyLink("derive samples from this sample", deriveURL)).append(" "); - } - - vbox.addView(new HtmlView(updateLinks)); - - ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); - runListView.setShowRecordSelectors(false); - runListView.getRunTable().setRuns(successorRuns); - runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); - runListView.setAllowableContainerFilterTypes(ContainerFilter.Type.Current, ContainerFilter.Type.CurrentAndSubfolders, ContainerFilter.Type.AllFolders); - runListView.setTitle("Runs associated with this material or a derived material"); - - ParentChildView pv = new ParentChildView(_material, getViewContext()); - vbox.addView(pv); - vbox.addView(runListView); - - return vbox; - } - } - - - // - // DataClass - // - - @RequiresPermission(ReadPermission.class) - public class ListDataClassAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - DataClassWebPart view = new DataClassWebPart(false, getViewContext(), null); - view.setFrame(WebPartView.FrameType.NONE); - view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); - - return view; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - addRootNavTrail(root); - root.addChild("Data Classes"); - } - } - - public static class DataClassForm extends ExpObjectForm - { - private String _name; - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - public ExpDataClassImpl getDataClass(@Nullable Container container) - { - ExpDataClassImpl dataClass = null; - - if (getName() != null) - { - dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getName()); - if (dataClass == null) - throw new NotFoundException("No data class found for name '" + getName() + "'."); - } - else if (getRowId() > 0) - { - dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getRowId()); - } - - if (dataClass == null) - throw new NotFoundException("No data class found."); - else if (container != null && !container.equals(dataClass.getContainer())) - throw new NotFoundException("Data class is not defined in the given container."); - - return dataClass; - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowDataClassAction extends SimpleViewAction - { - private ExpDataClassImpl _dataClass; - - @Override - public ModelAndView getView(DataClassForm form, BindException errors) - { - _dataClass = form.getDataClass(null); - return new VBox(getDataClassPropertiesView(), getDataClassContentsView(errors)); - } - - private DetailsView getDataClassPropertiesView() - { - ExpSchema expSchema = new ExpSchema(getUser(), _dataClass.getContainer()); - - TableInfo table = ExpSchema.TableType.DataClasses.createTable(expSchema, null, null); - QueryUpdateForm tvf = new QueryUpdateForm(table, getViewContext(), null); - tvf.setPkVal(_dataClass.getRowId()); - DetailsView detailsView = new DetailsView(tvf); - detailsView.setTitle("Data Class Properties"); - - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - boolean inDefinitionContainer = getContainer().equals(_dataClass.getContainer()); - - DomainKind domainKind = _dataClass.getDomain().getDomainKind(); - if (domainKind != null && domainKind.canEditDefinition(getUser(), _dataClass.getDomain())) - { - ActionURL updateURL = new ActionURL(EditDataClassAction.class, _dataClass.getContainer()); - updateURL.addParameter("rowId", _dataClass.getRowId()); - updateURL.addReturnUrl(urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId())); - - if (inDefinitionContainer) - { - ActionButton updateButton = new ActionButton(updateURL, "Edit Data Class", ActionButton.Action.LINK); - updateButton.setDisplayPermission(DesignDataClassPermission.class); - updateButton.setPrimary(true); - bb.add(updateButton); - } - else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) - { - ActionButton updateButton = new ActionButton("Edit Data Class"); - updateButton.setActionType(ActionButton.Action.SCRIPT); - updateButton.setScript("if (window.confirm('This data class is defined in the " + _dataClass.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + updateURL + "' }"); - updateButton.setPrimary(true); - bb.add(updateButton); - } - - ActionURL deleteURL = new ActionURL(DeleteDataClassAction.class, _dataClass.getContainer()); - deleteURL.addParameter("singleObjectRowId", _dataClass.getRowId()); - deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - ActionButton deleteButton = new ActionButton(deleteURL, "Delete Data Class", ActionButton.Action.LINK); - - if (inDefinitionContainer) - { - deleteButton.setDisplayPermission(DesignDataClassPermission.class); - bb.add(deleteButton); - } - else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) - { - bb.add(deleteButton); - } - } - detailsView.getDataRegion().setButtonBar(bb); - - if (!inDefinitionContainer) - { - ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId()); - LinkBuilder link = LinkBuilder.simpleLink(_dataClass.getContainer().getPath(), definitionURL); - SimpleDisplayColumn definedInCol = new SimpleDisplayColumn(link.toString()); - definedInCol.setCaption("Defined In:"); - detailsView.getDataRegion().addDisplayColumn(definedInCol); - } - - return detailsView; - } - - private QueryView getDataClassContentsView(BindException errors) - { - UserSchema dataClassSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_EXP_DATA); - QuerySettings settings = dataClassSchema.getSettings(getViewContext(), QueryView.DATAREGIONNAME_DEFAULT, _dataClass.getName()); - - return new QueryView(dataClassSchema, settings, errors) - { - @Override - public @NotNull LinkedHashSet getClientDependencies() - { - LinkedHashSet resources = super.getClientDependencies(); - resources.add(ClientDependency.fromPath("Ext4")); - resources.add(ClientDependency.fromPath("dataregion/confirmDelete.js")); - return resources; - } - - @Override - public ActionButton createDeleteButton() - { - ActionButton button = super.createDeleteButton(); - if (button != null) - { - String dependencyText = ExperimentService.get() - .getObjectReferencers() - .stream() - .map(referencer -> referencer.getObjectReferenceDescription(ExpData.class)) - .collect(Collectors.joining(" or ")); - - button.setScript("LABKEY.dataregion.confirmDelete(" + - PageFlowUtil.jsString(getDataRegionName()) + ", " + - PageFlowUtil.jsString(ExpSchema.SCHEMA_EXP_DATA.toString()) + ", " + - PageFlowUtil.jsString(getQueryDef().getName()) + ", " + - "'experiment', 'getDataOperationConfirmationData.api', " + - PageFlowUtil.jsString(getSelectionKey()) + ", " + - "'data object', 'data objects', '" + dependencyText + "', {dataOperation: 'Delete'})"); - button.setRequiresSelection(true); - } - return button; - } - }; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - addRootNavTrail(root); - root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - root.addChild(_dataClass.getName()); - } - } - - @RequiresPermission(DesignDataClassPermission.class) - public class DeleteDataClassAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - super.addNavTrail(root); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - List dataClasses = getDataClasses(deleteForm); - if (!ensureCorrectContainer(dataClasses)) - { - throw new UnauthorizedException(); - } - for (ExpRun run : getRuns(dataClasses)) - { - if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new UnauthorizedException(); - } - } - for (ExpDataClass dataClass : dataClasses) - { - dataClass.delete(getUser(), deleteForm.getUserComment()); - } - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List dataClasses = getDataClasses(deleteForm); - - if (!ensureCorrectContainer(dataClasses)) - { - throw new RedirectException(ExperimentUrlsImpl.get().getDataClassListURL(getContainer(), "To delete a data class, you must be in its folder or project.")); - } - - return new ConfirmDeleteView("Data Class", ShowDataClassAction.class, dataClasses, deleteForm, getRuns(dataClasses)); - } - - private List getDataClasses(DeleteForm deleteForm) - { - List dataClasses = new ArrayList<>(); - for (long rowId : deleteForm.getIds(false)) - { - ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), rowId); - if (dataClass != null) - { - dataClasses.add(dataClass); - } - } - return dataClasses; - } - - private boolean ensureCorrectContainer(List dataClasses) - { - for (ExpDataClass dataClass : dataClasses) - { - Container sourceContainer = dataClass.getContainer(); - if (!sourceContainer.equals(getContainer())) - { - return false; - } - } - return true; - } - - private List getRuns(List dataClasses) - { - if (!dataClasses.isEmpty()) - { - List runArray = ExperimentService.get().getRunsUsingDataClasses(dataClasses); - return ExperimentService.get().runsDeletedWithInput(runArray); - } - else - { - return Collections.emptyList(); - } - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetDataClassPropertiesAction extends ReadOnlyApiAction - { - @Override - public Object execute(DataClassForm form, BindException errors) throws Exception - { - ExpDataClass dataClass = form.getDataClass(getContainer()); - if (dataClass != null) - return new DataClassDomainKindProperties(dataClass); - else - throw new NotFoundException("Data class does not exist in this container for rowId " + form.getRowId() + "."); - } - } - - @RequiresPermission(DesignDataClassPermission.class) - public static class EditDataClassAction extends SimpleViewAction - { - private ExpDataClassImpl _dataClass; - - @Override - public ModelAndView getView(DataClassForm form, BindException errors) - { - boolean create = form.getLSID() == null && form.getRowId() == 0 && form.getName() == null; - if (!create) - _dataClass = form.getDataClass(getContainer()); - - return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("dataClassDesigner")); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - - root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - if (_dataClass == null) - { - root.addChild("Create Data Class"); - } - else - { - root.addChild(_dataClass.getName(), ExperimentUrlsImpl.get().getShowDataClassURL(getContainer(), _dataClass.getRowId())); - root.addChild("Update Data Class"); - } - } - } - - @RequiresPermission(DesignDataClassPermission.class) - public static class CreateDataClassFromTemplateAction extends FormViewAction - { - private ActionURL _successUrl; - private Map _domainTemplates; - - @Override - public void validateCommand(CreateDataClassFromTemplateForm form, Errors errors) - { - String name = null; - _domainTemplates = DomainTemplateGroup.getAllTemplates(getContainer()); - - if (!_domainTemplates.containsKey(form.getDomainTemplate())) - { - errors.reject(ERROR_MSG, "Unknown template selected: " + form.getDomainTemplate()); - } - else - { - DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); - name = template.getTemplateName(); - - // Issue 40230: if template includes sample type option, verify that it exists - if (template.getOptions().containsKey("sampleSet")) - { - String sampleTypeName = template.getOptions().get("sampleSet").toString(); - ExpSampleType sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), sampleTypeName); - if (sampleType == null) - errors.reject(ERROR_MSG, "Unable to find a sample type in this container with name: " + sampleTypeName + "."); - } - } - - if (StringUtils.isBlank(name)) - errors.reject(ERROR_MSG, "DataClass template selection is required."); - else if (ExperimentService.get().getDataClass(getContainer(), getUser(), name) != null) - errors.reject(ERROR_MSG, "DataClass '" + name + "' already exists."); - - } - - @Override - public ModelAndView getView(CreateDataClassFromTemplateForm form, boolean reshow, BindException errors) - { - Set templates = DomainTemplateGroup.getTemplatesForDomainKind(getContainer(), DataClassDomainKind.NAME); - form.setAvailableDomainTemplateNames(templates); - - Set messages = new HashSet<>(); - Map groups = DomainTemplateGroup.getAllGroups(getContainer()); - for (DomainTemplateGroup g : groups.values()) - messages.addAll(g.getErrors()); - form.setXmlParseErrors(messages); - - return new JspView<>("/org/labkey/experiment/createDataClassFromTemplate.jsp", form, errors); - } - - @Override - public boolean handlePost(CreateDataClassFromTemplateForm form, BindException errors) throws Exception - { - DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); - Domain domain = DomainUtil.createDomain(template, getContainer(), getUser(), form.getName()); - - _successUrl = domain.getDomainKind().urlEditDefinition(domain, getViewContext()); - return true; - } - - @Override - public URLHelper getSuccessURL(CreateDataClassFromTemplateForm form) - { - return _successUrl; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("dataClass"); - root.addChild("Create Data Class from Template"); - } - } - - public static class CreateDataClassFromTemplateForm extends DataClass - { - private String _domainTemplate; - private Set _availableDomainTemplateNames; - private Set _xmlParseErrors; - private final ReturnUrlForm _returnUrlForm = new ReturnUrlForm(); - - public String getDomainTemplate() - { - return _domainTemplate; - } - - public void setDomainTemplate(String domainTemplate) - { - _domainTemplate = domainTemplate; - } - - public Set getAvailableDomainTemplateNames() - { - return _availableDomainTemplateNames; - } - - public void setAvailableDomainTemplateNames(Set availableDomainTemplateNames) - { - _availableDomainTemplateNames = availableDomainTemplateNames; - } - - public Set getXmlParseErrors() - { - return _xmlParseErrors; - } - - public void setXmlParseErrors(Set xmlParseErrors) - { - _xmlParseErrors = xmlParseErrors; - } - - @Nullable - public String getReturnUrl() - { - return _returnUrlForm.getReturnUrl(); - } - - public void setReturnUrl(String s) - { - _returnUrlForm.setReturnUrl(s); - } - } - - public static class ConceptURIForm - { - private String _conceptURI; - - public String getConceptURI() - { - return _conceptURI; - } - - public void setConceptURI(String conceptURI) - { - _conceptURI = conceptURI; - } - } - - @RequiresPermission(AdminPermission.class) - public static class RemoveConceptMappingAction extends MutatingApiAction - { - @Override - public void validateForm(ConceptURIForm form, Errors errors) - { - if (form.getConceptURI() == null || ConceptURIProperties.getLookup(getContainer(), form.getConceptURI()) == null) - errors.reject(ERROR_MSG, "Concept URI not found: " + form.getConceptURI()); - } - - @Override - public Object execute(ConceptURIForm form, BindException errors) - { - ConceptURIProperties.removeLookup(getContainer(), form.getConceptURI()); - return new ApiSimpleResponse("success", true); - } - } - - @RequiresPermission(ReadPermission.class) - public static class RunAttachmentDownloadAction extends BaseDownloadAction - { - @Nullable - @Override - public Pair getAttachment(AttachmentForm form) - { - if (form.getLsid() == null || form.getName() == null) - throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); - - ExpRun run = ExperimentService.get().getExpRun(form.getLsid()); - if (run == null) - throw new NotFoundException("Run not found: " + form.getLsid()); - - if (!run.getContainer().equals(getContainer())) - { - if (run.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new RedirectException(getViewContext().cloneActionURL().setContainer(run.getContainer())); - else - throw new NotFoundException("Run not found"); - } - - AttachmentParent parent = new ExpRunAttachmentParent(run); - return new Pair<>(parent, form.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public static class DataClassAttachmentDownloadAction extends BaseDownloadAction - { - @Nullable - @Override - public Pair getAttachment(AttachmentForm form) - { - if (form.getLsid() == null || form.getName() == null) - throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); - - Lsid lsid = new Lsid(form.getLsid()); - ExpData data = ExperimentServiceImpl.get().getExpData(lsid.toString()); - if (data == null) - throw new NotFoundException("Error: Data object not found for the given LSID: " + lsid); - AttachmentParent parent = new ExpDataClassAttachmentParent(data.getContainer(), lsid); - - return new Pair<>(parent, form.getName()); - } - } - - public static class AttachmentForm extends LsidForm implements BaseDownloadAction.InlineDownloader - { - private String _name; - private boolean _inline = true; - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - @Override - public boolean isInline() - { - return _inline; - } - - public void setInline(boolean inline) - { - _inline = inline; - } - } - - // - // END DataClass actions - // - - public static ActionURL getRunGraphURL(Container c, long runId) - { - return new ActionURL(ShowRunGraphAction.class, c).addParameter("rowId", runId); - } - - - @RequiresPermission(ReadPermission.class) - public class ShowRunGraphAction extends AbstractShowRunAction - { - @Override - protected VBox createLowerView(ExpRunImpl experimentRun, BindException errors) - { - return new VBox( - createRunViewTabs(experimentRun, false, true, true), - new ExperimentRunGraphView(experimentRun, false)); - } - } - - - @RequiresPermission(ReadPermission.class) - public static class DownloadGraphAction extends SimpleViewAction - { - @Override - public ModelAndView getView(ExperimentRunForm form, BindException errors) throws Exception - { - boolean detail = form.isDetail(); - String focus = form.getFocus(); - String focusType = form.getFocusType(); - - ExpRunImpl experimentRun = (ExpRunImpl) form.lookupRun(); - ensureCorrectContainer(getContainer(), experimentRun, getViewContext()); - - ExperimentRunGraph.RunGraphFiles files; - try - { - files = ExperimentRunGraph.generateRunGraph(getViewContext(), experimentRun, detail, focus, focusType); - } - catch (ExperimentException e) - { - PageFlowUtil.streamTextAsImage(getViewContext().getResponse(), "ERROR: " + e.getMessage(), 600, 150, Color.RED); - return null; - } - - try - { - PageFlowUtil.streamFile(getViewContext().getResponse(), new File(files.getImageFile().getAbsolutePath()), false); - } - catch (FileNotFoundException e) - { - getViewContext().getResponse().sendRedirect(getViewContext().getRequest().getContextPath() + "/experiment/ExperimentRunNotFound.gif"); - } - finally - { - files.release(); - } - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - throw new UnsupportedOperationException(); - } - } - - private abstract class AbstractShowRunAction extends SimpleViewAction - { - private ExpRunImpl _experimentRun; - - @Override - public ModelAndView getView(ExperimentRunForm form, BindException errors) - { - _experimentRun = (ExpRunImpl) form.lookupRun(); - ensureCorrectContainer(getContainer(), _experimentRun, getViewContext()); - - VBox vbox = new VBox(); - - JspView detailsView = new JspView<>("/org/labkey/experiment/ExperimentRunDetails.jsp", _experimentRun); - detailsView.setTitle("Standard Properties"); - - var attachmentParent = new ExpRunAttachmentParent(_experimentRun); - var attachments = AttachmentService.get().getAttachments(attachmentParent) - .stream() - .map(att -> Pair.of(att.getName(), new ActionURL(RunAttachmentDownloadAction.class, _experimentRun.getContainer()).addParameter("name", att.getName()).addParameter("lsid", _experimentRun.getLSID()))) - .collect(toList()); - CustomPropertiesView cpv = new CustomPropertiesView(_experimentRun.getLSID(), getContainer(), attachments); - - vbox.addView(new StandardAndCustomPropertiesView(detailsView, cpv)); - - HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); - List runEditors = ExperimentService.get().getRunEditors(); - for (ExpRunEditor editor : runEditors) - { - if (editor.isProtocolEditor(form.lookupRun().getProtocol())) - { - updateLinks.append(LinkBuilder.labkeyLink("edit " + editor.getDisplayName() + " run", editor.getEditUrl(getContainer()).addParameter("rowId", form.getRowId()))); - } - } - - if (!updateLinks.isEmpty()) - { - HtmlView view = new HtmlView(updateLinks); - vbox.addView(view); - } - - VBox lowerView = createLowerView(_experimentRun, errors); - lowerView.setFrame(WebPartView.FrameType.PORTAL); - lowerView.setTitle("Run Details"); - NavTree tree = new NavTree(""); - File runRoot = _experimentRun.getFilePathRoot(); - if (NetworkDrive.exists(runRoot)) - { - if (!runRoot.isDirectory()) - { - runRoot = runRoot.getParentFile(); - } - PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(_experimentRun.getContainer()); - if (pipelineRoot != null) - { - if (pipelineRoot.isUnderRoot(runRoot)) - { - String path = pipelineRoot.relativePath(runRoot); - tree.addChild("View Files", urlProvider(PipelineUrls.class).urlBrowse(_experimentRun.getContainer(), null, path)); - } - } - } - - final String exportFilesFormId = "exportFilesForm"; - NavTree downloadFiles = new NavTree("Download all files"); - downloadFiles.setScript("document.getElementById('" + exportFilesFormId + "').submit();"); - tree.addChild(downloadFiles); - - // CONSIDER: Show modal dialog using ExperimentService.get().createRunExportView() - NavTree exportXarFiles = new NavTree("Export XAR"); - exportXarFiles.setScript("LABKEY.Experiment.exportRuns({runIds: [" + _experimentRun.getRowId() + "] });"); - tree.addChild(exportXarFiles); - - lowerView.setNavMenu(tree); - lowerView.setIsWebPart(false); - - vbox.addView(lowerView); - vbox.addView(new ExperimentRunGroupsView(getUser(), getContainer(), _experimentRun, getViewContext().getActionURL(), errors)); - - DOM.Renderable exportFilesForm = LK.FORM(at( - id, exportFilesFormId, - method, "POST", - action, new ActionURL(ExportRunFilesAction.class, _experimentRun.getContainer())), - INPUT(at(type, "hidden", - name, DataRegionSelection.DATA_REGION_SELECTION_KEY, - value, "ExportSingleRun")), - INPUT(at(type, "hidden", - name, DataRegion.SELECT_CHECKBOX_NAME, - value, _experimentRun.getRowId())), - INPUT(at(type, "hidden", - name, "zipFileName", - value, _experimentRun.getName() + ".zip"))); - - HtmlView hiddenFormView = new HtmlView(exportFilesForm); - vbox.addView(hiddenFormView); - - return vbox; - } - - protected abstract VBox createLowerView(ExpRunImpl experimentRun, BindException errors); - - @Override - public void addNavTrail(NavTree root) - { - root.addChild(_experimentRun.getName()); - } - } - - public static class ToggleRunExperimentMembershipForm - { - private int _runId; - private int _experimentId; - private boolean _included; - - public int getRunId() - { - return _runId; - } - - public void setRunId(int runId) - { - _runId = runId; - } - - public int getExperimentId() - { - return _experimentId; - } - - public void setExperimentId(int experimentId) - { - _experimentId = experimentId; - } - - public boolean isIncluded() - { - return _included; - } - - public void setIncluded(boolean included) - { - _included = included; - } - } - - @RequiresPermission(UpdatePermission.class) - public static class ToggleRunExperimentMembershipAction extends FormHandlerAction - { - @Override - public boolean handlePost(ToggleRunExperimentMembershipForm form, BindException errors) - { - ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); - // Check if the user has permission to update this run - if (run == null || !run.getContainer().hasPermission(getUser(), UpdatePermission.class)) - { - throw new NotFoundException(); - } - - ExpExperiment exp = ExperimentService.get().getExpExperiment(form.getExperimentId()); - if (exp == null) - { - throw new NotFoundException(); - } - // Check if this - if (!ExperimentService.get().getExperiments(run.getContainer(), getUser(), true, false).contains(exp)) - { - throw new NotFoundException(); - } - // Users must have permission to view, but not necessarily update, the container the holds the run group - if (!exp.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new UnauthorizedException(); - } - - if (form.isIncluded()) - { - exp.addRuns(getUser(), run); - } - else - { - exp.removeRun(getUser(), run); - } - - return true; - } - - @Override - public URLHelper getSuccessURL(ToggleRunExperimentMembershipForm form) - { - return null; - } - - @Override - public void validateCommand(ToggleRunExperimentMembershipForm target, Errors errors) - { - } - } - - private HtmlView createRunViewTabs(ExpRun expRun, boolean showGraphSummary, boolean showGraphDetail, boolean showText) - { - return new HtmlView( - TABLE(cl("labkey-tab-strip"), - TR( - createTabSpacer(false), - createTab("Graph Summary View", ExperimentUrlsImpl.get().getRunGraphURL(expRun), !showGraphSummary), - createTabSpacer(false), - createTab("Graph Detail View", ExperimentUrlsImpl.get().getRunGraphDetailURL(expRun), !showGraphDetail), - createTabSpacer(false), - createTab("Text View", ExperimentUrlsImpl.get().getRunTextURL(expRun), !showText), - createTabSpacer(true)))); - } - - private DOM.Renderable createTab(String text, ActionURL url, boolean selected) - { - return TD(cl(selected,"labkey-tab-selected", "labkey-tab"), - A(at(href, url), text)); - } - - private DOM.Renderable createTabSpacer(boolean fullWidth) - { - return TD(cl("labkey-tab-space").at(fullWidth, width, "100%"), - IMG(at(src, AppProps.getInstance().getContextPath() + "/_.gif", width, "5"))); - } - - @RequiresPermission(ReadPermission.class) - public class ShowRunTextAction extends AbstractShowRunAction - { - @Override - protected VBox createLowerView(ExpRunImpl expRun, BindException errors) - { - JspView applicationsView = new JspView<>("/org/labkey/experiment/ProtocolApplications.jsp", expRun); - applicationsView.setFrame(WebPartView.FrameType.TITLE); - applicationsView.setTitle("Protocol Applications"); - - HtmlView toggleView = createRunViewTabs(expRun, true, true, false); - - QuerySettings runDataInputsSettings = new QuerySettings(getViewContext(), "RunDataInputs", DataInputs.name()); - UsageQueryView runDataInputsView = new UsageQueryView("Data Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runDataInputsSettings, errors); - runDataInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); - - QuerySettings runDataOutputsSettings = new QuerySettings(getViewContext(), "RunDataOutputs", DataInputs.name()); - UsageQueryView runDataOutputsView = new UsageQueryView("Data Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runDataOutputsSettings, errors); - runDataOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); - - QuerySettings runMaterialInputsSetting = new QuerySettings(getViewContext(), "RunMaterialInputs", ExpSchema.TableType.MaterialInputs.name()); - UsageQueryView runMaterialInputsView = new UsageQueryView("Material Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runMaterialInputsSetting, errors); - runMaterialInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); - - QuerySettings runMaterialOutputsSettings = new QuerySettings(getViewContext(), "RunMaterialOutputs", ExpSchema.TableType.MaterialInputs.name()); - UsageQueryView runMaterialOutputsView = new UsageQueryView("Material Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runMaterialOutputsSettings, errors); - runMaterialOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); - - HBox inputsView = new HBox(runDataInputsView, runMaterialInputsView); - HBox registeredInputsView = new HBox(); - - var expService = ExperimentService.get(); - expService.getRunInputsViewProviders().forEach(provider -> - { - var queryView = provider.createView(getViewContext(), expRun, errors); - if (queryView != null) - { - registeredInputsView.addView(queryView); - } - }); - HBox outputsView = new HBox(runDataOutputsView, runMaterialOutputsView); - HBox registeredOutputsView = new HBox(); - expService.getRunOutputsViewProviders().forEach(provider -> - { - var queryView = provider.createView(getViewContext(), expRun, errors); - if (queryView != null) - { - registeredOutputsView.addView(queryView); - } - }); - - var vBox = new VBox(); - vBox.addView(toggleView); - vBox.addView(inputsView); - if (!registeredInputsView.isEmpty()) - vBox.addView(registeredInputsView); - vBox.addView(outputsView); - if (!registeredOutputsView.isEmpty()) - vBox.addView(registeredOutputsView); - vBox.addView(applicationsView); - - return vBox; - } - } - - private static class UsageQueryView extends QueryView - { - private final ExpRun _run; - private final ExpProtocol.ApplicationType _type; - - public UsageQueryView(String title, ViewContext context, ExpRun run, ExpProtocol.ApplicationType type, - QuerySettings settings, BindException errors) - { - super(new ExpSchema(context.getUser(), context.getContainer()), settings, errors); - setTitle(title); - setFrame(FrameType.TITLE); - _run = run; - _type = type; - setShowBorders(true); - setShadeAlternatingRows(true); - setShowExportButtons(false); - setShowPagination(false); - disableContainerFilterSelection(); - } - - @Override - protected TableInfo createTable() - { - String tableName = getSettings().getQueryName(); - ExpInputTable tableInfo = (ExpInputTable) getSchema().getTable(tableName, new ContainerFilter.AllFolders(getUser()), true, true); - tableInfo.setRun(_run, _type); - tableInfo.setLocked(true); - return tableInfo; - } - } - - - public static ActionURL getShowRunGraphDetailURL(Container c, long rowId) - { - ActionURL url = new ActionURL(ShowRunGraphDetailAction.class, c); - url.addParameter("rowId", rowId); - return url; - } - - - @RequiresPermission(ReadPermission.class) - public class ShowRunGraphDetailAction extends AbstractShowRunAction - { - @Override - protected VBox createLowerView(ExpRunImpl run, BindException errors) - { - ExperimentRunGraphView gw = new ExperimentRunGraphView(run, true); - if (null != getViewContext().getActionURL().getParameter("focus")) - gw.setFocus(getViewContext().getActionURL().getParameter("focus")); - if (null != getViewContext().getActionURL().getParameter("focusType")) - gw.setFocusType(getViewContext().getActionURL().getParameter("focusType")); - return new VBox(createRunViewTabs(run, true, false, true), gw); - } - } - - private abstract class AbstractDataAction extends SimpleViewAction - { - protected ExpDataImpl _data; - - @Override - public final ModelAndView getView(DataForm form, BindException errors) throws Exception - { - _data = form.lookupData(); - if (_data == null) - { - throw new NotFoundException("Could not find a data with RowId " + form.getRowId()); - } - - ensureCorrectContainer(getContainer(), _data, getViewContext()); - return getDataView(form, errors); - } - - protected abstract ModelAndView getDataView(DataForm form, BindException errors) throws Exception; - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Data " + _data.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowDataAction extends AbstractDataAction - { - @Override - public ModelAndView getDataView(DataForm form, BindException errors) - { - ExpRun run = _data.getRun(); - ExpProtocol sourceProtocol = _data.getSourceProtocol(); - ExpProtocolApplication sourceProtocolApplication = _data.getSourceApplication(); - ExpDataClass dataClass = _data.getDataClass(getUser()); - - ExpSchema schema = new ExpSchema(getUser(), getContainer()); - TableInfo table; - long pk; - if (dataClass == null) - { - table = schema.getDatasTable(); - pk = _data.getRowId(); - } - else - { - table = schema.getSchema(ExpSchema.NestedSchemas.data).getTable(dataClass.getName()); - pk = new TableSelector(table, Collections.singleton("rowId"), new SimpleFilter(FieldKey.fromParts("lsid"), _data.getLSID()), null).getObject(Integer.class); - } - - DataRegion dr = new DataRegion(); - dr.setTable(table); - List cols = table.getColumns().stream().filter(ColumnInfo::isShownInDetailsView).collect(toList()); - dr.addColumns(cols); - dr.removeColumns("RowId", "Created", "CreatedBy", "Modified", "ModifiedBy", "DataFileUrl", "Run", "LSID", "CpasType", "SourceApplicationId", "Folder", "Generated"); - dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); - dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); - dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); - dr.addDisplayColumn(new LineageGraphDisplayColumn(_data, run)); - DetailsView detailsView = new DetailsView(dr, pk); - detailsView.setTitle("Standard Properties"); - detailsView.setFrame(WebPartView.FrameType.PORTAL); - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - - ExperimentDataHandler handler = _data.findDataHandler(); - ActionURL viewDataURL = handler == null ? null : handler.getContentURL(_data); - if (viewDataURL != null) - { - bb.add(new ActionButton("View data", viewDataURL)); - } - - if (_data.isPathAccessible()) - { - bb.add(new ActionButton("View file", ExperimentUrlsImpl.get().getShowFileURL(_data, true))); - bb.add(new ActionButton("Download file", ExperimentUrlsImpl.get().getShowFileURL(_data, false))); - - if (getContainer().hasPermission(getUser(), InsertPermission.class)) - { - String relativePath = null; - PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); - if (root != null) - { - Path rootFile = root.getRootNioPath(); - Path dataFile = _data.getFilePath(); - if (dataFile != null) - { - Path pathRelative; - try - { - pathRelative = rootFile.relativize(dataFile); - if (null != pathRelative) - relativePath = pathRelative.toString(); - } - catch (IllegalArgumentException e) - { - // dataFile not relative to root - } - } - } - ActionURL browseURL = urlProvider(PipelineUrls.class).urlBrowse(getContainer(), getViewContext().getActionURL(), relativePath); - bb.add(new ActionButton("Browse in pipeline", browseURL)); - } - } - - // add links to any other exp.data that share the same dataFileUrl path - var altDataList = ExperimentService.get().getAllExpDataByURL(_data.getDataFileUrl(), getContainer()); - altDataList.removeIf(_data::equals); - if (!altDataList.isEmpty()) - { - MenuButton menu = new MenuButton("Alternate Data"); - for (ExpData altData : altDataList) - { - ExpRun altDataRun = altData.getRun(); - StringBuilder sb = new StringBuilder(altData.getName()); - if (altDataRun != null) - sb.append(" created by run '").append(altDataRun.getName()).append("' (").append(altDataRun.getProtocol().getName()).append(")"); - menu.addMenuItem(sb.toString(), altData.detailsURL()); - } - bb.add(menu); - } - - dr.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); - dr.setButtonBar(bb); - - CustomPropertiesView cpv = new CustomPropertiesView(_data.getLSID(), getContainer()); - HBox hbox = new StandardAndCustomPropertiesView(detailsView, cpv); - - VBox vbox = new VBox(hbox); - - ParentChildView pv = new ParentChildView(_data, getViewContext()); - vbox.addView(pv); - - ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); - runListView.getRunTable().setInputData(_data); - runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); - runListView.getRunTable().setLocked(true); - runListView.setTitle("Runs using this data as an input"); - vbox.addView(runListView); - - if (_data.isInlineImage() && _data.isFileOnDisk()) - { - ActionURL showFileURL = new ActionURL(ShowFileAction.class, getContainer()).addParameter("rowId", _data.getRowId()); - HtmlView imageView = new HtmlView(IMG(at(src, showFileURL))); - return new VBox(vbox, imageView); - } - return vbox; - } - } - - @RequiresPermission(AdminPermission.class) - public static class CheckDataFileAction extends MutatingApiAction - { - private ExpDataImpl _data; - - @Override - public void validateForm(DataFileForm form, Errors errors) - { - _data = form.lookupData(); - if (_data == null) - { - errors.reject(ERROR_MSG, "No ExpData found for id: " + form.getRowId()); - } - } - - @Override - public ApiResponse execute(DataFileForm form, BindException errors) - { - File dataFile = _data.getFile(); - Container dataContainer = _data.getContainer(); - boolean fileExists = _data.isFileOnDisk(); - boolean fileExistsAtCurrent = false; - File newDataFile = null; - - ApiSimpleResponse response = new ApiSimpleResponse(); - response.put("dataFileUrl", _data.getDataFileUrl()); - response.put("fileExists", fileExists); - response.put("containerPath", dataContainer.getPath()); - - if (!fileExists) - { - PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(dataContainer); - if (pipelineRoot != null && pipelineRoot.isValid() && dataFile != null) - { - newDataFile = pipelineRoot.resolvePath("/" + AssayFileWriter.DIR_NAME + "/" + dataFile.getName()); - fileExistsAtCurrent = NetworkDrive.exists(newDataFile); - response.put("fileExistsAtCurrent", fileExistsAtCurrent); - } - } - - // if the current dataFileUrl does not exist on disk and we have the file at the current - // pipeline root /assaydata dir, fix the dataFileUrl value - if (form.isAttemptFilePathFix()) - { - if (fileExistsAtCurrent) - { - ExpDataFileListener fileListener = new ExpDataFileListener(); - fileListener.fileMoved(dataFile, newDataFile, getUser(), dataContainer); - response.put("filePathFixed", true); - - // update the ExpData object so that we can get the new dataFileUrl - _data = form.lookupData(); - response.put("newDataFileUrl", _data.getDataFileUrl()); - } - else - { - response.put("filePathFixed", false); - } - } - - response.put("success", true); - return response; - } - } - - public static class DataFileForm extends DataForm - { - private boolean _attemptFilePathFix; - - public boolean isAttemptFilePathFix() - { - return _attemptFilePathFix; - } - - public void setAttemptFilePathFix(boolean attemptFilePathFix) - { - _attemptFilePathFix = attemptFilePathFix; - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowFileAction extends AbstractDataAction - { - @Override - protected ModelAndView getDataView(DataForm form, BindException errors) throws IOException - { - if (!_data.isPathAccessible()) - { - throw new NotFoundException("Data file " + _data.getDataFileUrl() + " does not exist on disk"); - } - - PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); - if (root != null && !root.isUnderRoot(_data.getFilePath())) - { - // Issue 35649: ImmPort module "publish" creates exp.data object in this container for paths that originate in a different container - FileContentService fileSvc = FileContentService.get(); - if (fileSvc == null) - throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); - - List containers = fileSvc.getContainersForFilePath(_data.getFilePath()); - if (containers.isEmpty() || containers.stream().noneMatch(c -> c.hasPermission(getUser(), ReadPermission.class))) - throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); - } - - //Issues 25667 and 31152 - if (form.isInline()) - { - ExperimentDataHandler h = _data.findDataHandler(); - if (h != null) - { - URLHelper url = h.getShowFileURL(_data); - if (url != null) - { - throw new RedirectException(url, false); - } - } - } - - try - { - Path realContent = _data.getFilePath(); - if (null == realContent) - throw new IllegalStateException("Path not found."); - - boolean inline = _data.isInlineImage() || form.isInline() || "inlineImage".equalsIgnoreCase(form.getFormat()); - if (_data.isInlineImage() && form.getMaxDimension() != null) - { - try (InputStream inputStream = Files.newInputStream(realContent)) - { - BufferedImage image = ImageIO.read(inputStream); - // If image, create a thumbnail, otherwise fall through as a regular download attempt - if (image != null) - { - int imageMax = Math.max(image.getHeight(), image.getWidth()); - if (imageMax > form.getMaxDimension().intValue()) - { - double scale = (double) form.getMaxDimension().intValue() / (double) imageMax; - ByteArrayOutputStream bOut = new ByteArrayOutputStream(); - ImageUtil.resizeImage(image, bOut, scale, 1); - PageFlowUtil.streamFileBytes(getViewContext().getResponse(), FileUtil.getFileName(realContent) + ".png", bOut.toByteArray(), !inline); - return null; - } - } - } - } - - boolean extended = "jsonTSVExtended".equalsIgnoreCase(form.getFormat()); - boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(form.getFormat()); - if ("jsonTSV".equalsIgnoreCase(form.getFormat()) || extended || ignoreTypes) - { - if (!FileUtil.hasCloudScheme(realContent)) // TODO: handle streaming from S3 to JSON - streamToJSON(FileSystemLike.wrapFile(realContent), form.getFormat(), -1, null); - return null; - } - - try (InputStream inputStream = Files.newInputStream(realContent)) - { - PageFlowUtil.streamFile(getViewContext().getResponse(), Collections.emptyMap(), FileUtil.getFileName(realContent), inputStream, !inline); - } - } - catch (IOException e) - { - try - { - // Try to write the exception back to the caller if we haven't already flushed the buffer - ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse()); - writer.writeResponse(e); - } - catch (IllegalStateException ise) - { - // Most likely that a disconnected client caused the IOException writing back the response - } - } - - return null; - } - } - - - public static class ParseForm - { - String format = "jsonTSV"; - int maxRows = -1; - - public String getFormat() - { - return format; - } - - public void setFormat(String format) - { - this.format = format; - } - - public int getMaxRows() - { - return maxRows; - } - - public void setMaxRows(int maxRow) - { - this.maxRows = maxRow; - } - } - - @RequiresNoPermission - public class ParseFileAction extends MutatingApiAction - { - @Override - public Object execute(ParseForm form, BindException errors) throws Exception - { - if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) - throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); - - MultipartFile formFile = getFileMap().get("file"); - if (formFile == null) - { - return true; - } - - FileLike tempFile = null; - try - { - tempFile = FileUtil.createTempFileLike("parse", formFile.getOriginalFilename()); - FileUtil.copyData(formFile.getInputStream(), tempFile.openOutputStream()); - streamToJSON(tempFile, form.getFormat(), form.getMaxRows(), formFile.getOriginalFilename()); - } - finally - { - if (null != tempFile) - tempFile.delete(); - } - return null; - } - } - - - // SampleTypeTest - private void streamToJSON(FileLike realContent, String format, int maxRow, String originalFileName) throws IOException - { - String lowerCaseFileName = realContent.getName().toLowerCase(); - boolean extended = "jsonTSVExtended".equalsIgnoreCase(format); - boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(format); - - JSONArray sheetsArray; - if (lowerCaseFileName.endsWith(".xls") || lowerCaseFileName.endsWith(".xlsx")) - { - try (InputStream in = realContent.openInputStream()) - { - sheetsArray = ExcelFactory.convertExcelToJSON(in, extended, maxRow); - } - } - else - { - DataLoaderFactory dlf = DataLoader.get().findFactory(realContent, null); - if (null == dlf) - { - throw new ApiUsageException("Unable to parse file " + realContent + ", it is likely of an unsupported file type"); - } - - try (InputStream in = realContent.openInputStream(); - DataLoader tabLoader = dlf.createLoader(in, true)) - { - tabLoader.setScanAheadLineCount(5000); - ColumnDescriptor[] cols = tabLoader.getColumns(); - - if (ignoreTypes) - for (ColumnDescriptor col : cols) - col.clazz = String.class; - - JSONArray rowsArray = new JSONArray(); - JSONArray headerArray = new JSONArray(); - for (ColumnDescriptor col : cols) - { - if (extended) - { - JSONObject valueObject = new JSONObject(); - valueObject.put("value", col.name); - headerArray.put(valueObject); - } - else - { - headerArray.put(col.name); - } - } - rowsArray.put(headerArray); - for (Map rowMap : tabLoader) - { - // headers count as a row to be consistent - if (maxRow > -1 && maxRow <= rowsArray.length() + 1) - break; - - JSONArray rowArray = new JSONArray(); - for (ColumnDescriptor col : cols) - { - Object value = rowMap.get(col.name); - if (extended) - { - JSONObject valueObject = new JSONObject(); - valueObject.put("value", value); - rowArray.put(valueObject); - } - else - { - rowArray.put(value); - } - } - rowsArray.put(rowArray); - } - - JSONObject sheetJSON = new JSONObject(); - sheetJSON.put("name", "flat"); - sheetJSON.put("data", rowsArray); - sheetsArray = new JSONArray(); - sheetsArray.put(sheetJSON); - } - } - - try (ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse())) - { - JSONObject workbookJSON = new JSONObject(); - workbookJSON.put("fileName", realContent.getName()); - workbookJSON.put("sheets", sheetsArray); - if (originalFileName != null) - workbookJSON.put("originalFileName", originalFileName); - writer.writeResponse(new ApiSimpleResponse(workbookJSON)); - } - } - - - public static class ConvertArraysToExcelForm - { - private String _json; - - public String getJson() - { - return _json; - } - - public void setJson(String json) - { - _json = json; - } - } - - @RequiresPermission(ReadPermission.class) - public static class ConvertArraysToExcelAction extends ExportAction - { - @Override - public void validate(ConvertArraysToExcelForm form, BindException errors) - { - if (form.getJson() == null) - { - errors.reject(ERROR_MSG, "Unable to convert to Excel - no spreadsheet data given"); - } - } - - @Override - public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception - { - try - { - JSONObject rootObject; - JSONArray sheetsArray; - if (form.getJson() == null || form.getJson().trim().isEmpty()) - { - // Create JSON so that we return an empty file - rootObject = new JSONObject(); - sheetsArray = new JSONArray(); - JSONObject sheetObject = new JSONObject(); - sheetsArray.put(sheetObject); - } - else - { - rootObject = new JSONObject(form.getJson()); - sheetsArray = rootObject.getJSONArray("sheets"); - } - String filename = rootObject.has("fileName") ? rootObject.getString("fileName") : "ExcelExport.xls"; - ExcelWriter.ExcelDocumentType docType = filename.toLowerCase().endsWith(".xlsx") ? ExcelWriter.ExcelDocumentType.xlsx : ExcelWriter.ExcelDocumentType.xls; - - try (Workbook workbook = ExcelFactory.createFromArray(sheetsArray, docType)) - { - response.setContentType(docType.getMimeType()); - ResponseHelper.setContentDisposition(response, ResponseHelper.ContentDispositionType.attachment, filename); - ResponseHelper.setPrivate(response); - workbook.write(response.getOutputStream()); - - JSONObject qInfo = rootObject.has("queryinfo") ? rootObject.getJSONObject("queryinfo") : null; - if (qInfo != null) - { - QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), - qInfo.getString("query"), getViewContext().getActionURL(), - rootObject.getString("auditMessage") + filename, - null); - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asExcel"); - } - } - } - catch (JSONException | ClassCastException e) - { - // We can get a ClassCastException if we expect an array and get a simple String, for example - ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to Excel - invalid input", e, false, false); - } - } - } - - @RequiresPermission(ReadPermission.class) - public static class ConvertArraysToTableAction extends ExportAction - { - @Override - public void validate(ConvertArraysToExcelForm form, BindException errors) - { - if (form.getJson() == null) - { - errors.reject(ERROR_MSG, "Unable to convert to table - no data given"); - } - } - - @Override - public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception - { - try - { - JSONObject rootObject; - JSONArray rowsArray; - if (form.getJson() == null || form.getJson().trim().isEmpty()) - { - // Create JSON so that we return an empty file - rootObject = new JSONObject(); - rowsArray = new JSONArray(); - } - else - { - rootObject = new JSONObject(form.getJson()); - rowsArray = rootObject.getJSONArray("rows"); - } - - TSVWriter.DELIM delimType = (!rootObject.isNull("delim") ? TSVWriter.DELIM.valueOf(rootObject.getString("delim")) : TSVWriter.DELIM.TAB); - TSVWriter.QUOTE quoteType = (!rootObject.isNull("quoteChar") ? TSVWriter.QUOTE.valueOf(rootObject.getString("quoteChar")) : TSVWriter.QUOTE.NONE); - String filenamePrefix = (!rootObject.isNull("fileNamePrefix") ? rootObject.getString("fileNamePrefix") : "Export"); - String filename = filenamePrefix + "." + delimType.extension; - String newlineChar = !rootObject.isNull("newlineChar") ? rootObject.getString("newlineChar") : "\n"; - - response.setCharacterEncoding(StringUtilsLabKey.DEFAULT_CHARSET.name()); - - try(var tsvWriter = new TSVJSONWriter(filenamePrefix, rowsArray)) - { - tsvWriter.setRowSeparator(newlineChar); - tsvWriter.setDelimiterCharacter(delimType); - tsvWriter.setQuoteCharacter(quoteType); - tsvWriter.write(response); - } - - JSONObject qInfo = rootObject.optJSONObject("queryinfo"); - if (qInfo != null) - { - QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), qInfo.getString("query"), - getViewContext().getActionURL(), - rootObject.getString("auditMessage") + filename, - rowsArray.length()); - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asDelimited"); - } - } - catch (JSONException e) - { - ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to table - invalid input", e, false, false); - } - } - } - - - public static class ConvertHtmlToExcelForm - { - private String _baseUrl; - private String _htmlFragment; - private String _name = "workbook.xls"; - - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - public String getBaseUrl() - { - return _baseUrl; - } - - public void setBaseUrl(String baseUrl) - { - _baseUrl = baseUrl; - } - - public String getHtmlFragment() - { - return _htmlFragment; - } - - public void setHtmlFragment(String htmlFragment) - { - _htmlFragment = htmlFragment; - } - } - - - @RequiresPermission(ReadPermission.class) - public static class ConvertHtmlToExcelAction extends FormViewAction - { - String _responseHtml = null; - - @Override - public void validateCommand(ConvertHtmlToExcelForm target, Errors errors) - { - } - - @Override - public ModelAndView getView(ConvertHtmlToExcelForm form, boolean reshow, BindException errors) - { - String html = - "

" + - "" + - new CsrfInput(getViewContext()) + - "
"; - return HtmlView.unsafe(html); - } - - @Override - public boolean handlePost(ConvertHtmlToExcelForm form, BindException errors) - { - ActionURL url = getViewContext().getActionURL(); - String base = url.getBaseServerURI(); - if (!base.endsWith("/")) base += "/"; - - String baseTag = ""; - SafeToRender css = PageFlowUtil.getStylesheetIncludes(getContainer()); - String htmlFragment = StringUtils.trimToEmpty(form.getHtmlFragment()); - String html = "" + baseTag + css + "" + htmlFragment + ""; - - // UNDONE: strip script - List tidyErrors = new ArrayList<>(); - String tidy = JSoupUtil.tidyHTML(html, false, tidyErrors); - - if (!tidyErrors.isEmpty()) - { - for (String err : tidyErrors) - { - errors.reject(ERROR_MSG, err); - } - return false; - } - - _responseHtml = tidy; - return true; - } - - @Override - public ModelAndView getSuccessView(ConvertHtmlToExcelForm form) - { - ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, form.getName()); - getPageConfig().setTemplate(PageConfig.Template.None); - HtmlView v = HtmlView.unsafe(_responseHtml); - v.setContentType("application/vnd.ms-excel"); - v.setFrame(WebPartView.FrameType.NONE); - return v; - } - - @Override - public URLHelper getSuccessURL(ConvertHtmlToExcelForm convertHtmlToExcelForm) - { - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - } - } - - - public static ActionURL getShowApplicationURL(Container c, long rowId) - { - ActionURL url = new ActionURL(ShowApplicationAction.class, c); - url.addParameter("rowId", rowId); - - return url; - } - - - @RequiresPermission(ReadPermission.class) - public class ShowApplicationAction extends SimpleViewAction - { - private ExpProtocolApplicationImpl _app; - private ExpRun _run; - - @Override - public ModelAndView getView(ExpObjectForm form, BindException errors) - { - _app = ExperimentServiceImpl.get().getExpProtocolApplication(form.getRowId()); - if (_app == null) - { - throw new NotFoundException("Could not find Protocol Application"); - } - _run = _app.getRun(); - if (_run == null) - { - throw new NotFoundException("No experiment run associated with Protocol Application"); - } - ensureCorrectContainer(getContainer(), _app, getViewContext()); - - ExpProtocol protocol = _app.getProtocol(); - - DataRegion dr = new DataRegion(); - dr.addColumns(ExperimentServiceImpl.get().getTinfoProtocolApplication().getUserEditableColumns()); - DetailsView detailsView = new DetailsView(dr, form.getRowId()); - dr.removeColumns("RunId", "ProtocolLSID", "RowId", "LSID"); - dr.addDisplayColumn(new ExperimentRunDisplayColumn(_run)); - dr.addDisplayColumn(new ProtocolDisplayColumn(protocol)); - dr.addDisplayColumn(new LineageGraphDisplayColumn(_app, _run)); - detailsView.setTitle("Protocol Application"); - - Container c = getContainer(); - ApplicationOutputGrid outMGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoMaterial()); - ApplicationOutputGrid outDGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoData()); - Map map = new HashMap<>(); - for (ProtocolApplicationParameter param : ExperimentService.get().getProtocolApplicationParameters(_app.getRowId())) - { - map.put(param.getOntologyEntryURI(), param); - } - - JspView> paramsView = new JspView<>("/org/labkey/experiment/Parameters.jsp", map); - paramsView.setTitle("Protocol Application Parameters"); - CustomPropertiesView cpv = new CustomPropertiesView(_app.getLSID(), c); - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), paramsView, outMGrid, outDGrid); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Experiment Run", ExperimentUrlsImpl.get().getRunGraphDetailURL(_run)); - root.addChild("Protocol Application " + _app.getName()); - } - } - - @RequiresPermission(ReadPermission.class) - public class ShowProtocolGridAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - return new ProtocolWebPart(false, getViewContext()); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Protocols"); - } - } - - @RequiresPermission(ReadPermission.class) - public class ProtocolDetailsAction extends SimpleViewAction - { - private ExpProtocolImpl _protocol; - - @Override - public ModelAndView getView(ExpObjectForm form, BindException errors) - { - _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getRowId()); - if (_protocol == null) - { - _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getLSID()); - } - - if (_protocol == null) - { - throw new NotFoundException("Unable to find a matching protocol"); - } - ensureCorrectContainer(getContainer(), _protocol, getViewContext()); - - JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", _protocol); - detailsView.setTitle("Standard Properties"); - - CustomPropertiesView cpv = new CustomPropertiesView(_protocol.getLSID(), getContainer()); - ProtocolParametersView parametersView = new ProtocolParametersView(_protocol); - - VBox protocolDetails = new VBox(); - protocolDetails.setFrame(WebPartView.FrameType.PORTAL); - protocolDetails.setTitle("Protocol Details"); - protocolDetails.addView(new ProtocolInputOutputsView(_protocol, errors)); - - JspView stepsView = new JspView<>("/org/labkey/experiment/ProtocolSteps.jsp", _protocol); - stepsView.setTitle("Protocol Steps"); - stepsView.setFrame(WebPartView.FrameType.TITLE); - protocolDetails.addView(stepsView); - - ExpSchema schema = new ExpSchema(getUser(), getContainer()); - ExperimentRunListView runView = new ExperimentRunListView(schema, ExperimentRunListView.getRunListQuerySettings(schema, getViewContext(), ExpSchema.TableType.Runs.name(), true), ExperimentRunType.ALL_RUNS_TYPE) - { - @Override - public DataView createDataView() - { - DataView result = super.createDataView(); - result.getRenderContext().setBaseFilter(new SimpleFilter(FieldKey.fromParts("Protocol", "LSID"), _protocol.getLSID())); - return result; - } - }; - - runView.setTitle("Runs Using This Protocol"); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails, runView); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); - root.addChild("Protocol: " + _protocol.getName()); - } - } - - public class ProtocolInputOutputsView extends VBox - { - ProtocolInputOutputsView(ExpProtocol protocol, Errors errors) - { - HBox inputsView = new HBox(); - addView(inputsView); - - HBox outputsView = new HBox(); - addView(outputsView); - - UserSchema expSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_NAME); - - class ProtocolInputGrid extends QueryView - { - public ProtocolInputGrid(String title, QuerySettings settings, @Nullable Errors errors) - { - super(expSchema, settings, errors); - - setFrame(FrameType.TITLE); - setTitle(title); - setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); - setShowBorders(true); - setShadeAlternatingRows(true); - setShowExportButtons(false); - setShowPagination(false); - disableContainerFilterSelection(); - } - } - - // INPUTS - - QuerySettings materialInputsSettings = expSchema.getSettings("mpi", ExpSchema.TableType.MaterialProtocolInputs.toString()); - materialInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - materialInputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) - )); - QueryView materialInputsView = new ProtocolInputGrid("Material Inputs", materialInputsSettings, errors); - inputsView.addView(materialInputsView); - - QuerySettings dataInputsSettings = expSchema.getSettings("dpi", ExpSchema.TableType.DataProtocolInputs.toString()); - dataInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - dataInputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) - )); - QueryView dataInputsView = new ProtocolInputGrid("Data Inputs", dataInputsSettings, errors); - inputsView.addView(dataInputsView); - - // OUTPUTS - - QuerySettings materialOutputsSettings = expSchema.getSettings("mpo", ExpSchema.TableType.MaterialProtocolInputs.toString()); - materialOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - materialOutputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) - )); - QueryView materialOutputsView = new ProtocolInputGrid("Material Outputs", materialOutputsSettings, errors); - outputsView.addView(materialOutputsView); - - QuerySettings dataOutputsSettings = expSchema.getSettings("dpo", ExpSchema.TableType.DataProtocolInputs.toString()); - dataOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); - dataOutputsSettings.setFieldKeys(Arrays.asList( - FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), - FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) - )); - QueryView dataOutputsView = new ProtocolInputGrid("Data Outputs", dataOutputsSettings, errors); - outputsView.addView(dataOutputsView); - } - } - - - @RequiresPermission(ReadPermission.class) - public class ProtocolPredecessorsAction extends SimpleViewAction - { - private ExpProtocol _parentProtocol; - private ProtocolActionStepDetail _actionStep; - - @Override - public ModelAndView getView(Object o, BindException errors) - { - ActionURL url = getViewContext().getActionURL(); - - String parentProtocolLSID = url.getParameter("ParentLSID"); - int actionSequence; - try - { - actionSequence = Integer.parseInt(url.getParameter("Sequence")); - } - catch (NumberFormatException e) - { - throw new NotFoundException("Could not find SequenceId " + url.getParameter("Sequence")); - } - - _parentProtocol = ExperimentService.get().getExpProtocol(parentProtocolLSID); - if (_parentProtocol == null) - { - throw new NotFoundException("Unable to find a matching protocol"); - } - - ensureCorrectContainer(getContainer(), _parentProtocol, getViewContext()); - - _actionStep = ExperimentServiceImpl.get().getProtocolActionStepDetail(parentProtocolLSID, actionSequence); - - if (_actionStep == null) - { - throw new NotFoundException("Unable to find a matching protocol action step"); - } - - ExpProtocol childProtocol = ExperimentService.get().getExpProtocol(_actionStep.getChildProtocolLSID()); - - JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", childProtocol); - detailsView.setTitle("Standard Properties"); - - CustomPropertiesView cpv = new CustomPropertiesView(childProtocol.getLSID(), getContainer()); - - ProtocolParametersView parametersView = new ProtocolParametersView(childProtocol); - - VBox protocolDetails = new VBox(); - protocolDetails.setFrame(WebPartView.FrameType.PORTAL); - protocolDetails.setTitle("Protocol Details"); - protocolDetails.addView(new ProtocolInputOutputsView(childProtocol, errors)); - protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "PredecessorChildLSID", "PredecessorSequence", "ActionSequence", "Protocol Predecessors")); - protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "ChildProtocolLSID", "ActionSequence", "PredecessorSequence", "Protocol Successors")); - - return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails); - } - - @Override - public void addNavTrail(NavTree root) - { - addRootNavTrail(root); - root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); - root.addChild("Parent Protocol '" + _parentProtocol.getName() + "'", ExperimentUrlsImpl.get().getProtocolDetailsURL(_parentProtocol)); - root.addChild("Protocol Step: " + _actionStep.getName()); - } - } - - public static class DataForm - { - private boolean _inline; - private long _rowId; - private String _lsid; - private Integer _maxDimension; - private String _format; - - public boolean isInline() - { - return _inline; - } - - public void setInline(boolean inline) - { - _inline = inline; - } - - public long getRowId() - { - return _rowId; - } - - public void setRowId(long rowId) - { - _rowId = rowId; - } - - public String getLsid() - { - return _lsid; - } - - public void setLsid(String lsid) - { - _lsid = lsid; - } - - public ExpDataImpl lookupData() - { - ExpDataImpl result = ExperimentServiceImpl.get().getExpData(getRowId()); - if (result == null && getLsid() != null) - { - result = ExperimentServiceImpl.get().getExpData(getLsid()); - } - return result; - } - - public Integer getMaxDimension() - { - return _maxDimension; - } - - public void setMaxDimension(Integer maxDimension) - { - _maxDimension = maxDimension; - } - - public String getFormat() - { - return _format; - } - - public void setFormat(String format) - { - _format = format; - } - } - - public static class ExpObjectForm extends QueryViewAction.QueryExportForm - { - private long _rowId; - private String _lsid; - - public String getLsid() - { - return _lsid; - } - - public void setLsid(String lsid) - { - _lsid = lsid; - } - - public String getLSID() - { - return getLsid(); - } - - public void setLSID(String lsid) - { - setLsid(lsid); - } - - public long getRowId() - { - return _rowId; - } - - public void setRowId(long rowId) - { - _rowId = rowId; - } - } - - @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) - public class DeleteSelectedExpRunsAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - // UNDONE: Need help topic on Runs - setHelpTopic("experiment"); - super.addNavTrail(root); - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List runs = new ArrayList<>(); - - Map idToRunMap = new LongHashMap<>(); - for (long runId : deleteForm.getIds(false)) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run != null) - { - if (!run.canDelete(getUser())) - throw new UnauthorizedException("You do not have permission to delete " + - (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") - + " in " + run.getContainer()); - - runs.add(run); - idToRunMap.put(run.getRowId(), run); - } - } - - Map referencedItems = new LongHashMap<>(); - List referenceDescriptions = new ArrayList<>(); - AssayService assayService = AssayService.get(); - if (!idToRunMap.isEmpty() && assayService != null ) - { - // using the first run as a representative, since all interactions here are (I believe) using the same protocol. - ExpProtocol protocol = runs.get(0).getProtocol(); - AssayProvider provider = assayService.getProvider(protocol); - if (provider != null) - { - SchemaKey key = AssayProtocolSchema.schemaName(provider, protocol); - ExperimentService.get().getObjectReferencers() - .forEach(referencer -> { - Collection referenced = referencer.getItemsWithReferences( - idToRunMap.keySet(), - key.toString(), - "Runs" - ); - referenced.forEach(id -> referencedItems.put(id, idToRunMap.get(id))); - referenceDescriptions.add(referencer.getObjectReferenceDescription(ExpRun.class)); - } - ); - } - - } - - List> permissionDatasetRows = new ArrayList<>(); - List> noPermissionDatasetRows = new ArrayList<>(); - if (StudyPublishService.get() != null) - { - for (Dataset dataset : StudyPublishService.get().getDatasetsForAssayRuns(runs, getUser())) - { - ActionURL url = urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId()); - TableInfo t = dataset.getTableInfo(getUser()); - if (null != t && t.hasPermission(getUser(),DeletePermission.class)) - { - permissionDatasetRows.add(new Pair<>(dataset, url)); - } - else - { - noPermissionDatasetRows.add(new Pair<>(dataset, url)); - } - } - } - - return new ConfirmDeleteView( - "run", - ShowRunGraphAction.class, - runs.stream().filter(run -> !referencedItems.containsKey(run.getRowId())).toList(), - deleteForm, - Collections.emptyList(), - "dataset(s) have one or more rows which", - permissionDatasetRows, - noPermissionDatasetRows, - referencedItems.values().stream().toList(), - referenceDescriptions.stream().filter(Objects::nonNull).collect(Collectors.joining(", or "))); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - ExperimentServiceImpl.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), deleteForm.getUserComment(), deleteForm.getIds(false), getTransactionAuditDetails()); - } - } - - public static class DeleteRunForm - { - private int _runId; - - public int getRunId() - { - return _runId; - } - - public void setRunId(int runId) - { - _runId = runId; - } - } - - /** - * Separate delete action from the client API - */ - @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) - public static class DeleteRunAction extends MutatingApiAction - { - @Override - public ApiResponse execute(DeleteRunForm form, BindException errors) - { - ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); - if (run == null) - { - throw new NotFoundException("Could not find run with ID " + form.getRunId()); - } - if (!run.canDelete(getUser())) - throw new UnauthorizedException("You do not have permission to delete " - + (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") + " in this container."); - - run.delete(getUser()); - return new ApiSimpleResponse("success", true); - } - } - - - @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) - public static class DeleteRunsAction extends AbstractDeleteAPIAction - { - @Override - protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) - { - Set runIdsToDelete = new HashSet<>(form.getIds(true)); - Set runIdsCascadeDeleted = new HashSet<>(); - - if (form.isCascade()) - { - for (long runId : runIdsToDelete) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run != null) - addReplacesRuns(run, runIdsCascadeDeleted); - } - - if (!runIdsCascadeDeleted.isEmpty()) - runIdsToDelete.addAll(runIdsCascadeDeleted); - } - - Map transactionAuditDetails = getTransactionAuditDetails(); - if (form.getRequestSource() != null) - transactionAuditDetails.put(TransactionAuditProvider.TransactionDetail.RequestSource, form.getRequestSource()); - if (form.getEditMethod() != null) - transactionAuditDetails.put(TransactionAuditProvider.TransactionDetail.EditMethod, form.getEditMethod()); - ExperimentService.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), form.getUserComment(), runIdsToDelete, transactionAuditDetails); - - ApiSimpleResponse response = new ApiSimpleResponse("success", true); - response.put("runIdsDeleted", runIdsToDelete); - if (!runIdsCascadeDeleted.isEmpty()) - response.put("runIdsCascadeDeleted", runIdsCascadeDeleted); - return response; - } - - private void addReplacesRuns(ExpRun run, Set runIds) - { - for (ExpRun replacedRun : run.getReplacesRuns()) - { - runIds.add(replacedRun.getRowId()); - addReplacesRuns(replacedRun, runIds); - } - } - } - - private abstract static class AbstractDeleteAPIAction extends MutatingApiAction - { - @Override - public void validateForm(CascadeDeleteForm form, Errors errors) - { - if (form.getSingleObjectRowId() == null && form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "Either singleObjectRowId, dataRegionSelectionKey, or rowIds is required"); - } - - @Override - public ApiResponse execute(CascadeDeleteForm form, BindException errors) throws Exception - { - ApiSimpleResponse response; - - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - tx.addCommitTask(form::clearSelected, POSTCOMMIT); - - response = deleteObjects(form); - tx.commit(); - } - - if (null != response.get("success")) - response.put("success", !errors.hasErrors()); - - return response; - } - - protected abstract ApiSimpleResponse deleteObjects(CascadeDeleteForm form) throws Exception; - } - - public static class CascadeDeleteForm extends DeleteForm - { - private boolean _cascade; - - public boolean isCascade() - { - return _cascade; - } - - public void setCascade(boolean cascade) - { - _cascade = cascade; - } - } - - private abstract static class AbstractDeleteAction extends FormViewAction - { - @Override - public void validateCommand(DeleteForm target, Errors errors) - { - } - - @Override - public boolean handlePost(DeleteForm deleteForm, BindException errors) throws Exception - { - if (!deleteForm.isForceDelete()) - { - return false; - } - else - { - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - tx.addCommitTask(deleteForm::clearSelected, POSTCOMMIT); - - deleteObjects(deleteForm); - tx.commit(); - } - catch (BatchValidationException v) - { - v.addToErrors(errors); - } - - return !errors.hasErrors(); - } - } - - @Override - public ActionURL getSuccessURL(DeleteForm form) - { - return form.getSuccessActionURL(ExperimentUrlsImpl.get().getOverviewURL(getContainer())); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Confirm Deletion"); - } - - protected abstract void deleteObjects(DeleteForm form) throws Exception; - } - - @RequiresPermission(DesignAssayPermission.class) - public static class DeleteProtocolByRowIdsAPIAction extends AbstractDeleteAPIAction - { - @Override - protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) - { - for (ExpProtocol protocol : getProtocolsForDeletion(form)) - { - if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) - throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); - - protocol.delete(getUser(), form.getUserComment()); - } - - return new ApiSimpleResponse(); - } - } - - public static List getProtocolsForDeletion(DeleteForm form) - { - List protocols = new ArrayList<>(); - for (long protocolId : form.getIds(false)) - { - ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); - if (protocol != null) - { - protocols.add(protocol); - } - } - return protocols; - } - - @RequiresPermission(DesignAssayPermission.class) - public class DeleteProtocolByRowIdsAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - // UNDONE: Need help topic on protocols - setHelpTopic("experiment"); - super.addNavTrail(root); - } - - @Override - public ModelAndView getView(DeleteForm form, boolean reshow, BindException errors) - { - List runs = ExperimentService.get().getExpRunsForProtocolIds(false, form.getIds(false)); - List protocols = getProtocolsForDeletion(form); - String noun = "Assay Design"; - List> deleteableDatasets = new ArrayList<>(); - List> noPermissionDatasets = new ArrayList<>(); - if (AssayService.get() != null && StudyService.get() != null) - { - for (ExpProtocol protocol : protocols) - { - if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) - throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); - - if (AssayService.get().getProvider(protocol) == null) - { - noun = "Protocol"; - } - for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(protocol.getRowId(), Dataset.PublishSource.Assay)) - { - Pair entry = new Pair<>(dataset, urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId())); - if (dataset.canDeleteDefinition(getUser())) - { - deleteableDatasets.add(entry); - } - else - { - noPermissionDatasets.add(entry); - } - } - } - } - - return new ConfirmDeleteView(noun, ProtocolDetailsAction.class, protocols, form, runs, "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); - } - - @Override - protected void deleteObjects(DeleteForm form) - { - for (ExpProtocol protocol : getProtocolsForDeletion(form)) - { - protocol.delete(getUser(), form.getUserComment()); - } - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetDataOperationConfirmationDataAction extends ReadOnlyApiAction - { - @Override - public void validateForm(DataOperationConfirmationForm form, Errors errors) - { - if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey"); - if (form.getDataOperation() == null) - errors.reject(ERROR_REQUIRED, "An operation type must be provided."); - } - - @Override - public Object execute(DataOperationConfirmationForm form, BindException errors) - { - Collection requestIds = form.getIds(false); - ExperimentServiceImpl service = ExperimentServiceImpl.get(); - List allData = service.getExpDatas(requestIds); - - Set notAllowedIds = new HashSet<>(); - if (form.getDataOperation() == ExpDataImpl.DataOperations.Delete) - service.getObjectReferencers().forEach(referencer -> - notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "exp.data"))); - - Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allData); - - Collection containers = new HashSet<>(); - Collection notPermittedIds = new ArrayList<>(); - Class permClass = form.getDataOperation().getPermissionClass(); - for (ExpDataImpl expData : allData) - { - Container c = expData.getContainer(); - if (c.hasPermission(getUser(), ReadPermission.class)) - containers.add(c); - if (permClass != null && !c.hasPermission(getUser(), permClass)) - notPermittedIds.add(expData.getRowId()); - } - - NameExpressionOptionService svc = NameExpressionOptionService.get(); - response.put("containers", containers.stream().map(c -> Map.of( - "id", c.getEntityId(), - "path", (Object) c.getPath(), - "permitted", permClass == null || c.hasPermission(getUser(), permClass), - "canEditName", svc.getAllowUserSpecificNamesValue(c) - )).toList()); - - response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); - - return success(response); - } - } - - - public static class DataOperationConfirmationForm extends DataViewSnapshotSelectionForm - { - private ExpDataImpl.DataOperations _dataOperation; - - public ExpDataImpl.DataOperations getDataOperation() - { - return _dataOperation; - } - - public void setDataOperation(ExpDataImpl.DataOperations dataOperation) - { - _dataOperation = dataOperation; - } - - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetMaterialOperationConfirmationDataAction extends ReadOnlyApiAction - { - @Override - public void validateForm(MaterialOperationConfirmationForm form, Errors errors) - { - if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); - if (form.getSampleOperation() == null) - errors.reject(ERROR_REQUIRED, "An operation type must be provided."); - } - - @Override - public Object execute(MaterialOperationConfirmationForm form, BindException errors) - { - Set requestIds = form.getIds(false); - ExperimentServiceImpl service = ExperimentServiceImpl.get(); - List allMaterials = service.getExpMaterials(requestIds); - - Set notAllowedIds = new HashSet<>(); - // We prevent deletion if a sample is used as a parent, has assay data, is used in a job, etc. - if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) - service.getObjectReferencers().forEach(referencer -> - notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "samples"))); - - if (SampleStatusService.get().supportsSampleStatus()) - notAllowedIds.addAll(service.findIdsNotPermittedForOperation(allMaterials, form.getSampleOperation())); - - Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allMaterials); - - Collection containers = new HashSet<>(); - Collection notPermittedIds = new ArrayList<>(); - Class permClass = form.getSampleOperation().getPermissionClass(); - for (ExpMaterial material : allMaterials) - { - Container c = material.getContainer(); - if (c.hasPermission(getUser(), ReadPermission.class)) - containers.add(c); - if (permClass != null && !c.hasPermission(getUser(), permClass)) - notPermittedIds.add(material.getRowId()); - } - - NameExpressionOptionService svc = NameExpressionOptionService.get(); - - response.put("containers", containers.stream().map(c -> Map.of( - "id", c.getEntityId(), - "path", (Object) c.getPath(), - "permitted", permClass == null || c.hasPermission(getUser(), permClass), - "canEditName", svc.getAllowUserSpecificNamesValue(c) - )).toList()); - - response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); - - if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) - // String 'associatedDatasets' must be synced to its handling in confirmDelete.js, confirmDelete() - response.put("associatedDatasets", ExperimentServiceImpl.includeLinkedToStudyText(allMaterials, requestIds, getUser(), getContainer())); - - return success(response); - } - } - - public static class MaterialOperationConfirmationForm extends DataViewSnapshotSelectionForm - { - private SampleTypeService.SampleOperations _sampleOperation; - - public SampleTypeService.SampleOperations getSampleOperation() - { - return _sampleOperation; - } - - public void setSampleOperation(SampleTypeService.SampleOperations sampleOperation) - { - _sampleOperation = sampleOperation; - } - } - - @RequiresPermission(DeletePermission.class) - public class DeleteSelectedDataAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - // UNDONE: Need help topic on Datas - setHelpTopic("experiment"); - super.addNavTrail(root); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) throws Exception - { - List datas = getDatas(deleteForm, false); - - for (ExpRun run : getRuns(datas)) - { - if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) - throw new UnauthorizedException(); - } - - // Issue 32076: Delete the exp.Data objects using QueryUpdateService so trigger scripts will be executed - Map, List> byDataClass = datas.stream().collect(Collectors.groupingBy(d -> Optional.ofNullable(d.getDataClass(null)))); - for (Optional opt : byDataClass.keySet()) - { - SchemaKey schemaKey; - String queryName; - ExpDataClass dc = opt.orElse(null); - List ds = byDataClass.get(opt); - if (dc == null) - { - // Reference to exp.Data table - schemaKey = ExpSchema.SCHEMA_EXP; - queryName = ExpSchema.TableType.Data.name(); - } - else - { - // Reference to exp.data. table - schemaKey = ExpSchema.SCHEMA_EXP_DATA; - queryName = dc.getName(); - } - - UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), schemaKey); - if (schema == null) - throw new IllegalStateException("Failed to get schema '" + schemaKey + "'"); - - TableInfo table = schema.getTable(queryName); - if (table == null) - throw new IllegalStateException("Failed to get table '" + queryName + "' in schema '" + schemaKey + "'"); - - QueryUpdateService qus = table.getUpdateService(); - if (qus == null) - throw new IllegalStateException(); - - qus.deleteRows(getUser(), getContainer(), toKeys(ds), null, null); - } - } - - protected List> toKeys(List datas) - { - return datas.stream().map(d -> CaseInsensitiveHashMap.of("rowId", d.getRowId())).collect(toList()); - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - if (errors.hasErrors()) - return new SimpleErrorView(errors, false); - - List datas = getDatas(deleteForm, false); - List runs = getRuns(datas); - - return new ConfirmDeleteView("Data", ShowDataAction.class, datas, deleteForm, runs); - } - - private List getRuns(List datas) - { - List runArray = ExperimentService.get().getRunsUsingDatas(datas); - return new ArrayList<>(ExperimentService.get().runsDeletedWithInput(runArray)); - } - - private List getDatas(DeleteForm deleteForm, boolean clear) - { - List datas = new ArrayList<>(); - for (long dataId : deleteForm.getIds(clear)) - { - ExpData data = ExperimentService.get().getExpData(dataId); - if (data != null) - { - datas.add(data); - } - } - return datas; - } - } - - @RequiresPermission(DeletePermission.class) - public class DeleteSelectedExperimentsAction extends AbstractDeleteAction - { - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - for (ExpExperiment exp : lookupExperiments(deleteForm)) - { - exp.delete(getUser()); - } - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List experiments = lookupExperiments(deleteForm); - - List runs = new ArrayList<>(); - boolean allBatches = true; - for (ExpExperiment experiment : experiments) - { - // Deleting a batch also deletes all of its runs - if (experiment.getBatchProtocol() != null) - { - runs.addAll(experiment.getRuns()); - } - else - { - allBatches = false; - } - } - - return new ConfirmDeleteView(allBatches ? "batch" : "run group", DetailsAction.class, experiments, deleteForm, runs); - } - - private List lookupExperiments(DeleteForm deleteForm) - { - List experiments = new ArrayList<>(); - for (long experimentId : deleteForm.getIds(false)) - { - ExpExperiment experiment = ExperimentService.get().getExpExperiment(experimentId); - if (experiment != null) - { - experiments.add(experiment); - } - } - return experiments; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - super.addNavTrail(root); - } - } - - @RequiresPermission(DesignSampleTypePermission.class) - public class DeleteSampleTypesAction extends AbstractDeleteAction - { - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - super.addNavTrail(root); - } - - @Override - protected void deleteObjects(DeleteForm deleteForm) - { - List sampleTypes = getSampleTypes(deleteForm); - if (sampleTypes.isEmpty()) - { - throw new NotFoundException("No sample types found for ids provided."); - } - if (!ensureCorrectContainer(sampleTypes)) - { - throw new UnauthorizedException(); - } - - for (ExpRun run : getRuns(sampleTypes)) - { - if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new UnauthorizedException(); - } - } - - for (ExpSampleType source : sampleTypes) - { - Domain domain = source.getDomain(); - if (!domain.getDomainKind().canDeleteDefinition(getUser(), domain)) - { - throw new UnauthorizedException(); - } - - source.delete(getUser(), deleteForm.getUserComment()); - } - } - - @Override - public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) - { - List sampleTypes = getSampleTypes(deleteForm); - if (!ensureCorrectContainer(sampleTypes)) - { - throw new RedirectException(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer(), "To delete a sample type, you must be in its folder or project.")); - } - - List> deleteableDatasets = new ArrayList<>(); - List> noPermissionDatasets = new ArrayList<>(); - if (StudyService.get() != null && StudyPublishService.get() != null) - { - for (ExpSampleType sampleType: sampleTypes) - { - for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(sampleType.getRowId(), Dataset.PublishSource.SampleType)) - { - ActionURL datasetURL = StudyService.get().getDatasetURL(getContainer(), dataset.getDatasetId()); - Pair entry = new Pair<>(dataset, datasetURL); - if (dataset.canDeleteDefinition(getUser())) - { - deleteableDatasets.add(entry); - } - else - { - noPermissionDatasets.add(entry); - } - } - } - } - return new ConfirmDeleteView("Sample Type", ShowSampleTypeAction.class, sampleTypes, deleteForm, getRuns(sampleTypes), "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); - } - - private List getSampleTypes(DeleteForm deleteForm) - { - List sources = new ArrayList<>(); - for (long rowId : deleteForm.getIds(false)) - { - ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId); - if (sampleType != null) - { - sources.add(sampleType); - } - } - return sources; - } - - private boolean ensureCorrectContainer(List sampleTypes) - { - for (ExpSampleType source : sampleTypes) - { - Container sourceContainer = source.getContainer(); - if (!sourceContainer.equals(getContainer())) - { - return false; - } - } - return true; - } - - private List getRuns(List sampleTypes) - { - if (!sampleTypes.isEmpty()) - { - List runArray = ExperimentService.get().getRunsUsingSampleTypes(sampleTypes.toArray(new ExpSampleType[0])); - return ExperimentService.get().runsDeletedWithInput(runArray); - } - else - { - return Collections.emptyList(); - } - } - } - - private DataRegion getSampleTypeRegion(ViewContext model) - { - TableInfo tableInfo = ExperimentServiceImpl.get().getTinfoSampleType(); - - QuerySettings settings = new QuerySettings(model, "SampleType"); - settings.setSelectionKey(DataRegionSelection.getSelectionKey(tableInfo.getSchema().getName(), tableInfo.getName(), "SampleType", settings.getDataRegionName())); - - DataRegion dr = new DataRegion(); - dr.setSettings(settings); - dr.addColumns(tableInfo.getUserEditableColumns()); - dr.removeColumns("lastindexed"); - dr.getDisplayColumn(0).setVisible(false); - - dr.getDisplayColumn("idcol1").setVisible(false); - dr.getDisplayColumn("idcol2").setVisible(false); - dr.getDisplayColumn("idcol3").setVisible(false); - dr.getDisplayColumn("lsid").setVisible(false); - dr.getDisplayColumn("materiallsidprefix").setVisible(false); - dr.getDisplayColumn("parentcol").setVisible(false); - - ActionURL url = new ActionURL(ShowSampleTypeAction.class, model.getContainer()); - dr.getDisplayColumn(1).setURL(url.addParameter("rowId", "${RowId}")); - dr.setShowRecordSelectors(getContainer().hasOneOf(getUser(), DeletePermission.class, UpdatePermission.class)); - - return dr; - } - - @RequiresPermission(ReadPermission.class) - @ActionNames("getSampleType,getSampleTypeApi") // Referenced in labkey-ui-components components/samples/actions.ts TODO: migrate getSampleTypeApi -> getSampleType - public static class GetSampleTypeAction extends ReadOnlyApiAction - { - @Override - public void validateForm(SampleTypeForm form, Errors errors) - { - if (form.getRowId() == null && form.getLSID() == null) - errors.reject(ERROR_REQUIRED, "RowId or LSID must be provided"); - } - - @Override - public Object execute(SampleTypeForm form, BindException errors) throws Exception - { - ExpSampleTypeImpl st = form.getSampleType(getContainer()); - - return getSampleTypeResponse(st); - } - } - - @NotNull - private static ApiSimpleResponse getSampleTypeResponse(ExpSampleType st) throws IOException - { - Map sampleType = new HashMap<>(); - sampleType.put("name", st.getName()); - sampleType.put("nameExpression", st.getNameExpression()); - sampleType.put("labelColor", st.getLabelColor()); - sampleType.put("metricUnit", st.getMetricUnit()); - sampleType.put("description", st.getDescription()); - sampleType.put("importAliases", st.getImportAliasMap()); - sampleType.put("lsid", st.getLSID()); - sampleType.put("rowId", st.getRowId()); - sampleType.put("domainId", st.getDomain().getTypeId()); - sampleType.put("category", st.getCategory()); - - return new ApiSimpleResponse(Map.of("sampleSet", sampleType, "success", true)); - } - - public static class DataTypesWithRequiredLineageForm - { - private Integer _parentDataTypeRowId; - private boolean _sampleParent; - - public Integer getParentDataTypeRowId() - { - return _parentDataTypeRowId; - } - - public void setParentDataTypeRowId(Integer parentDataTypeRowId) - { - this._parentDataTypeRowId = parentDataTypeRowId; - } - - public boolean isSampleParent() - { - return _sampleParent; - } - - public void setSampleParent(boolean sampleParent) - { - _sampleParent = sampleParent; - } - } - - @RequiresPermission(ReadPermission.class) - public static class GetDataTypesWithRequiredLineageAction extends ReadOnlyApiAction - { - @Override - public void validateForm(DataTypesWithRequiredLineageForm form, Errors errors) - { - if (form.getParentDataTypeRowId() == null) - errors.reject(ERROR_REQUIRED, "ParentDataTypeRowId must be provided"); - } - - @Override - public Object execute(DataTypesWithRequiredLineageForm form, BindException errors) throws Exception - { - return getDataTypesWithRequiredLineageResponse(form.getParentDataTypeRowId(), form.isSampleParent(), getContainer(), getUser()); - } - } - @NotNull - private static ApiSimpleResponse getDataTypesWithRequiredLineageResponse(Integer parentDataType, boolean isSampleParent, Container container, User user) - { - Pair, Set> requiredLineages = ExperimentServiceImpl.get().getDataTypesWithRequiredLineage(parentDataType, isSampleParent, container, user); - return new ApiSimpleResponse(Map.of("sampleTypes", requiredLineages.first, "dataClasses", requiredLineages.second,"success", true)); - } - - @RequiresPermission(DesignSampleTypePermission.class) - public static class EditSampleTypeAction extends SimpleViewAction - { - private ExpSampleTypeImpl _sampleType; - - @Override - public ModelAndView getView(SampleTypeForm form, BindException errors) - { - boolean create = form.getLSID() == null && form.getRowId() == null; - if (!create) - _sampleType = form.getSampleType(getContainer()); - - return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("sampleTypeDesigner")); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - if (_sampleType == null) - { - root.addChild("Create Sample Type"); - } - else - { - root.addChild(_sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(_sampleType)); - root.addChild("Update Sample Type"); - } - } - } - - public static class SampleTypeForm extends ReturnUrlForm - { - private Integer rowId; - private String lsid; - - public Integer getRowId() - { - return rowId; - } - - public void setRowId(Integer rowId) - { - this.rowId = rowId; - } - - public String getLSID() - { - return this.lsid; - } - - public void setLSID(String lsid) - { - this.lsid = lsid; - } - - public ExpSampleTypeImpl getSampleType(Container container) throws NotFoundException - { - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getLSID()); - if (sampleType == null) - sampleType = SampleTypeServiceImpl.get().getSampleType(getRowId()); - - if (sampleType == null) - { - throw new NotFoundException("Sample type not found: " + (getLSID() != null ? getLSID() : getRowId())); - } - - if (!container.equals(sampleType.getContainer())) - { - throw new NotFoundException("Sample type is not defined in the given container."); - } - - return sampleType; - } - } - - @RequiresPermission(InsertPermission.class) - public static class ImportSamplesAction extends AbstractExpDataImportAction - { - ExpSampleTypeImpl _sampleType; - boolean _isCrossTypeImport = false; - - @Override - public void validateForm(QueryForm queryForm, Errors errors) - { - _form = queryForm; - _insertOption = queryForm.getInsertOption(); - _isCrossTypeImport = getOptionParamValue(Params.crossTypeImport); - _form.setSchemaName(getTargetSchemaName()); - if (_isCrossTypeImport) - { - _form.setQueryName(getPipelineTargetQueryName()); - } - super.validateForm(queryForm, errors); - if (queryForm.getQueryName() == null) - errors.reject(ERROR_REQUIRED, "Sample type name is required"); - else - { - if (!_isCrossTypeImport) - { - _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), queryForm.getQueryName()); - if (_sampleType == null) - { - errors.reject(ERROR_GENERIC, "Sample type '" + queryForm.getQueryName() + " not found."); - } - } - } - } - - private String getTargetSchemaName() - { - return getOptionParamValue(Params.crossTypeImport) ? ExpSchema.SCHEMA_NAME : "samples"; - } - - @Override - protected UserSchema getTargetSchema() - { - return getOptionParamValue(Params.crossTypeImport) ? QueryService.get().getUserSchema(getUser(), getContainer(), getTargetSchemaName()) : super.getTargetSchema(); - } - - @Override - protected String getPipelineTargetQueryName() - { - return getOptionParamValue(Params.crossTypeImport) ? "materials" : super.getPipelineTargetQueryName(); - } - - @Override - protected Map getRenamedColumns() - { - Map renamedColumns = super.getRenamedColumns(); - renamedColumns.putAll(SampleTypeUpdateServiceDI.SAMPLE_ALT_IMPORT_NAME_COLS); - return renamedColumns; - } - - @Override - protected @Nullable Set getLineageImportAliases() throws IOException - { - Set aliases = new CaseInsensitiveHashSet(); - // Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import - aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT); - aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL); - boolean crossTypeImport = getOptionParamValue(AbstractQueryImportAction.Params.crossTypeImport); - // Issue 51894: We need to stop conversion to numbers for alias fields for all type - // If there are aliases defined for one type that are number fields in another type, this will prevent - // conversion to numbers during the initial partitioning, but the conversion will happen when the partition - // file is loaded. - if (crossTypeImport) - { - List sampleTypes = SampleTypeServiceImpl.get().getSampleTypes(getContainer(), true); - for (ExpSampleTypeImpl sampleType : sampleTypes) - aliases.addAll(sampleType.getImportAliases().keySet()); - } - else - { - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), _form.getQueryName()); - aliases.addAll(sampleType.getImportAliases().keySet()); - } - return aliases; - } - - @Override - protected int importData( - DataLoader dl, - FileStream file, - String originalName, - BatchValidationException errors, - @Nullable AuditBehaviorType auditBehaviorType, - TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, - @Nullable String auditUserComment - ) throws IOException - { - initContext(dl, errors, auditBehaviorType, auditUserComment); - - TableInfo tInfo = _target; - QueryUpdateService updateService = _updateService; - if (getOptionParamValue(Params.crossTypeImport)) - { - tInfo = ExperimentService.get().createMaterialTable(new SamplesSchema(getUser(), getContainer()), ContainerFilter.current(this), null); - updateService = tInfo.getUpdateService(); - } - - int count = importData(dl, tInfo, updateService, _context, auditEvent, getUser(), getContainer()); - - if (getOptionParamValue(Params.crossTypeImport)) - { - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeImport"); - if (_context.getInsertOption() == QueryUpdateService.InsertOption.UPDATE) - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeUpdate"); - else if (_context.getInsertOption() == QueryUpdateService.InsertOption.MERGE) - SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeMerge"); - } - - return count; - } - - @Override - public ModelAndView getView(QueryForm form, BindException errors) throws Exception - { - initRequest(form); - setHelpTopic("importSampleSets"); // page-wide help topic - setImportHelpTopic("importSampleSets"); // importOptions help topic - setTypeName("samples"); - return getDefaultImportView(form, errors); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ActionURL url = _form.urlFor(QueryAction.executeQuery); - if (_form.getQueryName() != null && url != null) - root.addChild(_form.getQueryName(), url); - root.addChild("Import Data"); - } - - @Override - protected JSONObject createSuccessResponse(int rowCount) - { - JSONObject json = super.createSuccessResponse(rowCount); - if (!_context.getResponseInfo().isEmpty()) - { - for (String key : _context.getResponseInfo().keySet()) - json.put(key, _context.getResponseInfo().get(key)); - } - return json; - } - - } - - public abstract static class AbstractExpDataImportAction extends AbstractQueryImportAction - { - protected QueryForm _form; - protected DataIteratorContext _context; - - @Override - public void validateForm(QueryForm form, Errors errors) - { - QueryDefinition query = form.getQueryDef(); - if (query.getContainerFilter() != null && query.getContainerFilter().getType() != null) - { - // cross folder import not supported - if (query.getContainerFilter().getType() != ContainerFilter.Type.Current) - errors.reject(ERROR_GENERIC, "ContainerFilter is not supported for import actions."); - } - } - - @Override - protected void initRequest(QueryForm form) throws ServletException - { - QueryDefinition query = form.getQueryDef(); - setContainerFilterForImport(query, getContainer(), getUser()); - List qpe = new ArrayList<>(); - TableInfo t = query.getTable(form.getSchema(), qpe, true); - - if (!qpe.isEmpty()) - throw qpe.get(0); - if (!getOptionParamValue(Params.crossTypeImport) && null != t) - { - setTarget(t); - setShowMergeOption(t.supportsInsertOption(QueryUpdateService.InsertOption.MERGE)); - setShowUpdateOption(t.supportsInsertOption(QueryUpdateService.InsertOption.UPDATE)); - } - - _auditBehaviorType = form.getAuditBehavior(); - _auditUserComment = form.getAuditUserComment(); - } - - @Override - protected Map getRenamedColumns() - { - final String renameParamPrefix = "importAlias."; - Map renameColumns = new CaseInsensitiveHashMap<>(); - PropertyValue[] pvs = _form.getInitParameters().getPropertyValues(); - for (PropertyValue pv : pvs) - { - String paramName = pv.getName(); - if (!paramName.startsWith(renameParamPrefix) || pv.getValue() == null) - continue; - - renameColumns.put(paramName.substring(renameParamPrefix.length()), (String) pv.getValue()); - } - return renameColumns; - } - - @Override - protected Set getLineageImportAliases() throws IOException - { - ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), _form.getQueryName()); - return new CaseInsensitiveHashSet(dataClass.getImportAliases().keySet()); - } - - protected void initContext(DataLoader dl, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, @Nullable String auditUserComment) - { - _context = createDataIteratorContext(_insertOption, getOptionParamsMap(), getLookupResolutionType(), auditBehaviorType, auditUserComment, errors, null, getContainer()); - - if (_context.isCrossFolderImport() && !getContainer().hasProductFolders()) - _context.setCrossFolderImport(false); - } - - @Override - protected int importData(DataLoader dl, FileStream file, String originalName, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, @Nullable String auditUserComment) throws IOException - { - initContext(dl, errors, auditBehaviorType, auditUserComment); - return importData(dl, _target, _updateService, _context, auditEvent, getUser(), getContainer()); - } - - @Override - protected String getQueryImportProviderName() - { - PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_PROVIDER_PARAM); - return pv == null ? null : (String) pv.getValue(); - } - - @Override - protected String getQueryImportDescription() - { - PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM); - return pv == null ? null : (String) pv.getValue(); - } - - @Override - protected String getQueryImportJobNotificationProviderName() - { - PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM); - return pv == null ? null : (String) pv.getValue(); - } - - @Override - protected boolean isBackgroundImportSupported() - { - return true; - } - - @Override - protected boolean allowLineageColumns() - { - return true; - } - - } - - @RequiresPermission(InsertPermission.class) - public static class ImportDataAction extends AbstractExpDataImportAction - { - @Override - public void validateForm(QueryForm queryForm, Errors errors) - { - _form = queryForm; - _form.setSchemaName("exp.data"); - _insertOption = queryForm.getInsertOption(); - super.validateForm(queryForm, errors); - if (queryForm.getQueryName() == null) - errors.reject(ERROR_REQUIRED, "Data class name is required"); - else - { - ExpDataClass dataClass = ExperimentService.get().getDataClass(getContainer(), getUser(), queryForm.getQueryName()); - if (dataClass == null) - { - errors.reject(ERROR_GENERIC, "Data class '" + queryForm.getQueryName() + " not found."); - } - } - } - - @Override - public ModelAndView getView(QueryForm form, BindException errors) throws Exception - { - initRequest(form); - setHelpTopic("dataClass"); // page wide help topic - setImportHelpTopic("dataClass#ui"); // importOptions help topic - setTypeName("data"); - return getDefaultImportView(form, errors); - } - - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); - ActionURL url = _form.urlFor(QueryAction.executeQuery); - if (_form.getQueryName() != null && url != null) - root.addChild(_form.getQueryName(), url); - root.addChild("Import Data"); - } - - } - - @RequiresPermission(UpdatePermission.class) - public class ShowUpdateAction extends SimpleViewAction - { - @Override - public ModelAndView getView(ExperimentForm form, BindException errors) - { - form.refreshFromDb(); - Experiment exp = form.getBean(); - if (exp == null) - { - throw new NotFoundException(); - } - ensureCorrectContainer(getContainer(), ExperimentService.get().getExpExperiment(exp.getRowId()), getViewContext()); - - return new ExperimentUpdateView(new DataRegion(), form, errors); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - addRootNavTrail(root); - root.addChild("Update Run Group"); - } - } - - @RequiresPermission(UpdatePermission.class) - public static class UpdateAction extends FormHandlerAction - { - private Experiment _exp; - - @Override - public void validateCommand(ExperimentForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ExperimentForm form, BindException errors) throws Exception - { - form.doUpdate(); - form.refreshFromDb(); - _exp = form.getBean(); - return true; - } - - @Override - public ActionURL getSuccessURL(ExperimentForm experimentForm) - { - return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), ExperimentService.get().getExpExperiment(_exp.getRowId())); - } - } - - public static class ExportBean - { - private final LSIDRelativizer _selectedRelativizer; - private final XarExportType _selectedExportType; - private final String _fileName; - private final String _dataRegionSelectionKey; - private final String _error; - private final Long _expRowId; - private final Long _protocolId; - private final ActionURL _postURL; - private final Set _roles; - - public ExportBean(LSIDRelativizer selectedRelativizer, XarExportType selectedExportType, String fileName, ExportOptionsForm form, Set roles, ActionURL postURL) - { - _selectedRelativizer = selectedRelativizer; - _selectedExportType = selectedExportType; - _fileName = fileName; - _dataRegionSelectionKey = form.getDataRegionSelectionKey(); - _error = form.getError(); - _expRowId = form.getExpRowId(); - _postURL = postURL; - _roles = roles; - _protocolId = form.getProtocolId(); - } - - public LSIDRelativizer getSelectedRelativizer() - { - return _selectedRelativizer; - } - - public XarExportType getSelectedExportType() - { - return _selectedExportType; - } - - public String getError() - { - return _error; - } - - public String getFileName() - { - return _fileName; - } - - public Set getRoles() - { - return _roles; - } - - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - public ActionURL getPostURL() - { - return _postURL; - } - - public Long getProtocolId() - { - return _protocolId; - } - - public Long getExpRowId() - { - return _expRowId; - } - } - - - private String fixupExportName(String runName) - { - runName = runName.replace('/', '-'); - runName = runName.replace('\\', '-'); - return runName; - } - - public static class ExportOptionsForm extends ExperimentRunListForm - { - private String _error; - private XarExportType _exportType; - private LSIDRelativizer _lsidOutputType; - private String _xarFileName; - private String _zipFileName; - private String _fileExportType; - private Long _protocolId; - private Integer _sampleTypeId; - private long[] _dataIds; - private String[] _roles = new String[0]; - - public String getError() - { - return _error; - } - - public void setError(String error) - { - _error = error; - } - - public XarExportType getExportType() - { - return _exportType; - } - - public LSIDRelativizer getLsidOutputType() - { - return _lsidOutputType; - } - - public String getFileExportType() - { - return _fileExportType; - } - - public void setFileExportType(String fileExportType) - { - _fileExportType = fileExportType; - } - - public String getXarFileName() - { - return _xarFileName; - } - - public void setXarFileName(String xarFileName) - { - _xarFileName = xarFileName; - } - - public String getZipFileName() - { - return _zipFileName; - } - - public void setZipFileName(String zipFileName) - { - _zipFileName = zipFileName; - } - - public void setExportType(XarExportType exportType) - { - _exportType = exportType; - } - - public void setLsidOutputType(LSIDRelativizer lsidOutputType) - { - _lsidOutputType = lsidOutputType; - } - - public Long getProtocolId() - { - return _protocolId; - } - - public void setProtocolId(Long protocolId) - { - _protocolId = protocolId; - } - - public String[] getRoles() - { - return _roles; - } - - public void setRoles(String[] roles) - { - _roles = roles; - } - - public Integer getSampleTypeId() - { - return _sampleTypeId; - } - - public void setSampleTypeId(Integer sampleTypeId) - { - _sampleTypeId = sampleTypeId; - } - - public long[] getDataIds() - { - return _dataIds; - } - - public void setDataIds(long[] dataIds) - { - _dataIds = dataIds; - } - - public List lookupProtocols(ViewContext context, boolean clearSelection) - { - List protocols = new ArrayList<>(); - - if (_protocolId != null) - { - ExpProtocol protocol = ExperimentService.get().getExpProtocol(_protocolId.intValue()); - if (protocol == null || !protocol.getContainer().equals(context.getContainer())) - { - throw new NotFoundException(); - } - protocols.add(protocol); - return protocols; - } - - for (Long protocolId : DataRegionSelection.getSelectedIntegers(context, clearSelection)) - { - try - { - ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); - if (protocol == null || !protocol.getContainer().equals(context.getContainer())) - { - throw new NotFoundException(); - } - protocols.add(protocol); - } - catch (NumberFormatException e) - { - throw new NotFoundException("Invalid protocol id: " + protocolId); - } - } - if (protocols.isEmpty()) - { - throw new NotFoundException("No protocols selected"); - } - return protocols; - } - } - - private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable String fileName) - throws ExperimentException, IOException, PipelineValidationException - { - return exportXAR(selection, null, null, fileName); - } - - private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable LSIDRelativizer lsidRelativizer, @Nullable XarExportType exportType, @Nullable String fileName) - throws ExperimentException, IOException, PipelineValidationException - { - if (lsidRelativizer == null) - lsidRelativizer = LSIDRelativizer.FOLDER_RELATIVE; - - if (exportType == null) - exportType = XarExportType.BROWSER_DOWNLOAD; - - if (fileName == null || fileName.isEmpty()) - fileName = "export.xar"; - - fileName = fixupExportName(fileName); - String xarXmlFileName = null; - if (Strings.CI.endsWith(fileName, ".xar")) - xarXmlFileName = fileName + ".xml"; - - switch (exportType) - { - case BROWSER_DOWNLOAD: - XarExporter exporter = new XarExporter(lsidRelativizer, selection, getUser(), xarXmlFileName, null, getContainer()); - - getViewContext().getResponse().setContentType("application/zip"); - ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, fileName); - ResponseHelper.setPrivate(getViewContext().getResponse()); - - exporter.writeAsArchive(getViewContext().getResponse().getOutputStream()); - return null; - case PIPELINE_FILE: - if (!PipelineService.get().hasValidPipelineRoot(getContainer())) - { - throw new IllegalStateException("You must set a valid pipeline root before you can export a XAR to it."); - } - PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); - XarExportPipelineJob job = new XarExportPipelineJob(getViewBackgroundInfo(), pipeRoot, fileName, lsidRelativizer, selection, xarXmlFileName); - PipelineService.get().queueJob(job); - PipelineStatusFile status = PipelineService.get().getStatusFile(job.getJobGUID()); - return PageFlowUtil.urlProvider(PipelineUrls.class).statusDetails(getContainer(), status.getRowId()); - default: - throw new IllegalArgumentException("Unknown export type: " + exportType); - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportProtocolsAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - List protocols = form.lookupProtocols(getViewContext(), false); - - long[] ids = new long[protocols.size()]; - for (int i = 0; i < ids.length; i++) - { - ids[i] = protocols.get(i).getRowId(); - } - XarExportSelection selection = new XarExportSelection(); - selection.addProtocolIds(ids); - - exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); - - if (form.getDataRegionSelectionKey() != null) - { - // Clear the selection - form.lookupProtocols(getViewContext(), true); - } - return true; - } - } - - public abstract static class AbstractExportAction extends FormViewAction - { - protected ActionURL _resultURL; - - @Override - public void validateCommand(ExportOptionsForm target, Errors errors) - { - } - - @Override - public ActionURL getSuccessURL(ExportOptionsForm exportOptionsForm) - { - return _resultURL; - } - - @Override - public ModelAndView getSuccessView(ExportOptionsForm exportOptionsForm) - { - return null; - } - - @Override - public ModelAndView getView(ExportOptionsForm form, boolean reshow, BindException errors) throws Exception - { - // FormViewAction can reinvoke getView() in response to a POST if we're not redirecting the browser, - // so avoid double-creating the export - if ("get".equalsIgnoreCase(getViewContext().getRequest().getMethod())) - handlePost(form, errors); - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - } - - public List lookupRuns(ExportOptionsForm form) - { - Set runIds; - if (form.getRunIds() != null && form.getRunIds().length > 0) - runIds = new HashSet<>(Arrays.asList(form.getRunIds())); - else - runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); - - if (runIds.isEmpty()) - { - throw new NotFoundException(); - } - List result = new ArrayList<>(); - - for (long id : runIds) - { - ExpRun run = ExperimentService.get().getExpRun(id); - if (run == null || !run.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new NotFoundException("Could not find run " + id); - } - result.add(run); - } - return result; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportRunsAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - XarExportSelection selection = new XarExportSelection(); - if (form.getExpRowId() != null) - { - ExpExperiment experiment = ExperimentService.get().getExpExperiment(form.getExpRowId()); - if (experiment != null && !experiment.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new NotFoundException("Run group " + form.getExpRowId()); - } - selection.addExperimentIds(experiment.getRowId()); - } - selection.addRuns(lookupRuns(form)); - - _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - return true; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportSampleTypeAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - Integer rowId = form.getSampleTypeId(); - if (rowId == null) - { - throw new NotFoundException("No sampleTypeId parameter specified"); - } - ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId.intValue()); - if (sampleType == null) - { - throw new NotFoundException("No such sample type with RowId " + rowId); - } - if (!sampleType.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new UnauthorizedException(); - } - - XarExportSelection selection = new XarExportSelection(); - selection.addSampleType(sampleType); - - _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), FileUtil.makeLegalName(sampleType.getName() + ".xar")); - return true; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportRunFilesAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - XarExportSelection selection = new XarExportSelection(); - selection.setIncludeXarXml(false); - if ("role".equalsIgnoreCase(form.getFileExportType())) - { - selection.addRoles(form.getRoles()); - } - selection.addRuns(lookupRuns(form)); - - _resultURL = exportXAR(selection, form.getZipFileName()); - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - return true; - } - } - - @RequiresPermission(ReadPermission.class) - public class ExportFilesAction extends AbstractExportAction - { - @Override - public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception - { - long[] dataIds = form.getDataIds(); - if (dataIds == null || dataIds.length == 0) - { - throw new NotFoundException(); - } - - try - { - for (long id : dataIds) - { - ExpData data = ExperimentService.get().getExpData(id); - if (data == null || !data.getContainer().hasPermission(getUser(), ReadPermission.class)) - { - throw new NotFoundException("Could not find file " + id); - } - } - - XarExportSelection selection = new XarExportSelection(); - selection.setIncludeXarXml(false); - selection.addDataIds(dataIds); - - _resultURL = exportXAR(selection, form.getZipFileName()); - return true; - } - catch (NumberFormatException e) - { - throw new NotFoundException(Arrays.toString(dataIds)); - } - } - } - - public static class ExperimentRunListForm implements DataRegionSelection.DataSelectionKeyForm - { - private String _dataRegionSelectionKey; - private Long _expRowId; - private Long[] _runIds; - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String key) - { - _dataRegionSelectionKey = key; - } - - public Long getExpRowId() - { - return _expRowId; - } - - public void setExpRowId(Long expRowId) - { - _expRowId = expRowId; - } - - public Long[] getRunIds() - { - return _runIds; - } - - public void setRunIds(Long[] runIds) - { - _runIds = runIds; - } - - public ExpExperiment lookupExperiment() - { - return getExpRowId() == null ? null : ExperimentService.get().getExpExperiment(getExpRowId().intValue()); - } - } - - private void addSelectedRunsToExperiment(ExpExperiment exp, String dataRegionSelectionKey) - { - Collection runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), dataRegionSelectionKey, true); - List runs = new ArrayList<>(); - for (long runId : runIds) - { - ExpRun run = ExperimentServiceImpl.get().getExpRun(runId); - if (run != null) - { - runs.add(run); - } - } - exp.addRuns(getUser(), runs.toArray(new ExpRun[0])); - } - - - @RequiresPermission(InsertPermission.class) - public class AddRunsToExperimentAction extends FormHandlerAction - { - @Override - public void validateCommand(ExperimentRunListForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ExperimentRunListForm form, BindException errors) - { - addSelectedRunsToExperiment(form.lookupExperiment(), form.getDataRegionSelectionKey()); - return true; - } - - @Override - public ActionURL getSuccessURL(ExperimentRunListForm form) - { - return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); - } - } - - @RequiresPermission(DeletePermission.class) - public static class RemoveSelectedExpRunsAction extends FormHandlerAction - { - @Override - public void validateCommand(ExperimentRunListForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ExperimentRunListForm form, BindException errors) - { - ExpExperiment exp = form.lookupExperiment(); - if (exp == null || !exp.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new NotFoundException("Could not find run group with RowId " + form.getExpRowId()); - } - - for (long runId : DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false)) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run == null || !run.getContainer().hasPermission(getUser(), DeletePermission.class)) - { - throw new NotFoundException("Could not find run with RowId " + runId); - } - exp.removeRun(getUser(), run); - } - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - return true; - } - - @Override - public ActionURL getSuccessURL(ExperimentRunListForm form) - { - return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); - } - } - - public static ActionURL getResolveLsidURL(Container c, @NotNull String type, @NotNull String lsid) - { - ActionURL url = new ActionURL(ResolveLSIDAction.class, c); - url.addParameter("type", type); - url.addParameter("lsid", lsid); - - return url; - } - - - @RequiresPermission(ReadPermission.class) - public static class ResolveLSIDAction extends SimpleViewAction - { - @Override - public ModelAndView getView(LsidForm form, BindException errors) - { - String message = ""; - if (!PageFlowUtil.empty(form.getLsid())) - { - try - { - String lsid = Lsid.canonical(form.getLsid().trim()); - ActionURL url = LsidManager.get().getDisplayURL(lsid); - if (url == null && form.getType() != null) - { - url = switch (form.getType().toLowerCase()) - { - case "data" -> LsidType.Data.getDisplayURL(new Lsid(lsid)); - case "material" -> LsidType.Material.getDisplayURL(new Lsid(lsid)); - default -> url; - }; - } - if (null != url) - { - throw new RedirectException(url); - } - message = "Could not map LSID to URL"; - } - catch (IllegalArgumentException e) - { - message = "Invalid LSID"; - } - } - - return new HtmlView("Enter LSID", - DOM.createHtmlFragment( - message, - DOM.FORM(at(action, getViewContext().cloneActionURL().setAction(ResolveLSIDAction.class)), - "LSID: ", - DOM.INPUT(at(type, "text", name, "lsid", size, "80", value, form.getLsid())), - PageFlowUtil.button("Go").submit(true)))); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Resolve LSID"); - } - } - - public static class LsidForm - { - private String _lsid; - - public String getType() - { - return _type; - } - - public void setType(String type) - { - _type = type; - } - - private String _type; - - public void setLsid(String lsid) - { - _lsid = lsid; - } - - public String getLsid() - { - return _lsid; - } - } - - public static class SetFlagForm extends LsidForm - { - private String _comment; - private boolean _redirect = true; - - public String getComment() - { - return _comment; - } - - public void setComment(String comment) - { - _comment = comment; - } - - public boolean isRedirect() - { - return _redirect; - } - - public void setRedirect(boolean redirect) - { - _redirect = redirect; - } - } - - /** - * Check for update on the object itself - */ - @RequiresNoPermission - public static class SetFlagAction extends FormHandlerAction - { - @Override - public void validateCommand(SetFlagForm target, Errors errors) - { - } - - @Override - public boolean handlePost(SetFlagForm form, BindException errors) throws Exception - { - String lsid = form.getLsid(); - if (lsid == null) - throw new NotFoundException(); - ExpObject obj = ExperimentService.get().findObjectFromLSID(lsid); - if (obj == null) - throw new NotFoundException(); - Container container = obj.getContainer(); - if (!container.hasPermission(getUser(), UpdatePermission.class)) - { - throw new UnauthorizedException(); - } - - obj.setComment(getUser(), form.getComment()); - return true; - } - - @Override - public URLHelper getSuccessURL(SetFlagForm form) - { - return null; - } - } - - @RequiresPermission(InsertPermission.class) - public class DeriveSamplesChooseTargetAction extends SimpleViewAction - { - private List _materials; - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; - if (sampleType != null) - { - root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); - } - root.addChild("Derive Samples"); - } - - @Override - public void validate(DeriveMaterialForm form, BindException errors) - { - _materials = form.lookupMaterials(); - if (_materials.isEmpty()) - { - throw new NotFoundException("Could not find any matching materials"); - } - } - - @Override - public ModelAndView getView(DeriveMaterialForm form, BindException errors) - { - Container c = getContainer(); - PipeRoot root = PipelineService.get().findPipelineRoot(c); - - if (root == null || !root.isValid()) - { - ActionURL pipelineURL = urlProvider(PipelineUrls.class).urlSetup(c); - return new HtmlView(DIV("You must ", - DOM.A(DOM.at(href, pipelineURL), "configure a valid pipeline root for this folder"), - " before deriving samples.")); - } - else - { - Set materialInputRoles = new TreeSet<>(ExperimentService.get().getMaterialInputRoles(getContainer(), getUser())); - Map materialsWithRoles = new LinkedHashMap<>(); - for (ExpMaterial material : _materials) - { - materialsWithRoles.put(material, null); - } - - List sampleTypes = getUploadableSampleTypes(); - - DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), sampleTypes, materialsWithRoles, form.getOutputCount(), materialInputRoles, null); - return new JspView<>("/org/labkey/experiment/deriveSamplesChooseTarget.jsp", bean); - } - } - } - - public static class DeriveSamplesChooseTargetBean implements DataRegionSelection.DataSelectionKeyForm - { - private String _dataRegionSelectionKey; - - private final Integer _targetSampleTypeId; - private final List _sampleTypes; - private final Map _sourceMaterials; - private final int _sampleCount; - private final Collection _inputRoles; - private final DerivedSamplePropertyHelper _propertyHelper; - - public static final String CUSTOM_ROLE = "--CUSTOM--"; - - public DeriveSamplesChooseTargetBean(String dataRegionSelectionKey, Integer targetSampleTypeId, List sampleTypes, Map sourceMaterials, int sampleCount, Collection inputRoles, DerivedSamplePropertyHelper helper) - { - _dataRegionSelectionKey = dataRegionSelectionKey; - _targetSampleTypeId = targetSampleTypeId; - _sampleTypes = sampleTypes; - _sourceMaterials = sourceMaterials; - _sampleCount = sampleCount; - _inputRoles = inputRoles; - _propertyHelper = helper; - } - - public Integer getTargetSampleTypeId() - { - return _targetSampleTypeId; - } - - public DerivedSamplePropertyHelper getPropertyHelper() - { - return _propertyHelper; - } - - public int getSampleCount() - { - return _sampleCount; - } - - public Map getSourceMaterials() - { - return _sourceMaterials; - } - - public List getSampleTypes() - { - return _sampleTypes; - } - - public Collection getInputRoles() - { - return _inputRoles; - } - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String key) - { - _dataRegionSelectionKey = key; - } - } - - private List getUploadableSampleTypes() - { - // Make a copy so we can modify it - List sampleTypes = new ArrayList<>(SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true)); - sampleTypes.removeIf(sampleType -> !sampleType.canImportMoreSamples()); - return sampleTypes; - } - - @RequiresPermission(InsertPermission.class) - public class DeriveSamplesAction extends FormViewAction - { - private List _materials; - private ActionURL _successUrl; - private final Map _inputMaterials = new LinkedHashMap<>(); - - @Override - public ModelAndView getView(DeriveMaterialForm form, boolean reshow, BindException errors) - { - _materials = form.lookupMaterials(); - if (_materials.isEmpty()) - { - throw new NotFoundException("Could not find any matching materials"); - } - - Container c = getContainer(); - - if (form.getOutputCount() <= 0) - { - form.setOutputCount(1); - } - - if (form.getTargetSampleTypeId() == 0) - throw new NotFoundException("Target sample type required for the derived samples"); - - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); - if (sampleType == null) - throw new NotFoundException("Could not find sample type with rowId " + form.getTargetSampleTypeId()); - - InsertView insertView = new InsertView(new DataRegion(), errors); - - DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), c, getUser()); - helper.addSampleColumns(insertView, getUser()); - - int[] rowIds = form.getRowIds(); - for (int i = 0; i < rowIds.length; i++) - { - insertView.getDataRegion().addHiddenFormField("rowIds", Integer.toString(rowIds[i])); - insertView.getDataRegion().addHiddenFormField("inputRole" + i, form.getInputRole(i) == null ? "" : form.getInputRole(i)); - insertView.getDataRegion().addHiddenFormField("customRole" + i, form.getCustomRole(i) == null ? "" : form.getCustomRole(i)); - } - - insertView.getDataRegion().addHiddenFormField("targetSampleTypeId", Integer.toString(form.getTargetSampleTypeId())); - insertView.getDataRegion().addHiddenFormField("outputCount", Integer.toString(form.getOutputCount())); - if (form.getDataRegionSelectionKey() != null) - insertView.getDataRegion().addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, form.getDataRegionSelectionKey()); - insertView.setInitialValues(ViewServlet.adaptParameterMap(getViewContext().getRequest().getParameterMap())); - ButtonBar bar = new ButtonBar(); - bar.setStyle(ButtonBar.Style.separateButtons); - ActionButton submitButton = new ActionButton(DeriveSamplesAction.class, "Submit"); - submitButton.setActionType(ActionButton.Action.POST); - bar.add(submitButton); - insertView.getDataRegion().setButtonBar(bar); - insertView.setTitle("Output Samples"); - - Map materialsWithRoles = new LinkedHashMap<>(); - List materials = form.lookupMaterials(); - for (int i = 0; i < materials.size(); i++) - { - materialsWithRoles.put(materials.get(i), form.determineLabel(i)); - } - - DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), getUploadableSampleTypes(), materialsWithRoles, form.getOutputCount(), Collections.emptyList(), helper); - JspView view = new JspView<>("/org/labkey/experiment/summarizeMaterialInputs.jsp", bean); - view.setTitle("Input Samples"); - - return new VBox(view, insertView); - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("sampleSets"); - addRootNavTrail(root); - root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); - ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; - if (sampleType != null) - { - root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); - } - root.addChild("Derive Samples"); - } - - @Override - public void validateCommand(DeriveMaterialForm form, Errors errors) - { - List materials = form.lookupMaterials(); - - List lockedSamples = new ArrayList<>(); - for (int i = 0; i < materials.size(); i++) - { - ExpMaterial m = materials.get(i); - if (!m.isOperationPermitted(SampleTypeService.SampleOperations.EditLineage)) - { - lockedSamples.add(m); - } - String inputRole = form.determineLabel(i); - if (inputRole == null || inputRole.isEmpty()) - { - ExpSampleType st = m.getSampleType(); - inputRole = st != null ? st.getName() : ExpMaterialRunInput.DEFAULT_ROLE; - } - _inputMaterials.put(materials.get(i), inputRole); - } - - if (!lockedSamples.isEmpty()) - { - errors.reject(ERROR_MSG, SampleTypeService.get().getOperationNotPermittedMessage(lockedSamples, SampleTypeService.SampleOperations.EditLineage)); - } - } - - @Override - public boolean handlePost(DeriveMaterialForm form, BindException errors) - { - ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); - - DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), getContainer(), getUser()); - - Map, Map> allProperties; - try - { - boolean valid = true; - for (Map.Entry> entry : helper.getPostedPropertyValues(getViewContext().getRequest()).entrySet()) - valid = UploadWizardAction.validatePostedProperties(getViewContext(), entry.getValue(), errors) && valid; - if (!valid) - return false; - - allProperties = helper.getSampleProperties(getViewContext().getRequest(), _inputMaterials.keySet()); - } - catch (DuplicateMaterialException e) - { - errors.addError(new ObjectError(e.getColName(), null, null, e.getMessage())); - return false; - } - catch (ExperimentException e) - { - errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); - return false; - } - - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - Map outputMaterials = new HashMap<>(); - int i = 0; - for (Map.Entry, Map> entry : allProperties.entrySet()) - { - Lsid lsid = entry.getKey().first; - String name = entry.getKey().second; - assert name != null; - - ExpMaterialImpl outputMaterial = ExperimentServiceImpl.get().createExpMaterial(getContainer(), lsid.toString(), name); - if (sampleType != null) - { - outputMaterial.setCpasType(sampleType.getLSID()); - } - outputMaterial.save(getUser()); - - if (sampleType != null) - { - Map pvs = new HashMap<>(); - for (Map.Entry propertyEntry : entry.getValue().entrySet()) - pvs.put(propertyEntry.getKey().getName(), propertyEntry.getValue()); - outputMaterial.setProperties(getUser(), pvs, false); - } - - outputMaterials.put(outputMaterial, helper.getSampleNames().get(i++)); - } - - ExperimentService.get().deriveSamples(_inputMaterials, outputMaterials, getViewBackgroundInfo(), _log); - - tx.commit(); - - // automatically link samples to study, if configured - StudyPublishService.get().autoLinkDerivedSamples(sampleType, outputMaterials.keySet().stream().map(ExpObject::getRowId).collect(toList()), getContainer(), getUser()); - - _successUrl = ExperimentUrlsImpl.get().getShowSampleURL(getContainer(), outputMaterials.keySet().iterator().next()); - - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - } - catch (Exception e) - { - errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); - return false; - } - - return true; - } - - @Override - public URLHelper getSuccessURL(DeriveMaterialForm deriveMaterialForm) - { - return _successUrl; - } - } - - public static class DeriveMaterialForm implements HasViewContext, DataRegionSelection.DataSelectionKeyForm - { - private String _dataRegionSelectionKey; - private int _outputCount = 1; - private int _targetSampleTypeId; - private int[] _rowIds; - private String _name; - - private ViewContext _context; - - @Override - public void setViewContext(ViewContext context) - { - _context = context; - } - - @Override - public ViewContext getViewContext() - { - return _context; - } - - public List lookupMaterials() - { - List result = new ArrayList<>(); - for (int rowId : getRowIds()) - { - ExpMaterial material = ExperimentService.get().getExpMaterial(rowId); - if (material != null) - { - if (material.getContainer().hasPermission(_context.getUser(), ReadPermission.class)) - { - result.add(material); - } - else - { - throw new UnauthorizedException(); - } - } - else - { - throw new NotFoundException("No material with RowId " + rowId); - } - } - result.sort(Comparator.comparing(Identifiable::getName)); - return result; - } - - public String getName() - { - return _name; - } - - public void setName(String name) - { - _name = name; - } - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String dataRegionSelectionKey) - { - _dataRegionSelectionKey = dataRegionSelectionKey; - } - - public int[] getRowIds() - { - if (_rowIds == null) - { - _rowIds = PageFlowUtil.toInts(DataRegionSelection.getSelected(getViewContext(), getDataRegionSelectionKey(), false)); - } - return _rowIds; - } - - public void setRowIds(int[] rowIds) - { - _rowIds = rowIds; - } - - public int getOutputCount() - { - return _outputCount; - } - - public void setOutputCount(int outputCount) - { - _outputCount = outputCount; - } - - public int getTargetSampleTypeId() - { - return _targetSampleTypeId; - } - - public void setTargetSampleTypeId(int targetSampleTypeId) - { - _targetSampleTypeId = targetSampleTypeId; - } - - public String getInputRole(int i) - { - return _context.getRequest().getParameter("inputRole" + i); - } - - public String getCustomRole(int i) - { - return _context.getRequest().getParameter("customRole" + i); - } - - public String determineLabel(int index) - { - String result = getInputRole(index); - if (DeriveSamplesChooseTargetBean.CUSTOM_ROLE.equals(result)) - { - result = getCustomRole(index); - } - if (result != null) - { - result = result.trim(); - } - return result; - } - } - - - public static class ExpInput - { - public String role; - public int rowId; - public Lsid lsid; - } - - public static class DerivationSpec - { - public String role; - public Map values; - } - - public static class DerivationForm - { - public List dataInputs; - public List materialInputs; - - public int dataOutputCount; - public Lsid targetDataClass; - public Map dataDefault; - public List dataOutputs; - - public int materialOutputCount; - public Lsid targetSampleType; - public Map materialDefault; - public List materialOutputs; - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(InsertPermission.class) - public static class DeriveAction extends MutatingApiAction - { - @Override - public void validateForm(DerivationForm form, Errors errors) - { - if (errors.hasErrors()) - return; - - if (form.materialOutputCount > 0 && form.materialOutputs != null && !form.materialOutputs.isEmpty()) - errors.reject(ERROR_MSG, "Either 'materialOutputCount' or 'materialOutputs' property can be specified, but not both."); - - if (form.dataOutputCount > 0 && form.dataOutputs != null && !form.dataOutputs.isEmpty()) - errors.reject(ERROR_MSG, "Either 'dataOutputCount' or 'dataOutputs' property can be specified, but not both."); - - boolean hasMaterialOutputs = form.materialOutputCount > 0 || form.materialOutputs != null && !form.materialOutputs.isEmpty(); - boolean hasDataOutputs = form.dataOutputCount > 0 || form.dataOutputs != null && !form.dataOutputs.isEmpty(); - - if (!hasMaterialOutputs && !hasDataOutputs) - errors.reject(ERROR_MSG, "At least one data output or material output is required"); - - if (hasMaterialOutputs && form.targetSampleType == null) - errors.reject(ERROR_MSG, "targetSampleType lsid required for material outputs"); - - if (hasDataOutputs && form.targetDataClass == null) - errors.reject(ERROR_MSG, "targetDataClass lsid required for data outputs"); - } - - @Override - public Object execute(DerivationForm form, BindException errors) throws Exception - { - // Find material inputs - Map materialInputs = new LinkedHashMap<>(); - if (form.materialInputs != null) - { - for (ExpInput in : form.materialInputs) - { - ExpMaterial m = null; - if (in.lsid != null) - { - m = ExperimentService.get().getExpMaterial(in.lsid.toString()); - if (m == null) - errors.reject(ERROR_MSG, "Can't resolve sample '" + in.lsid + "'"); - } - else if (in.rowId > 0) - { - m = ExperimentService.get().getExpMaterial(in.rowId); - if (m == null) - errors.reject(ERROR_MSG, "Can't resolve sample '" + in.rowId + "'"); - } - - if (m == null) - { - errors.reject(ERROR_MSG, "Material input lsid or rowId required"); - continue; - } - - ExpSampleType st = m.getSampleType(); - if (st == null) - { - errors.reject(ERROR_MSG, "Material input is not a member of a SampleType"); - continue; - } - - String role = in.role; - if (role == null || role.isEmpty()) - { - role = st.getName(); - } - materialInputs.put(m, role); - } - } - - // Find input data - Map dataInputs = new LinkedHashMap<>(); - if (form.dataInputs != null) - { - for (ExpInput in : form.dataInputs) - { - ExpData d = null; - if (in.lsid != null) - { - d = ExperimentService.get().getExpData(in.lsid.toString()); - if (d == null) - errors.reject(ERROR_MSG, "Can't resolve data '" + in.lsid + "'"); - } - else if (in.rowId > 0) - { - d = ExperimentService.get().getExpData(in.rowId); - if (d == null) - errors.reject(ERROR_MSG, "Can't resolve data '" + in.rowId + "'"); - } - - if (d == null) - { - errors.reject(ERROR_MSG, "Data input lsid or rowId required"); - continue; - } - - ExpDataClass dc = d.getDataClass(getUser()); - if (dc == null) - { - errors.reject(ERROR_MSG, "Data input is not a member of a DataClass"); - continue; - } - - String role = in.role; - if (role == null || role.isEmpty()) - { - role = dc.getName(); - } - dataInputs.put(d, role); - } - } - - ExpSampleType outSampleType; - if (form.targetSampleType != null) - { - // TODO: check in scope and has permission - outSampleType = SampleTypeService.get().getSampleType(form.targetSampleType.toString()); - if (outSampleType == null) - errors.reject(ERROR_MSG, "Sample type not found: " + form.targetSampleType.toString()); - } - else - { - outSampleType = null; - } - - ExpDataClass outDataClass; - if (form.targetDataClass != null) - { - // TODO: check in scope and has permission - outDataClass = ExperimentServiceImpl.get().getDataClass(form.targetDataClass.toString()); - if (outDataClass == null) - errors.reject(ERROR_MSG, "DataClass not found: " + form.targetDataClass.toString()); - } - else - { - outDataClass = null; - } - - if (errors.hasErrors()) - return null; - - // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names - // Create "MaterialInputs/" columns with a value containing a comma-separated list of Material names - final Map> parentInputNames = new HashMap<>(); - Set inputTypes = new CaseInsensitiveHashSet(); - for (ExpMaterial material : materialInputs.keySet()) - { - ExpSampleType st = material.getSampleType(); - String keyName = ExpMaterial.MATERIAL_INPUT_PARENT + "/" + st.getName(); - inputTypes.add(keyName); - parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(material.getName()); - } - - // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names - // Create "DataInputs/" columns with a value containing a comma-separated list of ExpData names - for (ExpData d : dataInputs.keySet()) - { - ExpDataClass dc = d.getDataClass(getUser()); - String keyName = ExpData.DATA_INPUT_PARENT + "/" + dc.getName(); - inputTypes.add(keyName); - parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(d.getName()); - } - - - try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) - { - Set requiredParentTypes = new CaseInsensitiveHashSet(); - - // output materials - Map outputMaterials = new HashMap<>(); - int materialOutputCount = Math.max(form.materialOutputCount, form.materialOutputs != null ? form.materialOutputs.size() : 0); - if (materialOutputCount > 0 && outSampleType != null) - { - requiredParentTypes.addAll(outSampleType.getRequiredImportAliases().values()); - DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.materialDefault, form.materialOutputs, materialOutputCount, ExpMaterial.DEFAULT_CPAS_TYPE) - { - @Override - protected TableInfo createTable() - { - SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); - return schema.getTable(outSampleType.getName()); - } - - @Override - protected List getExpObject(List> insertedRows) - { - List rowIds = insertedRows.stream().map(r -> MapUtils.getLong(r,"rowid")).collect(toList()); - return ExperimentService.get().getExpMaterials(rowIds); - } - }; - - outputMaterials = derived.createOutputs(); - } - - - // create output data - Map outputData = new HashMap<>(); - int dataOutputCount = Math.max(form.dataOutputCount, form.dataOutputs != null ? form.dataOutputs.size() : 0); - if (dataOutputCount > 0 && outDataClass != null) - { - requiredParentTypes.addAll(outDataClass.getRequiredImportAliases().values()); - DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.dataDefault, form.dataOutputs, dataOutputCount, ExpData.DEFAULT_CPAS_TYPE) - { - @Override - protected TableInfo createTable() - { - ExpSchema expSchema = new ExpSchema(getUser(), getContainer()); - UserSchema dataSchema = expSchema.getUserSchema(ExpSchema.NestedSchemas.data.name()); - return dataSchema.getTable(outDataClass.getName()); - } - - @Override - protected List getExpObject(List> insertedRows) - { - List lsids = insertedRows.stream().map(r -> (String) r.get("lsid")).collect(toList()); - return ExperimentService.get().getExpDatasByLSID(lsids); - } - }; - - outputData = derived.createOutputs(); - } - - if (outputMaterials.isEmpty() && outputData.isEmpty()) - throw new IllegalStateException("Expected to create " + materialOutputCount + " materials and " + dataOutputCount + " datas"); - - boolean hasMissingRequiredParent = false; - for (String required : requiredParentTypes) - { - if (!inputTypes.contains(required)) - { - hasMissingRequiredParent = true; - break; - } - } - if (hasMissingRequiredParent) - throw new IllegalStateException("Inputs are required: " + String.join(",", requiredParentTypes)); - - // finally, create the derived run if there are any parents - ExpRun run = null; - if (!materialInputs.isEmpty() || !dataInputs.isEmpty()) - run = ExperimentService.get().derive(materialInputs, dataInputs, outputMaterials, outputData, new ViewBackgroundInfo(getContainer(), getUser(), null), _log); - tx.commit(); - - StringBuilder successMessage = new StringBuilder("Created "); - if (!outputMaterials.isEmpty()) - successMessage.append(outputMaterials.size()).append(" materials"); - if (!outputData.isEmpty()) - successMessage.append(outputData.size()).append(" data"); - - JSONObject ret; - if (run != null) - ret = ExperimentJSONConverter.serializeRun(run, null, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); - else - ret = ExperimentJSONConverter.serializeRunOutputs(outputData.keySet(), outputMaterials.keySet(), getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); - - return success(successMessage.toString(), ret); - } - } - - // Helper class that prepares and executes the QueryUpdateService.insertRows() on the data or material table. - private abstract class DerivedOutputs - { - private final @NotNull Map> _parentInputNames; - private final @Nullable Map _defaultValues; - private final @Nullable List _values; - private final int _outputCount; - private final String _rolePrefix; - - - public DerivedOutputs(@NotNull Map> parentInputNames, @Nullable Map defaultValues, @Nullable List values, int outputCount, String rolePrefix) - { - _parentInputNames = parentInputNames; - _defaultValues = defaultValues; - _values = values; - _outputCount = outputCount; - _rolePrefix = rolePrefix; - } - - public Pair>, List> prepareRows() - { - List> rows = new ArrayList<>(); - List roles = new ArrayList<>(); - int unknownOutputDataCount = 0; - - for (int i = 0; i < _outputCount; i++) - { - Map row = new CaseInsensitiveHashMap<>(); - if (_defaultValues != null) - row.putAll(_defaultValues); - DerivationSpec spec = _values != null && i < _values.size() ? _values.get(i) : null; - String role = null; - if (spec != null) - { - row.putAll(spec.values); - role = spec.role; - } - - // NOTE: Input parents are added to each row, but are only used for name generation and not for derivation. - // NOTE: We will derive the inserted samples in a single derivation run after the sample/date have been inserted. - row.putAll(_parentInputNames); - - rows.add(row); - - if (StringUtils.trimToNull(role) == null) - { - role = _rolePrefix + (unknownOutputDataCount == 0 ? "" : Integer.toString(unknownOutputDataCount + 1)); - unknownOutputDataCount++; - } - roles.add(role); - } - return Pair.of(rows, roles); - } - - protected abstract TableInfo createTable(); - - protected abstract List getExpObject(List> insertedRows); - - public Map createOutputs() throws BatchValidationException, DuplicateKeyException, SQLException, QueryUpdateServiceException - { - Pair>, List> pair = prepareRows(); - List> rows = pair.first; - List roles = pair.second; - - TableInfo table = createTable(); - QueryUpdateService qus = table.getUpdateService(); - if (qus == null) - throw new IllegalStateException(); - - Map configParams = new HashMap<>(); - // Skip derivation during insert -- DeriveAction will call ExperimentService.get().derive() after samples are inserted - configParams.put(SampleTypeUpdateServiceDI.Options.SkipDerivation, true); - - BatchValidationException qusErrors = new BatchValidationException(); - List> insertedRows = qus.insertRows(getUser(), getContainer(), rows, qusErrors, configParams, null); - if (qusErrors.hasErrors()) - throw qusErrors; - - if (insertedRows.size() != roles.size()) - throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); - - List outputs = getExpObject(insertedRows); - if (outputs.size() != roles.size()) - throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); - - Map outputMap = new HashMap<>(); - for (int i = 0; i < outputs.size(); i++) - { - String role = roles.get(i); - T data = outputs.get(i); - outputMap.put(data, role); - } - - return outputMap; - } - } - } - - public static class CreateExperimentForm extends ExperimentForm implements DataRegionSelection.DataSelectionKeyForm - { - private boolean _addSelectedRuns; - private String _dataRegionSelectionKey; - - public boolean isAddSelectedRuns() - { - return _addSelectedRuns; - } - - public void setAddSelectedRuns(boolean addSelectedRuns) - { - _addSelectedRuns = addSelectedRuns; - } - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String dataRegionSelectionKey) - { - _dataRegionSelectionKey = dataRegionSelectionKey; - } - } - - @RequiresPermission(InsertPermission.class) - @ActionNames("createRunGroup, createExperiment") - public class CreateRunGroupAction extends FormViewAction - { - @Override - public ModelAndView getView(CreateExperimentForm form, boolean reshow, BindException errors) - { - // HACK - convert ExperimentForm to not be a BeanViewForm - form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); - form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - - DataRegion drg = new DataRegion(); - - drg.addHiddenFormField(ActionURL.Param.returnUrl, getViewContext().getRequest().getParameter(ActionURL.Param.returnUrl.name())); - drg.addHiddenFormField("addSelectedRuns", Boolean.toString("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns")))); - form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - // Fix issue 27562 - include session-stored selection - if (form.getDataRegionSelectionKey() != null) - { - for (String rowId : DataRegionSelection.getSelected(getViewContext(), form.getDataRegionSelectionKey(), false)) - { - drg.addHiddenFormField(DataRegion.SELECT_CHECKBOX_NAME, rowId); - } - } - drg.addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - - drg.addColumns(ExperimentServiceImpl.get().getTinfoExperiment(), "RowId,Name,LSID,ContactId,ExperimentDescriptionURL,Hypothesis,Comments,Created"); - - DisplayColumn col = drg.getDisplayColumn("RowId"); - col.setVisible(false); - drg.getDisplayColumn("LSID").setVisible(false); - drg.getDisplayColumn("Created").setVisible(false); - - ButtonBar bb = new ButtonBar(); - bb.setStyle(ButtonBar.Style.separateButtons); - ActionButton insertButton = new ActionButton(new ActionURL(CreateRunGroupAction.class, getContainer()), "Submit", ActionButton.Action.POST); - bb.add(insertButton); - - drg.setButtonBar(bb); - - return new InsertView(drg, errors); - } - - - @Override - public boolean handlePost(CreateExperimentForm form, BindException errors) throws Exception - { - // This is strange... but the "Create new run group..." menu item on the run grid always POSTs, probably to - // allow for long lists of run IDs. This "noPost" parameter on the initial POST is used to inform the action - // that it wants to display the form, not try to save anything yet. - if (!"true".equals(getViewContext().getRequest().getParameter("noPost"))) - { - form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); - form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); - - Experiment exp = form.getBean(); - if (exp.getName() == null || exp.getName().trim().isEmpty()) - { - errors.reject(ERROR_MSG, "You must specify a name for the experiment"); - } - else - { - int maxNameLength = ExperimentService.get().getTinfoExperimentRun().getColumn("Name").getScale(); - if (exp.getName().length() > maxNameLength) - { - errors.reject(ERROR_MSG, "Name of the experiment must be " + maxNameLength + " characters or less."); - } - } - - String lsid; - int suffix = 1; - do - { - String template = "urn:lsid:" + XarContext.LSID_AUTHORITY_SUBSTITUTION + ":Experiment.Folder-" + XarContext.CONTAINER_ID_SUBSTITUTION + ":" + exp.getName(); - if (suffix > 1) - { - template = template + suffix; - } - suffix++; - lsid = LsidUtils.resolveLsidFromTemplate(template, new XarContext("Experiment Creation", getContainer(), getUser()), ExpExperiment.DEFAULT_CPAS_TYPE); - } - while (ExperimentService.get().getExpExperiment(lsid) != null); - exp.setLSID(lsid); - exp.setContainer(getContainer()); - - if (errors.getErrorCount() == 0) - { - ExpExperimentImpl wrapper = new ExpExperimentImpl(exp); - wrapper.save(getUser()); - - if (form.isAddSelectedRuns()) - { - addSelectedRunsToExperiment(wrapper, form.getDataRegionSelectionKey()); - } - - if (form.getReturnUrl() != null) - { - throw new RedirectException(form.getReturnUrl()); - } - throw new RedirectException(ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); - } - } - return true; - } - - @Override - public void addNavTrail(NavTree root) - { - setHelpTopic("runGroups"); - root.addChild("Create Run Group"); - } - - @Override - public URLHelper getSuccessURL(CreateExperimentForm createExperimentForm) - { - return null; // null is used to show the form in the case where IDs are POSTed from the grid - } - - @Override - public void validateCommand(CreateExperimentForm target, Errors errors) { } - } - - public static class MoveRunsForm implements DataRegionSelection.DataSelectionKeyForm - { - private String _targetContainerId; - private String _dataRegionSelectionKey; - - @Override - public String getDataRegionSelectionKey() - { - return _dataRegionSelectionKey; - } - - @Override - public void setDataRegionSelectionKey(String key) - { - _dataRegionSelectionKey = key; - } - - public String getTargetContainerId() - { - return _targetContainerId; - } - - public void setTargetContainerId(String targetContainerId) - { - _targetContainerId = targetContainerId; - } - } - - @RequiresPermission(DeletePermission.class) - public class MoveRunsLocationAction extends SimpleViewAction - { - @Override - public ModelAndView getView(MoveRunsForm form, BindException errors) - { - ActionURL moveURL = new ActionURL(MoveRunsAction.class, getContainer()); - PipelineRootContainerTree ct = new PipelineRootContainerTree(getUser(), moveURL) - { - private boolean _clickHandlerRegistered = false; - - @Override - protected void renderCellContents(StringBuilder html, Container c, ActionURL url, boolean hasRoot) - { - boolean renderLink = hasRoot && !c.equals(getContainer()); - - if (renderLink) - { - html.append(""); - } - html.append(PageFlowUtil.filter(c.getName())); - if (renderLink) - { - html.append(""); - } - - if (!_clickHandlerRegistered) - { - HttpView.currentPageConfig().addHandlerForQuerySelector("a.move-target-container", "click", "moveTo(this.attributes.getNamedItem('data-objectid').value);" ); - _clickHandlerRegistered = true; - } - } - }; - ct.setInitialLevel(1); - - MoveRunsBean bean = new MoveRunsBean(ct, form.getDataRegionSelectionKey()); - JspView result = new JspView<>("/org/labkey/experiment/moveRunsLocation.jsp", bean); - result.setTitle("Choose Destination Folder"); - result.setFrame(WebPartView.FrameType.PORTAL); - return result; - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Move Runs"); - } - } - - - @RequiresPermission(DeletePermission.class) - public class MoveRunsAction extends FormHandlerAction - { - private Container _targetContainer; - - @Override - public void validateCommand(MoveRunsForm target, Errors errors) - { - } - - @Override - public boolean handlePost(MoveRunsForm form, BindException errors) - { - _targetContainer = ContainerManager.getForId(form.getTargetContainerId()); - if (_targetContainer == null || !_targetContainer.hasPermission(getUser(), InsertPermission.class)) - { - throw new UnauthorizedException(); - } - - Set runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); - List runs = new ArrayList<>(); - for (Long runId : runIds) - { - ExpRun run = ExperimentService.get().getExpRun(runId); - if (run != null) - { - runs.add(run); - } - } - - ViewBackgroundInfo info = getViewBackgroundInfo(); - info.setContainer(_targetContainer); - - try - { - ExperimentService.get().moveRuns(info, getContainer(), runs); - if (form.getDataRegionSelectionKey() != null) - DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); - } - catch (IOException e) - { - throw new NotFoundException("Failed to initialize move. Check that the pipeline root is configured correctly. " + e); - } - return true; - } - - @Override - public ActionURL getSuccessURL(MoveRunsForm form) - { - return urlProvider(PipelineUrls.class).urlBegin(_targetContainer); - } - } - - public static class ShowExternalDocsForm - { - private String _objectURI; - private String _propertyURI; - - public String getObjectURI() - { - return _objectURI; - } - - public void setObjectURI(String objectURI) - { - _objectURI = objectURI; - } - - public String getPropertyURI() - { - return _propertyURI; - } - - public void setPropertyURI(String propertyURI) - { - _propertyURI = propertyURI; - } - } - - @RequiresPermission(ReadPermission.class) - public static class ShowExternalDocsAction extends SimpleViewAction - { - @Override - public ModelAndView getView(ShowExternalDocsForm form, BindException errors) throws Exception - { - Map props = OntologyManager.getPropertyObjects(getContainer(), form.getObjectURI()); - ObjectProperty prop = props.get(form.getPropertyURI()); - if (prop == null || !getContainer().equals(prop.getContainer())) - { - throw new NotFoundException(); - } - URI uri = new URI(prop.getStringValue()); - File f = new File(uri); - if (!f.exists()) - { - throw new NotFoundException(); - } - - PageFlowUtil.streamFile(getViewContext().getResponse(), new File(f.getAbsolutePath()), false); - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - } - } - - - // TODO: DotGraph has been adding a "runId" parameter, but ShowGraphMoreListAction - public static ActionURL getShowGraphMoreListURL(Container c, @Nullable Long runId, @NotNull String objtype) - { - ActionURL url = new ActionURL(ShowGraphMoreListAction.class, c); - - if (null != runId) - url.addParameter("runId", runId); - - url.addParameter("objtype", objtype); - - return url; - } - - - @RequiresPermission(ReadPermission.class) - public static class ShowGraphMoreListAction extends SimpleViewAction - { - private ExperimentRunForm _form; - - @Override - public ModelAndView getView(ExperimentRunForm form, BindException errors) - { - _form = form; - return new GraphMoreGrid(getContainer(), errors, getViewContext().getActionURL()); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild(new NavTree("Experiments", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer()))); - ExpRun run = ExperimentService.get().getExpRun(_form.getRowId()); - if (run != null) - { - root.addChild(new NavTree("Experiment Run", ExperimentUrlsImpl.get().getRunGraphURL(_form.lookupRun()))); - } - root.addChild(new NavTree("Selected Protocol Applications")); - } - } - - @RequiresPermission(DesignAssayPermission.class) - public class AssayXarFileAction extends MutatingApiAction - { - - @Override - public Object execute(Object o, BindException errors) throws Exception - { - ApiSimpleResponse response = new ApiSimpleResponse(); - - if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) - throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); - - if (!PipelineService.get().hasValidPipelineRoot(getContainer())) - { - return false; - } - - MultipartFile formFile = getFileMap().get("file"); - if (formFile == null) - { - errors.reject(ERROR_MSG, "No file was posted by the browser."); - return false; - } - - byte[] bytes = formFile.getBytes(); - if (bytes.length == 0) - { - errors.reject(ERROR_MSG, "No file was posted by the browser."); - return false; - } - - PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); - FileLike systemDir = pipeRoot.ensureSystemDirectory(); - FileLike uploadDir = systemDir.resolveChild("UploadedXARs"); - FileUtil.createDirectories(uploadDir); - if (!uploadDir.isDirectory()) - { - errors.reject(ERROR_MSG, "Unable to create a 'system/UploadedXARs' directory under the pipeline root"); - return false; - } - String userDirName = getUser().getEmail(); - if (userDirName == null || userDirName.isEmpty()) - { - userDirName = GUEST_DIRECTORY_NAME; - } - FileLike userDir = uploadDir.resolveChild(userDirName); - FileUtil.createDirectories(userDir); - if (!userDir.isDirectory()) - { - errors.reject(ERROR_MSG, "Unable to create an 'UploadedXARs/" + userDirName + "' directory under the pipeline root"); - return false; - } - - FileLike xarFile = userDir.resolveChild(formFile.getOriginalFilename()); - - // As this is multi-part will need to use finally to close, to prevent a stream closure exception - try (OutputStream out = new BufferedOutputStream(xarFile.openOutputStream())) - { - out.write(bytes); - } - catch (IOException e) - { - errors.reject(ERROR_MSG, "Unable to write uploaded XAR file to " + xarFile); - return false; - } - //noinspection EmptyCatchBlock - - ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), xarFile, - "Uploaded file", true, pipeRoot); - PipelineService.get().queueJob(job); - - response.put("success", true); - return response; - } - } - - @RequiresPermission(InsertPermission.class) - public class ImportXarFileAction extends FormHandlerAction - { - @Override - public void validateCommand(ImportXarForm target, Errors errors) - { - } - - @Override - public boolean handlePost(ImportXarForm form, BindException errors) throws Exception - { - for (FileLike f : form.getValidatedFiles(getContainer())) - { - if (f.isFile()) - { - ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); - - // TODO: Configure module resources with the appropriate log location per container - if (form.getModule() != null) - { - FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); - job.setLogFile(logFile); - } - - PipelineService.get().queueJob(job); - } - else - { - throw new NotFoundException("Expected a file but found a directory: " + f.getName()); - } - } - - return true; - } - - @Override - public URLHelper getSuccessURL(ImportXarForm importXarForm) - { - return getContainer().getStartURL(getUser()); - } - } - - - @RequiresPermission(InsertPermission.class) - public class ImportXarAction extends MutatingApiAction - { - @Override - public Object execute(ImportXarForm form, BindException errors) throws Exception - { - ApiSimpleResponse response = new ApiSimpleResponse(); - - List> archives = new ArrayList<>(); - for (FileLike f : form.getValidatedFiles(getContainer())) - { - Map archive = new HashMap<>(); - ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); - - // TODO: Configure module resources with the appropriate log location per container - if (form.getModule() != null) - { - FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); - job.setLogFile(logFile); - } - - PipelineService.get().queueJob(job); - - archive.put("file", f.getName()); - archive.put("job", job.getJobGUID()); - archive.put("path", form.getPath()); // echo back the public path - - archives.add(archive); - } - - response.put("success", true); - response.put("archives", archives); - - return response; - } - } - - - /** - * User: jeckels - * Date: Jan 27, 2008 - */ - public static class ExperimentUrlsImpl implements ExperimentUrls - { - public ActionURL getOverviewURL(Container c) - { - return new ActionURL(BeginAction.class, c); - } - - @Override - public ActionURL getExperimentDetailsURL(Container c, ExpExperiment expExperiment) - { - return new ActionURL(DetailsAction.class, c).addParameter("rowId", expExperiment.getRowId()); - } - - public ActionURL getShowSampleURL(Container c, ExpMaterial material) - { - return getMaterialDetailsBaseURL(c, null).addParameter("rowId", material.getRowId()); - } - - @Override - public ActionURL getExportProtocolURL(Container container, ExpProtocol protocol) - { - return new ActionURL(ExperimentController.ExportProtocolsAction.class, container). - addParameter("protocolId", protocol.getRowId()). - addParameter("xarFileName", protocol.getName() + ".xar"); - } - - @Override - public ActionURL getMoveRunsLocationURL(Container container) - { - return new ActionURL(ExperimentController.MoveRunsLocationAction.class, container); - } - - @Override - public ActionURL getProtocolDetailsURL(ExpProtocol protocol) - { - return new ActionURL(ProtocolDetailsAction.class, protocol.getContainer()).addParameter("rowId", protocol.getRowId()); - } - - @Override - public ActionURL getProtocolApplicationDetailsURL(ExpProtocolApplication app) - { - return getShowApplicationURL(app.getContainer(), app.getRowId()); - } - - public ActionURL getProtocolGridURL(Container c) - { - return new ActionURL(ShowProtocolGridAction.class, c); - } - - public ActionURL getRunGraphDetailURL(ExpRun run) - { - return getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpData focus) - { - return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_DATA); - } - - public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpMaterial focus) - { - return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_MATERIAL); - } - - public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpProtocolApplication focus) - { - return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_PROT_APP); - } - - private ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpObject focus, String typeCode) - { - ActionURL result = getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); - result.addParameter("detail", "true"); - if (focus != null) - { - result.addParameter("focus", typeCode + focus.getRowId()); - } - return result; - } - - @Override - public ActionURL getRunGraphURL(Container container, long runId) - { - return ExperimentController.getRunGraphURL(container, runId); - } - - @Override - public ActionURL getRunGraphURL(ExpRun run) - { - return getRunGraphURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getRunTextURL(Container c, long runId) - { - return new ActionURL(ShowRunTextAction.class, c).addParameter("rowId", runId); - } - - @Override - public ActionURL getRunTextURL(ExpRun run) - { - return getRunTextURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getDeleteExperimentsURL(Container container, URLHelper returnUrl) - { - return new ActionURL(DeleteSelectedExperimentsAction.class, container).addReturnUrl(returnUrl); - } - - @Override - public ActionURL getDeleteProtocolURL(@NotNull ExpProtocol protocol, URLHelper returnUrl) - { - ActionURL result = new ActionURL(DeleteProtocolByRowIdsAction.class, protocol.getContainer()); - result.addParameter("singleObjectRowId", protocol.getRowId()); - if (returnUrl != null) - { - result.addReturnUrl(returnUrl); - } - return result; - } - - @Override - public ActionURL getAddRunsToExperimentURL(Container c, ExpExperiment exp) - { - return new ActionURL(AddRunsToExperimentAction.class, c).addParameter("expRowId", exp.getRowId()); - } - - @Override - public ActionURL getShowRunsURL(Container c, ExperimentRunType type) - { - ActionURL result = new ActionURL(ShowRunsAction.class, c); - result.addParameter("experimentRunFilter", type.getDescription()); - return result; - } - - public ActionURL getShowExperimentsURL(Container c) - { - return new ActionURL(ShowRunGroupsAction.class, c); - } - - @Override - public ActionURL getShowSampleTypeListURL(Container c) - { - return getShowSampleTypeListURL(c, null); - } - - @Override - public ActionURL getShowSampleTypeURL(ExpSampleType sampleType) - { - return getShowSampleTypeURL(sampleType, sampleType.getContainer()); - } - - @Override - public ActionURL getShowSampleTypeURL(ExpSampleType sampleType, Container container) - { - return new ActionURL(ShowSampleTypeAction.class, container).addParameter("rowId", sampleType.getRowId()); - } - - public ActionURL getExperimentListURL(Container container) - { - return new ActionURL(ShowRunGroupsAction.class, container); - } - - public ActionURL getShowSampleTypeListURL(Container c, String errorMessage) - { - ActionURL url = new ActionURL(ListSampleTypesAction.class, c); - if (errorMessage != null) - { - url.addParameter("errorMessage", errorMessage); - } - return url; - } - - @Override - public ActionURL getDataClassListURL(Container c) - { - return getDataClassListURL(c, null); - } - - public ActionURL getDataClassListURL(Container c, String errorMessage) - { - ActionURL url = new ActionURL(ListDataClassAction.class, c); - if (errorMessage != null) - { - url.addParameter("errorMessage", errorMessage); - } - return url; - } - - @Override - public ActionURL getDeleteDatasURL(Container c, URLHelper returnUrl) - { - ActionURL url = new ActionURL(DeleteSelectedDataAction.class, c); - if (returnUrl != null) - url.addReturnUrl(returnUrl); - return url; - } - - public ActionURL getDeleteSelectedExperimentsURL(Container c, URLHelper returnUrl) - { - ActionURL result = new ActionURL(DeleteSelectedExperimentsAction.class, c); - if (returnUrl != null) - result.addReturnUrl(returnUrl); - return result; - } - - @Override - public ActionURL getDeleteSelectedExpRunsURL(Container container, URLHelper returnUrl) - { - return new ActionURL(DeleteSelectedExpRunsAction.class, container).addReturnUrl(returnUrl); - } - - public ActionURL getShowUpdateURL(ExpExperiment experiment) - { - return new ActionURL(ShowUpdateAction.class, experiment.getContainer()).addParameter("rowId", experiment.getRowId()); - } - - @Override - public ActionURL getRemoveSelectedExpRunsURL(Container container, URLHelper returnUrl, ExpExperiment exp) - { - return new ActionURL(RemoveSelectedExpRunsAction.class, container).addReturnUrl(returnUrl).addParameter("expRowId", exp.getRowId()); - } - - @Override - public ActionURL getCreateRunGroupURL(Container container, URLHelper returnUrl, boolean addSelectedRuns) - { - ActionURL result = new ActionURL(CreateRunGroupAction.class, container); - if (returnUrl != null) - { - result.addReturnUrl(returnUrl); - } - if (addSelectedRuns) - { - result.addParameter("addSelectedRuns", "true"); - } - return result; - } - - - public static ExperimentUrlsImpl get() - { - return (ExperimentUrlsImpl) urlProvider(ExperimentUrls.class); - } - - public ActionURL getDownloadGraphURL(ExpRun run, boolean detail, String focus, String focusType) - { - ActionURL result = new ActionURL(DownloadGraphAction.class, run.getContainer()); - result.addParameter("rowId", run.getRowId()).addParameter("detail", detail); - if (focus != null) - { - result.addParameter("focus", focus); - } - if (focusType != null) - { - result.addParameter("focusType", focusType); - } - return result; - } - - public ActionURL getBeginURL(Container container) - { - return new ActionURL(BeginAction.class, container); - } - - @Override - public ActionURL getDomainEditorURL(Container container, String domainURI, boolean createOrEdit) - { - Domain domain = PropertyService.get().getDomain(container, domainURI); - if (domain != null) - return getDomainEditorURL(container, domain); - - ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); - url.addParameter("domainURI", domainURI); - if (createOrEdit) - url.addParameter("createOrEdit", true); - return url; - } - - @Override - public ActionURL getDomainEditorURL(Container container, Domain domain) - { - ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); - url.addParameter("domainId", domain.getTypeId()); - return url; - } - - @Override - public ActionURL getCreateDataClassURL(Container container) - { - return new ActionURL(EditDataClassAction.class, container); - } - - @Override - public ActionURL getShowDataClassURL(Container container, long rowId) - { - ActionURL url = new ActionURL(ShowDataClassAction.class, container); - url.addParameter("rowId", rowId); - return url; - } - - @Override - public ActionURL getShowFileURL(ExpData data, boolean inline) - { - ActionURL result = getShowFileURL(data.getContainer()).addParameter("rowId", data.getRowId()); - if (inline) - { - result.addParameter("inline", inline); - } - return result; - } - - @Override - public ActionURL getMaterialDetailsURL(ExpMaterial material) - { - return getMaterialDetailsURL(material.getContainer(), material.getRowId()); - } - - @Override - public ActionURL getMaterialDetailsURL(Container c, long materialRowId) - { - return getMaterialDetailsBaseURL(c, null).addParameter("rowId", materialRowId); - } - - @Override - public ActionURL getMaterialDetailsBaseURL(Container c, @Nullable String materialIdFieldKey) - { - return new ActionURL(ShowMaterialAction.class, c); - } - - @Override - public ActionURL getCreateSampleTypeURL(Container container) - { - return new ActionURL(EditSampleTypeAction.class, container); - } - - @Override - public ActionURL getImportSamplesURL(Container container, String sampleTypeName) - { - ActionURL url = new ActionURL(ImportSamplesAction.class, container); - url.addParameter("query.queryName", sampleTypeName); - url.addParameter("schemaName", "exp.materials"); - return url; - } - - @Override - public ActionURL getImportDataURL(Container container, String dataClassName) - { - ActionURL url = new ActionURL(ImportDataAction.class, container); - url.addParameter("query.queryName", dataClassName); - url.addParameter("schemaName", "exp.data"); - return url; - } - - @Override - public ActionURL getDataDetailsURL(ExpData data) - { - return new ActionURL(ShowDataAction.class, data.getContainer()).addParameter("rowId", data.getRowId()); - } - - @Override - public ActionURL getShowFileURL(Container c) - { - return new ActionURL(ShowFileAction.class, c); - } - - @Override - public ActionURL getSetFlagURL(Container container) - { - return new ActionURL(SetFlagAction.class, container); - } - - @Override - public ActionURL getShowRunGraphURL(ExpRun run) - { - return ExperimentController.getRunGraphURL(run.getContainer(), run.getRowId()); - } - - @Override - public ActionURL getRepairTypeURL(Container container) - { - return new ActionURL(TypesController.RepairAction.class, container); - } - - @Override - public ActionURL getUpdateMaterialQueryRowAction(Container c, TableInfo table) - { - ActionURL url = new ActionURL(UpdateMaterialQueryRowAction.class, c); - url.addParameter("schemaName", "samples"); - url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); - - return url; - } - - @Override - public ActionURL getInsertMaterialQueryRowAction(Container c, TableInfo table) - { - ActionURL url = new ActionURL(InsertMaterialQueryRowAction.class, c); - url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); - - return url; - } - - @Override - public ActionURL getDataClassAttachmentDownloadAction(Container c) - { - return new ActionURL(ExperimentController.DataClassAttachmentDownloadAction.class, c); - } - - } - - private static abstract class BaseResolveLsidApiAction extends ReadOnlyApiAction - { - protected Set _seeds; - - @Override - public void validateForm(F form, Errors errors) - { - if (null != form.getLsids()) - { - _seeds = new LinkedHashSet<>(form.getLsids().size()); - for (String lsid : form.getLsids()) - { - Identifiable id = LsidManager.get().getObject(lsid); - if (id == null) - throw new NotFoundException("Unable to resolve object: " + lsid); - - // ensure the user has read permission in the seed container - if (!getContainer().equals(id.getContainer())) - { - if (!id.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new UnauthorizedException("User does not have permission to read object: " + lsid); - } - - _seeds.add(id); - } - } - else - { - throw new ApiUsageException("Starting lsids required"); - } - } - } - - @RequiresPermission(ReadPermission.class) - public static class ResolveAction extends BaseResolveLsidApiAction - { - @Override - public Object execute(ResolveLsidsForm form, BindException errors) - { - var settings = new ExperimentJSONConverter.Settings(form.isIncludeProperties(), form.isIncludeInputsAndOutputs(), form.isIncludeRunSteps()); - var data = _seeds.stream().map(n -> ExperimentJSONConverter.serialize(n, getUser(), settings)).collect(toList()); - return new ApiSimpleResponse("data", data); - } - } - - @RequiresPermission(ReadPermission.class) - public static class LineageAction extends BaseResolveLsidApiAction - { - @Override - public Object execute(ExpLineageOptions options, BindException errors) throws Exception - { - ExpLineageServiceImpl.get().streamLineage(getContainer(), getUser(), getViewContext().getResponse(), _seeds, options); - return null; - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class RebuildEdgesAction extends MutatingApiAction - { - @Override - public Object execute(ExperimentRunForm form, BindException errors) - { - if (form.getRowId() != 0 || form.getLsid() != null) - { - ExpRun run = form.lookupRun(); - if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new UnauthorizedException("Not permitted"); - - ExperimentServiceImpl.get().syncRunEdges(run); - } - else - { - // should this require site admin permissions? - ExperimentServiceImpl.get().rebuildAllRunEdges(); - } - return success(); - } - } - - private static class VerifyEdgesForm extends ExperimentRunForm - { - private Integer _limit; - - public Integer getLimit() - { - return _limit; - } - - public void setLimit(Integer limit) - { - _limit = limit; - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class VerifyEdgesAction extends ReadOnlyApiAction - { - @Override - public Object execute(VerifyEdgesForm form, BindException errors) - { - if (form.getRowId() != 0 || form.getLsid() != null) - { - ExpRun run = form.lookupRun(); - if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) - throw new UnauthorizedException("Not permitted"); - - ExperimentServiceImpl.get().verifyRunEdges(run); - } - else - { - ExperimentServiceImpl.get().verifyAllEdges(getContainer(), form.getLimit()); - } - return success(); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class RebuildAncestorsAction extends MutatingApiAction - { - @Override - public Object execute(Object form, BindException errors) - { - ClosureQueryHelper.truncateAndRecreate(); - return success(); - } - } - - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class CheckDataClassesIndexedAction extends ReadOnlyApiAction - { - @Override - public Object execute(Object o, BindException errors) throws Exception - { - List> notInIndex = new ArrayList<>(100); - - List list = ExperimentService.get().getDataClasses(getContainer(), getUser(), false); - for (ExpDataClass dc : list) - { - for (ExpData d : dc.getDatas()) - { - String docId = d.getDocumentId(); - if (docId != null) - { - SearchService.SearchHit hit = SearchService.get().find(docId); - if (hit == null) - { - JSONObject props = ExperimentJSONConverter.serializeData(d, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); - props.put("docid", docId); - notInIndex.add(props.toMap()); - } - } - } - } - - return success(notInIndex); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(AdminPermission.class) - public static class CheckEdgesAction extends ReadOnlyApiAction - { - @Override - public Object execute(Object o, BindException errors) throws Exception - { - List result; - DbSchema schema = ExperimentService.get().getSchema(); - TableInfo edgeTable = schema.getTable("Edge"); - - if (null != edgeTable.getColumn("fromObjectId")) - { - var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") - .resultSetStream() - .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) - .collect(toList()); - var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); - result = cycles.stream().map(e -> new Integer[]{e.first, e.second}).collect(toList()); - } - else - { - var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromLsid, toLsid FROM exp.Edge") - .resultSetStream() - .map(r -> { try { return new Pair<>(r.getString(1), r.getString(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) - .collect(toList()); - var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); - result = cycles.stream().map(e -> new String[]{e.first, e.second}).collect(toList()); - } - - JSONObject ret = new JSONObject(); - ret.put("result", result); - ret.put("success", true); - return ret; - } - } - - @RequiresPermission(UpdatePermission.class) - public static class UpdateMaterialQueryRowAction extends UserSchemaAction - { - @Override - protected QueryForm createQueryForm(ViewContext context) - { - QueryForm form = new QueryForm("samples", null); - form.setViewContext(getViewContext()); - form.bindParameters(getViewContext().getBindPropertyValues()); - return form; - } - - @Override - public BindException bindParameters(PropertyValues m) throws Exception - { - BindException bind = super.bindParameters(m); - - QueryUpdateForm tableForm = (QueryUpdateForm)bind.getTarget(); - - int sampleId; - try - { - sampleId = Integer.parseInt((String) tableForm.getPkVal()); - } - catch (NumberFormatException e) - { - throw new NotFoundException("Invalid RowId: " + tableForm.getPkVal()); - } - - ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); - if (material == null) - throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); - - return bind; - } - - @Override - public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) - { - int sampleId = Integer.parseInt((String) tableForm.getPkVal()); - - ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); - if (material == null) - throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); - - boolean isAliquot = !StringUtils.isEmpty(material.getAliquotedFromLSID()); - - TableInfo tableInfo = tableForm.getTable(); - Map scopedFields = new CaseInsensitiveHashMap<>(); - for (DomainProperty dp : tableInfo.getDomain().getProperties()) - { - if (!ExpSchema.DerivationDataScopeType.All.name().equalsIgnoreCase(dp.getDerivationDataScope())) - scopedFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); - } - - for (var column : tableInfo.getColumns()) - { - String columnName = column.getName(); - if (scopedFields.containsKey(columnName)) - { - boolean isAliquotField = scopedFields.get(columnName); - boolean show = (isAliquot && isAliquotField) || (!isAliquot && !isAliquotField); - ((BaseColumnInfo)column).setUserEditable(show); - ((BaseColumnInfo)column).setHidden(!show); - } - } - - ButtonBar bb = createSubmitCancelButtonBar(tableForm); - UpdateView view = new UpdateView(tableForm, errors); - view.getDataRegion().setButtonBar(bb); - return view; - } - - @Override - public boolean handlePost(QueryUpdateForm tableForm, BindException errors) - { - doInsertUpdate(tableForm, errors, false); - return 0 == errors.getErrorCount(); - } - - @Override - public void addNavTrail(NavTree root) - { - super.addNavTrail(root); - root.addChild("Edit " + _form.getQueryName()); - } - } - - @RequiresPermission(InsertPermission.class) - public static class InsertMaterialQueryRowAction extends UserSchemaAction - { - @Override - protected QueryForm createQueryForm(ViewContext context) - { - QueryForm form = new QueryForm("samples", null); - form.setViewContext(getViewContext()); - form.bindParameters(getViewContext().getBindPropertyValues()); - - return form; - } - - @Override - public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) - { - TableInfo tableInfo = tableForm.getTable(); - Map propertyFields = new CaseInsensitiveHashMap<>(); - for (DomainProperty dp : tableInfo.getDomain().getProperties()) - { - propertyFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); - } - - for (var column : tableInfo.getColumns()) - { - String columnName = column.getName(); - if (propertyFields.containsKey(columnName)) - { - boolean isAliquotField = propertyFields.get(columnName); - ((BaseColumnInfo)column).setUserEditable(!isAliquotField); - ((BaseColumnInfo)column).setHidden(isAliquotField); - } - } - - InsertView view = new InsertView(tableForm, errors); - view.getDataRegion().setButtonBar(createSubmitCancelButtonBar(tableForm)); - return view; - } - - @Override - public boolean handlePost(QueryUpdateForm tableForm, BindException errors) - { - doInsertUpdate(tableForm, errors, true); - return 0 == errors.getErrorCount(); - } - - @Override - public void addNavTrail(NavTree root) - { - super.addNavTrail(root); - root.addChild("Insert " + _form.getQueryName()); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class SaveFindIdsAction extends ReadOnlyApiAction - { - - public static final String FIND_BY_IDS_SESSION_KEY_PREFIX = "findByIds"; - - @Override - public Object execute(FindByIdsForm form, BindException errors) throws Exception - { - HttpServletRequest request = getViewContext().getRequest(); - String key = form.getSessionKey(); - boolean removePrevious = false; - - if (key == null) - { - removePrevious = true; - key = FIND_BY_IDS_SESSION_KEY_PREFIX + "_" + UniqueID.getServerSessionScopedUID(); - } - - if (request != null) - { - if (removePrevious) - SessionHelper.clearAttributesWithPrefix(request, FIND_BY_IDS_SESSION_KEY_PREFIX); - HttpSession session = request.getSession(false); - if (session != null) - { - @SuppressWarnings("unchecked") - List existingIds = (List) session.getAttribute(key); - - // deduplicate from existing ids - if (existingIds != null && form.getSessionKey() != null) - { - existingIds.addAll(form.getIds().stream().filter(id -> !existingIds.contains(id)).toList()); - session.setAttribute(key, existingIds); - } - else - { - session.setAttribute(key, form.getIds()); - } - return success("Saved ids to session key", key); - } - } - - return new SimpleResponse<>(false, "Unable to save to session. Session or request may be null."); - } - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class SaveOrderedSamplesQueryAction extends ReadOnlyApiAction - { - private static final String SAMPLE_ID_PREFIX = "s:"; - private static final String UNIQUE_ID_PREFIX = "u:"; - - private List _ids; - private Map> _uniqueIdLsids; - - @Override - public void validateForm(FindByIdsForm form, Errors errors) - { - if (form.getSessionKey() == null) - errors.reject(ERROR_REQUIRED, "sessionKey must be provided"); - else - { - _ids = getFindIdsFromSession(form.getSessionKey()); - if (_ids == null || _ids.isEmpty()) - errors.reject(ERROR_REQUIRED, "No ids found corresponding to session key " + form.getSessionKey()); - } - } - - private void ensureUniqueIdLsids() - { - boolean hasUniqueId = _ids.stream().anyMatch(s -> s.startsWith(UNIQUE_ID_PREFIX)); - if (hasUniqueId && _uniqueIdLsids == null) - { - List uniqueIds = _ids.stream().map(s -> s.substring(UNIQUE_ID_PREFIX.length())).toList(); - _uniqueIdLsids = ExperimentService.get().getUniqueIdLsids(uniqueIds, getUser(), getContainer()); - } - } - - @Override - public Object execute(FindByIdsForm form, BindException errors) throws Exception - { - ensureUniqueIdLsids(); - - SQLFragment select = getOrderedRowsSql(); - // need to set the key field so selections are possible - // need the SampleTypeUnits so we will display using that unit - String metadata = - """ - - - - - true - true - - - true - - - true - - -
- """; - QueryDefinition def = QueryService.get().saveSessionQuery(getViewContext(), getContainer(), ExperimentServiceImpl.getExpSchema().getName(), select.getSQL(), metadata); - return success("Session query created", Map.of("queryName", def.getName(), "ids", _ids)); - } - - - private List getFindIdsFromSession(String sessionKey) - { - HttpServletRequest request = getViewContext().getRequest(); - List ids = new ArrayList<>(); - if (request != null) - { - HttpSession session = request.getSession(false); - if (session != null) - { - ids = (List) session.getAttribute(sessionKey); - } - } - return ids; - } - - private SQLFragment getOrderedRowsSql() - { - boolean isFMEnabled = InventoryService.isFreezerManagementEnabled(getContainer()); - String samplesTable = isFMEnabled ? "inventory.SampleItems" : "exp.materials"; - List orderedIdCols = new ArrayList<>(Arrays.asList("Id AS ProvidedID", "RowId", "Ordinal")); - List sampleColumns = new ArrayList<>(); - if (!isFMEnabled) - { - sampleColumns.addAll(Arrays.asList( - "S.Name AS SampleID", - "S.MaterialExpDate AS ExpirationDate", - "S.SampleSet as SampleType", - "S.SampleState", - "S.isAliquot", - "S.Created", - "S.CreatedBy" - )); - } - else - { - sampleColumns.addAll(Arrays.asList( - "S.Name AS SampleID", - "S.MaterialExpDate AS ExpirationDate", - "S.LabelColor", - "S.SampleSet", - "S.SampleState", - "S.StoredAmount", - "S.Units", - "S.SampleTypeUnits", - "S.FreezeThawCount", - "S.StorageStatus", - "S.CheckedOutBy", - "S.StorageLocation", - "S.StorageRow", - "S.StorageCol", - "S.StoragePositionNumber", - "S.IsAliquot", - "S.Created", - "S.CreatedBy" - )); - } - - - String sampleIdComma = ""; - String uniqueIdComma = ""; - int index = 1; - SQLFragment sampleIdValuesSql = new SQLFragment(); - SQLFragment uniqueIdValuesSql = new SQLFragment(); - for (String id : _ids) - { - if (id.startsWith(SAMPLE_ID_PREFIX)) - { - sampleIdValuesSql.append(sampleIdComma).append("\t(").appendValue(index); - sampleIdValuesSql.append(", "); - sampleIdValuesSql.append(LabKeySql.quoteString(id.substring(SAMPLE_ID_PREFIX.length()))); - sampleIdValuesSql.append(", "); - sampleIdValuesSql.append(LabKeySql.quoteString("null")); - sampleIdValuesSql.append(")"); - sampleIdComma = "\n,"; - } - else if (id.startsWith(UNIQUE_ID_PREFIX)) - { - String idClean = id.substring(UNIQUE_ID_PREFIX.length()); - - List lsids = _uniqueIdLsids.get(idClean); - if (lsids != null) - { - for (String lsid : lsids) - { - uniqueIdValuesSql.append(uniqueIdComma).append("\t(").appendValue(index); - uniqueIdValuesSql.append(", "); - uniqueIdValuesSql.append(LabKeySql.quoteString(idClean)); - uniqueIdValuesSql.append(", "); - uniqueIdValuesSql.append(LabKeySql.quoteString(lsid)); - uniqueIdValuesSql.append(")"); - uniqueIdComma = "\n,"; - } - } - } - index++; - } - - boolean haveData = !sampleIdValuesSql.isEmpty() || !_uniqueIdLsids.isEmpty(); - SQLFragment sql = new SQLFragment(); - if (!sampleIdValuesSql.isEmpty()) - { - sql.append("WITH _ordered_ids_ AS (\nSELECT * FROM (VALUES\n"); - sql.append(sampleIdValuesSql); - sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter - } - if (!uniqueIdValuesSql.isEmpty()) - { - if (!sampleIdValuesSql.isEmpty()) - sql.append(",\n"); - else - sql.append("WITH "); - - sql.append("_ordered_unique_ids_ AS (\nSELECT * FROM (VALUES\n"); - sql.append(uniqueIdValuesSql); - sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter - } - - sql.append("SELECT "); - sql.append("\n\tOID.").append(StringUtils.join(orderedIdCols, ",\n\tOID.")); - sql.append(",\n\t").append(StringUtils.join( sampleColumns, ",\n\t")); - sql.append("\nFROM\n("); - if (!sampleIdValuesSql.isEmpty()) - { - sql.append("SELECT\n\tM.RowId,\n\t_ordered_ids_.column1 as Ordinal,\n\t_ordered_ids_.column2 as Id,\n\t_ordered_ids_.column2 as lsid"); - sql.append("\nFROM _ordered_ids_\n"); - sql.append("INNER JOIN exp.materials M ON _ordered_ids_.column2 = M.Name"); - sql.append("\n"); - } - if (!uniqueIdValuesSql.isEmpty()) - { - if (!sampleIdValuesSql.isEmpty()) - sql.append("\nUNION ALL\n\n"); - - sql.append("SELECT\n\tM.RowId,\n\t_ordered_unique_ids_.column1 as Ordinal,\n\t_ordered_unique_ids_.column2 as Id,\n\t_ordered_unique_ids_.column3 as lsid"); - sql.append("\nFROM _ordered_unique_ids_\n"); - sql.append("INNER JOIN exp.materials M ON _ordered_unique_ids_.column3 = M.lsid"); - sql.append("\n"); - } - if (!haveData) // no data to return but return data in the expected shape. - { - sql = new SQLFragment("SELECT\n"); - sql.append(orderedIdCols.stream() - .map(col -> { - int asIndex = col.indexOf("AS"); - if (asIndex > 0) - return "NULL AS " + col.substring(asIndex+ 3); - else - return "NULL AS " + col; - }) - .collect(Collectors.joining(",\t\n"))); - sql.append(",\t\n").append(StringUtils.join(sampleColumns, ",\t\n")); - sql.append("\nFROM ").append(samplesTable).append(" S WHERE 1 = 2"); - return sql; - } - else - { - sql.append(") OID"); - if (isFMEnabled) - sql.append("\nLEFT JOIN inventory.SampleItems S on S.RowId = OID.RowId"); - else - sql.append("\nINNER JOIN exp.materials S on S.RowId = OID.RowId"); - sql.append("\n\nORDER BY Ordinal"); - return sql; - } - } - } - - public static class FindByIdsForm extends FindSessionKeyForm - { - List _ids; - - public List getIds() - { - return _ids; - } - - public void setIds(List ids) - { - _ids = ids; - } - } - - - public static class FindSessionKeyForm - { - private String _sessionKey; - - public String getSessionKey() - { - return _sessionKey; - } - - public void setSessionKey(String sessionKey) - { - _sessionKey = sessionKey; - } - } - - static void validateEntitySequenceForm(EntitySequenceForm form, Errors errors) - { - String kindName = form.getKindName(); - if (StringUtils.isEmpty(kindName) || form.getSeqType() == null) - { - errors.reject(ERROR_REQUIRED, "KindName and SeqType must be provided"); - return; - } - - if (form.getSeqType() == NameGenerator.EntityCounter.genId) - { - if (form.getRowId() == null) - errors.reject(ERROR_REQUIRED, "Data type RowId must be provided for genId"); - } - else if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName)) - { - errors.reject(ERROR_MSG, form.getSeqType() + " is not supported for " + kindName); - } - - if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName) && !DataClassDomainKind.NAME.equalsIgnoreCase(kindName)) - errors.reject(ERROR_MSG, "Invalid KindName. Should be either " + SampleTypeDomainKind.NAME + " or " + DataClassDomainKind.NAME + "."); - - } - - @RequiresPermission(ReadPermission.class) - public static class GetEntitySequenceAction extends ReadOnlyApiAction - { - @Override - public void validateForm(EntitySequenceForm form, Errors errors) - { - validateEntitySequenceForm(form, errors); - } - - @Override - public Object execute(EntitySequenceForm form, BindException errors) throws Exception - { - long value = -1; - if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - if (form.getSeqType() == NameGenerator.EntityCounter.genId) - { - ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); - if (sampleType != null) - value = sampleType.getCurrentGenId(); - } - else - { - value = SampleTypeService.get().getCurrentCount(form.getSeqType(), getContainer()); - } - - } - else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); - if (dataClass != null) - value = dataClass.getCurrentGenId(); - } - - ApiSimpleResponse resp = new ApiSimpleResponse(); - resp.put("success", value > -1); - resp.put("value", value); - return resp; - } - } - - @RequiresPermission(ReadPermission.class) // actual permission checked later - public static class SetEntitySequenceAction extends MutatingApiAction - { - @Override - public void validateForm(EntitySequenceForm form, Errors errors) - { - validateEntitySequenceForm(form, errors); - - if (form.getNewValue() == null || form.getNewValue() < 0) - errors.reject(ERROR_MSG, "Invalid newValue."); - } - - @Override - public Object execute(EntitySequenceForm form, BindException errors) - { - ApiSimpleResponse resp = new ApiSimpleResponse(); - resp.put("success", true); - - try - { - Domain domain = null; - if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - if (form.getSeqType() == NameGenerator.EntityCounter.genId) - { - if (!getContainer().hasPermission(getUser(), DesignSampleTypePermission.class)) - throw new UnauthorizedException("Insufficient permissions."); - - ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); - if (sampleType != null) - { - sampleType.ensureMinGenId(form.getNewValue()); - domain = sampleType.getDomain(); - } - else - { - resp.put("success", false); - resp.put("error", "Sample type does not exist."); - } - } - else - { - if (!getContainer().hasPermission(getUser(), AdminPermission.class)) - throw new UnauthorizedException("Insufficient permissions."); - - SampleTypeService.get().ensureMinSampleCount(form.getNewValue(), form.getSeqType(), getContainer()); - } - } - else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) - { - if (!getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) - throw new BadRequestException("Insufficient permissions."); - - ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); - if (dataClass != null) - { - dataClass.ensureMinGenId(form.getNewValue(), getContainer()); - domain = dataClass.getDomain(); - } - else - { - resp.put("success", false); - resp.put("error", "DataClass does not exist."); - } - } - - if (domain != null) - { - DomainAuditProvider.DomainAuditEvent event = new DomainAuditProvider.DomainAuditEvent(getContainer(), "The genId for domain " + domain.getName() + " has been updated to " + form.getNewValue() + "."); - event.setDomainUri(domain.getTypeURI()); - event.setDomainName(domain.getName()); - AuditLogService.get().addEvent(getUser(), event); - } - } - catch (ExperimentException e) - { - resp.put("success", false); - resp.put("error", e.getMessage()); - } - - return resp; - } - } - - public static class EntitySequenceForm - { - private String _kindName; - private NameGenerator.EntityCounter _seqType; - private Integer _rowId; - private Long _newValue; - - public Integer getRowId() - { - return _rowId; - } - - public void setRowId(Integer rowId) - { - _rowId = rowId; - } - - public String getKindName() - { - return _kindName; - } - - public void setKindName(String kindName) - { - _kindName = kindName; - } - - public Long getNewValue() - { - return _newValue; - } - - public void setNewValue(Long newValue) - { - this._newValue = newValue; - } - - public NameGenerator.EntityCounter getSeqType() - { - return _seqType; - } - - public void setSeqType(String seqType) - { - _seqType = NameGenerator.EntityCounter.valueOf(seqType); - } - - } - - @Marshal(Marshaller.Jackson) - @RequiresPermission(ReadPermission.class) - public static class GetCrossFolderDataSelectionAction extends ReadOnlyApiAction - { - @Override - public void validateForm(CrossFolderSelectionForm form, Errors errors) - { - if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) - errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); - if (!"samples".equalsIgnoreCase(form.getDataType()) && !"exp.data".equalsIgnoreCase(form.getDataType())&& !"assay".equalsIgnoreCase(form.getDataType())) - errors.reject(ERROR_REQUIRED, "Data type (sample, data or assayrun) must be specified."); - } - - @Override - public Object execute(CrossFolderSelectionForm form, BindException errors) - { - Pair result = ExperimentServiceImpl.getCurrentAndCrossFolderDataCount(form.getIds(false), form.getDataType(), getContainer()); - - ApiSimpleResponse resp = new ApiSimpleResponse(); - resp.put("success", true); - resp.put("currentFolderSelectionCount", result.first); - resp.put("crossFolderSelectionCount", result.second); - - return success(resp); - } - } - - public static class CrossFolderSelectionForm extends DataViewSnapshotSelectionForm - { - private String _dataType; - private String _picklistName; - - public String getDataType() - { - return _dataType; - } - - public void setDataType(String dataType) - { - _dataType = dataType; - } - - public String getPicklistName() - { - return _picklistName; - } - - public void setPicklistName(String picklistName) - { - _picklistName = picklistName; - } - - @Override - public Set getIds(boolean clear) - { - Set selectedIds; - - if (_rowIds != null) - selectedIds = _rowIds; - else if (isUseSnapshotSelection()) - selectedIds = new HashSet<>(DataRegionSelection.getSnapshotSelectedIntegers(getViewContext(), getDataRegionSelectionKey())); - else - selectedIds = DataRegionSelection.getSelectedIntegers(getViewContext(), getDataRegionSelectionKey(), clear); - - if (_picklistName != null) - { - User user = getViewContext().getUser(); - Container container = getViewContext().getContainer(); - UserSchema schema = ListService.get().getUserSchema(user, container); - TableInfo tInfo = schema.getTable(_picklistName); - if (tInfo != null) - { - SimpleFilter filter = SimpleFilter.createContainerFilter(container); - filter.addInClause(FieldKey.fromParts("id"), selectedIds); - TableSelector selector = new TableSelector(tInfo, Collections.singleton("SampleID"), filter, null); - return new HashSet<>(selector.getArrayList(Long.class)); - } - } - return selectedIds; - } - } - - @RequiresPermission(AdminPermission.class) - public static class RecomputeAliquotRollup extends SimpleViewAction - { - @Override - public void addNavTrail(NavTree root) - { - } - - @Override - public ModelAndView getView(Object o, BindException errors) throws SQLException - { - try (var ignore = SpringActionController.ignoreSqlUpdates()) - { - Container container = getContainer(); - User user = getUser(); - - List sampleTypes = SampleTypeService.get() - .getSampleTypes(container, user, true); - - HtmlStringBuilder builder = HtmlStringBuilder.of(); - builder.unsafeAppend(""); - - SampleTypeService service = SampleTypeService.get(); - for (ExpSampleType sampleType : sampleTypes) - { - int updatedCount; - updatedCount = service.recomputeSampleTypeRollup(sampleType, container); - // we could check "if (0 < updatedCount) refresh(rollup)", but since this is a "manual" usage lets just always refresh - SampleTypeServiceImpl.get().refreshSampleTypeMaterializedView(sampleType, update); - builder.unsafeAppend(""); - } - - builder.unsafeAppend("
Sample Type#Recomputed
") - .append(sampleType.getName()) - .unsafeAppend("") - .append(updatedCount) - .unsafeAppend("
"); - return new HtmlView("Aliquot Rollup Recalculation Result", builder); - } - } - } - - /* Also see API CheckEdgesAction */ - @RequiresPermission(TroubleshooterPermission.class) - public static class CycleCheckAction extends FormViewAction - { - List cycleObjectIds = null; - - @Override - public void validateCommand(Object target, Errors errors) - { - - } - - @Override - public ModelAndView getView(Object o, boolean reshow, BindException errors) - { - if (!reshow) - { - return new HtmlView( - DIV("This operation can use a lot of memory.", - LK.FORM(at(method,"POST"), - PageFlowUtil.button("Continue").submit(true))) - ); - } - - if (null == cycleObjectIds) - return new HtmlView(HtmlString.of("No cycles found")); - - Map map = new LongHashMap<>(); - var cf = new ContainerFilter.AllFolders(getUser()); - var materials = ExperimentServiceImpl.get().getExpMaterialsByObjectId(cf, cycleObjectIds); - materials.forEach( (m) -> map.put(m.getObjectId(), m)); - var datas = ExperimentServiceImpl.get().getExpDatasByObjectId(cf, cycleObjectIds); - datas.forEach( (d) -> map.put(d.getObjectId(), d)); - var runs = ExperimentServiceImpl.get().getRunsByObjectId(cf, cycleObjectIds); - runs.forEach( (r) -> map.put(r.getObjectId(), r)); - - ExperimentUrls urls = ExperimentUrls.get(); - return new HtmlView( - DIV("Cycle found involving these objects.", - UL(cycleObjectIds.stream().map((objectid) -> - { - ExpObject exp = map.get(objectid); - if (exp instanceof ExpMaterial mat) - return LI(A(at(target, "_blank", href, urls.getMaterialDetailsURL(mat)), objectid + " : material - " + mat.getName())); - else if (exp instanceof ExpRun run) - return LI(A(at(target, "_blank", href, urls.getRunTextURL(run)), objectid + " : run - " + run.getName())); - else if (exp instanceof ExpData data) - return LI(A(at(target, "_blank", href, urls.getDataDetailsURL(data)), objectid + " : run - " + data.getName())); - else - return LI(String.valueOf(objectid)); - })) - ) - ); - } - - @Override - public boolean handlePost(Object o, BindException errors) - { - var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") - .resultSetStream() - .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) - .collect(toList()); - var cyclesEdges = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); - - var set = new LinkedHashSet(); - cyclesEdges.forEach( (edge) -> { - set.add(edge.first); - set.add(edge.second); - }); - cycleObjectIds = set.stream().toList(); - return false; - } - - @Override - public URLHelper getSuccessURL(Object o) - { - return null; - } - - @Override - public void addNavTrail(NavTree root) - { - - } - } - - @RequiresPermission(AdminPermission.class) - public static class MissingFilesCheckAction extends ReadOnlyApiAction - { - @Override - public Object execute(Object o, BindException errors) throws Exception - { - Map> info = ExperimentServiceImpl.get().doMissingFilesCheck(getUser(), getContainer(), true); - JSONObject results = new JSONObject(); - for (String containerId : info.keySet()) - { - JSONObject containerResults = new JSONObject(); - for (String sourceName : info.get(containerId).keySet()) - containerResults.put(sourceName, info.get(containerId).get(sourceName).toJSON()); - results.put(containerId, containerResults); - } - - ApiSimpleResponse response = new ApiSimpleResponse(); - response.put("success", true); - response.put("result", results); - return response; - } - } - -} +/* + * Copyright (c) 2008-2019 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.labkey.experiment.controllers.exp; + +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import jakarta.servlet.http.HttpSession; +import org.apache.commons.collections4.MapUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.Strings; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.poi.ss.usermodel.Workbook; +import org.jetbrains.annotations.NotNull; +import org.jetbrains.annotations.Nullable; +import org.json.JSONArray; +import org.json.JSONException; +import org.json.JSONObject; +import org.labkey.api.action.ApiJsonWriter; +import org.labkey.api.action.ApiResponse; +import org.labkey.api.action.ApiSimpleResponse; +import org.labkey.api.action.ApiUsageException; +import org.labkey.api.action.ExportAction; +import org.labkey.api.action.FormHandlerAction; +import org.labkey.api.action.FormViewAction; +import org.labkey.api.action.HasViewContext; +import org.labkey.api.action.Marshal; +import org.labkey.api.action.Marshaller; +import org.labkey.api.action.MutatingApiAction; +import org.labkey.api.action.QueryViewAction; +import org.labkey.api.action.ReadOnlyApiAction; +import org.labkey.api.action.ReturnUrlForm; +import org.labkey.api.action.SimpleApiJsonForm; +import org.labkey.api.action.SimpleErrorView; +import org.labkey.api.action.SimpleResponse; +import org.labkey.api.action.SimpleViewAction; +import org.labkey.api.action.SpringActionController; +import org.labkey.api.assay.AssayFileWriter; +import org.labkey.api.assay.AssayProtocolSchema; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.actions.UploadWizardAction; +import org.labkey.api.assay.security.DesignAssayPermission; +import org.labkey.api.attachments.AttachmentParent; +import org.labkey.api.attachments.AttachmentService; +import org.labkey.api.attachments.BaseDownloadAction; +import org.labkey.api.audit.AbstractAuditTypeProvider; +import org.labkey.api.audit.AuditLogService; +import org.labkey.api.audit.DetailedAuditTypeEvent; +import org.labkey.api.audit.SampleTimelineAuditEvent; +import org.labkey.api.audit.TransactionAuditProvider; +import org.labkey.api.collections.CaseInsensitiveHashMap; +import org.labkey.api.collections.CaseInsensitiveHashSet; +import org.labkey.api.collections.LongHashMap; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.CompareType; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.ContainerManager; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.DataRegionSelection; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.DbScope; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.ExcelWriter; +import org.labkey.api.data.MenuButton; +import org.labkey.api.data.NameGenerator; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.ShowRows; +import org.labkey.api.data.SimpleDisplayColumn; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.SqlSelector; +import org.labkey.api.data.TSVJSONWriter; +import org.labkey.api.data.TSVWriter; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.TableSelector; +import org.labkey.api.dataiterator.DataIteratorContext; +import org.labkey.api.exp.AbstractParameter; +import org.labkey.api.exp.DeleteForm; +import org.labkey.api.exp.DuplicateMaterialException; +import org.labkey.api.exp.ExperimentDataHandler; +import org.labkey.api.exp.ExperimentException; +import org.labkey.api.exp.ExperimentRunForm; +import org.labkey.api.exp.ExperimentRunListView; +import org.labkey.api.exp.ExperimentRunType; +import org.labkey.api.exp.Identifiable; +import org.labkey.api.exp.Lsid; +import org.labkey.api.exp.LsidManager; +import org.labkey.api.exp.LsidType; +import org.labkey.api.exp.ObjectProperty; +import org.labkey.api.exp.OntologyManager; +import org.labkey.api.exp.ProtocolApplicationParameter; +import org.labkey.api.exp.XarContext; +import org.labkey.api.exp.api.DataClassDomainKindProperties; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExpDataClass; +import org.labkey.api.exp.api.ExpExperiment; +import org.labkey.api.exp.api.ExpLineageOptions; +import org.labkey.api.exp.api.ExpMaterial; +import org.labkey.api.exp.api.ExpMaterialRunInput; +import org.labkey.api.exp.api.ExpObject; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExpProtocolApplication; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExpRunAttachmentParent; +import org.labkey.api.exp.api.ExpRunEditor; +import org.labkey.api.exp.api.ExpRunItem; +import org.labkey.api.exp.api.ExpSampleType; +import org.labkey.api.exp.api.ExperimentJSONConverter; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.exp.api.ExperimentUrls; +import org.labkey.api.exp.api.NameExpressionOptionService; +import org.labkey.api.exp.api.ResolveLsidsForm; +import org.labkey.api.exp.api.SampleTypeDomainKind; +import org.labkey.api.exp.api.SampleTypeService; +import org.labkey.api.exp.list.ListService; +import org.labkey.api.exp.property.Domain; +import org.labkey.api.exp.property.DomainAuditProvider; +import org.labkey.api.exp.property.DomainKind; +import org.labkey.api.exp.property.DomainProperty; +import org.labkey.api.exp.property.DomainTemplate; +import org.labkey.api.exp.property.DomainTemplateGroup; +import org.labkey.api.exp.property.DomainUtil; +import org.labkey.api.exp.property.PropertyService; +import org.labkey.api.exp.query.ExpDataProtocolInputTable; +import org.labkey.api.exp.query.ExpInputTable; +import org.labkey.api.exp.query.ExpMaterialProtocolInputTable; +import org.labkey.api.exp.query.ExpSchema; +import org.labkey.api.exp.query.SamplesSchema; +import org.labkey.api.exp.xar.LSIDRelativizer; +import org.labkey.api.exp.xar.LsidUtils; +import org.labkey.api.files.FileContentService; +import org.labkey.api.gwt.client.AuditBehaviorType; +import org.labkey.api.inventory.InventoryService; +import org.labkey.api.module.ModuleHtmlView; +import org.labkey.api.module.ModuleLoader; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineService; +import org.labkey.api.pipeline.PipelineStatusFile; +import org.labkey.api.pipeline.PipelineUrls; +import org.labkey.api.pipeline.PipelineValidationException; +import org.labkey.api.qc.SampleStatusService; +import org.labkey.api.query.AbstractQueryImportAction; +import org.labkey.api.query.BatchValidationException; +import org.labkey.api.query.DetailsURL; +import org.labkey.api.query.DuplicateKeyException; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryAction; +import org.labkey.api.query.QueryDefinition; +import org.labkey.api.query.QueryException; +import org.labkey.api.query.QueryForm; +import org.labkey.api.query.QueryParam; +import org.labkey.api.query.QueryService; +import org.labkey.api.query.QuerySettings; +import org.labkey.api.query.QueryUpdateForm; +import org.labkey.api.query.QueryUpdateService; +import org.labkey.api.query.QueryUpdateServiceException; +import org.labkey.api.query.QueryView; +import org.labkey.api.query.SchemaKey; +import org.labkey.api.query.UserSchema; +import org.labkey.api.query.UserSchemaAction; +import org.labkey.api.reader.ColumnDescriptor; +import org.labkey.api.reader.DataLoader; +import org.labkey.api.reader.DataLoaderFactory; +import org.labkey.api.reader.ExcelFactory; +import org.labkey.api.search.SearchService; +import org.labkey.api.security.ActionNames; +import org.labkey.api.security.RequiresAnyOf; +import org.labkey.api.security.RequiresNoPermission; +import org.labkey.api.security.RequiresPermission; +import org.labkey.api.security.SecurableResource; +import org.labkey.api.security.User; +import org.labkey.api.security.permissions.AdminPermission; +import org.labkey.api.security.permissions.DeletePermission; +import org.labkey.api.security.permissions.DesignDataClassPermission; +import org.labkey.api.security.permissions.DesignSampleTypePermission; +import org.labkey.api.security.permissions.InsertPermission; +import org.labkey.api.security.permissions.Permission; +import org.labkey.api.security.permissions.ReadPermission; +import org.labkey.api.security.permissions.SampleWorkflowDeletePermission; +import org.labkey.api.security.permissions.SiteAdminPermission; +import org.labkey.api.security.permissions.TroubleshooterPermission; +import org.labkey.api.security.permissions.UpdatePermission; +import org.labkey.api.settings.AppProps; +import org.labkey.api.settings.ConceptURIProperties; +import org.labkey.api.sql.LabKeySql; +import org.labkey.api.study.Dataset; +import org.labkey.api.study.StudyService; +import org.labkey.api.study.StudyUrls; +import org.labkey.api.study.publish.StudyPublishService; +import org.labkey.api.usageMetrics.SimpleMetricsService; +import org.labkey.api.util.DOM; +import org.labkey.api.util.DOM.LK; +import org.labkey.api.util.ErrorRenderer; +import org.labkey.api.util.ExceptionUtil; +import org.labkey.api.util.FileStream; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.HtmlString; +import org.labkey.api.util.HtmlStringBuilder; +import org.labkey.api.util.ImageUtil; +import org.labkey.api.util.JSoupUtil; +import org.labkey.api.util.LinkBuilder; +import org.labkey.api.util.NetworkDrive; +import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.util.Pair; +import org.labkey.api.util.ResponseHelper; +import org.labkey.api.util.SafeToRender; +import org.labkey.api.util.SessionHelper; +import org.labkey.api.util.StringExpression; +import org.labkey.api.util.StringUtilsLabKey; +import org.labkey.api.util.URLHelper; +import org.labkey.api.util.UniqueID; +import org.labkey.api.util.CsrfInput; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.BadRequestException; +import org.labkey.api.view.DataView; +import org.labkey.api.view.DataViewSnapshotSelectionForm; +import org.labkey.api.view.DetailsView; +import org.labkey.api.view.HBox; +import org.labkey.api.view.HtmlView; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.InsertView; +import org.labkey.api.view.JspView; +import org.labkey.api.view.NavTree; +import org.labkey.api.view.NotFoundException; +import org.labkey.api.view.RedirectException; +import org.labkey.api.view.UnauthorizedException; +import org.labkey.api.view.UpdateView; +import org.labkey.api.view.VBox; +import org.labkey.api.view.ViewBackgroundInfo; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.ViewServlet; +import org.labkey.api.view.WebPartView; +import org.labkey.api.view.template.ClientDependency; +import org.labkey.api.view.template.PageConfig; +import org.labkey.experiment.ChooseExperimentTypeBean; +import org.labkey.experiment.ConfirmDeleteView; +import org.labkey.experiment.CustomPropertiesView; +import org.labkey.experiment.DataClassWebPart; +import org.labkey.experiment.DerivedSamplePropertyHelper; +import org.labkey.experiment.DotGraph; +import org.labkey.experiment.ExpDataFileListener; +import org.labkey.experiment.ExperimentRunDisplayColumn; +import org.labkey.experiment.ExperimentRunGraph; +import org.labkey.experiment.LineageGraphDisplayColumn; +import org.labkey.experiment.MissingFilesCheckInfo; +import org.labkey.experiment.MoveRunsBean; +import org.labkey.experiment.ParentChildView; +import org.labkey.experiment.ProtocolApplicationDisplayColumn; +import org.labkey.experiment.ProtocolDisplayColumn; +import org.labkey.experiment.ProtocolWebPart; +import org.labkey.experiment.RunGroupWebPart; +import org.labkey.experiment.SampleTypeDisplayColumn; +import org.labkey.experiment.SampleTypeWebPart; +import org.labkey.experiment.StandardAndCustomPropertiesView; +import org.labkey.experiment.XarExportPipelineJob; +import org.labkey.experiment.XarExportType; +import org.labkey.experiment.XarExporter; +import org.labkey.experiment.api.ClosureQueryHelper; +import org.labkey.experiment.api.DataClass; +import org.labkey.experiment.api.DataClassDomainKind; +import org.labkey.experiment.api.ExpDataClassAttachmentParent; +import org.labkey.experiment.api.ExpDataClassImpl; +import org.labkey.experiment.api.ExpDataImpl; +import org.labkey.experiment.api.ExpExperimentImpl; +import org.labkey.experiment.api.ExpMaterialImpl; +import org.labkey.experiment.api.ExpProtocolApplicationImpl; +import org.labkey.experiment.api.ExpProtocolImpl; +import org.labkey.experiment.api.ExpRunImpl; +import org.labkey.experiment.api.ExpSampleTypeImpl; +import org.labkey.experiment.api.Experiment; +import org.labkey.experiment.api.ExperimentServiceImpl; +import org.labkey.experiment.api.GraphAlgorithms; +import org.labkey.experiment.api.ProtocolActionStepDetail; +import org.labkey.experiment.api.SampleTypeServiceImpl; +import org.labkey.experiment.api.SampleTypeUpdateServiceDI; +import org.labkey.experiment.controllers.property.PropertyController; +import org.labkey.experiment.lineage.ExpLineageServiceImpl; +import org.labkey.experiment.pipeline.ExperimentPipelineJob; +import org.labkey.experiment.types.TypesController; +import org.labkey.experiment.xar.XarExportSelection; +import org.labkey.vfs.FileLike; +import org.labkey.vfs.FileSystemLike; +import org.springframework.beans.PropertyValue; +import org.springframework.beans.PropertyValues; +import org.springframework.validation.BindException; +import org.springframework.validation.Errors; +import org.springframework.validation.ObjectError; +import org.springframework.web.multipart.MultipartFile; +import org.springframework.web.multipart.MultipartHttpServletRequest; +import org.springframework.web.servlet.ModelAndView; + +import javax.imageio.ImageIO; +import java.awt.*; +import java.awt.image.BufferedImage; +import java.io.BufferedOutputStream; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.net.URI; +import java.nio.file.Files; +import java.nio.file.Path; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Iterator; +import java.util.LinkedHashMap; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.Set; +import java.util.TreeSet; +import java.util.function.Function; +import java.util.stream.Collectors; + +import static java.util.stream.Collectors.toList; +import static org.labkey.api.data.DbScope.CommitTaskOption.POSTCOMMIT; +import static org.labkey.api.exp.query.ExpSchema.TableType.DataInputs; +import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM; +import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM; +import static org.labkey.api.query.QueryImportPipelineJob.QUERY_IMPORT_PIPELINE_PROVIDER_PARAM; +import static org.labkey.api.util.DOM.A; +import static org.labkey.api.util.DOM.Attribute.action; +import static org.labkey.api.util.DOM.Attribute.href; +import static org.labkey.api.util.DOM.Attribute.id; +import static org.labkey.api.util.DOM.Attribute.method; +import static org.labkey.api.util.DOM.Attribute.name; +import static org.labkey.api.util.DOM.Attribute.size; +import static org.labkey.api.util.DOM.Attribute.src; +import static org.labkey.api.util.DOM.Attribute.target; +import static org.labkey.api.util.DOM.Attribute.type; +import static org.labkey.api.util.DOM.Attribute.value; +import static org.labkey.api.util.DOM.Attribute.width; +import static org.labkey.api.util.DOM.DIV; +import static org.labkey.api.util.DOM.IMG; +import static org.labkey.api.util.DOM.INPUT; +import static org.labkey.api.util.DOM.LI; +import static org.labkey.api.util.DOM.TABLE; +import static org.labkey.api.util.DOM.TD; +import static org.labkey.api.util.DOM.TR; +import static org.labkey.api.util.DOM.UL; +import static org.labkey.api.util.DOM.at; +import static org.labkey.api.util.DOM.cl; +import static org.labkey.experiment.ExpDataIterators.setContainerFilterForImport; +import static org.labkey.experiment.api.SampleTypeServiceImpl.SampleChangeType.update; + +public class ExperimentController extends SpringActionController +{ + private static final Logger _log = LogManager.getLogger(ExperimentController.class); + private static final DefaultActionResolver _actionResolver = new DefaultActionResolver( + ExperimentController.class + ); + private static final String GUEST_DIRECTORY_NAME = "guest"; + + public ExperimentController() + { + setActionResolver(_actionResolver); + } + + public static void ensureCorrectContainer(Container requestContainer, ExpObject object, ViewContext viewContext) + { + Container objectContainer = object.getContainer(); + if (!requestContainer.equals(objectContainer)) + { + ActionURL url = viewContext.cloneActionURL(); + url.setContainer(objectContainer); + throw new RedirectException(url); + } + } + + // Complete no-op, but leave in place in case we decide to adjust the base nav trail + private void addRootNavTrail(NavTree root) + { + // Intentionally don't add an "Experiment" node to the list because it's too overloaded. All content on the + // default action can be added to a portal page if desired. + } + + @Override + public PageConfig defaultPageConfig() + { + // set default help topic for controller + PageConfig config = super.defaultPageConfig(); + config.setHelpTopic("experiment"); + return config; + } + + @ActionNames("begin,gridView") + @RequiresPermission(ReadPermission.class) + public class BeginAction extends SimpleViewAction + { + @Override + public VBox getView(Object o, BindException errors) + { + VBox result = new VBox(); + + VBox runListView = createRunListView(20); + result.addView(runListView); + + RunGroupWebPart runGroups = new RunGroupWebPart(getViewContext(), false); + runGroups.showHeader(); + result.addView(runGroups); + + result.addView(new ProtocolWebPart(false, getViewContext())); + result.addView(new SampleTypeWebPart(false, getViewContext())); + result.addView(new DataClassWebPart(false, getViewContext(), null)); + + return result; + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Experiment"); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowRunsAction extends SimpleViewAction + { + @Override + public VBox getView(Object o, BindException errors) + { + return createRunListView(100); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Experiment Runs"); + } + } + + private VBox createRunListView(int defaultMaxRows) + { + Set types = ExperimentService.get().getExperimentRunTypes(getContainer()); + ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")), getViewContext().getActionURL().clone(), Collections.emptyList()); + JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean); + + ExperimentRunListView view = ExperimentService.get().createExperimentRunWebPart(getViewContext(), bean.getSelectedFilter()); + view.setFrame(WebPartView.FrameType.NONE); + + // When paginated and the user hasn't explicitly set a maxRows, use the default maxRows size. + QuerySettings settings = view.getSettings(); + if (!settings.isMaxRowsSet() && settings.getShowRows() == ShowRows.PAGINATED) + { + settings.setMaxRows(defaultMaxRows); + } + + VBox result = new VBox(chooserView, view); + result.setFrame(WebPartView.FrameType.PORTAL); + return result; + } + + @RequiresPermission(ReadPermission.class) + @ActionNames("showRunGroups, showExperiments") + public class ShowRunGroupsAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + RunGroupWebPart webPart = new RunGroupWebPart(getViewContext(), false); + webPart.setFrame(WebPartView.FrameType.NONE); + return webPart; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + addRootNavTrail(root); + root.addChild("Run Groups"); + } + } + + public record Field(String domainURI, String domainName, String name, Container container) {} + public record MiniExpObject(Object rowId, String name) {} + public record TimelineSummary(MiniExpObject miniExpObject, String mostRecentValue) {} + public record ProblemType(String tableName, String fieldName, String pkName) { + public Object toHtml(List summaries) + { + return DOM.DIV( + DOM.H4(tableName), + DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), + DOM.THEAD(DOM.TH(pkName), DOM.TH(fieldName)), + summaries.stream().map(summary -> + DOM.TR(DOM.TD(summary.miniExpObject.name), DOM.TD(summary.mostRecentValue))) + )); + } + } + + @RequiresPermission(SiteAdminPermission.class) + public static class ReportLostFieldValuesAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + // Find all the fields that could have lost data due to issue 52666 + TableInfo t = new ExpSchema(getUser(), ContainerManager.getRoot()).getTable(ExpSchema.TableType.Fields.name(), ContainerFilter.getUnsafeEverythingFilter()); + List fields = new TableSelector(t, + new SimpleFilter(FieldKey.fromParts("StorageColumnNameMatch"), false). + addCondition(FieldKey.fromParts("DomainURI"), ":AssayDomain-Data.", CompareType.DOES_NOT_CONTAIN), + null). + getArrayList(Field.class); + + // Prep audit table for querying + UserSchema auditSchema = AuditLogService.get().createSchema(getUser(), ContainerManager.getRoot()); + + Map> sampleTypeSummaries = new HashMap<>(); + Map> dataClassSummaries = new HashMap<>(); + Map> listSummaries = new HashMap<>(); + + Map> problematicFields = new LinkedHashMap<>(); + + for (Field field : fields) + { + String domainURI = field.domainURI; + String fieldName = field.name; + Container container = field.container; + Domain domain = PropertyService.get().getDomain(container, domainURI); + if (domain != null && domain.getDomainKind() != null) + { + TableInfo table = domain.getDomainKind().getTableInfo(getUser(), container, domain, ContainerFilter.getUnsafeEverythingFilter()); + + if (table != null) + { + // Drill into sample types + if (domain.getDomainKind().getClass().equals(SampleTypeDomainKind.class)) + { + // rows that currently have no value for the field with potential for data loss + List rowsWithNull = new TableSelector(table, + new HashSet<>(List.of("RowId", "Name")), + new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), + null). + getArrayList(MiniExpObject.class); + + List fixupsNeeded = checkData( + rowsWithNull, + fieldName, + obj -> new SimpleFilter(FieldKey.fromParts("SampleId"), obj.rowId), + auditSchema.getTable(SampleTimelineAuditEvent.EVENT_TYPE, ContainerFilter.getUnsafeEverythingFilter())); + if (!fixupsNeeded.isEmpty()) + { + sampleTypeSummaries.put(new ProblemType(table.getName(), fieldName, "SampleID"), fixupsNeeded); + } + } + // and data classes/sample sources + if (domain.getDomainKind().getClass().equals(DataClassDomainKind.class)) + { + // rows samples that current have no value for the field with potential for data loss + List rowsWithNull = new TableSelector(table, + new HashSet<>(List.of("RowId", "Name")), + new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), + null). + getArrayList(MiniExpObject.class); + + List fixupsNeeded = checkData( + rowsWithNull, + fieldName, + obj -> new SimpleFilter(FieldKey.fromParts("RowPk"), Objects.toString(obj.rowId)). + addCondition(FieldKey.fromParts("SchemaName"), "exp.data"). + addCondition(FieldKey.fromParts("QueryName"), domain.getName()), + auditSchema.getTable("QueryUpdateAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); + + if (!fixupsNeeded.isEmpty()) + { + dataClassSummaries.put(new ProblemType(table.getName(), fieldName, "SourceID"), fixupsNeeded); + } + } + // and lists + if ("lists".equals(table.getUserSchema().getName())) + { + // rows samples that current have no value for the field with potential for data loss + List rowsWithNull = new ArrayList<>(); + + ColumnInfo entityIdCol = table.getColumn("EntityId"); + ColumnInfo pkCol = table.getPkColumns().get(0); + + new TableSelector(table, + List.of(entityIdCol, pkCol), + new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), + null). + forEachResults(r -> + { + Object entityId = entityIdCol.getValue(r); + Object pk = pkCol.getValue(r); + rowsWithNull.add(new MiniExpObject(entityId, pk.toString())); + }); + + + List fixupsNeeded = checkData( + rowsWithNull, + fieldName, + obj -> new SimpleFilter(FieldKey.fromParts("ListItemEntityId"), obj.rowId), + auditSchema.getTable("ListAuditEvent", ContainerFilter.getUnsafeEverythingFilter())); + + if (!fixupsNeeded.isEmpty()) + { + listSummaries.put(new ProblemType(table.getName(), fieldName, table.getPkColumnNames().get(0)), fixupsNeeded); + } + } + + long totalRows = new TableSelector(table).getRowCount(); + long emptyRows = new TableSelector(table, new SimpleFilter(new CompareType.CompareClause(FieldKey.fromParts(fieldName), CompareType.ISBLANK, null)), null).getRowCount(); + problematicFields.put(field, Pair.of(totalRows, emptyRows)); + } + else + { + problematicFields.put(field, Pair.of(null, null)); + } + } + } + + return new HtmlView("Fixups Needed", + DOM.createHtmlFragment( + DOM.H2("Potentially Problematic Fields"), + problematicFields.isEmpty() ? "No problematic fields detected!" : + DOM.TABLE(at(cl("table-condensed", "labkey-data-region", "table-bordered")), + DOM.THEAD(DOM.TH("Domain Name"), DOM.TH("Domain URI"), DOM.TH("Field Name"), DOM.TH("Container"), DOM.TH("Total Rows"), DOM.TH("Rows with Nulls")), + problematicFields.entrySet().stream().map(e -> { + Field f = e.getKey(); + Pair counts = e.getValue(); + return DOM.TR( + DOM.TD(f.domainName), + DOM.TD(f.domainURI), + DOM.TD(f.name), + DOM.TD(f.container.getPath()), + DOM.TD(counts.first), + DOM.TD(counts.second) + ); + } + )), + + DOM.H2("Sample Types"), + sampleTypeSummaries.isEmpty() ? "No problems detected!" : + sampleTypeSummaries.entrySet().stream().map(e -> + e.getKey().toHtml(e.getValue())), + + DOM.H2("Data Classes"), + dataClassSummaries.isEmpty() ? "No problems detected!" : + dataClassSummaries.entrySet().stream().map(e -> + e.getKey().toHtml(e.getValue())), + + DOM.H2("Lists"), + listSummaries.isEmpty() ? "No problems detected!" : + listSummaries.entrySet().stream().map(e -> + e.getKey().toHtml(e.getValue())) + )); + } + + @NotNull + private List checkData(List rowsWithNull, String fieldName, Function filterGenerator, TableInfo auditTable) + { + List fixupsNeeded = new ArrayList<>(); + + // For each sample without a value today, check the audit history + for (MiniExpObject row : rowsWithNull) + { + // Order by RowId to get them in the sequence they happened in + var events = new TableSelector(auditTable, filterGenerator.apply(row), new Sort("RowId")).getArrayList(DetailedAuditTypeEvent.class); + // Remember the most recently set value + String mostRecentValue = null; + for (DetailedAuditTypeEvent event : events) + { + Map newValues = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(event.getNewRecordMap())); + if (newValues.containsKey(fieldName)) + { + // Will be the empty string if the value was intentionally set to blank + mostRecentValue = newValues.get(fieldName); + } + } + // If the value had been set before, and its most recent insert/update wasn't setting it blank, + // it's most likely a lost value + if (mostRecentValue != null && !mostRecentValue.isEmpty()) + { + fixupsNeeded.add(new TimelineSummary(row, mostRecentValue)); + } + } + return fixupsNeeded; + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Accidentally Nulled Field Report"); + } + } + + @RequiresPermission(ReadPermission.class) + public static class CreateHiddenRunGroupAction extends MutatingApiAction + { + @Override + public ApiResponse execute(SimpleApiJsonForm form, BindException errors) throws Exception + { + JSONObject json = form.getJsonObject(); + String selectionKey = json.optString("selectionKey", null); + List runs = new ArrayList<>(); + + // Accept either an explicit list of run IDs + if (json.has("runIds")) + { + JSONArray runIds = json.getJSONArray("runIds"); + for (int i = 0; i < runIds.length(); i++) + { + ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(runIds.getInt(i)); + if (run != null) + { + runs.add(run); + } + } + } + // Or a reference to a DataRegion selection key + else if (selectionKey != null) + { + Set ids = DataRegionSelection.getSelectedIntegers(getViewContext(), selectionKey, false); + for (Long id : ids) + { + ExpRunImpl run = ExperimentServiceImpl.get().getExpRun(id); + if (run != null) + { + runs.add(run); + } + } + } + if (runs.isEmpty()) + { + throw new NotFoundException(); + } + + ExpExperiment group = ExperimentService.get().createHiddenRunGroup(getContainer(), getUser(), runs.toArray(new ExpRun[0])); + if (selectionKey != null) + DataRegionSelection.clearAll(getViewContext(), selectionKey); + + ApiSimpleResponse response = new ApiSimpleResponse(); + response.putBean(group, "rowId", "LSID", "name", "hidden"); + return response; + } + } + + + @RequiresPermission(ReadPermission.class) + public class DetailsAction extends QueryViewAction + { + private ExpExperimentImpl _experiment; + + public DetailsAction() + { + super(ExpObjectForm.class); + } + + private Pair> createViews(ExpObjectForm form, BindException errors) + { + _experiment = ExperimentServiceImpl.get().getExpExperiment(form.getRowId()); + if (_experiment == null) + { + throw new NotFoundException("Could not find an experiment with RowId " + form.getRowId()); + } + + if (!_experiment.getContainer().equals(getContainer())) + { + throw new RedirectException(getViewContext().cloneActionURL().setContainer(_experiment.getContainer())); + } + + List protocols = _experiment.getAllProtocols(); + + Set types = new TreeSet<>(ExperimentService.get().getExperimentRunTypes(getContainer())); + ExperimentRunType selectedType = ExperimentRunType.getSelectedFilter(types, getViewContext().getRequest().getParameter("experimentRunFilter")); + + ChooseExperimentTypeBean bean = new ChooseExperimentTypeBean(types, selectedType, getViewContext().getActionURL().clone(), protocols); + JspView chooserView = new JspView<>("/org/labkey/experiment/experimentRunQueryHeader.jsp", bean, errors); + + ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), bean.getSelectedFilter(), true); + runListView.getRunTable().setExperiment(_experiment); + runListView.setShowRemoveFromExperimentButton(true); + runListView.setShowDeleteButton(true); + runListView.setShowAddToRunGroupButton(true); + runListView.setShowExportButtons(true); + runListView.setShowMoveRunsButton(true); + return new Pair<>(runListView, chooserView); + } + + @Override + protected ModelAndView getHtmlView(ExpObjectForm form, BindException errors) throws Exception + { + Pair> views = createViews(form, errors); + + CustomPropertiesView customPropertiesView = new CustomPropertiesView(_experiment.getLSID(), getContainer()); + + TableInfo runGroupsTable = new ExpSchema(getUser(), getContainer()).getTable(ExpSchema.TableType.RunGroups); + + DetailsView detailsView = new DetailsView(new DataRegion(), _experiment.getRowId()); + detailsView.getDataRegion().setTable(runGroupsTable); + detailsView.getDataRegion().addColumns(runGroupsTable, "RowId,Name,Created,Modified,Contact,ExperimentDescriptionURL,Hypothesis,Comments"); + detailsView.getDataRegion().getDisplayColumn(0).setVisible(false); + detailsView.getDataRegion().getDisplayColumn(2).setWidth("60%"); + + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + ActionButton b = new ActionButton(ExperimentUrlsImpl.get().getShowUpdateURL(_experiment), "Edit"); + b.setDisplayPermission(UpdatePermission.class); + bb.add(b); + detailsView.getDataRegion().setButtonBar(bb); + if (_experiment.getBatchProtocol() != null) + { + detailsView.setTitle("Batch Details"); + detailsView.getDataRegion().addColumns(runGroupsTable, "BatchProtocolId"); + } + else + { + detailsView.setTitle("Run Group Details"); + } + + VBox runsVBox = new VBox(views.second, createInitializedQueryView(form, errors, false, null)); + runsVBox.setTitle("Experiment Runs"); + runsVBox.setFrame(WebPartView.FrameType.PORTAL); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, customPropertiesView), runsVBox); + } + + @Override + protected ExperimentRunListView createQueryView(ExpObjectForm form, BindException errors, boolean forExport, String dataRegion) + { + return createViews(form, errors).first; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + addRootNavTrail(root); + root.addChild("Run Groups", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); + root.addChild(_experiment.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ListSampleTypesAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + SampleTypeWebPart view = new SampleTypeWebPart(false, getViewContext()); + view.setFrame(WebPartView.FrameType.NONE); + view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); + + return view; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types"); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowSampleTypeAction extends SimpleViewAction + { + private ExpSampleTypeImpl _sampleType; + + @Override + public ModelAndView getView(ExpObjectForm form, BindException errors) + { + _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getRowId()); + if (_sampleType == null && form.getLsid() != null) + { + if (form.getLsid().equalsIgnoreCase("Material") || form.getLsid().equalsIgnoreCase("Sample")) + { + // Not a real sample type - just show all the materials instead + throw new RedirectException(new ActionURL(ShowAllMaterialsAction.class, getContainer())); + } + // Check if the URL specifies the LSID, and stick the bean back into the form + _sampleType = SampleTypeServiceImpl.get().getSampleType(form.getLsid()); + } + + if (_sampleType == null) + { + throw new NotFoundException("No matching sample type found"); + } + + List allScopedSampleTypes = (List) SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true); + if (!allScopedSampleTypes.contains(_sampleType)) + { + ensureCorrectContainer(getContainer(), _sampleType, getViewContext()); + } + + SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); + QuerySettings settings = schema.getSettings(getViewContext(), "Material", _sampleType.getName()); + QueryView queryView = new SampleTypeContentsView(_sampleType, schema, settings, errors); + + DetailsView detailsView = new DetailsView(getSampleTypeRegion(getViewContext()), _sampleType.getRowId()); + detailsView.getDataRegion().getDisplayColumn("Name").setURL((ActionURL)null); + detailsView.getDataRegion().getDisplayColumn("LSID").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("MaterialLSIDPrefix").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("LabelColor").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("MetricUnit").setVisible(false); + detailsView.getDataRegion().getDisplayColumn("Category").setVisible(false); + + detailsView.setTitle("Sample Type Properties"); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).setStyle(ButtonBar.Style.separateButtons); + + Container autoLinkContainer = _sampleType.getAutoLinkTargetContainer(); + if (null != autoLinkContainer) + { + DisplayColumn autoLinkTargetColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkTargetContainer"); + autoLinkTargetColumn.setVisible(false); + + SimpleDisplayColumn displayAutoLinkTargetColumn = new SimpleDisplayColumn(); + displayAutoLinkTargetColumn.setCaption("Auto Link Target Container:"); + String path = autoLinkContainer.getPath(); + displayAutoLinkTargetColumn.setDisplayHtml(path.equals("/") ? "" : path); + detailsView.getDataRegion().addDisplayColumn(displayAutoLinkTargetColumn); + } + + DisplayColumn autoLinkCategoryColumn = detailsView.getDataRegion().getDisplayColumn("autoLinkCategory"); + autoLinkCategoryColumn.setVisible(false); + SimpleDisplayColumn displayAutoLinkCategoryColumn = new SimpleDisplayColumn(); + displayAutoLinkCategoryColumn.setCaption("Auto Link Category:"); + displayAutoLinkCategoryColumn.setDisplayHtml(_sampleType.getAutoLinkCategory()); + detailsView.getDataRegion().addDisplayColumn(displayAutoLinkCategoryColumn); + + if (_sampleType.hasNameAsIdCol()) + { + SimpleDisplayColumn nameIdCol = new SimpleDisplayColumn(); + nameIdCol.setCaption("Has Name Id Column:"); + nameIdCol.setDisplayHtml("true"); + detailsView.getDataRegion().addDisplayColumn(nameIdCol); + } + + if (_sampleType.hasIdColumns()) + { + SimpleDisplayColumn idCols = new SimpleDisplayColumn(); + idCols.setCaption("Id Column(s):"); + String names = _sampleType.getIdCols().stream() + .filter(Objects::nonNull) + .map(DomainProperty::getName) + .collect(Collectors.joining(", ")); + if (!names.isEmpty()) + { + idCols.setDisplayHtml(PageFlowUtil.filter(names)); + detailsView.getDataRegion().addDisplayColumn(idCols); + } + } + + if (_sampleType.getParentCol() != null) + { + SimpleDisplayColumn parentCol = new SimpleDisplayColumn(PageFlowUtil.filter(_sampleType.getParentCol().getName())); + parentCol.setCaption("Parent Column:"); + detailsView.getDataRegion().addDisplayColumn(parentCol); + } + + try + { + SimpleDisplayColumn importAliasCol = new SimpleDisplayColumn(); + importAliasCol.setCaption("Parent Import Alias(es):"); + if (!_sampleType.getImportAliases().isEmpty()) + importAliasCol.setDisplayHtml(PageFlowUtil.filter(StringUtils.join(_sampleType.getImportAliases().keySet(), ", "))); + detailsView.getDataRegion().addDisplayColumn(importAliasCol); + } + catch (IOException e) + { + // unable to parse import alias map from JSON + } + + if (!getContainer().equals(_sampleType.getContainer())) + { + ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowSampleTypeURL(_sampleType); + SimpleDisplayColumn definedInCol = new SimpleDisplayColumn("" + + PageFlowUtil.filter(_sampleType.getContainer().getPath()) + + ""); + definedInCol.setCaption("Defined In:"); + detailsView.getDataRegion().addDisplayColumn(definedInCol); + } + + // Not all sample types can be edited + DomainKind domainKind = _sampleType.getDomain().getDomainKind(); + if (domainKind != null && domainKind.canEditDefinition(getUser(), _sampleType.getDomain())) + { + if (domainKind instanceof SampleTypeDomainKind) + { + ActionURL updateURL = new ActionURL(EditSampleTypeAction.class, _sampleType.getContainer()); + updateURL.addParameter("RowId", _sampleType.getRowId()); + updateURL.addReturnUrl(getViewContext().getActionURL()); + + if (!getContainer().equals(_sampleType.getContainer())) + { + String editLink = updateURL.toString(); + ActionButton updateButton = new ActionButton("Edit Type"); + updateButton.setActionType(ActionButton.Action.SCRIPT); + updateButton.setScript("if (window.confirm('This sample type is defined in the " + _sampleType.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + editLink + "' }"); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); + } + else + { + ActionButton updateButton = new ActionButton(updateURL, "Edit Type", ActionButton.Action.LINK); + updateButton.setDisplayPermission(DesignSampleTypePermission.class); + updateButton.setPrimary(true); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(updateButton); + } + + ActionURL deleteURL = new ActionURL(DeleteSampleTypesAction.class, _sampleType.getContainer()); + deleteURL.addParameter("singleObjectRowId", _sampleType.getRowId()); + deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ActionButton deleteButton = new ActionButton(deleteURL, "Delete Type", ActionButton.Action.LINK); + deleteButton.setDisplayPermission(DesignSampleTypePermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(deleteButton); + } + else + { + ActionURL editURL = domainKind.urlEditDefinition(_sampleType.getDomain(), new ViewBackgroundInfo(_sampleType.getContainer(), getUser(), getViewContext().getActionURL())); + if (editURL != null) + { + editURL.addReturnUrl(getViewContext().getActionURL()); + ActionButton editTypeButton = new ActionButton(editURL, "Edit Fields"); + editTypeButton.setDisplayPermission(UpdatePermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(editTypeButton); + } + } + } + + if (_sampleType.canImportMoreSamples()) + { + TableInfo table = queryView.getTable(); + if (table != null) + { + ActionURL importURL = table.getImportDataURL(getContainer()); + if (importURL != null) + { + importURL = importURL.clone(); + importURL.addReturnUrl(getViewContext().getActionURL()); + ActionButton uploadButton = new ActionButton(importURL, "Import More Samples", ActionButton.Action.LINK); + uploadButton.setDisplayPermission(UpdatePermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(uploadButton); + } + } + } + + var publish = StudyPublishService.get(); + if (AuditLogService.get().isViewable() && publish != null) + { + ContainerFilter cf = ContainerFilter.Type.CurrentAndSubfolders.create(getContainer(), getUser()); + ActionURL linkToStudyHistoryURL = publish.getPublishHistory(getContainer(), Dataset.PublishSource.SampleType, _sampleType.getRowId(), cf); + ActionButton linkToStudyHistoryButton = new ActionButton(linkToStudyHistoryURL, "Link to Study History", ActionButton.Action.LINK); + linkToStudyHistoryButton.setDisplayPermission(InsertPermission.class); + detailsView.getDataRegion().getButtonBar(DataRegion.MODE_DETAILS).add(linkToStudyHistoryButton); + } + + return new VBox(detailsView, queryView); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + ActionURL url = ExperimentUrls.get().getShowSampleTypeListURL(getContainer()); + addRootNavTrail(root); + root.addChild("Sample Types", url); + root.addChild("Sample Type " + _sampleType.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowAllMaterialsAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + ExpSchema schema = new ExpSchema(getUser(), getContainer()); + QuerySettings settings = schema.getSettings(getViewContext(), "Materials", ExpSchema.TableType.Materials.toString()); + QueryView view = new QueryView(schema, settings, errors) + { + @Override + protected void populateButtonBar(DataView view, ButtonBar bar) + { + super.populateButtonBar(view, bar); + bar.add(SampleTypeContentsView.getDeriveSamplesButton(getContainer(),null)); + } + }; + view.setShowDetailsColumn(false); + return view; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("All Materials"); + } + } + + /** + * Only shows standard and custom properties, not parent and child samples. Used for indexing + */ + @RequiresPermission(ReadPermission.class) + public class ShowMaterialSimpleAction extends SimpleViewAction + { + protected ExpMaterialImpl _material; + + @Override + public VBox getView(ExpObjectForm form, BindException errors) throws Exception + { + Container c = getContainer(); + _material = ExperimentServiceImpl.get().getExpMaterial(form.getRowId()); + if (_material == null && form.getLsid() != null) + { + _material = ExperimentServiceImpl.get().getExpMaterial(form.getLsid()); + } + if (_material == null) + { + throw new NotFoundException("Could not find a material with RowId " + form.getRowId()); + } + + ensureCorrectContainer(getContainer(), _material, getViewContext()); + + ExpRunImpl run = _material.getRun(); + ExpProtocol sourceProtocol = _material.getSourceProtocol(); + ExpProtocolApplication sourceProtocolApplication = _material.getSourceApplication(); + + DataRegion dr = new DataRegion(); + dr.addColumns(ExperimentServiceImpl.get().getTinfoMaterial().getUserEditableColumns()); + dr.removeColumns("RowId", "RunId", "LastIndexed", "LSID", "SourceApplicationId", "CpasType"); + + //dr.addColumns(extraProps); + dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); + dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); + dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); + dr.addDisplayColumn(new LineageGraphDisplayColumn(_material, run)); + dr.addDisplayColumn(new SampleTypeDisplayColumn(_material)); + + //TODO: Can't yet edit materials uploaded from a material source + dr.setButtonBar(new ButtonBar()); + DetailsView detailsView = new DetailsView(dr, _material.getRowId()); + detailsView.setTitle("Standard Properties"); + detailsView.setFrame(WebPartView.FrameType.PORTAL); + + CustomPropertiesView cpv = new CustomPropertiesView(_material, c, getUser()); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv)); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ExpSampleType sampleType = _material.getSampleType(); + if (sampleType != null) + { + root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); + } + root.addChild("Sample " + _material.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowMaterialAction extends ShowMaterialSimpleAction + { + @Override + public VBox getView(ExpObjectForm form, BindException errors) throws Exception + { + VBox vbox = super.getView(form, errors); + + List materialsToInvestigate = new ArrayList<>(); + final Set successorRuns = new HashSet<>(); + materialsToInvestigate.add(_material); + Set investigatedMaterials = new HashSet<>(); + do + { + // Query for all the next tier of materials at once - issue 45402 + List followupRuns = ExperimentService.get().getRunsUsingMaterials(materialsToInvestigate); + + // Mark this set as investigated and reset for the next cycle + investigatedMaterials.addAll(materialsToInvestigate); + materialsToInvestigate = new ArrayList<>(); + + for (ExpRun r : followupRuns) + { + // Only expand the material outputs of the run if it's our first time visiting it + if (successorRuns.add(r)) + { + materialsToInvestigate.addAll(r.getMaterialOutputs()); + } + } + + if (successorRuns.size() > 1000) + { + // Give up - there may be a cycle or other problematic data + break; + } + + // Cull the ones we've already looked up + materialsToInvestigate.removeAll(investigatedMaterials); + } + while (!materialsToInvestigate.isEmpty()); + + HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); + ExpSampleType st = _material.getSampleType(); + if (st != null && st.getContainer() != null && st.getContainer().hasPermission(getUser(), UpdatePermission.class)) + { + // XXX: ridiculous amount of work to get a update url expression for the sample type's table. + UserSchema samplesSchema = QueryService.get().getUserSchema(getUser(), st.getContainer(), "Samples"); + QueryDefinition queryDef = samplesSchema.getQueryDefForTable(st.getName()); + StringExpression expr = queryDef.urlExpr(QueryAction.updateQueryRow, null); + if (expr != null) + { + // Since we're building a detailsURL outside the context of a "row" need to set the correct + // container context on the generated expr. + ((DetailsURL) expr).setContainerContext(st.getContainer()); + String url = expr.eval(Collections.singletonMap(new FieldKey(null, "RowId"), _material.getRowId())); + updateLinks.append(LinkBuilder.labkeyLink("edit", url)).append(" "); + } + } + + if (getContainer().hasPermission(getUser(), InsertPermission.class)) + { + ActionURL deriveURL = new ActionURL(DeriveSamplesChooseTargetAction.class, getContainer()); + deriveURL.addParameter("rowIds", _material.getRowId()); + if (st != null) + deriveURL.addParameter("targetSampleTypeId", st.getRowId()); + + updateLinks.append(LinkBuilder.labkeyLink("derive samples from this sample", deriveURL)).append(" "); + } + + vbox.addView(new HtmlView(updateLinks)); + + ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); + runListView.setShowRecordSelectors(false); + runListView.getRunTable().setRuns(successorRuns); + runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); + runListView.setAllowableContainerFilterTypes(ContainerFilter.Type.Current, ContainerFilter.Type.CurrentAndSubfolders, ContainerFilter.Type.AllFolders); + runListView.setTitle("Runs associated with this material or a derived material"); + + ParentChildView pv = new ParentChildView(_material, getViewContext()); + vbox.addView(pv); + vbox.addView(runListView); + + return vbox; + } + } + + + // + // DataClass + // + + @RequiresPermission(ReadPermission.class) + public class ListDataClassAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + DataClassWebPart view = new DataClassWebPart(false, getViewContext(), null); + view.setFrame(WebPartView.FrameType.NONE); + view.setErrorMessage(getViewContext().getRequest().getParameter("errorMessage")); + + return view; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + addRootNavTrail(root); + root.addChild("Data Classes"); + } + } + + public static class DataClassForm extends ExpObjectForm + { + private String _name; + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + public ExpDataClassImpl getDataClass(@Nullable Container container) + { + ExpDataClassImpl dataClass = null; + + if (getName() != null) + { + dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getName()); + if (dataClass == null) + throw new NotFoundException("No data class found for name '" + getName() + "'."); + } + else if (getRowId() > 0) + { + dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), getRowId()); + } + + if (dataClass == null) + throw new NotFoundException("No data class found."); + else if (container != null && !container.equals(dataClass.getContainer())) + throw new NotFoundException("Data class is not defined in the given container."); + + return dataClass; + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowDataClassAction extends SimpleViewAction + { + private ExpDataClassImpl _dataClass; + + @Override + public ModelAndView getView(DataClassForm form, BindException errors) + { + _dataClass = form.getDataClass(null); + return new VBox(getDataClassPropertiesView(), getDataClassContentsView(errors)); + } + + private DetailsView getDataClassPropertiesView() + { + ExpSchema expSchema = new ExpSchema(getUser(), _dataClass.getContainer()); + + TableInfo table = ExpSchema.TableType.DataClasses.createTable(expSchema, null, null); + QueryUpdateForm tvf = new QueryUpdateForm(table, getViewContext(), null); + tvf.setPkVal(_dataClass.getRowId()); + DetailsView detailsView = new DetailsView(tvf); + detailsView.setTitle("Data Class Properties"); + + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + boolean inDefinitionContainer = getContainer().equals(_dataClass.getContainer()); + + DomainKind domainKind = _dataClass.getDomain().getDomainKind(); + if (domainKind != null && domainKind.canEditDefinition(getUser(), _dataClass.getDomain())) + { + ActionURL updateURL = new ActionURL(EditDataClassAction.class, _dataClass.getContainer()); + updateURL.addParameter("rowId", _dataClass.getRowId()); + updateURL.addReturnUrl(urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId())); + + if (inDefinitionContainer) + { + ActionButton updateButton = new ActionButton(updateURL, "Edit Data Class", ActionButton.Action.LINK); + updateButton.setDisplayPermission(DesignDataClassPermission.class); + updateButton.setPrimary(true); + bb.add(updateButton); + } + else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) + { + ActionButton updateButton = new ActionButton("Edit Data Class"); + updateButton.setActionType(ActionButton.Action.SCRIPT); + updateButton.setScript("if (window.confirm('This data class is defined in the " + _dataClass.getContainer().getPath() + " folder. Would you still like to edit it?')) { window.location = '" + updateURL + "' }"); + updateButton.setPrimary(true); + bb.add(updateButton); + } + + ActionURL deleteURL = new ActionURL(DeleteDataClassAction.class, _dataClass.getContainer()); + deleteURL.addParameter("singleObjectRowId", _dataClass.getRowId()); + deleteURL.addReturnUrl(ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + ActionButton deleteButton = new ActionButton(deleteURL, "Delete Data Class", ActionButton.Action.LINK); + + if (inDefinitionContainer) + { + deleteButton.setDisplayPermission(DesignDataClassPermission.class); + bb.add(deleteButton); + } + else if (_dataClass.getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) + { + bb.add(deleteButton); + } + } + detailsView.getDataRegion().setButtonBar(bb); + + if (!inDefinitionContainer) + { + ActionURL definitionURL = urlProvider(ExperimentUrls.class).getShowDataClassURL(_dataClass.getContainer(), _dataClass.getRowId()); + LinkBuilder link = LinkBuilder.simpleLink(_dataClass.getContainer().getPath(), definitionURL); + SimpleDisplayColumn definedInCol = new SimpleDisplayColumn(link.toString()); + definedInCol.setCaption("Defined In:"); + detailsView.getDataRegion().addDisplayColumn(definedInCol); + } + + return detailsView; + } + + private QueryView getDataClassContentsView(BindException errors) + { + UserSchema dataClassSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_EXP_DATA); + QuerySettings settings = dataClassSchema.getSettings(getViewContext(), QueryView.DATAREGIONNAME_DEFAULT, _dataClass.getName()); + + return new QueryView(dataClassSchema, settings, errors) + { + @Override + public @NotNull LinkedHashSet getClientDependencies() + { + LinkedHashSet resources = super.getClientDependencies(); + resources.add(ClientDependency.fromPath("Ext4")); + resources.add(ClientDependency.fromPath("dataregion/confirmDelete.js")); + return resources; + } + + @Override + public ActionButton createDeleteButton() + { + ActionButton button = super.createDeleteButton(); + if (button != null) + { + String dependencyText = ExperimentService.get() + .getObjectReferencers() + .stream() + .map(referencer -> referencer.getObjectReferenceDescription(ExpData.class)) + .collect(Collectors.joining(" or ")); + + button.setScript("LABKEY.dataregion.confirmDelete(" + + PageFlowUtil.jsString(getDataRegionName()) + ", " + + PageFlowUtil.jsString(ExpSchema.SCHEMA_EXP_DATA.toString()) + ", " + + PageFlowUtil.jsString(getQueryDef().getName()) + ", " + + "'experiment', 'getDataOperationConfirmationData.api', " + + PageFlowUtil.jsString(getSelectionKey()) + ", " + + "'data object', 'data objects', '" + dependencyText + "', {dataOperation: 'Delete'})"); + button.setRequiresSelection(true); + } + return button; + } + }; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + addRootNavTrail(root); + root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + root.addChild(_dataClass.getName()); + } + } + + @RequiresPermission(DesignDataClassPermission.class) + public class DeleteDataClassAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + super.addNavTrail(root); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + List dataClasses = getDataClasses(deleteForm); + if (!ensureCorrectContainer(dataClasses)) + { + throw new UnauthorizedException(); + } + for (ExpRun run : getRuns(dataClasses)) + { + if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new UnauthorizedException(); + } + } + for (ExpDataClass dataClass : dataClasses) + { + dataClass.delete(getUser(), deleteForm.getUserComment()); + } + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List dataClasses = getDataClasses(deleteForm); + + if (!ensureCorrectContainer(dataClasses)) + { + throw new RedirectException(ExperimentUrlsImpl.get().getDataClassListURL(getContainer(), "To delete a data class, you must be in its folder or project.")); + } + + return new ConfirmDeleteView("Data Class", ShowDataClassAction.class, dataClasses, deleteForm, getRuns(dataClasses)); + } + + private List getDataClasses(DeleteForm deleteForm) + { + List dataClasses = new ArrayList<>(); + for (long rowId : deleteForm.getIds(false)) + { + ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), rowId); + if (dataClass != null) + { + dataClasses.add(dataClass); + } + } + return dataClasses; + } + + private boolean ensureCorrectContainer(List dataClasses) + { + for (ExpDataClass dataClass : dataClasses) + { + Container sourceContainer = dataClass.getContainer(); + if (!sourceContainer.equals(getContainer())) + { + return false; + } + } + return true; + } + + private List getRuns(List dataClasses) + { + if (!dataClasses.isEmpty()) + { + List runArray = ExperimentService.get().getRunsUsingDataClasses(dataClasses); + return ExperimentService.get().runsDeletedWithInput(runArray); + } + else + { + return Collections.emptyList(); + } + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetDataClassPropertiesAction extends ReadOnlyApiAction + { + @Override + public Object execute(DataClassForm form, BindException errors) throws Exception + { + ExpDataClass dataClass = form.getDataClass(getContainer()); + if (dataClass != null) + return new DataClassDomainKindProperties(dataClass); + else + throw new NotFoundException("Data class does not exist in this container for rowId " + form.getRowId() + "."); + } + } + + @RequiresPermission(DesignDataClassPermission.class) + public static class EditDataClassAction extends SimpleViewAction + { + private ExpDataClassImpl _dataClass; + + @Override + public ModelAndView getView(DataClassForm form, BindException errors) + { + boolean create = form.getLSID() == null && form.getRowId() == 0 && form.getName() == null; + if (!create) + _dataClass = form.getDataClass(getContainer()); + + return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("dataClassDesigner")); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + + root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + if (_dataClass == null) + { + root.addChild("Create Data Class"); + } + else + { + root.addChild(_dataClass.getName(), ExperimentUrlsImpl.get().getShowDataClassURL(getContainer(), _dataClass.getRowId())); + root.addChild("Update Data Class"); + } + } + } + + @RequiresPermission(DesignDataClassPermission.class) + public static class CreateDataClassFromTemplateAction extends FormViewAction + { + private ActionURL _successUrl; + private Map _domainTemplates; + + @Override + public void validateCommand(CreateDataClassFromTemplateForm form, Errors errors) + { + String name = null; + _domainTemplates = DomainTemplateGroup.getAllTemplates(getContainer()); + + if (!_domainTemplates.containsKey(form.getDomainTemplate())) + { + errors.reject(ERROR_MSG, "Unknown template selected: " + form.getDomainTemplate()); + } + else + { + DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); + name = template.getTemplateName(); + + // Issue 40230: if template includes sample type option, verify that it exists + if (template.getOptions().containsKey("sampleSet")) + { + String sampleTypeName = template.getOptions().get("sampleSet").toString(); + ExpSampleType sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), sampleTypeName); + if (sampleType == null) + errors.reject(ERROR_MSG, "Unable to find a sample type in this container with name: " + sampleTypeName + "."); + } + } + + if (StringUtils.isBlank(name)) + errors.reject(ERROR_MSG, "DataClass template selection is required."); + else if (ExperimentService.get().getDataClass(getContainer(), getUser(), name) != null) + errors.reject(ERROR_MSG, "DataClass '" + name + "' already exists."); + + } + + @Override + public ModelAndView getView(CreateDataClassFromTemplateForm form, boolean reshow, BindException errors) + { + Set templates = DomainTemplateGroup.getTemplatesForDomainKind(getContainer(), DataClassDomainKind.NAME); + form.setAvailableDomainTemplateNames(templates); + + Set messages = new HashSet<>(); + Map groups = DomainTemplateGroup.getAllGroups(getContainer()); + for (DomainTemplateGroup g : groups.values()) + messages.addAll(g.getErrors()); + form.setXmlParseErrors(messages); + + return new JspView<>("/org/labkey/experiment/createDataClassFromTemplate.jsp", form, errors); + } + + @Override + public boolean handlePost(CreateDataClassFromTemplateForm form, BindException errors) throws Exception + { + DomainTemplate template = _domainTemplates.get(form.getDomainTemplate()); + Domain domain = DomainUtil.createDomain(template, getContainer(), getUser(), form.getName()); + + _successUrl = domain.getDomainKind().urlEditDefinition(domain, getViewContext()); + return true; + } + + @Override + public URLHelper getSuccessURL(CreateDataClassFromTemplateForm form) + { + return _successUrl; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("dataClass"); + root.addChild("Create Data Class from Template"); + } + } + + public static class CreateDataClassFromTemplateForm extends DataClass + { + private String _domainTemplate; + private Set _availableDomainTemplateNames; + private Set _xmlParseErrors; + private final ReturnUrlForm _returnUrlForm = new ReturnUrlForm(); + + public String getDomainTemplate() + { + return _domainTemplate; + } + + public void setDomainTemplate(String domainTemplate) + { + _domainTemplate = domainTemplate; + } + + public Set getAvailableDomainTemplateNames() + { + return _availableDomainTemplateNames; + } + + public void setAvailableDomainTemplateNames(Set availableDomainTemplateNames) + { + _availableDomainTemplateNames = availableDomainTemplateNames; + } + + public Set getXmlParseErrors() + { + return _xmlParseErrors; + } + + public void setXmlParseErrors(Set xmlParseErrors) + { + _xmlParseErrors = xmlParseErrors; + } + + @Nullable + public String getReturnUrl() + { + return _returnUrlForm.getReturnUrl(); + } + + public void setReturnUrl(String s) + { + _returnUrlForm.setReturnUrl(s); + } + } + + public static class ConceptURIForm + { + private String _conceptURI; + + public String getConceptURI() + { + return _conceptURI; + } + + public void setConceptURI(String conceptURI) + { + _conceptURI = conceptURI; + } + } + + @RequiresPermission(AdminPermission.class) + public static class RemoveConceptMappingAction extends MutatingApiAction + { + @Override + public void validateForm(ConceptURIForm form, Errors errors) + { + if (form.getConceptURI() == null || ConceptURIProperties.getLookup(getContainer(), form.getConceptURI()) == null) + errors.reject(ERROR_MSG, "Concept URI not found: " + form.getConceptURI()); + } + + @Override + public Object execute(ConceptURIForm form, BindException errors) + { + ConceptURIProperties.removeLookup(getContainer(), form.getConceptURI()); + return new ApiSimpleResponse("success", true); + } + } + + @RequiresPermission(ReadPermission.class) + public static class RunAttachmentDownloadAction extends BaseDownloadAction + { + @Nullable + @Override + public Pair getAttachment(AttachmentForm form) + { + if (form.getLsid() == null || form.getName() == null) + throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); + + ExpRun run = ExperimentService.get().getExpRun(form.getLsid()); + if (run == null) + throw new NotFoundException("Run not found: " + form.getLsid()); + + if (!run.getContainer().equals(getContainer())) + { + if (run.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new RedirectException(getViewContext().cloneActionURL().setContainer(run.getContainer())); + else + throw new NotFoundException("Run not found"); + } + + AttachmentParent parent = new ExpRunAttachmentParent(run); + return new Pair<>(parent, form.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public static class DataClassAttachmentDownloadAction extends BaseDownloadAction + { + @Nullable + @Override + public Pair getAttachment(AttachmentForm form) + { + if (form.getLsid() == null || form.getName() == null) + throw new NotFoundException("Error: missing required param 'lsid' or 'name'."); + + Lsid lsid = new Lsid(form.getLsid()); + ExpData data = ExperimentServiceImpl.get().getExpData(lsid.toString()); + if (data == null) + throw new NotFoundException("Error: Data object not found for the given LSID: " + lsid); + AttachmentParent parent = new ExpDataClassAttachmentParent(data.getContainer(), lsid); + + return new Pair<>(parent, form.getName()); + } + } + + public static class AttachmentForm extends LsidForm implements BaseDownloadAction.InlineDownloader + { + private String _name; + private boolean _inline = true; + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + @Override + public boolean isInline() + { + return _inline; + } + + public void setInline(boolean inline) + { + _inline = inline; + } + } + + // + // END DataClass actions + // + + public static ActionURL getRunGraphURL(Container c, long runId) + { + return new ActionURL(ShowRunGraphAction.class, c).addParameter("rowId", runId); + } + + + @RequiresPermission(ReadPermission.class) + public class ShowRunGraphAction extends AbstractShowRunAction + { + @Override + protected VBox createLowerView(ExpRunImpl experimentRun, BindException errors) + { + return new VBox( + createRunViewTabs(experimentRun, false, true, true), + new ExperimentRunGraphView(experimentRun, false)); + } + } + + + @RequiresPermission(ReadPermission.class) + public static class DownloadGraphAction extends SimpleViewAction + { + @Override + public ModelAndView getView(ExperimentRunForm form, BindException errors) throws Exception + { + boolean detail = form.isDetail(); + String focus = form.getFocus(); + String focusType = form.getFocusType(); + + ExpRunImpl experimentRun = (ExpRunImpl) form.lookupRun(); + ensureCorrectContainer(getContainer(), experimentRun, getViewContext()); + + ExperimentRunGraph.RunGraphFiles files; + try + { + files = ExperimentRunGraph.generateRunGraph(getViewContext(), experimentRun, detail, focus, focusType); + } + catch (ExperimentException e) + { + PageFlowUtil.streamTextAsImage(getViewContext().getResponse(), "ERROR: " + e.getMessage(), 600, 150, Color.RED); + return null; + } + + try + { + PageFlowUtil.streamFile(getViewContext().getResponse(), new File(files.getImageFile().getAbsolutePath()), false); + } + catch (FileNotFoundException e) + { + getViewContext().getResponse().sendRedirect(getViewContext().getRequest().getContextPath() + "/experiment/ExperimentRunNotFound.gif"); + } + finally + { + files.release(); + } + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + throw new UnsupportedOperationException(); + } + } + + private abstract class AbstractShowRunAction extends SimpleViewAction + { + private ExpRunImpl _experimentRun; + + @Override + public ModelAndView getView(ExperimentRunForm form, BindException errors) + { + _experimentRun = (ExpRunImpl) form.lookupRun(); + ensureCorrectContainer(getContainer(), _experimentRun, getViewContext()); + + VBox vbox = new VBox(); + + JspView detailsView = new JspView<>("/org/labkey/experiment/ExperimentRunDetails.jsp", _experimentRun); + detailsView.setTitle("Standard Properties"); + + var attachmentParent = new ExpRunAttachmentParent(_experimentRun); + var attachments = AttachmentService.get().getAttachments(attachmentParent) + .stream() + .map(att -> Pair.of(att.getName(), new ActionURL(RunAttachmentDownloadAction.class, _experimentRun.getContainer()).addParameter("name", att.getName()).addParameter("lsid", _experimentRun.getLSID()))) + .collect(toList()); + CustomPropertiesView cpv = new CustomPropertiesView(_experimentRun.getLSID(), getContainer(), attachments); + + vbox.addView(new StandardAndCustomPropertiesView(detailsView, cpv)); + + HtmlStringBuilder updateLinks = HtmlStringBuilder.of(); + List runEditors = ExperimentService.get().getRunEditors(); + for (ExpRunEditor editor : runEditors) + { + if (editor.isProtocolEditor(form.lookupRun().getProtocol())) + { + updateLinks.append(LinkBuilder.labkeyLink("edit " + editor.getDisplayName() + " run", editor.getEditUrl(getContainer()).addParameter("rowId", form.getRowId()))); + } + } + + if (!updateLinks.isEmpty()) + { + HtmlView view = new HtmlView(updateLinks); + vbox.addView(view); + } + + VBox lowerView = createLowerView(_experimentRun, errors); + lowerView.setFrame(WebPartView.FrameType.PORTAL); + lowerView.setTitle("Run Details"); + NavTree tree = new NavTree(""); + File runRoot = _experimentRun.getFilePathRoot(); + if (NetworkDrive.exists(runRoot)) + { + if (!runRoot.isDirectory()) + { + runRoot = runRoot.getParentFile(); + } + PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(_experimentRun.getContainer()); + if (pipelineRoot != null) + { + if (pipelineRoot.isUnderRoot(runRoot)) + { + String path = pipelineRoot.relativePath(runRoot); + tree.addChild("View Files", urlProvider(PipelineUrls.class).urlBrowse(_experimentRun.getContainer(), null, path)); + } + } + } + + final String exportFilesFormId = "exportFilesForm"; + NavTree downloadFiles = new NavTree("Download all files"); + downloadFiles.setScript("document.getElementById('" + exportFilesFormId + "').submit();"); + tree.addChild(downloadFiles); + + // CONSIDER: Show modal dialog using ExperimentService.get().createRunExportView() + NavTree exportXarFiles = new NavTree("Export XAR"); + exportXarFiles.setScript("LABKEY.Experiment.exportRuns({runIds: [" + _experimentRun.getRowId() + "] });"); + tree.addChild(exportXarFiles); + + lowerView.setNavMenu(tree); + lowerView.setIsWebPart(false); + + vbox.addView(lowerView); + vbox.addView(new ExperimentRunGroupsView(getUser(), getContainer(), _experimentRun, getViewContext().getActionURL(), errors)); + + DOM.Renderable exportFilesForm = LK.FORM(at( + id, exportFilesFormId, + method, "POST", + action, new ActionURL(ExportRunFilesAction.class, _experimentRun.getContainer())), + INPUT(at(type, "hidden", + name, DataRegionSelection.DATA_REGION_SELECTION_KEY, + value, "ExportSingleRun")), + INPUT(at(type, "hidden", + name, DataRegion.SELECT_CHECKBOX_NAME, + value, _experimentRun.getRowId())), + INPUT(at(type, "hidden", + name, "zipFileName", + value, _experimentRun.getName() + ".zip"))); + + HtmlView hiddenFormView = new HtmlView(exportFilesForm); + vbox.addView(hiddenFormView); + + return vbox; + } + + protected abstract VBox createLowerView(ExpRunImpl experimentRun, BindException errors); + + @Override + public void addNavTrail(NavTree root) + { + root.addChild(_experimentRun.getName()); + } + } + + public static class ToggleRunExperimentMembershipForm + { + private int _runId; + private int _experimentId; + private boolean _included; + + public int getRunId() + { + return _runId; + } + + public void setRunId(int runId) + { + _runId = runId; + } + + public int getExperimentId() + { + return _experimentId; + } + + public void setExperimentId(int experimentId) + { + _experimentId = experimentId; + } + + public boolean isIncluded() + { + return _included; + } + + public void setIncluded(boolean included) + { + _included = included; + } + } + + @RequiresPermission(UpdatePermission.class) + public static class ToggleRunExperimentMembershipAction extends FormHandlerAction + { + @Override + public boolean handlePost(ToggleRunExperimentMembershipForm form, BindException errors) + { + ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); + // Check if the user has permission to update this run + if (run == null || !run.getContainer().hasPermission(getUser(), UpdatePermission.class)) + { + throw new NotFoundException(); + } + + ExpExperiment exp = ExperimentService.get().getExpExperiment(form.getExperimentId()); + if (exp == null) + { + throw new NotFoundException(); + } + // Check if this + if (!ExperimentService.get().getExperiments(run.getContainer(), getUser(), true, false).contains(exp)) + { + throw new NotFoundException(); + } + // Users must have permission to view, but not necessarily update, the container the holds the run group + if (!exp.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new UnauthorizedException(); + } + + if (form.isIncluded()) + { + exp.addRuns(getUser(), run); + } + else + { + exp.removeRun(getUser(), run); + } + + return true; + } + + @Override + public URLHelper getSuccessURL(ToggleRunExperimentMembershipForm form) + { + return null; + } + + @Override + public void validateCommand(ToggleRunExperimentMembershipForm target, Errors errors) + { + } + } + + private HtmlView createRunViewTabs(ExpRun expRun, boolean showGraphSummary, boolean showGraphDetail, boolean showText) + { + return new HtmlView( + TABLE(cl("labkey-tab-strip"), + TR( + createTabSpacer(false), + createTab("Graph Summary View", ExperimentUrlsImpl.get().getRunGraphURL(expRun), !showGraphSummary), + createTabSpacer(false), + createTab("Graph Detail View", ExperimentUrlsImpl.get().getRunGraphDetailURL(expRun), !showGraphDetail), + createTabSpacer(false), + createTab("Text View", ExperimentUrlsImpl.get().getRunTextURL(expRun), !showText), + createTabSpacer(true)))); + } + + private DOM.Renderable createTab(String text, ActionURL url, boolean selected) + { + return TD(cl(selected,"labkey-tab-selected", "labkey-tab"), + A(at(href, url), text)); + } + + private DOM.Renderable createTabSpacer(boolean fullWidth) + { + return TD(cl("labkey-tab-space").at(fullWidth, width, "100%"), + IMG(at(src, AppProps.getInstance().getContextPath() + "/_.gif", width, "5"))); + } + + @RequiresPermission(ReadPermission.class) + public class ShowRunTextAction extends AbstractShowRunAction + { + @Override + protected VBox createLowerView(ExpRunImpl expRun, BindException errors) + { + JspView applicationsView = new JspView<>("/org/labkey/experiment/ProtocolApplications.jsp", expRun); + applicationsView.setFrame(WebPartView.FrameType.TITLE); + applicationsView.setTitle("Protocol Applications"); + + HtmlView toggleView = createRunViewTabs(expRun, true, true, false); + + QuerySettings runDataInputsSettings = new QuerySettings(getViewContext(), "RunDataInputs", DataInputs.name()); + UsageQueryView runDataInputsView = new UsageQueryView("Data Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runDataInputsSettings, errors); + runDataInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); + + QuerySettings runDataOutputsSettings = new QuerySettings(getViewContext(), "RunDataOutputs", DataInputs.name()); + UsageQueryView runDataOutputsView = new UsageQueryView("Data Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runDataOutputsSettings, errors); + runDataOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); + + QuerySettings runMaterialInputsSetting = new QuerySettings(getViewContext(), "RunMaterialInputs", ExpSchema.TableType.MaterialInputs.name()); + UsageQueryView runMaterialInputsView = new UsageQueryView("Material Inputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRun, runMaterialInputsSetting, errors); + runMaterialInputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); + + QuerySettings runMaterialOutputsSettings = new QuerySettings(getViewContext(), "RunMaterialOutputs", ExpSchema.TableType.MaterialInputs.name()); + UsageQueryView runMaterialOutputsView = new UsageQueryView("Material Outputs", getViewContext(), expRun, ExpProtocol.ApplicationType.ExperimentRunOutput, runMaterialOutputsSettings, errors); + runMaterialOutputsView.setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); + + HBox inputsView = new HBox(runDataInputsView, runMaterialInputsView); + HBox registeredInputsView = new HBox(); + + var expService = ExperimentService.get(); + expService.getRunInputsViewProviders().forEach(provider -> + { + var queryView = provider.createView(getViewContext(), expRun, errors); + if (queryView != null) + { + registeredInputsView.addView(queryView); + } + }); + HBox outputsView = new HBox(runDataOutputsView, runMaterialOutputsView); + HBox registeredOutputsView = new HBox(); + expService.getRunOutputsViewProviders().forEach(provider -> + { + var queryView = provider.createView(getViewContext(), expRun, errors); + if (queryView != null) + { + registeredOutputsView.addView(queryView); + } + }); + + var vBox = new VBox(); + vBox.addView(toggleView); + vBox.addView(inputsView); + if (!registeredInputsView.isEmpty()) + vBox.addView(registeredInputsView); + vBox.addView(outputsView); + if (!registeredOutputsView.isEmpty()) + vBox.addView(registeredOutputsView); + vBox.addView(applicationsView); + + return vBox; + } + } + + private static class UsageQueryView extends QueryView + { + private final ExpRun _run; + private final ExpProtocol.ApplicationType _type; + + public UsageQueryView(String title, ViewContext context, ExpRun run, ExpProtocol.ApplicationType type, + QuerySettings settings, BindException errors) + { + super(new ExpSchema(context.getUser(), context.getContainer()), settings, errors); + setTitle(title); + setFrame(FrameType.TITLE); + _run = run; + _type = type; + setShowBorders(true); + setShadeAlternatingRows(true); + setShowExportButtons(false); + setShowPagination(false); + disableContainerFilterSelection(); + } + + @Override + protected TableInfo createTable() + { + String tableName = getSettings().getQueryName(); + ExpInputTable tableInfo = (ExpInputTable) getSchema().getTable(tableName, new ContainerFilter.AllFolders(getUser()), true, true); + tableInfo.setRun(_run, _type); + tableInfo.setLocked(true); + return tableInfo; + } + } + + + public static ActionURL getShowRunGraphDetailURL(Container c, long rowId) + { + ActionURL url = new ActionURL(ShowRunGraphDetailAction.class, c); + url.addParameter("rowId", rowId); + return url; + } + + + @RequiresPermission(ReadPermission.class) + public class ShowRunGraphDetailAction extends AbstractShowRunAction + { + @Override + protected VBox createLowerView(ExpRunImpl run, BindException errors) + { + ExperimentRunGraphView gw = new ExperimentRunGraphView(run, true); + if (null != getViewContext().getActionURL().getParameter("focus")) + gw.setFocus(getViewContext().getActionURL().getParameter("focus")); + if (null != getViewContext().getActionURL().getParameter("focusType")) + gw.setFocusType(getViewContext().getActionURL().getParameter("focusType")); + return new VBox(createRunViewTabs(run, true, false, true), gw); + } + } + + private abstract class AbstractDataAction extends SimpleViewAction + { + protected ExpDataImpl _data; + + @Override + public final ModelAndView getView(DataForm form, BindException errors) throws Exception + { + _data = form.lookupData(); + if (_data == null) + { + throw new NotFoundException("Could not find a data with RowId " + form.getRowId()); + } + + ensureCorrectContainer(getContainer(), _data, getViewContext()); + return getDataView(form, errors); + } + + protected abstract ModelAndView getDataView(DataForm form, BindException errors) throws Exception; + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Data " + _data.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowDataAction extends AbstractDataAction + { + @Override + public ModelAndView getDataView(DataForm form, BindException errors) + { + ExpRun run = _data.getRun(); + ExpProtocol sourceProtocol = _data.getSourceProtocol(); + ExpProtocolApplication sourceProtocolApplication = _data.getSourceApplication(); + ExpDataClass dataClass = _data.getDataClass(getUser()); + + ExpSchema schema = new ExpSchema(getUser(), getContainer()); + TableInfo table; + long pk; + if (dataClass == null) + { + table = schema.getDatasTable(); + pk = _data.getRowId(); + } + else + { + table = schema.getSchema(ExpSchema.NestedSchemas.data).getTable(dataClass.getName()); + pk = new TableSelector(table, Collections.singleton("rowId"), new SimpleFilter(FieldKey.fromParts("lsid"), _data.getLSID()), null).getObject(Integer.class); + } + + DataRegion dr = new DataRegion(); + dr.setTable(table); + List cols = table.getColumns().stream().filter(ColumnInfo::isShownInDetailsView).collect(toList()); + dr.addColumns(cols); + dr.removeColumns("RowId", "Created", "CreatedBy", "Modified", "ModifiedBy", "DataFileUrl", "Run", "LSID", "CpasType", "SourceApplicationId", "Folder", "Generated"); + dr.addDisplayColumn(new ExperimentRunDisplayColumn(run, "Source Experiment Run")); + dr.addDisplayColumn(new ProtocolDisplayColumn(sourceProtocol, "Source Protocol")); + dr.addDisplayColumn(new ProtocolApplicationDisplayColumn(sourceProtocolApplication, "Source Protocol Application")); + dr.addDisplayColumn(new LineageGraphDisplayColumn(_data, run)); + DetailsView detailsView = new DetailsView(dr, pk); + detailsView.setTitle("Standard Properties"); + detailsView.setFrame(WebPartView.FrameType.PORTAL); + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + + ExperimentDataHandler handler = _data.findDataHandler(); + ActionURL viewDataURL = handler == null ? null : handler.getContentURL(_data); + if (viewDataURL != null) + { + bb.add(new ActionButton("View data", viewDataURL)); + } + + if (_data.isPathAccessible()) + { + bb.add(new ActionButton("View file", ExperimentUrlsImpl.get().getShowFileURL(_data, true))); + bb.add(new ActionButton("Download file", ExperimentUrlsImpl.get().getShowFileURL(_data, false))); + + if (getContainer().hasPermission(getUser(), InsertPermission.class)) + { + String relativePath = null; + PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); + if (root != null) + { + Path rootFile = root.getRootNioPath(); + Path dataFile = _data.getFilePath(); + if (dataFile != null) + { + Path pathRelative; + try + { + pathRelative = rootFile.relativize(dataFile); + if (null != pathRelative) + relativePath = pathRelative.toString(); + } + catch (IllegalArgumentException e) + { + // dataFile not relative to root + } + } + } + ActionURL browseURL = urlProvider(PipelineUrls.class).urlBrowse(getContainer(), getViewContext().getActionURL(), relativePath); + bb.add(new ActionButton("Browse in pipeline", browseURL)); + } + } + + // add links to any other exp.data that share the same dataFileUrl path + var altDataList = ExperimentService.get().getAllExpDataByURL(_data.getDataFileUrl(), getContainer()); + altDataList.removeIf(_data::equals); + if (!altDataList.isEmpty()) + { + MenuButton menu = new MenuButton("Alternate Data"); + for (ExpData altData : altDataList) + { + ExpRun altDataRun = altData.getRun(); + StringBuilder sb = new StringBuilder(altData.getName()); + if (altDataRun != null) + sb.append(" created by run '").append(altDataRun.getName()).append("' (").append(altDataRun.getProtocol().getName()).append(")"); + menu.addMenuItem(sb.toString(), altData.detailsURL()); + } + bb.add(menu); + } + + dr.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP); + dr.setButtonBar(bb); + + CustomPropertiesView cpv = new CustomPropertiesView(_data.getLSID(), getContainer()); + HBox hbox = new StandardAndCustomPropertiesView(detailsView, cpv); + + VBox vbox = new VBox(hbox); + + ParentChildView pv = new ParentChildView(_data, getViewContext()); + vbox.addView(pv); + + ExperimentRunListView runListView = ExperimentRunListView.createView(getViewContext(), ExperimentRunType.ALL_RUNS_TYPE, true); + runListView.getRunTable().setInputData(_data); + runListView.getRunTable().setContainerFilter(new ContainerFilter.AllFolders(getUser())); + runListView.getRunTable().setLocked(true); + runListView.setTitle("Runs using this data as an input"); + vbox.addView(runListView); + + if (_data.isInlineImage() && _data.isFileOnDisk()) + { + ActionURL showFileURL = new ActionURL(ShowFileAction.class, getContainer()).addParameter("rowId", _data.getRowId()); + HtmlView imageView = new HtmlView(IMG(at(src, showFileURL))); + return new VBox(vbox, imageView); + } + return vbox; + } + } + + @RequiresPermission(AdminPermission.class) + public static class CheckDataFileAction extends MutatingApiAction + { + private ExpDataImpl _data; + + @Override + public void validateForm(DataFileForm form, Errors errors) + { + _data = form.lookupData(); + if (_data == null) + { + errors.reject(ERROR_MSG, "No ExpData found for id: " + form.getRowId()); + } + } + + @Override + public ApiResponse execute(DataFileForm form, BindException errors) + { + File dataFile = _data.getFile(); + Container dataContainer = _data.getContainer(); + boolean fileExists = _data.isFileOnDisk(); + boolean fileExistsAtCurrent = false; + File newDataFile = null; + + ApiSimpleResponse response = new ApiSimpleResponse(); + response.put("dataFileUrl", _data.getDataFileUrl()); + response.put("fileExists", fileExists); + response.put("containerPath", dataContainer.getPath()); + + if (!fileExists) + { + PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(dataContainer); + if (pipelineRoot != null && pipelineRoot.isValid() && dataFile != null) + { + newDataFile = pipelineRoot.resolvePath("/" + AssayFileWriter.DIR_NAME + "/" + dataFile.getName()); + fileExistsAtCurrent = NetworkDrive.exists(newDataFile); + response.put("fileExistsAtCurrent", fileExistsAtCurrent); + } + } + + // if the current dataFileUrl does not exist on disk and we have the file at the current + // pipeline root /assaydata dir, fix the dataFileUrl value + if (form.isAttemptFilePathFix()) + { + if (fileExistsAtCurrent) + { + ExpDataFileListener fileListener = new ExpDataFileListener(); + fileListener.fileMoved(dataFile, newDataFile, getUser(), dataContainer); + response.put("filePathFixed", true); + + // update the ExpData object so that we can get the new dataFileUrl + _data = form.lookupData(); + response.put("newDataFileUrl", _data.getDataFileUrl()); + } + else + { + response.put("filePathFixed", false); + } + } + + response.put("success", true); + return response; + } + } + + public static class DataFileForm extends DataForm + { + private boolean _attemptFilePathFix; + + public boolean isAttemptFilePathFix() + { + return _attemptFilePathFix; + } + + public void setAttemptFilePathFix(boolean attemptFilePathFix) + { + _attemptFilePathFix = attemptFilePathFix; + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowFileAction extends AbstractDataAction + { + @Override + protected ModelAndView getDataView(DataForm form, BindException errors) throws IOException + { + if (!_data.isPathAccessible()) + { + throw new NotFoundException("Data file " + _data.getDataFileUrl() + " does not exist on disk"); + } + + PipeRoot root = PipelineService.get().findPipelineRoot(getContainer()); + if (root != null && !root.isUnderRoot(_data.getFilePath())) + { + // Issue 35649: ImmPort module "publish" creates exp.data object in this container for paths that originate in a different container + FileContentService fileSvc = FileContentService.get(); + if (fileSvc == null) + throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); + + List containers = fileSvc.getContainersForFilePath(_data.getFilePath()); + if (containers.isEmpty() || containers.stream().noneMatch(c -> c.hasPermission(getUser(), ReadPermission.class))) + throw new UnauthorizedException("Data file is not under the pipeline root for this folder"); + } + + //Issues 25667 and 31152 + if (form.isInline()) + { + ExperimentDataHandler h = _data.findDataHandler(); + if (h != null) + { + URLHelper url = h.getShowFileURL(_data); + if (url != null) + { + throw new RedirectException(url, false); + } + } + } + + try + { + Path realContent = _data.getFilePath(); + if (null == realContent) + throw new IllegalStateException("Path not found."); + + boolean inline = _data.isInlineImage() || form.isInline() || "inlineImage".equalsIgnoreCase(form.getFormat()); + if (_data.isInlineImage() && form.getMaxDimension() != null) + { + try (InputStream inputStream = Files.newInputStream(realContent)) + { + BufferedImage image = ImageIO.read(inputStream); + // If image, create a thumbnail, otherwise fall through as a regular download attempt + if (image != null) + { + int imageMax = Math.max(image.getHeight(), image.getWidth()); + if (imageMax > form.getMaxDimension().intValue()) + { + double scale = (double) form.getMaxDimension().intValue() / (double) imageMax; + ByteArrayOutputStream bOut = new ByteArrayOutputStream(); + ImageUtil.resizeImage(image, bOut, scale, 1); + PageFlowUtil.streamFileBytes(getViewContext().getResponse(), FileUtil.getFileName(realContent) + ".png", bOut.toByteArray(), !inline); + return null; + } + } + } + } + + boolean extended = "jsonTSVExtended".equalsIgnoreCase(form.getFormat()); + boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(form.getFormat()); + if ("jsonTSV".equalsIgnoreCase(form.getFormat()) || extended || ignoreTypes) + { + if (!FileUtil.hasCloudScheme(realContent)) // TODO: handle streaming from S3 to JSON + streamToJSON(FileSystemLike.wrapFile(realContent), form.getFormat(), -1, null); + return null; + } + + try (InputStream inputStream = Files.newInputStream(realContent)) + { + PageFlowUtil.streamFile(getViewContext().getResponse(), Collections.emptyMap(), FileUtil.getFileName(realContent), inputStream, !inline); + } + } + catch (IOException e) + { + try + { + // Try to write the exception back to the caller if we haven't already flushed the buffer + ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse()); + writer.writeResponse(e); + } + catch (IllegalStateException ise) + { + // Most likely that a disconnected client caused the IOException writing back the response + } + } + + return null; + } + } + + + public static class ParseForm + { + String format = "jsonTSV"; + int maxRows = -1; + + public String getFormat() + { + return format; + } + + public void setFormat(String format) + { + this.format = format; + } + + public int getMaxRows() + { + return maxRows; + } + + public void setMaxRows(int maxRow) + { + this.maxRows = maxRow; + } + } + + @RequiresNoPermission + public class ParseFileAction extends MutatingApiAction + { + @Override + public Object execute(ParseForm form, BindException errors) throws Exception + { + if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) + throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); + + MultipartFile formFile = getFileMap().get("file"); + if (formFile == null) + { + return true; + } + + FileLike tempFile = null; + try + { + tempFile = FileUtil.createTempFileLike("parse", formFile.getOriginalFilename()); + FileUtil.copyData(formFile.getInputStream(), tempFile.openOutputStream()); + streamToJSON(tempFile, form.getFormat(), form.getMaxRows(), formFile.getOriginalFilename()); + } + finally + { + if (null != tempFile) + tempFile.delete(); + } + return null; + } + } + + + // SampleTypeTest + private void streamToJSON(FileLike realContent, String format, int maxRow, String originalFileName) throws IOException + { + String lowerCaseFileName = realContent.getName().toLowerCase(); + boolean extended = "jsonTSVExtended".equalsIgnoreCase(format); + boolean ignoreTypes = "jsonTSVIgnoreTypes".equalsIgnoreCase(format); + + JSONArray sheetsArray; + if (lowerCaseFileName.endsWith(".xls") || lowerCaseFileName.endsWith(".xlsx")) + { + try (InputStream in = realContent.openInputStream()) + { + sheetsArray = ExcelFactory.convertExcelToJSON(in, extended, maxRow); + } + } + else + { + DataLoaderFactory dlf = DataLoader.get().findFactory(realContent, null); + if (null == dlf) + { + throw new ApiUsageException("Unable to parse file " + realContent + ", it is likely of an unsupported file type"); + } + + try (InputStream in = realContent.openInputStream(); + DataLoader tabLoader = dlf.createLoader(in, true)) + { + tabLoader.setScanAheadLineCount(5000); + ColumnDescriptor[] cols = tabLoader.getColumns(); + + if (ignoreTypes) + for (ColumnDescriptor col : cols) + col.clazz = String.class; + + JSONArray rowsArray = new JSONArray(); + JSONArray headerArray = new JSONArray(); + for (ColumnDescriptor col : cols) + { + if (extended) + { + JSONObject valueObject = new JSONObject(); + valueObject.put("value", col.name); + headerArray.put(valueObject); + } + else + { + headerArray.put(col.name); + } + } + rowsArray.put(headerArray); + for (Map rowMap : tabLoader) + { + // headers count as a row to be consistent + if (maxRow > -1 && maxRow <= rowsArray.length() + 1) + break; + + JSONArray rowArray = new JSONArray(); + for (ColumnDescriptor col : cols) + { + Object value = rowMap.get(col.name); + if (extended) + { + JSONObject valueObject = new JSONObject(); + valueObject.put("value", value); + rowArray.put(valueObject); + } + else + { + rowArray.put(value); + } + } + rowsArray.put(rowArray); + } + + JSONObject sheetJSON = new JSONObject(); + sheetJSON.put("name", "flat"); + sheetJSON.put("data", rowsArray); + sheetsArray = new JSONArray(); + sheetsArray.put(sheetJSON); + } + } + + try (ApiJsonWriter writer = new ApiJsonWriter(getViewContext().getResponse())) + { + JSONObject workbookJSON = new JSONObject(); + workbookJSON.put("fileName", realContent.getName()); + workbookJSON.put("sheets", sheetsArray); + if (originalFileName != null) + workbookJSON.put("originalFileName", originalFileName); + writer.writeResponse(new ApiSimpleResponse(workbookJSON)); + } + } + + + public static class ConvertArraysToExcelForm + { + private String _json; + + public String getJson() + { + return _json; + } + + public void setJson(String json) + { + _json = json; + } + } + + @RequiresPermission(ReadPermission.class) + public static class ConvertArraysToExcelAction extends ExportAction + { + @Override + public void validate(ConvertArraysToExcelForm form, BindException errors) + { + if (form.getJson() == null) + { + errors.reject(ERROR_MSG, "Unable to convert to Excel - no spreadsheet data given"); + } + } + + @Override + public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception + { + try + { + JSONObject rootObject; + JSONArray sheetsArray; + if (form.getJson() == null || form.getJson().trim().isEmpty()) + { + // Create JSON so that we return an empty file + rootObject = new JSONObject(); + sheetsArray = new JSONArray(); + JSONObject sheetObject = new JSONObject(); + sheetsArray.put(sheetObject); + } + else + { + rootObject = new JSONObject(form.getJson()); + sheetsArray = rootObject.getJSONArray("sheets"); + } + String filename = rootObject.has("fileName") ? rootObject.getString("fileName") : "ExcelExport.xls"; + ExcelWriter.ExcelDocumentType docType = filename.toLowerCase().endsWith(".xlsx") ? ExcelWriter.ExcelDocumentType.xlsx : ExcelWriter.ExcelDocumentType.xls; + + try (Workbook workbook = ExcelFactory.createFromArray(sheetsArray, docType)) + { + response.setContentType(docType.getMimeType()); + ResponseHelper.setContentDisposition(response, ResponseHelper.ContentDispositionType.attachment, filename); + ResponseHelper.setPrivate(response); + workbook.write(response.getOutputStream()); + + JSONObject qInfo = rootObject.has("queryinfo") ? rootObject.getJSONObject("queryinfo") : null; + if (qInfo != null) + { + QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), + qInfo.getString("query"), getViewContext().getActionURL(), + rootObject.getString("auditMessage") + filename, + null); + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asExcel"); + } + } + } + catch (JSONException | ClassCastException e) + { + // We can get a ClassCastException if we expect an array and get a simple String, for example + ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to Excel - invalid input", e, false, false); + } + } + } + + @RequiresPermission(ReadPermission.class) + public static class ConvertArraysToTableAction extends ExportAction + { + @Override + public void validate(ConvertArraysToExcelForm form, BindException errors) + { + if (form.getJson() == null) + { + errors.reject(ERROR_MSG, "Unable to convert to table - no data given"); + } + } + + @Override + public void export(ConvertArraysToExcelForm form, HttpServletResponse response, BindException errors) throws Exception + { + try + { + JSONObject rootObject; + JSONArray rowsArray; + if (form.getJson() == null || form.getJson().trim().isEmpty()) + { + // Create JSON so that we return an empty file + rootObject = new JSONObject(); + rowsArray = new JSONArray(); + } + else + { + rootObject = new JSONObject(form.getJson()); + rowsArray = rootObject.getJSONArray("rows"); + } + + TSVWriter.DELIM delimType = (!rootObject.isNull("delim") ? TSVWriter.DELIM.valueOf(rootObject.getString("delim")) : TSVWriter.DELIM.TAB); + TSVWriter.QUOTE quoteType = (!rootObject.isNull("quoteChar") ? TSVWriter.QUOTE.valueOf(rootObject.getString("quoteChar")) : TSVWriter.QUOTE.NONE); + String filenamePrefix = (!rootObject.isNull("fileNamePrefix") ? rootObject.getString("fileNamePrefix") : "Export"); + String filename = filenamePrefix + "." + delimType.extension; + String newlineChar = !rootObject.isNull("newlineChar") ? rootObject.getString("newlineChar") : "\n"; + + response.setCharacterEncoding(StringUtilsLabKey.DEFAULT_CHARSET.name()); + + try(var tsvWriter = new TSVJSONWriter(filenamePrefix, rowsArray)) + { + tsvWriter.setRowSeparator(newlineChar); + tsvWriter.setDelimiterCharacter(delimType); + tsvWriter.setQuoteCharacter(quoteType); + tsvWriter.write(response); + } + + JSONObject qInfo = rootObject.optJSONObject("queryinfo"); + if (qInfo != null) + { + QueryService.get().addAuditEvent(getUser(), getContainer(), qInfo.getString("schema"), qInfo.getString("query"), + getViewContext().getActionURL(), + rootObject.getString("auditMessage") + filename, + rowsArray.length()); + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "convertTable", "asDelimited"); + } + } + catch (JSONException e) + { + ExceptionUtil.renderErrorView(getViewContext(), getPageConfig(), ErrorRenderer.ErrorType.notFound, HttpServletResponse.SC_BAD_REQUEST, "Failed to convert to table - invalid input", e, false, false); + } + } + } + + + public static class ConvertHtmlToExcelForm + { + private String _baseUrl; + private String _htmlFragment; + private String _name = "workbook.xls"; + + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + public String getBaseUrl() + { + return _baseUrl; + } + + public void setBaseUrl(String baseUrl) + { + _baseUrl = baseUrl; + } + + public String getHtmlFragment() + { + return _htmlFragment; + } + + public void setHtmlFragment(String htmlFragment) + { + _htmlFragment = htmlFragment; + } + } + + + @RequiresPermission(ReadPermission.class) + public static class ConvertHtmlToExcelAction extends FormViewAction + { + String _responseHtml = null; + + @Override + public void validateCommand(ConvertHtmlToExcelForm target, Errors errors) + { + } + + @Override + public ModelAndView getView(ConvertHtmlToExcelForm form, boolean reshow, BindException errors) + { + String html = + "

" + + "" + + new CsrfInput(getViewContext()) + + "
"; + return HtmlView.unsafe(html); + } + + @Override + public boolean handlePost(ConvertHtmlToExcelForm form, BindException errors) + { + ActionURL url = getViewContext().getActionURL(); + String base = url.getBaseServerURI(); + if (!base.endsWith("/")) base += "/"; + + String baseTag = ""; + SafeToRender css = PageFlowUtil.getStylesheetIncludes(getContainer()); + String htmlFragment = StringUtils.trimToEmpty(form.getHtmlFragment()); + String html = "" + baseTag + css + "" + htmlFragment + ""; + + // UNDONE: strip script + List tidyErrors = new ArrayList<>(); + String tidy = JSoupUtil.tidyHTML(html, false, tidyErrors); + + if (!tidyErrors.isEmpty()) + { + for (String err : tidyErrors) + { + errors.reject(ERROR_MSG, err); + } + return false; + } + + _responseHtml = tidy; + return true; + } + + @Override + public ModelAndView getSuccessView(ConvertHtmlToExcelForm form) + { + ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, form.getName()); + getPageConfig().setTemplate(PageConfig.Template.None); + HtmlView v = HtmlView.unsafe(_responseHtml); + v.setContentType("application/vnd.ms-excel"); + v.setFrame(WebPartView.FrameType.NONE); + return v; + } + + @Override + public URLHelper getSuccessURL(ConvertHtmlToExcelForm convertHtmlToExcelForm) + { + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + } + } + + + public static ActionURL getShowApplicationURL(Container c, long rowId) + { + ActionURL url = new ActionURL(ShowApplicationAction.class, c); + url.addParameter("rowId", rowId); + + return url; + } + + + @RequiresPermission(ReadPermission.class) + public class ShowApplicationAction extends SimpleViewAction + { + private ExpProtocolApplicationImpl _app; + private ExpRun _run; + + @Override + public ModelAndView getView(ExpObjectForm form, BindException errors) + { + _app = ExperimentServiceImpl.get().getExpProtocolApplication(form.getRowId()); + if (_app == null) + { + throw new NotFoundException("Could not find Protocol Application"); + } + _run = _app.getRun(); + if (_run == null) + { + throw new NotFoundException("No experiment run associated with Protocol Application"); + } + ensureCorrectContainer(getContainer(), _app, getViewContext()); + + ExpProtocol protocol = _app.getProtocol(); + + DataRegion dr = new DataRegion(); + dr.addColumns(ExperimentServiceImpl.get().getTinfoProtocolApplication().getUserEditableColumns()); + DetailsView detailsView = new DetailsView(dr, form.getRowId()); + dr.removeColumns("RunId", "ProtocolLSID", "RowId", "LSID"); + dr.addDisplayColumn(new ExperimentRunDisplayColumn(_run)); + dr.addDisplayColumn(new ProtocolDisplayColumn(protocol)); + dr.addDisplayColumn(new LineageGraphDisplayColumn(_app, _run)); + detailsView.setTitle("Protocol Application"); + + Container c = getContainer(); + ApplicationOutputGrid outMGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoMaterial()); + ApplicationOutputGrid outDGrid = new ApplicationOutputGrid(c, _app.getRowId(), ExperimentServiceImpl.get().getTinfoData()); + Map map = new HashMap<>(); + for (ProtocolApplicationParameter param : ExperimentService.get().getProtocolApplicationParameters(_app.getRowId())) + { + map.put(param.getOntologyEntryURI(), param); + } + + JspView> paramsView = new JspView<>("/org/labkey/experiment/Parameters.jsp", map); + paramsView.setTitle("Protocol Application Parameters"); + CustomPropertiesView cpv = new CustomPropertiesView(_app.getLSID(), c); + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), paramsView, outMGrid, outDGrid); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Experiment Run", ExperimentUrlsImpl.get().getRunGraphDetailURL(_run)); + root.addChild("Protocol Application " + _app.getName()); + } + } + + @RequiresPermission(ReadPermission.class) + public class ShowProtocolGridAction extends SimpleViewAction + { + @Override + public ModelAndView getView(Object o, BindException errors) + { + return new ProtocolWebPart(false, getViewContext()); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Protocols"); + } + } + + @RequiresPermission(ReadPermission.class) + public class ProtocolDetailsAction extends SimpleViewAction + { + private ExpProtocolImpl _protocol; + + @Override + public ModelAndView getView(ExpObjectForm form, BindException errors) + { + _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getRowId()); + if (_protocol == null) + { + _protocol = ExperimentServiceImpl.get().getExpProtocol(form.getLSID()); + } + + if (_protocol == null) + { + throw new NotFoundException("Unable to find a matching protocol"); + } + ensureCorrectContainer(getContainer(), _protocol, getViewContext()); + + JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", _protocol); + detailsView.setTitle("Standard Properties"); + + CustomPropertiesView cpv = new CustomPropertiesView(_protocol.getLSID(), getContainer()); + ProtocolParametersView parametersView = new ProtocolParametersView(_protocol); + + VBox protocolDetails = new VBox(); + protocolDetails.setFrame(WebPartView.FrameType.PORTAL); + protocolDetails.setTitle("Protocol Details"); + protocolDetails.addView(new ProtocolInputOutputsView(_protocol, errors)); + + JspView stepsView = new JspView<>("/org/labkey/experiment/ProtocolSteps.jsp", _protocol); + stepsView.setTitle("Protocol Steps"); + stepsView.setFrame(WebPartView.FrameType.TITLE); + protocolDetails.addView(stepsView); + + ExpSchema schema = new ExpSchema(getUser(), getContainer()); + ExperimentRunListView runView = new ExperimentRunListView(schema, ExperimentRunListView.getRunListQuerySettings(schema, getViewContext(), ExpSchema.TableType.Runs.name(), true), ExperimentRunType.ALL_RUNS_TYPE) + { + @Override + public DataView createDataView() + { + DataView result = super.createDataView(); + result.getRenderContext().setBaseFilter(new SimpleFilter(FieldKey.fromParts("Protocol", "LSID"), _protocol.getLSID())); + return result; + } + }; + + runView.setTitle("Runs Using This Protocol"); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails, runView); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); + root.addChild("Protocol: " + _protocol.getName()); + } + } + + public class ProtocolInputOutputsView extends VBox + { + ProtocolInputOutputsView(ExpProtocol protocol, Errors errors) + { + HBox inputsView = new HBox(); + addView(inputsView); + + HBox outputsView = new HBox(); + addView(outputsView); + + UserSchema expSchema = QueryService.get().getUserSchema(getUser(), getContainer(), ExpSchema.SCHEMA_NAME); + + class ProtocolInputGrid extends QueryView + { + public ProtocolInputGrid(String title, QuerySettings settings, @Nullable Errors errors) + { + super(expSchema, settings, errors); + + setFrame(FrameType.TITLE); + setTitle(title); + setButtonBarPosition(DataRegion.ButtonBarPosition.NONE); + setShowBorders(true); + setShadeAlternatingRows(true); + setShowExportButtons(false); + setShowPagination(false); + disableContainerFilterSelection(); + } + } + + // INPUTS + + QuerySettings materialInputsSettings = expSchema.getSettings("mpi", ExpSchema.TableType.MaterialProtocolInputs.toString()); + materialInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + materialInputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) + )); + QueryView materialInputsView = new ProtocolInputGrid("Material Inputs", materialInputsSettings, errors); + inputsView.addView(materialInputsView); + + QuerySettings dataInputsSettings = expSchema.getSettings("dpi", ExpSchema.TableType.DataProtocolInputs.toString()); + dataInputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + dataInputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) + )); + QueryView dataInputsView = new ProtocolInputGrid("Data Inputs", dataInputsSettings, errors); + inputsView.addView(dataInputsView); + + // OUTPUTS + + QuerySettings materialOutputsSettings = expSchema.getSettings("mpo", ExpSchema.TableType.MaterialProtocolInputs.toString()); + materialOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + materialOutputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpMaterialProtocolInputTable.Column.SampleSet.toString()) + )); + QueryView materialOutputsView = new ProtocolInputGrid("Material Outputs", materialOutputsSettings, errors); + outputsView.addView(materialOutputsView); + + QuerySettings dataOutputsSettings = expSchema.getSettings("dpo", ExpSchema.TableType.DataProtocolInputs.toString()); + dataOutputsSettings.getBaseFilter().addCondition(FieldKey.fromParts(ExpDataProtocolInputTable.Column.Protocol.toString()), protocol.getRowId()); + dataOutputsSettings.setFieldKeys(Arrays.asList( + FieldKey.fromParts(ExpDataProtocolInputTable.Column.Name.toString()), + FieldKey.fromParts(ExpDataProtocolInputTable.Column.DataClass.toString()) + )); + QueryView dataOutputsView = new ProtocolInputGrid("Data Outputs", dataOutputsSettings, errors); + outputsView.addView(dataOutputsView); + } + } + + + @RequiresPermission(ReadPermission.class) + public class ProtocolPredecessorsAction extends SimpleViewAction + { + private ExpProtocol _parentProtocol; + private ProtocolActionStepDetail _actionStep; + + @Override + public ModelAndView getView(Object o, BindException errors) + { + ActionURL url = getViewContext().getActionURL(); + + String parentProtocolLSID = url.getParameter("ParentLSID"); + int actionSequence; + try + { + actionSequence = Integer.parseInt(url.getParameter("Sequence")); + } + catch (NumberFormatException e) + { + throw new NotFoundException("Could not find SequenceId " + url.getParameter("Sequence")); + } + + _parentProtocol = ExperimentService.get().getExpProtocol(parentProtocolLSID); + if (_parentProtocol == null) + { + throw new NotFoundException("Unable to find a matching protocol"); + } + + ensureCorrectContainer(getContainer(), _parentProtocol, getViewContext()); + + _actionStep = ExperimentServiceImpl.get().getProtocolActionStepDetail(parentProtocolLSID, actionSequence); + + if (_actionStep == null) + { + throw new NotFoundException("Unable to find a matching protocol action step"); + } + + ExpProtocol childProtocol = ExperimentService.get().getExpProtocol(_actionStep.getChildProtocolLSID()); + + JspView detailsView = new JspView<>("/org/labkey/experiment/ProtocolDetails.jsp", childProtocol); + detailsView.setTitle("Standard Properties"); + + CustomPropertiesView cpv = new CustomPropertiesView(childProtocol.getLSID(), getContainer()); + + ProtocolParametersView parametersView = new ProtocolParametersView(childProtocol); + + VBox protocolDetails = new VBox(); + protocolDetails.setFrame(WebPartView.FrameType.PORTAL); + protocolDetails.setTitle("Protocol Details"); + protocolDetails.addView(new ProtocolInputOutputsView(childProtocol, errors)); + protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "PredecessorChildLSID", "PredecessorSequence", "ActionSequence", "Protocol Predecessors")); + protocolDetails.addView(new ProtocolSuccessorPredecessorView(parentProtocolLSID, actionSequence, getContainer(), "ChildProtocolLSID", "ActionSequence", "PredecessorSequence", "Protocol Successors")); + + return new VBox(new StandardAndCustomPropertiesView(detailsView, cpv), parametersView, protocolDetails); + } + + @Override + public void addNavTrail(NavTree root) + { + addRootNavTrail(root); + root.addChild("Protocols", ExperimentUrlsImpl.get().getProtocolGridURL(getContainer())); + root.addChild("Parent Protocol '" + _parentProtocol.getName() + "'", ExperimentUrlsImpl.get().getProtocolDetailsURL(_parentProtocol)); + root.addChild("Protocol Step: " + _actionStep.getName()); + } + } + + public static class DataForm + { + private boolean _inline; + private long _rowId; + private String _lsid; + private Integer _maxDimension; + private String _format; + + public boolean isInline() + { + return _inline; + } + + public void setInline(boolean inline) + { + _inline = inline; + } + + public long getRowId() + { + return _rowId; + } + + public void setRowId(long rowId) + { + _rowId = rowId; + } + + public String getLsid() + { + return _lsid; + } + + public void setLsid(String lsid) + { + _lsid = lsid; + } + + public ExpDataImpl lookupData() + { + ExpDataImpl result = ExperimentServiceImpl.get().getExpData(getRowId()); + if (result == null && getLsid() != null) + { + result = ExperimentServiceImpl.get().getExpData(getLsid()); + } + return result; + } + + public Integer getMaxDimension() + { + return _maxDimension; + } + + public void setMaxDimension(Integer maxDimension) + { + _maxDimension = maxDimension; + } + + public String getFormat() + { + return _format; + } + + public void setFormat(String format) + { + _format = format; + } + } + + public static class ExpObjectForm extends QueryViewAction.QueryExportForm + { + private long _rowId; + private String _lsid; + + public String getLsid() + { + return _lsid; + } + + public void setLsid(String lsid) + { + _lsid = lsid; + } + + public String getLSID() + { + return getLsid(); + } + + public void setLSID(String lsid) + { + setLsid(lsid); + } + + public long getRowId() + { + return _rowId; + } + + public void setRowId(long rowId) + { + _rowId = rowId; + } + } + + @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) + public class DeleteSelectedExpRunsAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + // UNDONE: Need help topic on Runs + setHelpTopic("experiment"); + super.addNavTrail(root); + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List runs = new ArrayList<>(); + + Map idToRunMap = new LongHashMap<>(); + for (long runId : deleteForm.getIds(false)) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run != null) + { + if (!run.canDelete(getUser())) + throw new UnauthorizedException("You do not have permission to delete " + + (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") + + " in " + run.getContainer()); + + runs.add(run); + idToRunMap.put(run.getRowId(), run); + } + } + + Map referencedItems = new LongHashMap<>(); + List referenceDescriptions = new ArrayList<>(); + AssayService assayService = AssayService.get(); + if (!idToRunMap.isEmpty() && assayService != null ) + { + // using the first run as a representative, since all interactions here are (I believe) using the same protocol. + ExpProtocol protocol = runs.get(0).getProtocol(); + AssayProvider provider = assayService.getProvider(protocol); + if (provider != null) + { + SchemaKey key = AssayProtocolSchema.schemaName(provider, protocol); + ExperimentService.get().getObjectReferencers() + .forEach(referencer -> { + Collection referenced = referencer.getItemsWithReferences( + idToRunMap.keySet(), + key.toString(), + "Runs" + ); + referenced.forEach(id -> referencedItems.put(id, idToRunMap.get(id))); + referenceDescriptions.add(referencer.getObjectReferenceDescription(ExpRun.class)); + } + ); + } + + } + + List> permissionDatasetRows = new ArrayList<>(); + List> noPermissionDatasetRows = new ArrayList<>(); + if (StudyPublishService.get() != null) + { + for (Dataset dataset : StudyPublishService.get().getDatasetsForAssayRuns(runs, getUser())) + { + ActionURL url = urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId()); + TableInfo t = dataset.getTableInfo(getUser()); + if (null != t && t.hasPermission(getUser(),DeletePermission.class)) + { + permissionDatasetRows.add(new Pair<>(dataset, url)); + } + else + { + noPermissionDatasetRows.add(new Pair<>(dataset, url)); + } + } + } + + return new ConfirmDeleteView( + "run", + ShowRunGraphAction.class, + runs.stream().filter(run -> !referencedItems.containsKey(run.getRowId())).toList(), + deleteForm, + Collections.emptyList(), + "dataset(s) have one or more rows which", + permissionDatasetRows, + noPermissionDatasetRows, + referencedItems.values().stream().toList(), + referenceDescriptions.stream().filter(Objects::nonNull).collect(Collectors.joining(", or "))); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + ExperimentServiceImpl.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), deleteForm.getUserComment(), deleteForm.getIds(false), getTransactionAuditDetails()); + } + } + + public static class DeleteRunForm + { + private int _runId; + + public int getRunId() + { + return _runId; + } + + public void setRunId(int runId) + { + _runId = runId; + } + } + + /** + * Separate delete action from the client API + */ + @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) + public static class DeleteRunAction extends MutatingApiAction + { + @Override + public ApiResponse execute(DeleteRunForm form, BindException errors) + { + ExpRun run = ExperimentService.get().getExpRun(form.getRunId()); + if (run == null) + { + throw new NotFoundException("Could not find run with ID " + form.getRunId()); + } + if (!run.canDelete(getUser())) + throw new UnauthorizedException("You do not have permission to delete " + + (ExpProtocol.isSampleWorkflowProtocol(run.getProtocol().getLSID()) ? "jobs" : "runs") + " in this container."); + + run.delete(getUser()); + return new ApiSimpleResponse("success", true); + } + } + + + @RequiresAnyOf({DeletePermission.class, SampleWorkflowDeletePermission.class}) + public static class DeleteRunsAction extends AbstractDeleteAPIAction + { + @Override + protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) + { + Set runIdsToDelete = new HashSet<>(form.getIds(true)); + Set runIdsCascadeDeleted = new HashSet<>(); + + if (form.isCascade()) + { + for (long runId : runIdsToDelete) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run != null) + addReplacesRuns(run, runIdsCascadeDeleted); + } + + if (!runIdsCascadeDeleted.isEmpty()) + runIdsToDelete.addAll(runIdsCascadeDeleted); + } + + Map transactionAuditDetails = getTransactionAuditDetails(); + if (form.getRequestSource() != null) + transactionAuditDetails.put(TransactionAuditProvider.TransactionDetail.RequestSource, form.getRequestSource()); + if (form.getEditMethod() != null) + transactionAuditDetails.put(TransactionAuditProvider.TransactionDetail.EditMethod, form.getEditMethod()); + ExperimentService.get().deleteExperimentRunsByRowIds(getContainer(), getUser(), form.getUserComment(), runIdsToDelete, transactionAuditDetails); + + ApiSimpleResponse response = new ApiSimpleResponse("success", true); + response.put("runIdsDeleted", runIdsToDelete); + if (!runIdsCascadeDeleted.isEmpty()) + response.put("runIdsCascadeDeleted", runIdsCascadeDeleted); + return response; + } + + private void addReplacesRuns(ExpRun run, Set runIds) + { + for (ExpRun replacedRun : run.getReplacesRuns()) + { + runIds.add(replacedRun.getRowId()); + addReplacesRuns(replacedRun, runIds); + } + } + } + + private abstract static class AbstractDeleteAPIAction extends MutatingApiAction + { + @Override + public void validateForm(CascadeDeleteForm form, Errors errors) + { + if (form.getSingleObjectRowId() == null && form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "Either singleObjectRowId, dataRegionSelectionKey, or rowIds is required"); + } + + @Override + public ApiResponse execute(CascadeDeleteForm form, BindException errors) throws Exception + { + ApiSimpleResponse response; + + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + tx.addCommitTask(form::clearSelected, POSTCOMMIT); + + response = deleteObjects(form); + tx.commit(); + } + + if (null != response.get("success")) + response.put("success", !errors.hasErrors()); + + return response; + } + + protected abstract ApiSimpleResponse deleteObjects(CascadeDeleteForm form) throws Exception; + } + + public static class CascadeDeleteForm extends DeleteForm + { + private boolean _cascade; + + public boolean isCascade() + { + return _cascade; + } + + public void setCascade(boolean cascade) + { + _cascade = cascade; + } + } + + private abstract static class AbstractDeleteAction extends FormViewAction + { + @Override + public void validateCommand(DeleteForm target, Errors errors) + { + } + + @Override + public boolean handlePost(DeleteForm deleteForm, BindException errors) throws Exception + { + if (!deleteForm.isForceDelete()) + { + return false; + } + else + { + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + tx.addCommitTask(deleteForm::clearSelected, POSTCOMMIT); + + deleteObjects(deleteForm); + tx.commit(); + } + catch (BatchValidationException v) + { + v.addToErrors(errors); + } + + return !errors.hasErrors(); + } + } + + @Override + public ActionURL getSuccessURL(DeleteForm form) + { + return form.getSuccessActionURL(ExperimentUrlsImpl.get().getOverviewURL(getContainer())); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Confirm Deletion"); + } + + protected abstract void deleteObjects(DeleteForm form) throws Exception; + } + + @RequiresPermission(DesignAssayPermission.class) + public static class DeleteProtocolByRowIdsAPIAction extends AbstractDeleteAPIAction + { + @Override + protected ApiSimpleResponse deleteObjects(CascadeDeleteForm form) + { + for (ExpProtocol protocol : getProtocolsForDeletion(form)) + { + if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) + throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); + + protocol.delete(getUser(), form.getUserComment()); + } + + return new ApiSimpleResponse(); + } + } + + public static List getProtocolsForDeletion(DeleteForm form) + { + List protocols = new ArrayList<>(); + for (long protocolId : form.getIds(false)) + { + ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); + if (protocol != null) + { + protocols.add(protocol); + } + } + return protocols; + } + + @RequiresPermission(DesignAssayPermission.class) + public class DeleteProtocolByRowIdsAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + // UNDONE: Need help topic on protocols + setHelpTopic("experiment"); + super.addNavTrail(root); + } + + @Override + public ModelAndView getView(DeleteForm form, boolean reshow, BindException errors) + { + List runs = ExperimentService.get().getExpRunsForProtocolIds(false, form.getIds(false)); + List protocols = getProtocolsForDeletion(form); + String noun = "Assay Design"; + List> deleteableDatasets = new ArrayList<>(); + List> noPermissionDatasets = new ArrayList<>(); + if (AssayService.get() != null && StudyService.get() != null) + { + for (ExpProtocol protocol : protocols) + { + if (!protocol.getContainer().hasPermission(getUser(), DesignAssayPermission.class)) + throw new UnauthorizedException("You do not have sufficient permissions to delete this assay design."); + + if (AssayService.get().getProvider(protocol) == null) + { + noun = "Protocol"; + } + for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(protocol.getRowId(), Dataset.PublishSource.Assay)) + { + Pair entry = new Pair<>(dataset, urlProvider(StudyUrls.class).getDatasetURL(dataset.getContainer(), dataset.getDatasetId())); + if (dataset.canDeleteDefinition(getUser())) + { + deleteableDatasets.add(entry); + } + else + { + noPermissionDatasets.add(entry); + } + } + } + } + + return new ConfirmDeleteView(noun, ProtocolDetailsAction.class, protocols, form, runs, "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); + } + + @Override + protected void deleteObjects(DeleteForm form) + { + for (ExpProtocol protocol : getProtocolsForDeletion(form)) + { + protocol.delete(getUser(), form.getUserComment()); + } + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetDataOperationConfirmationDataAction extends ReadOnlyApiAction + { + @Override + public void validateForm(DataOperationConfirmationForm form, Errors errors) + { + if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey"); + if (form.getDataOperation() == null) + errors.reject(ERROR_REQUIRED, "An operation type must be provided."); + } + + @Override + public Object execute(DataOperationConfirmationForm form, BindException errors) + { + Collection requestIds = form.getIds(false); + ExperimentServiceImpl service = ExperimentServiceImpl.get(); + List allData = service.getExpDatas(requestIds); + + Set notAllowedIds = new HashSet<>(); + if (form.getDataOperation() == ExpDataImpl.DataOperations.Delete) + service.getObjectReferencers().forEach(referencer -> + notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "exp.data"))); + + Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allData); + + Collection containers = new HashSet<>(); + Collection notPermittedIds = new ArrayList<>(); + Class permClass = form.getDataOperation().getPermissionClass(); + for (ExpDataImpl expData : allData) + { + Container c = expData.getContainer(); + if (c.hasPermission(getUser(), ReadPermission.class)) + containers.add(c); + if (permClass != null && !c.hasPermission(getUser(), permClass)) + notPermittedIds.add(expData.getRowId()); + } + + NameExpressionOptionService svc = NameExpressionOptionService.get(); + response.put("containers", containers.stream().map(c -> Map.of( + "id", c.getEntityId(), + "path", (Object) c.getPath(), + "permitted", permClass == null || c.hasPermission(getUser(), permClass), + "canEditName", svc.getAllowUserSpecificNamesValue(c) + )).toList()); + + response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); + + return success(response); + } + } + + + public static class DataOperationConfirmationForm extends DataViewSnapshotSelectionForm + { + private ExpDataImpl.DataOperations _dataOperation; + + public ExpDataImpl.DataOperations getDataOperation() + { + return _dataOperation; + } + + public void setDataOperation(ExpDataImpl.DataOperations dataOperation) + { + _dataOperation = dataOperation; + } + + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetMaterialOperationConfirmationDataAction extends ReadOnlyApiAction + { + @Override + public void validateForm(MaterialOperationConfirmationForm form, Errors errors) + { + if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); + if (form.getSampleOperation() == null) + errors.reject(ERROR_REQUIRED, "An operation type must be provided."); + } + + @Override + public Object execute(MaterialOperationConfirmationForm form, BindException errors) + { + Set requestIds = form.getIds(false); + ExperimentServiceImpl service = ExperimentServiceImpl.get(); + List allMaterials = service.getExpMaterials(requestIds); + + Set notAllowedIds = new HashSet<>(); + // We prevent deletion if a sample is used as a parent, has assay data, is used in a job, etc. + if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) + service.getObjectReferencers().forEach(referencer -> + notAllowedIds.addAll(referencer.getItemsWithReferences(requestIds, "samples"))); + + if (SampleStatusService.get().supportsSampleStatus()) + notAllowedIds.addAll(service.findIdsNotPermittedForOperation(allMaterials, form.getSampleOperation())); + + Map>> response = ExperimentServiceImpl.partitionRequestedOperationObjects(getUser(), requestIds, notAllowedIds, allMaterials); + + Collection containers = new HashSet<>(); + Collection notPermittedIds = new ArrayList<>(); + Class permClass = form.getSampleOperation().getPermissionClass(); + for (ExpMaterial material : allMaterials) + { + Container c = material.getContainer(); + if (c.hasPermission(getUser(), ReadPermission.class)) + containers.add(c); + if (permClass != null && !c.hasPermission(getUser(), permClass)) + notPermittedIds.add(material.getRowId()); + } + + NameExpressionOptionService svc = NameExpressionOptionService.get(); + + response.put("containers", containers.stream().map(c -> Map.of( + "id", c.getEntityId(), + "path", (Object) c.getPath(), + "permitted", permClass == null || c.hasPermission(getUser(), permClass), + "canEditName", svc.getAllowUserSpecificNamesValue(c) + )).toList()); + + response.put("notPermitted", notPermittedIds.stream().map(id -> Map.of("RowId", (Object) id)).toList()); + + if (form.getSampleOperation() == SampleTypeService.SampleOperations.Delete) + // String 'associatedDatasets' must be synced to its handling in confirmDelete.js, confirmDelete() + response.put("associatedDatasets", ExperimentServiceImpl.includeLinkedToStudyText(allMaterials, requestIds, getUser(), getContainer())); + + return success(response); + } + } + + public static class MaterialOperationConfirmationForm extends DataViewSnapshotSelectionForm + { + private SampleTypeService.SampleOperations _sampleOperation; + + public SampleTypeService.SampleOperations getSampleOperation() + { + return _sampleOperation; + } + + public void setSampleOperation(SampleTypeService.SampleOperations sampleOperation) + { + _sampleOperation = sampleOperation; + } + } + + @RequiresPermission(DeletePermission.class) + public class DeleteSelectedDataAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + // UNDONE: Need help topic on Datas + setHelpTopic("experiment"); + super.addNavTrail(root); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) throws Exception + { + List datas = getDatas(deleteForm, false); + + for (ExpRun run : getRuns(datas)) + { + if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) + throw new UnauthorizedException(); + } + + // Issue 32076: Delete the exp.Data objects using QueryUpdateService so trigger scripts will be executed + Map, List> byDataClass = datas.stream().collect(Collectors.groupingBy(d -> Optional.ofNullable(d.getDataClass(null)))); + for (Optional opt : byDataClass.keySet()) + { + SchemaKey schemaKey; + String queryName; + ExpDataClass dc = opt.orElse(null); + List ds = byDataClass.get(opt); + if (dc == null) + { + // Reference to exp.Data table + schemaKey = ExpSchema.SCHEMA_EXP; + queryName = ExpSchema.TableType.Data.name(); + } + else + { + // Reference to exp.data. table + schemaKey = ExpSchema.SCHEMA_EXP_DATA; + queryName = dc.getName(); + } + + UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), schemaKey); + if (schema == null) + throw new IllegalStateException("Failed to get schema '" + schemaKey + "'"); + + TableInfo table = schema.getTable(queryName); + if (table == null) + throw new IllegalStateException("Failed to get table '" + queryName + "' in schema '" + schemaKey + "'"); + + QueryUpdateService qus = table.getUpdateService(); + if (qus == null) + throw new IllegalStateException(); + + qus.deleteRows(getUser(), getContainer(), toKeys(ds), null, null); + } + } + + protected List> toKeys(List datas) + { + return datas.stream().map(d -> CaseInsensitiveHashMap.of("rowId", d.getRowId())).collect(toList()); + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + if (errors.hasErrors()) + return new SimpleErrorView(errors, false); + + List datas = getDatas(deleteForm, false); + List runs = getRuns(datas); + + return new ConfirmDeleteView("Data", ShowDataAction.class, datas, deleteForm, runs); + } + + private List getRuns(List datas) + { + List runArray = ExperimentService.get().getRunsUsingDatas(datas); + return new ArrayList<>(ExperimentService.get().runsDeletedWithInput(runArray)); + } + + private List getDatas(DeleteForm deleteForm, boolean clear) + { + List datas = new ArrayList<>(); + for (long dataId : deleteForm.getIds(clear)) + { + ExpData data = ExperimentService.get().getExpData(dataId); + if (data != null) + { + datas.add(data); + } + } + return datas; + } + } + + @RequiresPermission(DeletePermission.class) + public class DeleteSelectedExperimentsAction extends AbstractDeleteAction + { + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + for (ExpExperiment exp : lookupExperiments(deleteForm)) + { + exp.delete(getUser()); + } + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List experiments = lookupExperiments(deleteForm); + + List runs = new ArrayList<>(); + boolean allBatches = true; + for (ExpExperiment experiment : experiments) + { + // Deleting a batch also deletes all of its runs + if (experiment.getBatchProtocol() != null) + { + runs.addAll(experiment.getRuns()); + } + else + { + allBatches = false; + } + } + + return new ConfirmDeleteView(allBatches ? "batch" : "run group", DetailsAction.class, experiments, deleteForm, runs); + } + + private List lookupExperiments(DeleteForm deleteForm) + { + List experiments = new ArrayList<>(); + for (long experimentId : deleteForm.getIds(false)) + { + ExpExperiment experiment = ExperimentService.get().getExpExperiment(experimentId); + if (experiment != null) + { + experiments.add(experiment); + } + } + return experiments; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + super.addNavTrail(root); + } + } + + @RequiresPermission(DesignSampleTypePermission.class) + public class DeleteSampleTypesAction extends AbstractDeleteAction + { + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + super.addNavTrail(root); + } + + @Override + protected void deleteObjects(DeleteForm deleteForm) + { + List sampleTypes = getSampleTypes(deleteForm); + if (sampleTypes.isEmpty()) + { + throw new NotFoundException("No sample types found for ids provided."); + } + if (!ensureCorrectContainer(sampleTypes)) + { + throw new UnauthorizedException(); + } + + for (ExpRun run : getRuns(sampleTypes)) + { + if (!run.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new UnauthorizedException(); + } + } + + for (ExpSampleType source : sampleTypes) + { + Domain domain = source.getDomain(); + if (!domain.getDomainKind().canDeleteDefinition(getUser(), domain)) + { + throw new UnauthorizedException(); + } + + source.delete(getUser(), deleteForm.getUserComment()); + } + } + + @Override + public ModelAndView getView(DeleteForm deleteForm, boolean reshow, BindException errors) + { + List sampleTypes = getSampleTypes(deleteForm); + if (!ensureCorrectContainer(sampleTypes)) + { + throw new RedirectException(ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer(), "To delete a sample type, you must be in its folder or project.")); + } + + List> deleteableDatasets = new ArrayList<>(); + List> noPermissionDatasets = new ArrayList<>(); + if (StudyService.get() != null && StudyPublishService.get() != null) + { + for (ExpSampleType sampleType: sampleTypes) + { + for (Dataset dataset : StudyPublishService.get().getDatasetsForPublishSource(sampleType.getRowId(), Dataset.PublishSource.SampleType)) + { + ActionURL datasetURL = StudyService.get().getDatasetURL(getContainer(), dataset.getDatasetId()); + Pair entry = new Pair<>(dataset, datasetURL); + if (dataset.canDeleteDefinition(getUser())) + { + deleteableDatasets.add(entry); + } + else + { + noPermissionDatasets.add(entry); + } + } + } + } + return new ConfirmDeleteView("Sample Type", ShowSampleTypeAction.class, sampleTypes, deleteForm, getRuns(sampleTypes), "Dataset", deleteableDatasets, noPermissionDatasets, Collections.emptyList(), null); + } + + private List getSampleTypes(DeleteForm deleteForm) + { + List sources = new ArrayList<>(); + for (long rowId : deleteForm.getIds(false)) + { + ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId); + if (sampleType != null) + { + sources.add(sampleType); + } + } + return sources; + } + + private boolean ensureCorrectContainer(List sampleTypes) + { + for (ExpSampleType source : sampleTypes) + { + Container sourceContainer = source.getContainer(); + if (!sourceContainer.equals(getContainer())) + { + return false; + } + } + return true; + } + + private List getRuns(List sampleTypes) + { + if (!sampleTypes.isEmpty()) + { + List runArray = ExperimentService.get().getRunsUsingSampleTypes(sampleTypes.toArray(new ExpSampleType[0])); + return ExperimentService.get().runsDeletedWithInput(runArray); + } + else + { + return Collections.emptyList(); + } + } + } + + private DataRegion getSampleTypeRegion(ViewContext model) + { + TableInfo tableInfo = ExperimentServiceImpl.get().getTinfoSampleType(); + + QuerySettings settings = new QuerySettings(model, "SampleType"); + settings.setSelectionKey(DataRegionSelection.getSelectionKey(tableInfo.getSchema().getName(), tableInfo.getName(), "SampleType", settings.getDataRegionName())); + + DataRegion dr = new DataRegion(); + dr.setSettings(settings); + dr.addColumns(tableInfo.getUserEditableColumns()); + dr.removeColumns("lastindexed"); + dr.getDisplayColumn(0).setVisible(false); + + dr.getDisplayColumn("idcol1").setVisible(false); + dr.getDisplayColumn("idcol2").setVisible(false); + dr.getDisplayColumn("idcol3").setVisible(false); + dr.getDisplayColumn("lsid").setVisible(false); + dr.getDisplayColumn("materiallsidprefix").setVisible(false); + dr.getDisplayColumn("parentcol").setVisible(false); + + ActionURL url = new ActionURL(ShowSampleTypeAction.class, model.getContainer()); + dr.getDisplayColumn(1).setURL(url.addParameter("rowId", "${RowId}")); + dr.setShowRecordSelectors(getContainer().hasOneOf(getUser(), DeletePermission.class, UpdatePermission.class)); + + return dr; + } + + @RequiresPermission(ReadPermission.class) + @ActionNames("getSampleType,getSampleTypeApi") // Referenced in labkey-ui-components components/samples/actions.ts TODO: migrate getSampleTypeApi -> getSampleType + public static class GetSampleTypeAction extends ReadOnlyApiAction + { + @Override + public void validateForm(SampleTypeForm form, Errors errors) + { + if (form.getRowId() == null && form.getLSID() == null) + errors.reject(ERROR_REQUIRED, "RowId or LSID must be provided"); + } + + @Override + public Object execute(SampleTypeForm form, BindException errors) throws Exception + { + ExpSampleTypeImpl st = form.getSampleType(getContainer()); + + return getSampleTypeResponse(st); + } + } + + @NotNull + private static ApiSimpleResponse getSampleTypeResponse(ExpSampleType st) throws IOException + { + Map sampleType = new HashMap<>(); + sampleType.put("name", st.getName()); + sampleType.put("nameExpression", st.getNameExpression()); + sampleType.put("labelColor", st.getLabelColor()); + sampleType.put("metricUnit", st.getMetricUnit()); + sampleType.put("description", st.getDescription()); + sampleType.put("importAliases", st.getImportAliasMap()); + sampleType.put("lsid", st.getLSID()); + sampleType.put("rowId", st.getRowId()); + sampleType.put("domainId", st.getDomain().getTypeId()); + sampleType.put("category", st.getCategory()); + + return new ApiSimpleResponse(Map.of("sampleSet", sampleType, "success", true)); + } + + public static class DataTypesWithRequiredLineageForm + { + private Integer _parentDataTypeRowId; + private boolean _sampleParent; + + public Integer getParentDataTypeRowId() + { + return _parentDataTypeRowId; + } + + public void setParentDataTypeRowId(Integer parentDataTypeRowId) + { + this._parentDataTypeRowId = parentDataTypeRowId; + } + + public boolean isSampleParent() + { + return _sampleParent; + } + + public void setSampleParent(boolean sampleParent) + { + _sampleParent = sampleParent; + } + } + + @RequiresPermission(ReadPermission.class) + public static class GetDataTypesWithRequiredLineageAction extends ReadOnlyApiAction + { + @Override + public void validateForm(DataTypesWithRequiredLineageForm form, Errors errors) + { + if (form.getParentDataTypeRowId() == null) + errors.reject(ERROR_REQUIRED, "ParentDataTypeRowId must be provided"); + } + + @Override + public Object execute(DataTypesWithRequiredLineageForm form, BindException errors) throws Exception + { + return getDataTypesWithRequiredLineageResponse(form.getParentDataTypeRowId(), form.isSampleParent(), getContainer(), getUser()); + } + } + @NotNull + private static ApiSimpleResponse getDataTypesWithRequiredLineageResponse(Integer parentDataType, boolean isSampleParent, Container container, User user) + { + Pair, Set> requiredLineages = ExperimentServiceImpl.get().getDataTypesWithRequiredLineage(parentDataType, isSampleParent, container, user); + return new ApiSimpleResponse(Map.of("sampleTypes", requiredLineages.first, "dataClasses", requiredLineages.second,"success", true)); + } + + @RequiresPermission(DesignSampleTypePermission.class) + public static class EditSampleTypeAction extends SimpleViewAction + { + private ExpSampleTypeImpl _sampleType; + + @Override + public ModelAndView getView(SampleTypeForm form, BindException errors) + { + boolean create = form.getLSID() == null && form.getRowId() == null; + if (!create) + _sampleType = form.getSampleType(getContainer()); + + return ModuleHtmlView.get(ModuleLoader.getInstance().getModule("core"), ModuleHtmlView.getGeneratedViewPath("sampleTypeDesigner")); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + if (_sampleType == null) + { + root.addChild("Create Sample Type"); + } + else + { + root.addChild(_sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(_sampleType)); + root.addChild("Update Sample Type"); + } + } + } + + public static class SampleTypeForm extends ReturnUrlForm + { + private Integer rowId; + private String lsid; + + public Integer getRowId() + { + return rowId; + } + + public void setRowId(Integer rowId) + { + this.rowId = rowId; + } + + public String getLSID() + { + return this.lsid; + } + + public void setLSID(String lsid) + { + this.lsid = lsid; + } + + public ExpSampleTypeImpl getSampleType(Container container) throws NotFoundException + { + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getLSID()); + if (sampleType == null) + sampleType = SampleTypeServiceImpl.get().getSampleType(getRowId()); + + if (sampleType == null) + { + throw new NotFoundException("Sample type not found: " + (getLSID() != null ? getLSID() : getRowId())); + } + + if (!container.equals(sampleType.getContainer())) + { + throw new NotFoundException("Sample type is not defined in the given container."); + } + + return sampleType; + } + } + + @RequiresPermission(InsertPermission.class) + public static class ImportSamplesAction extends AbstractExpDataImportAction + { + ExpSampleTypeImpl _sampleType; + boolean _isCrossTypeImport = false; + + @Override + public void validateForm(QueryForm queryForm, Errors errors) + { + _form = queryForm; + _insertOption = queryForm.getInsertOption(); + _isCrossTypeImport = getOptionParamValue(Params.crossTypeImport); + _form.setSchemaName(getTargetSchemaName()); + if (_isCrossTypeImport) + { + _form.setQueryName(getPipelineTargetQueryName()); + } + super.validateForm(queryForm, errors); + if (queryForm.getQueryName() == null) + errors.reject(ERROR_REQUIRED, "Sample type name is required"); + else + { + if (!_isCrossTypeImport) + { + _sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), queryForm.getQueryName()); + if (_sampleType == null) + { + errors.reject(ERROR_GENERIC, "Sample type '" + queryForm.getQueryName() + " not found."); + } + } + } + } + + private String getTargetSchemaName() + { + return getOptionParamValue(Params.crossTypeImport) ? ExpSchema.SCHEMA_NAME : "samples"; + } + + @Override + protected UserSchema getTargetSchema() + { + return getOptionParamValue(Params.crossTypeImport) ? QueryService.get().getUserSchema(getUser(), getContainer(), getTargetSchemaName()) : super.getTargetSchema(); + } + + @Override + protected String getPipelineTargetQueryName() + { + return getOptionParamValue(Params.crossTypeImport) ? "materials" : super.getPipelineTargetQueryName(); + } + + @Override + protected Map getRenamedColumns() + { + Map renamedColumns = super.getRenamedColumns(); + renamedColumns.putAll(SampleTypeUpdateServiceDI.SAMPLE_ALT_IMPORT_NAME_COLS); + return renamedColumns; + } + + @Override + protected @Nullable Set getLineageImportAliases() throws IOException + { + Set aliases = new CaseInsensitiveHashSet(); + // Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import + aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT); + aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL); + boolean crossTypeImport = getOptionParamValue(AbstractQueryImportAction.Params.crossTypeImport); + // Issue 51894: We need to stop conversion to numbers for alias fields for all type + // If there are aliases defined for one type that are number fields in another type, this will prevent + // conversion to numbers during the initial partitioning, but the conversion will happen when the partition + // file is loaded. + if (crossTypeImport) + { + List sampleTypes = SampleTypeServiceImpl.get().getSampleTypes(getContainer(), true); + for (ExpSampleTypeImpl sampleType : sampleTypes) + aliases.addAll(sampleType.getImportAliases().keySet()); + } + else + { + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), _form.getQueryName()); + aliases.addAll(sampleType.getImportAliases().keySet()); + } + return aliases; + } + + @Override + protected int importData( + DataLoader dl, + FileStream file, + String originalName, + BatchValidationException errors, + @Nullable AuditBehaviorType auditBehaviorType, + TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, + @Nullable String auditUserComment + ) throws IOException + { + initContext(dl, errors, auditBehaviorType, auditUserComment); + + TableInfo tInfo = _target; + QueryUpdateService updateService = _updateService; + if (getOptionParamValue(Params.crossTypeImport)) + { + tInfo = ExperimentService.get().createMaterialTable(new SamplesSchema(getUser(), getContainer()), ContainerFilter.current(this), null); + updateService = tInfo.getUpdateService(); + } + + int count = importData(dl, tInfo, updateService, _context, auditEvent, getUser(), getContainer()); + + if (getOptionParamValue(Params.crossTypeImport)) + { + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeImport"); + if (_context.getInsertOption() == QueryUpdateService.InsertOption.UPDATE) + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeUpdate"); + else if (_context.getInsertOption() == QueryUpdateService.InsertOption.MERGE) + SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, "sampleImport", "crossTypeMerge"); + } + + return count; + } + + @Override + public ModelAndView getView(QueryForm form, BindException errors) throws Exception + { + initRequest(form); + setHelpTopic("importSampleSets"); // page-wide help topic + setImportHelpTopic("importSampleSets"); // importOptions help topic + setTypeName("samples"); + return getDefaultImportView(form, errors); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ActionURL url = _form.urlFor(QueryAction.executeQuery); + if (_form.getQueryName() != null && url != null) + root.addChild(_form.getQueryName(), url); + root.addChild("Import Data"); + } + + @Override + protected JSONObject createSuccessResponse(int rowCount) + { + JSONObject json = super.createSuccessResponse(rowCount); + if (!_context.getResponseInfo().isEmpty()) + { + for (String key : _context.getResponseInfo().keySet()) + json.put(key, _context.getResponseInfo().get(key)); + } + return json; + } + + } + + public abstract static class AbstractExpDataImportAction extends AbstractQueryImportAction + { + protected QueryForm _form; + protected DataIteratorContext _context; + + @Override + public void validateForm(QueryForm form, Errors errors) + { + QueryDefinition query = form.getQueryDef(); + if (query.getContainerFilter() != null && query.getContainerFilter().getType() != null) + { + // cross folder import not supported + if (query.getContainerFilter().getType() != ContainerFilter.Type.Current) + errors.reject(ERROR_GENERIC, "ContainerFilter is not supported for import actions."); + } + } + + @Override + protected void initRequest(QueryForm form) throws ServletException + { + QueryDefinition query = form.getQueryDef(); + setContainerFilterForImport(query, getContainer(), getUser()); + List qpe = new ArrayList<>(); + TableInfo t = query.getTable(form.getSchema(), qpe, true); + + if (!qpe.isEmpty()) + throw qpe.get(0); + if (!getOptionParamValue(Params.crossTypeImport) && null != t) + { + setTarget(t); + setShowMergeOption(t.supportsInsertOption(QueryUpdateService.InsertOption.MERGE)); + setShowUpdateOption(t.supportsInsertOption(QueryUpdateService.InsertOption.UPDATE)); + } + + _auditBehaviorType = form.getAuditBehavior(); + _auditUserComment = form.getAuditUserComment(); + } + + @Override + protected Map getRenamedColumns() + { + final String renameParamPrefix = "importAlias."; + Map renameColumns = new CaseInsensitiveHashMap<>(); + PropertyValue[] pvs = _form.getInitParameters().getPropertyValues(); + for (PropertyValue pv : pvs) + { + String paramName = pv.getName(); + if (!paramName.startsWith(renameParamPrefix) || pv.getValue() == null) + continue; + + renameColumns.put(paramName.substring(renameParamPrefix.length()), (String) pv.getValue()); + } + return renameColumns; + } + + @Override + protected Set getLineageImportAliases() throws IOException + { + ExpDataClass dataClass = ExperimentServiceImpl.get().getDataClass(getContainer(), getUser(), _form.getQueryName()); + return new CaseInsensitiveHashSet(dataClass.getImportAliases().keySet()); + } + + protected void initContext(DataLoader dl, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, @Nullable String auditUserComment) + { + _context = createDataIteratorContext(_insertOption, getOptionParamsMap(), getLookupResolutionType(), auditBehaviorType, auditUserComment, errors, null, getContainer()); + + if (_context.isCrossFolderImport() && !getContainer().hasProductFolders()) + _context.setCrossFolderImport(false); + } + + @Override + protected int importData(DataLoader dl, FileStream file, String originalName, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, TransactionAuditProvider.@Nullable TransactionAuditEvent auditEvent, @Nullable String auditUserComment) throws IOException + { + initContext(dl, errors, auditBehaviorType, auditUserComment); + return importData(dl, _target, _updateService, _context, auditEvent, getUser(), getContainer()); + } + + @Override + protected String getQueryImportProviderName() + { + PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_PROVIDER_PARAM); + return pv == null ? null : (String) pv.getValue(); + } + + @Override + protected String getQueryImportDescription() + { + PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_PIPELINE_DESCRIPTION_PARAM); + return pv == null ? null : (String) pv.getValue(); + } + + @Override + protected String getQueryImportJobNotificationProviderName() + { + PropertyValue pv = _form.getInitParameters().getPropertyValue(QUERY_IMPORT_NOTIFICATION_PROVIDER_PARAM); + return pv == null ? null : (String) pv.getValue(); + } + + @Override + protected boolean isBackgroundImportSupported() + { + return true; + } + + @Override + protected boolean allowLineageColumns() + { + return true; + } + + } + + @RequiresPermission(InsertPermission.class) + public static class ImportDataAction extends AbstractExpDataImportAction + { + @Override + public void validateForm(QueryForm queryForm, Errors errors) + { + _form = queryForm; + _form.setSchemaName("exp.data"); + _insertOption = queryForm.getInsertOption(); + super.validateForm(queryForm, errors); + if (queryForm.getQueryName() == null) + errors.reject(ERROR_REQUIRED, "Data class name is required"); + else + { + ExpDataClass dataClass = ExperimentService.get().getDataClass(getContainer(), getUser(), queryForm.getQueryName()); + if (dataClass == null) + { + errors.reject(ERROR_GENERIC, "Data class '" + queryForm.getQueryName() + " not found."); + } + } + } + + @Override + public ModelAndView getView(QueryForm form, BindException errors) throws Exception + { + initRequest(form); + setHelpTopic("dataClass"); // page wide help topic + setImportHelpTopic("dataClass#ui"); // importOptions help topic + setTypeName("data"); + return getDefaultImportView(form, errors); + } + + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Data Classes", ExperimentUrlsImpl.get().getDataClassListURL(getContainer())); + ActionURL url = _form.urlFor(QueryAction.executeQuery); + if (_form.getQueryName() != null && url != null) + root.addChild(_form.getQueryName(), url); + root.addChild("Import Data"); + } + + } + + @RequiresPermission(UpdatePermission.class) + public class ShowUpdateAction extends SimpleViewAction + { + @Override + public ModelAndView getView(ExperimentForm form, BindException errors) + { + form.refreshFromDb(); + Experiment exp = form.getBean(); + if (exp == null) + { + throw new NotFoundException(); + } + ensureCorrectContainer(getContainer(), ExperimentService.get().getExpExperiment(exp.getRowId()), getViewContext()); + + return new ExperimentUpdateView(new DataRegion(), form, errors); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + addRootNavTrail(root); + root.addChild("Update Run Group"); + } + } + + @RequiresPermission(UpdatePermission.class) + public static class UpdateAction extends FormHandlerAction + { + private Experiment _exp; + + @Override + public void validateCommand(ExperimentForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ExperimentForm form, BindException errors) throws Exception + { + form.doUpdate(); + form.refreshFromDb(); + _exp = form.getBean(); + return true; + } + + @Override + public ActionURL getSuccessURL(ExperimentForm experimentForm) + { + return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), ExperimentService.get().getExpExperiment(_exp.getRowId())); + } + } + + public static class ExportBean + { + private final LSIDRelativizer _selectedRelativizer; + private final XarExportType _selectedExportType; + private final String _fileName; + private final String _dataRegionSelectionKey; + private final String _error; + private final Long _expRowId; + private final Long _protocolId; + private final ActionURL _postURL; + private final Set _roles; + + public ExportBean(LSIDRelativizer selectedRelativizer, XarExportType selectedExportType, String fileName, ExportOptionsForm form, Set roles, ActionURL postURL) + { + _selectedRelativizer = selectedRelativizer; + _selectedExportType = selectedExportType; + _fileName = fileName; + _dataRegionSelectionKey = form.getDataRegionSelectionKey(); + _error = form.getError(); + _expRowId = form.getExpRowId(); + _postURL = postURL; + _roles = roles; + _protocolId = form.getProtocolId(); + } + + public LSIDRelativizer getSelectedRelativizer() + { + return _selectedRelativizer; + } + + public XarExportType getSelectedExportType() + { + return _selectedExportType; + } + + public String getError() + { + return _error; + } + + public String getFileName() + { + return _fileName; + } + + public Set getRoles() + { + return _roles; + } + + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + public ActionURL getPostURL() + { + return _postURL; + } + + public Long getProtocolId() + { + return _protocolId; + } + + public Long getExpRowId() + { + return _expRowId; + } + } + + + private String fixupExportName(String runName) + { + runName = runName.replace('/', '-'); + runName = runName.replace('\\', '-'); + return runName; + } + + public static class ExportOptionsForm extends ExperimentRunListForm + { + private String _error; + private XarExportType _exportType; + private LSIDRelativizer _lsidOutputType; + private String _xarFileName; + private String _zipFileName; + private String _fileExportType; + private Long _protocolId; + private Integer _sampleTypeId; + private long[] _dataIds; + private String[] _roles = new String[0]; + + public String getError() + { + return _error; + } + + public void setError(String error) + { + _error = error; + } + + public XarExportType getExportType() + { + return _exportType; + } + + public LSIDRelativizer getLsidOutputType() + { + return _lsidOutputType; + } + + public String getFileExportType() + { + return _fileExportType; + } + + public void setFileExportType(String fileExportType) + { + _fileExportType = fileExportType; + } + + public String getXarFileName() + { + return _xarFileName; + } + + public void setXarFileName(String xarFileName) + { + _xarFileName = xarFileName; + } + + public String getZipFileName() + { + return _zipFileName; + } + + public void setZipFileName(String zipFileName) + { + _zipFileName = zipFileName; + } + + public void setExportType(XarExportType exportType) + { + _exportType = exportType; + } + + public void setLsidOutputType(LSIDRelativizer lsidOutputType) + { + _lsidOutputType = lsidOutputType; + } + + public Long getProtocolId() + { + return _protocolId; + } + + public void setProtocolId(Long protocolId) + { + _protocolId = protocolId; + } + + public String[] getRoles() + { + return _roles; + } + + public void setRoles(String[] roles) + { + _roles = roles; + } + + public Integer getSampleTypeId() + { + return _sampleTypeId; + } + + public void setSampleTypeId(Integer sampleTypeId) + { + _sampleTypeId = sampleTypeId; + } + + public long[] getDataIds() + { + return _dataIds; + } + + public void setDataIds(long[] dataIds) + { + _dataIds = dataIds; + } + + public List lookupProtocols(ViewContext context, boolean clearSelection) + { + List protocols = new ArrayList<>(); + + if (_protocolId != null) + { + ExpProtocol protocol = ExperimentService.get().getExpProtocol(_protocolId.intValue()); + if (protocol == null || !protocol.getContainer().equals(context.getContainer())) + { + throw new NotFoundException(); + } + protocols.add(protocol); + return protocols; + } + + for (Long protocolId : DataRegionSelection.getSelectedIntegers(context, clearSelection)) + { + try + { + ExpProtocol protocol = ExperimentService.get().getExpProtocol(protocolId); + if (protocol == null || !protocol.getContainer().equals(context.getContainer())) + { + throw new NotFoundException(); + } + protocols.add(protocol); + } + catch (NumberFormatException e) + { + throw new NotFoundException("Invalid protocol id: " + protocolId); + } + } + if (protocols.isEmpty()) + { + throw new NotFoundException("No protocols selected"); + } + return protocols; + } + } + + private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable String fileName) + throws ExperimentException, IOException, PipelineValidationException + { + return exportXAR(selection, null, null, fileName); + } + + private ActionURL exportXAR(@NotNull XarExportSelection selection, @Nullable LSIDRelativizer lsidRelativizer, @Nullable XarExportType exportType, @Nullable String fileName) + throws ExperimentException, IOException, PipelineValidationException + { + if (lsidRelativizer == null) + lsidRelativizer = LSIDRelativizer.FOLDER_RELATIVE; + + if (exportType == null) + exportType = XarExportType.BROWSER_DOWNLOAD; + + if (fileName == null || fileName.isEmpty()) + fileName = "export.xar"; + + fileName = fixupExportName(fileName); + String xarXmlFileName = null; + if (Strings.CI.endsWith(fileName, ".xar")) + xarXmlFileName = fileName + ".xml"; + + switch (exportType) + { + case BROWSER_DOWNLOAD: + XarExporter exporter = new XarExporter(lsidRelativizer, selection, getUser(), xarXmlFileName, null, getContainer()); + + getViewContext().getResponse().setContentType("application/zip"); + ResponseHelper.setContentDisposition(getViewContext().getResponse(), ResponseHelper.ContentDispositionType.attachment, fileName); + ResponseHelper.setPrivate(getViewContext().getResponse()); + + exporter.writeAsArchive(getViewContext().getResponse().getOutputStream()); + return null; + case PIPELINE_FILE: + if (!PipelineService.get().hasValidPipelineRoot(getContainer())) + { + throw new IllegalStateException("You must set a valid pipeline root before you can export a XAR to it."); + } + PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); + XarExportPipelineJob job = new XarExportPipelineJob(getViewBackgroundInfo(), pipeRoot, fileName, lsidRelativizer, selection, xarXmlFileName); + PipelineService.get().queueJob(job); + PipelineStatusFile status = PipelineService.get().getStatusFile(job.getJobGUID()); + return PageFlowUtil.urlProvider(PipelineUrls.class).statusDetails(getContainer(), status.getRowId()); + default: + throw new IllegalArgumentException("Unknown export type: " + exportType); + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportProtocolsAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + List protocols = form.lookupProtocols(getViewContext(), false); + + long[] ids = new long[protocols.size()]; + for (int i = 0; i < ids.length; i++) + { + ids[i] = protocols.get(i).getRowId(); + } + XarExportSelection selection = new XarExportSelection(); + selection.addProtocolIds(ids); + + exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); + + if (form.getDataRegionSelectionKey() != null) + { + // Clear the selection + form.lookupProtocols(getViewContext(), true); + } + return true; + } + } + + public abstract static class AbstractExportAction extends FormViewAction + { + protected ActionURL _resultURL; + + @Override + public void validateCommand(ExportOptionsForm target, Errors errors) + { + } + + @Override + public ActionURL getSuccessURL(ExportOptionsForm exportOptionsForm) + { + return _resultURL; + } + + @Override + public ModelAndView getSuccessView(ExportOptionsForm exportOptionsForm) + { + return null; + } + + @Override + public ModelAndView getView(ExportOptionsForm form, boolean reshow, BindException errors) throws Exception + { + // FormViewAction can reinvoke getView() in response to a POST if we're not redirecting the browser, + // so avoid double-creating the export + if ("get".equalsIgnoreCase(getViewContext().getRequest().getMethod())) + handlePost(form, errors); + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + } + + public List lookupRuns(ExportOptionsForm form) + { + Set runIds; + if (form.getRunIds() != null && form.getRunIds().length > 0) + runIds = new HashSet<>(Arrays.asList(form.getRunIds())); + else + runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); + + if (runIds.isEmpty()) + { + throw new NotFoundException(); + } + List result = new ArrayList<>(); + + for (long id : runIds) + { + ExpRun run = ExperimentService.get().getExpRun(id); + if (run == null || !run.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new NotFoundException("Could not find run " + id); + } + result.add(run); + } + return result; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportRunsAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + XarExportSelection selection = new XarExportSelection(); + if (form.getExpRowId() != null) + { + ExpExperiment experiment = ExperimentService.get().getExpExperiment(form.getExpRowId()); + if (experiment != null && !experiment.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new NotFoundException("Run group " + form.getExpRowId()); + } + selection.addExperimentIds(experiment.getRowId()); + } + selection.addRuns(lookupRuns(form)); + + _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), form.getXarFileName()); + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + return true; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportSampleTypeAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + Integer rowId = form.getSampleTypeId(); + if (rowId == null) + { + throw new NotFoundException("No sampleTypeId parameter specified"); + } + ExpSampleType sampleType = SampleTypeService.get().getSampleType(getContainer(), getUser(), rowId.intValue()); + if (sampleType == null) + { + throw new NotFoundException("No such sample type with RowId " + rowId); + } + if (!sampleType.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new UnauthorizedException(); + } + + XarExportSelection selection = new XarExportSelection(); + selection.addSampleType(sampleType); + + _resultURL = exportXAR(selection, form.getLsidOutputType(), form.getExportType(), FileUtil.makeLegalName(sampleType.getName() + ".xar")); + return true; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportRunFilesAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + XarExportSelection selection = new XarExportSelection(); + selection.setIncludeXarXml(false); + if ("role".equalsIgnoreCase(form.getFileExportType())) + { + selection.addRoles(form.getRoles()); + } + selection.addRuns(lookupRuns(form)); + + _resultURL = exportXAR(selection, form.getZipFileName()); + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + return true; + } + } + + @RequiresPermission(ReadPermission.class) + public class ExportFilesAction extends AbstractExportAction + { + @Override + public boolean handlePost(ExportOptionsForm form, BindException errors) throws Exception + { + long[] dataIds = form.getDataIds(); + if (dataIds == null || dataIds.length == 0) + { + throw new NotFoundException(); + } + + try + { + for (long id : dataIds) + { + ExpData data = ExperimentService.get().getExpData(id); + if (data == null || !data.getContainer().hasPermission(getUser(), ReadPermission.class)) + { + throw new NotFoundException("Could not find file " + id); + } + } + + XarExportSelection selection = new XarExportSelection(); + selection.setIncludeXarXml(false); + selection.addDataIds(dataIds); + + _resultURL = exportXAR(selection, form.getZipFileName()); + return true; + } + catch (NumberFormatException e) + { + throw new NotFoundException(Arrays.toString(dataIds)); + } + } + } + + public static class ExperimentRunListForm implements DataRegionSelection.DataSelectionKeyForm + { + private String _dataRegionSelectionKey; + private Long _expRowId; + private Long[] _runIds; + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String key) + { + _dataRegionSelectionKey = key; + } + + public Long getExpRowId() + { + return _expRowId; + } + + public void setExpRowId(Long expRowId) + { + _expRowId = expRowId; + } + + public Long[] getRunIds() + { + return _runIds; + } + + public void setRunIds(Long[] runIds) + { + _runIds = runIds; + } + + public ExpExperiment lookupExperiment() + { + return getExpRowId() == null ? null : ExperimentService.get().getExpExperiment(getExpRowId().intValue()); + } + } + + private void addSelectedRunsToExperiment(ExpExperiment exp, String dataRegionSelectionKey) + { + Collection runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), dataRegionSelectionKey, true); + List runs = new ArrayList<>(); + for (long runId : runIds) + { + ExpRun run = ExperimentServiceImpl.get().getExpRun(runId); + if (run != null) + { + runs.add(run); + } + } + exp.addRuns(getUser(), runs.toArray(new ExpRun[0])); + } + + + @RequiresPermission(InsertPermission.class) + public class AddRunsToExperimentAction extends FormHandlerAction + { + @Override + public void validateCommand(ExperimentRunListForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ExperimentRunListForm form, BindException errors) + { + addSelectedRunsToExperiment(form.lookupExperiment(), form.getDataRegionSelectionKey()); + return true; + } + + @Override + public ActionURL getSuccessURL(ExperimentRunListForm form) + { + return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); + } + } + + @RequiresPermission(DeletePermission.class) + public static class RemoveSelectedExpRunsAction extends FormHandlerAction + { + @Override + public void validateCommand(ExperimentRunListForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ExperimentRunListForm form, BindException errors) + { + ExpExperiment exp = form.lookupExperiment(); + if (exp == null || !exp.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new NotFoundException("Could not find run group with RowId " + form.getExpRowId()); + } + + for (long runId : DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false)) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run == null || !run.getContainer().hasPermission(getUser(), DeletePermission.class)) + { + throw new NotFoundException("Could not find run with RowId " + runId); + } + exp.removeRun(getUser(), run); + } + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + return true; + } + + @Override + public ActionURL getSuccessURL(ExperimentRunListForm form) + { + return ExperimentUrlsImpl.get().getExperimentDetailsURL(getContainer(), form.lookupExperiment()); + } + } + + public static ActionURL getResolveLsidURL(Container c, @NotNull String type, @NotNull String lsid) + { + ActionURL url = new ActionURL(ResolveLSIDAction.class, c); + url.addParameter("type", type); + url.addParameter("lsid", lsid); + + return url; + } + + + @RequiresPermission(ReadPermission.class) + public static class ResolveLSIDAction extends SimpleViewAction + { + @Override + public ModelAndView getView(LsidForm form, BindException errors) + { + String message = ""; + if (!PageFlowUtil.empty(form.getLsid())) + { + try + { + String lsid = Lsid.canonical(form.getLsid().trim()); + ActionURL url = LsidManager.get().getDisplayURL(lsid); + if (url == null && form.getType() != null) + { + url = switch (form.getType().toLowerCase()) + { + case "data" -> LsidType.Data.getDisplayURL(new Lsid(lsid)); + case "material" -> LsidType.Material.getDisplayURL(new Lsid(lsid)); + default -> url; + }; + } + if (null != url) + { + throw new RedirectException(url); + } + message = "Could not map LSID to URL"; + } + catch (IllegalArgumentException e) + { + message = "Invalid LSID"; + } + } + + return new HtmlView("Enter LSID", + DOM.createHtmlFragment( + message, + DOM.FORM(at(action, getViewContext().cloneActionURL().setAction(ResolveLSIDAction.class)), + "LSID: ", + DOM.INPUT(at(type, "text", name, "lsid", size, "80", value, form.getLsid())), + PageFlowUtil.button("Go").submit(true)))); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Resolve LSID"); + } + } + + public static class LsidForm + { + private String _lsid; + + public String getType() + { + return _type; + } + + public void setType(String type) + { + _type = type; + } + + private String _type; + + public void setLsid(String lsid) + { + _lsid = lsid; + } + + public String getLsid() + { + return _lsid; + } + } + + public static class SetFlagForm extends LsidForm + { + private String _comment; + private boolean _redirect = true; + + public String getComment() + { + return _comment; + } + + public void setComment(String comment) + { + _comment = comment; + } + + public boolean isRedirect() + { + return _redirect; + } + + public void setRedirect(boolean redirect) + { + _redirect = redirect; + } + } + + /** + * Check for update on the object itself + */ + @RequiresNoPermission + public static class SetFlagAction extends FormHandlerAction + { + @Override + public void validateCommand(SetFlagForm target, Errors errors) + { + } + + @Override + public boolean handlePost(SetFlagForm form, BindException errors) throws Exception + { + String lsid = form.getLsid(); + if (lsid == null) + throw new NotFoundException(); + ExpObject obj = ExperimentService.get().findObjectFromLSID(lsid); + if (obj == null) + throw new NotFoundException(); + Container container = obj.getContainer(); + if (!container.hasPermission(getUser(), UpdatePermission.class)) + { + throw new UnauthorizedException(); + } + + obj.setComment(getUser(), form.getComment()); + return true; + } + + @Override + public URLHelper getSuccessURL(SetFlagForm form) + { + return null; + } + } + + @RequiresPermission(InsertPermission.class) + public class DeriveSamplesChooseTargetAction extends SimpleViewAction + { + private List _materials; + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; + if (sampleType != null) + { + root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); + } + root.addChild("Derive Samples"); + } + + @Override + public void validate(DeriveMaterialForm form, BindException errors) + { + _materials = form.lookupMaterials(); + if (_materials.isEmpty()) + { + throw new NotFoundException("Could not find any matching materials"); + } + } + + @Override + public ModelAndView getView(DeriveMaterialForm form, BindException errors) + { + Container c = getContainer(); + PipeRoot root = PipelineService.get().findPipelineRoot(c); + + if (root == null || !root.isValid()) + { + ActionURL pipelineURL = urlProvider(PipelineUrls.class).urlSetup(c); + return new HtmlView(DIV("You must ", + DOM.A(DOM.at(href, pipelineURL), "configure a valid pipeline root for this folder"), + " before deriving samples.")); + } + else + { + Set materialInputRoles = new TreeSet<>(ExperimentService.get().getMaterialInputRoles(getContainer(), getUser())); + Map materialsWithRoles = new LinkedHashMap<>(); + for (ExpMaterial material : _materials) + { + materialsWithRoles.put(material, null); + } + + List sampleTypes = getUploadableSampleTypes(); + + DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), sampleTypes, materialsWithRoles, form.getOutputCount(), materialInputRoles, null); + return new JspView<>("/org/labkey/experiment/deriveSamplesChooseTarget.jsp", bean); + } + } + } + + public static class DeriveSamplesChooseTargetBean implements DataRegionSelection.DataSelectionKeyForm + { + private String _dataRegionSelectionKey; + + private final Integer _targetSampleTypeId; + private final List _sampleTypes; + private final Map _sourceMaterials; + private final int _sampleCount; + private final Collection _inputRoles; + private final DerivedSamplePropertyHelper _propertyHelper; + + public static final String CUSTOM_ROLE = "--CUSTOM--"; + + public DeriveSamplesChooseTargetBean(String dataRegionSelectionKey, Integer targetSampleTypeId, List sampleTypes, Map sourceMaterials, int sampleCount, Collection inputRoles, DerivedSamplePropertyHelper helper) + { + _dataRegionSelectionKey = dataRegionSelectionKey; + _targetSampleTypeId = targetSampleTypeId; + _sampleTypes = sampleTypes; + _sourceMaterials = sourceMaterials; + _sampleCount = sampleCount; + _inputRoles = inputRoles; + _propertyHelper = helper; + } + + public Integer getTargetSampleTypeId() + { + return _targetSampleTypeId; + } + + public DerivedSamplePropertyHelper getPropertyHelper() + { + return _propertyHelper; + } + + public int getSampleCount() + { + return _sampleCount; + } + + public Map getSourceMaterials() + { + return _sourceMaterials; + } + + public List getSampleTypes() + { + return _sampleTypes; + } + + public Collection getInputRoles() + { + return _inputRoles; + } + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String key) + { + _dataRegionSelectionKey = key; + } + } + + private List getUploadableSampleTypes() + { + // Make a copy so we can modify it + List sampleTypes = new ArrayList<>(SampleTypeService.get().getSampleTypes(getContainer(), getUser(), true)); + sampleTypes.removeIf(sampleType -> !sampleType.canImportMoreSamples()); + return sampleTypes; + } + + @RequiresPermission(InsertPermission.class) + public class DeriveSamplesAction extends FormViewAction + { + private List _materials; + private ActionURL _successUrl; + private final Map _inputMaterials = new LinkedHashMap<>(); + + @Override + public ModelAndView getView(DeriveMaterialForm form, boolean reshow, BindException errors) + { + _materials = form.lookupMaterials(); + if (_materials.isEmpty()) + { + throw new NotFoundException("Could not find any matching materials"); + } + + Container c = getContainer(); + + if (form.getOutputCount() <= 0) + { + form.setOutputCount(1); + } + + if (form.getTargetSampleTypeId() == 0) + throw new NotFoundException("Target sample type required for the derived samples"); + + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); + if (sampleType == null) + throw new NotFoundException("Could not find sample type with rowId " + form.getTargetSampleTypeId()); + + InsertView insertView = new InsertView(new DataRegion(), errors); + + DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), c, getUser()); + helper.addSampleColumns(insertView, getUser()); + + int[] rowIds = form.getRowIds(); + for (int i = 0; i < rowIds.length; i++) + { + insertView.getDataRegion().addHiddenFormField("rowIds", Integer.toString(rowIds[i])); + insertView.getDataRegion().addHiddenFormField("inputRole" + i, form.getInputRole(i) == null ? "" : form.getInputRole(i)); + insertView.getDataRegion().addHiddenFormField("customRole" + i, form.getCustomRole(i) == null ? "" : form.getCustomRole(i)); + } + + insertView.getDataRegion().addHiddenFormField("targetSampleTypeId", Integer.toString(form.getTargetSampleTypeId())); + insertView.getDataRegion().addHiddenFormField("outputCount", Integer.toString(form.getOutputCount())); + if (form.getDataRegionSelectionKey() != null) + insertView.getDataRegion().addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, form.getDataRegionSelectionKey()); + insertView.setInitialValues(ViewServlet.adaptParameterMap(getViewContext().getRequest().getParameterMap())); + ButtonBar bar = new ButtonBar(); + bar.setStyle(ButtonBar.Style.separateButtons); + ActionButton submitButton = new ActionButton(DeriveSamplesAction.class, "Submit"); + submitButton.setActionType(ActionButton.Action.POST); + bar.add(submitButton); + insertView.getDataRegion().setButtonBar(bar); + insertView.setTitle("Output Samples"); + + Map materialsWithRoles = new LinkedHashMap<>(); + List materials = form.lookupMaterials(); + for (int i = 0; i < materials.size(); i++) + { + materialsWithRoles.put(materials.get(i), form.determineLabel(i)); + } + + DeriveSamplesChooseTargetBean bean = new DeriveSamplesChooseTargetBean(form.getDataRegionSelectionKey(), form.getTargetSampleTypeId(), getUploadableSampleTypes(), materialsWithRoles, form.getOutputCount(), Collections.emptyList(), helper); + JspView view = new JspView<>("/org/labkey/experiment/summarizeMaterialInputs.jsp", bean); + view.setTitle("Input Samples"); + + return new VBox(view, insertView); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("sampleSets"); + addRootNavTrail(root); + root.addChild("Sample Types", ExperimentUrlsImpl.get().getShowSampleTypeListURL(getContainer())); + ExpSampleType sampleType = _materials != null && !_materials.isEmpty() ? _materials.get(0).getSampleType() : null; + if (sampleType != null) + { + root.addChild(sampleType.getName(), ExperimentUrlsImpl.get().getShowSampleTypeURL(sampleType)); + } + root.addChild("Derive Samples"); + } + + @Override + public void validateCommand(DeriveMaterialForm form, Errors errors) + { + List materials = form.lookupMaterials(); + + List lockedSamples = new ArrayList<>(); + for (int i = 0; i < materials.size(); i++) + { + ExpMaterial m = materials.get(i); + if (!m.isOperationPermitted(SampleTypeService.SampleOperations.EditLineage)) + { + lockedSamples.add(m); + } + String inputRole = form.determineLabel(i); + if (inputRole == null || inputRole.isEmpty()) + { + ExpSampleType st = m.getSampleType(); + inputRole = st != null ? st.getName() : ExpMaterialRunInput.DEFAULT_ROLE; + } + _inputMaterials.put(materials.get(i), inputRole); + } + + if (!lockedSamples.isEmpty()) + { + errors.reject(ERROR_MSG, SampleTypeService.get().getOperationNotPermittedMessage(lockedSamples, SampleTypeService.SampleOperations.EditLineage)); + } + } + + @Override + public boolean handlePost(DeriveMaterialForm form, BindException errors) + { + ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), form.getTargetSampleTypeId()); + + DerivedSamplePropertyHelper helper = new DerivedSamplePropertyHelper(sampleType, form.getOutputCount(), getContainer(), getUser()); + + Map, Map> allProperties; + try + { + boolean valid = true; + for (Map.Entry> entry : helper.getPostedPropertyValues(getViewContext().getRequest()).entrySet()) + valid = UploadWizardAction.validatePostedProperties(getViewContext(), entry.getValue(), errors) && valid; + if (!valid) + return false; + + allProperties = helper.getSampleProperties(getViewContext().getRequest(), _inputMaterials.keySet()); + } + catch (DuplicateMaterialException e) + { + errors.addError(new ObjectError(e.getColName(), null, null, e.getMessage())); + return false; + } + catch (ExperimentException e) + { + errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); + return false; + } + + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + Map outputMaterials = new HashMap<>(); + int i = 0; + for (Map.Entry, Map> entry : allProperties.entrySet()) + { + Lsid lsid = entry.getKey().first; + String name = entry.getKey().second; + assert name != null; + + ExpMaterialImpl outputMaterial = ExperimentServiceImpl.get().createExpMaterial(getContainer(), lsid.toString(), name); + if (sampleType != null) + { + outputMaterial.setCpasType(sampleType.getLSID()); + } + outputMaterial.save(getUser()); + + if (sampleType != null) + { + Map pvs = new HashMap<>(); + for (Map.Entry propertyEntry : entry.getValue().entrySet()) + pvs.put(propertyEntry.getKey().getName(), propertyEntry.getValue()); + outputMaterial.setProperties(getUser(), pvs, false); + } + + outputMaterials.put(outputMaterial, helper.getSampleNames().get(i++)); + } + + ExperimentService.get().deriveSamples(_inputMaterials, outputMaterials, getViewBackgroundInfo(), _log); + + tx.commit(); + + // automatically link samples to study, if configured + StudyPublishService.get().autoLinkDerivedSamples(sampleType, outputMaterials.keySet().stream().map(ExpObject::getRowId).collect(toList()), getContainer(), getUser()); + + _successUrl = ExperimentUrlsImpl.get().getShowSampleURL(getContainer(), outputMaterials.keySet().iterator().next()); + + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + } + catch (Exception e) + { + errors.reject(SpringActionController.ERROR_MSG, e.getMessage()); + return false; + } + + return true; + } + + @Override + public URLHelper getSuccessURL(DeriveMaterialForm deriveMaterialForm) + { + return _successUrl; + } + } + + public static class DeriveMaterialForm implements HasViewContext, DataRegionSelection.DataSelectionKeyForm + { + private String _dataRegionSelectionKey; + private int _outputCount = 1; + private int _targetSampleTypeId; + private int[] _rowIds; + private String _name; + + private ViewContext _context; + + @Override + public void setViewContext(ViewContext context) + { + _context = context; + } + + @Override + public ViewContext getViewContext() + { + return _context; + } + + public List lookupMaterials() + { + List result = new ArrayList<>(); + for (int rowId : getRowIds()) + { + ExpMaterial material = ExperimentService.get().getExpMaterial(rowId); + if (material != null) + { + if (material.getContainer().hasPermission(_context.getUser(), ReadPermission.class)) + { + result.add(material); + } + else + { + throw new UnauthorizedException(); + } + } + else + { + throw new NotFoundException("No material with RowId " + rowId); + } + } + result.sort(Comparator.comparing(Identifiable::getName)); + return result; + } + + public String getName() + { + return _name; + } + + public void setName(String name) + { + _name = name; + } + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String dataRegionSelectionKey) + { + _dataRegionSelectionKey = dataRegionSelectionKey; + } + + public int[] getRowIds() + { + if (_rowIds == null) + { + _rowIds = PageFlowUtil.toInts(DataRegionSelection.getSelected(getViewContext(), getDataRegionSelectionKey(), false)); + } + return _rowIds; + } + + public void setRowIds(int[] rowIds) + { + _rowIds = rowIds; + } + + public int getOutputCount() + { + return _outputCount; + } + + public void setOutputCount(int outputCount) + { + _outputCount = outputCount; + } + + public int getTargetSampleTypeId() + { + return _targetSampleTypeId; + } + + public void setTargetSampleTypeId(int targetSampleTypeId) + { + _targetSampleTypeId = targetSampleTypeId; + } + + public String getInputRole(int i) + { + return _context.getRequest().getParameter("inputRole" + i); + } + + public String getCustomRole(int i) + { + return _context.getRequest().getParameter("customRole" + i); + } + + public String determineLabel(int index) + { + String result = getInputRole(index); + if (DeriveSamplesChooseTargetBean.CUSTOM_ROLE.equals(result)) + { + result = getCustomRole(index); + } + if (result != null) + { + result = result.trim(); + } + return result; + } + } + + + public static class ExpInput + { + public String role; + public int rowId; + public Lsid lsid; + } + + public static class DerivationSpec + { + public String role; + public Map values; + } + + public static class DerivationForm + { + public List dataInputs; + public List materialInputs; + + public int dataOutputCount; + public Lsid targetDataClass; + public Map dataDefault; + public List dataOutputs; + + public int materialOutputCount; + public Lsid targetSampleType; + public Map materialDefault; + public List materialOutputs; + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(InsertPermission.class) + public static class DeriveAction extends MutatingApiAction + { + @Override + public void validateForm(DerivationForm form, Errors errors) + { + if (errors.hasErrors()) + return; + + if (form.materialOutputCount > 0 && form.materialOutputs != null && !form.materialOutputs.isEmpty()) + errors.reject(ERROR_MSG, "Either 'materialOutputCount' or 'materialOutputs' property can be specified, but not both."); + + if (form.dataOutputCount > 0 && form.dataOutputs != null && !form.dataOutputs.isEmpty()) + errors.reject(ERROR_MSG, "Either 'dataOutputCount' or 'dataOutputs' property can be specified, but not both."); + + boolean hasMaterialOutputs = form.materialOutputCount > 0 || form.materialOutputs != null && !form.materialOutputs.isEmpty(); + boolean hasDataOutputs = form.dataOutputCount > 0 || form.dataOutputs != null && !form.dataOutputs.isEmpty(); + + if (!hasMaterialOutputs && !hasDataOutputs) + errors.reject(ERROR_MSG, "At least one data output or material output is required"); + + if (hasMaterialOutputs && form.targetSampleType == null) + errors.reject(ERROR_MSG, "targetSampleType lsid required for material outputs"); + + if (hasDataOutputs && form.targetDataClass == null) + errors.reject(ERROR_MSG, "targetDataClass lsid required for data outputs"); + } + + @Override + public Object execute(DerivationForm form, BindException errors) throws Exception + { + // Find material inputs + Map materialInputs = new LinkedHashMap<>(); + if (form.materialInputs != null) + { + for (ExpInput in : form.materialInputs) + { + ExpMaterial m = null; + if (in.lsid != null) + { + m = ExperimentService.get().getExpMaterial(in.lsid.toString()); + if (m == null) + errors.reject(ERROR_MSG, "Can't resolve sample '" + in.lsid + "'"); + } + else if (in.rowId > 0) + { + m = ExperimentService.get().getExpMaterial(in.rowId); + if (m == null) + errors.reject(ERROR_MSG, "Can't resolve sample '" + in.rowId + "'"); + } + + if (m == null) + { + errors.reject(ERROR_MSG, "Material input lsid or rowId required"); + continue; + } + + ExpSampleType st = m.getSampleType(); + if (st == null) + { + errors.reject(ERROR_MSG, "Material input is not a member of a SampleType"); + continue; + } + + String role = in.role; + if (role == null || role.isEmpty()) + { + role = st.getName(); + } + materialInputs.put(m, role); + } + } + + // Find input data + Map dataInputs = new LinkedHashMap<>(); + if (form.dataInputs != null) + { + for (ExpInput in : form.dataInputs) + { + ExpData d = null; + if (in.lsid != null) + { + d = ExperimentService.get().getExpData(in.lsid.toString()); + if (d == null) + errors.reject(ERROR_MSG, "Can't resolve data '" + in.lsid + "'"); + } + else if (in.rowId > 0) + { + d = ExperimentService.get().getExpData(in.rowId); + if (d == null) + errors.reject(ERROR_MSG, "Can't resolve data '" + in.rowId + "'"); + } + + if (d == null) + { + errors.reject(ERROR_MSG, "Data input lsid or rowId required"); + continue; + } + + ExpDataClass dc = d.getDataClass(getUser()); + if (dc == null) + { + errors.reject(ERROR_MSG, "Data input is not a member of a DataClass"); + continue; + } + + String role = in.role; + if (role == null || role.isEmpty()) + { + role = dc.getName(); + } + dataInputs.put(d, role); + } + } + + ExpSampleType outSampleType; + if (form.targetSampleType != null) + { + // TODO: check in scope and has permission + outSampleType = SampleTypeService.get().getSampleType(form.targetSampleType.toString()); + if (outSampleType == null) + errors.reject(ERROR_MSG, "Sample type not found: " + form.targetSampleType.toString()); + } + else + { + outSampleType = null; + } + + ExpDataClass outDataClass; + if (form.targetDataClass != null) + { + // TODO: check in scope and has permission + outDataClass = ExperimentServiceImpl.get().getDataClass(form.targetDataClass.toString()); + if (outDataClass == null) + errors.reject(ERROR_MSG, "DataClass not found: " + form.targetDataClass.toString()); + } + else + { + outDataClass = null; + } + + if (errors.hasErrors()) + return null; + + // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names + // Create "MaterialInputs/" columns with a value containing a comma-separated list of Material names + final Map> parentInputNames = new HashMap<>(); + Set inputTypes = new CaseInsensitiveHashSet(); + for (ExpMaterial material : materialInputs.keySet()) + { + ExpSampleType st = material.getSampleType(); + String keyName = ExpMaterial.MATERIAL_INPUT_PARENT + "/" + st.getName(); + inputTypes.add(keyName); + parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(material.getName()); + } + + // TODO: support list of resolved ExpData or ExpMaterial instead of string concatenated names + // Create "DataInputs/" columns with a value containing a comma-separated list of ExpData names + for (ExpData d : dataInputs.keySet()) + { + ExpDataClass dc = d.getDataClass(getUser()); + String keyName = ExpData.DATA_INPUT_PARENT + "/" + dc.getName(); + inputTypes.add(keyName); + parentInputNames.computeIfAbsent(keyName, (x) -> new LinkedHashSet<>()).add(d.getName()); + } + + + try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction()) + { + Set requiredParentTypes = new CaseInsensitiveHashSet(); + + // output materials + Map outputMaterials = new HashMap<>(); + int materialOutputCount = Math.max(form.materialOutputCount, form.materialOutputs != null ? form.materialOutputs.size() : 0); + if (materialOutputCount > 0 && outSampleType != null) + { + requiredParentTypes.addAll(outSampleType.getRequiredImportAliases().values()); + DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.materialDefault, form.materialOutputs, materialOutputCount, ExpMaterial.DEFAULT_CPAS_TYPE) + { + @Override + protected TableInfo createTable() + { + SamplesSchema schema = new SamplesSchema(getUser(), getContainer()); + return schema.getTable(outSampleType.getName()); + } + + @Override + protected List getExpObject(List> insertedRows) + { + List rowIds = insertedRows.stream().map(r -> MapUtils.getLong(r,"rowid")).collect(toList()); + return ExperimentService.get().getExpMaterials(rowIds); + } + }; + + outputMaterials = derived.createOutputs(); + } + + + // create output data + Map outputData = new HashMap<>(); + int dataOutputCount = Math.max(form.dataOutputCount, form.dataOutputs != null ? form.dataOutputs.size() : 0); + if (dataOutputCount > 0 && outDataClass != null) + { + requiredParentTypes.addAll(outDataClass.getRequiredImportAliases().values()); + DerivedOutputs derived = new DerivedOutputs<>(parentInputNames, form.dataDefault, form.dataOutputs, dataOutputCount, ExpData.DEFAULT_CPAS_TYPE) + { + @Override + protected TableInfo createTable() + { + ExpSchema expSchema = new ExpSchema(getUser(), getContainer()); + UserSchema dataSchema = expSchema.getUserSchema(ExpSchema.NestedSchemas.data.name()); + return dataSchema.getTable(outDataClass.getName()); + } + + @Override + protected List getExpObject(List> insertedRows) + { + List lsids = insertedRows.stream().map(r -> (String) r.get("lsid")).collect(toList()); + return ExperimentService.get().getExpDatasByLSID(lsids); + } + }; + + outputData = derived.createOutputs(); + } + + if (outputMaterials.isEmpty() && outputData.isEmpty()) + throw new IllegalStateException("Expected to create " + materialOutputCount + " materials and " + dataOutputCount + " datas"); + + boolean hasMissingRequiredParent = false; + for (String required : requiredParentTypes) + { + if (!inputTypes.contains(required)) + { + hasMissingRequiredParent = true; + break; + } + } + if (hasMissingRequiredParent) + throw new IllegalStateException("Inputs are required: " + String.join(",", requiredParentTypes)); + + // finally, create the derived run if there are any parents + ExpRun run = null; + if (!materialInputs.isEmpty() || !dataInputs.isEmpty()) + run = ExperimentService.get().derive(materialInputs, dataInputs, outputMaterials, outputData, new ViewBackgroundInfo(getContainer(), getUser(), null), _log); + tx.commit(); + + StringBuilder successMessage = new StringBuilder("Created "); + if (!outputMaterials.isEmpty()) + successMessage.append(outputMaterials.size()).append(" materials"); + if (!outputData.isEmpty()) + successMessage.append(outputData.size()).append(" data"); + + JSONObject ret; + if (run != null) + ret = ExperimentJSONConverter.serializeRun(run, null, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); + else + ret = ExperimentJSONConverter.serializeRunOutputs(outputData.keySet(), outputMaterials.keySet(), getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); + + return success(successMessage.toString(), ret); + } + } + + // Helper class that prepares and executes the QueryUpdateService.insertRows() on the data or material table. + private abstract class DerivedOutputs + { + private final @NotNull Map> _parentInputNames; + private final @Nullable Map _defaultValues; + private final @Nullable List _values; + private final int _outputCount; + private final String _rolePrefix; + + + public DerivedOutputs(@NotNull Map> parentInputNames, @Nullable Map defaultValues, @Nullable List values, int outputCount, String rolePrefix) + { + _parentInputNames = parentInputNames; + _defaultValues = defaultValues; + _values = values; + _outputCount = outputCount; + _rolePrefix = rolePrefix; + } + + public Pair>, List> prepareRows() + { + List> rows = new ArrayList<>(); + List roles = new ArrayList<>(); + int unknownOutputDataCount = 0; + + for (int i = 0; i < _outputCount; i++) + { + Map row = new CaseInsensitiveHashMap<>(); + if (_defaultValues != null) + row.putAll(_defaultValues); + DerivationSpec spec = _values != null && i < _values.size() ? _values.get(i) : null; + String role = null; + if (spec != null) + { + row.putAll(spec.values); + role = spec.role; + } + + // NOTE: Input parents are added to each row, but are only used for name generation and not for derivation. + // NOTE: We will derive the inserted samples in a single derivation run after the sample/date have been inserted. + row.putAll(_parentInputNames); + + rows.add(row); + + if (StringUtils.trimToNull(role) == null) + { + role = _rolePrefix + (unknownOutputDataCount == 0 ? "" : Integer.toString(unknownOutputDataCount + 1)); + unknownOutputDataCount++; + } + roles.add(role); + } + return Pair.of(rows, roles); + } + + protected abstract TableInfo createTable(); + + protected abstract List getExpObject(List> insertedRows); + + public Map createOutputs() throws BatchValidationException, DuplicateKeyException, SQLException, QueryUpdateServiceException + { + Pair>, List> pair = prepareRows(); + List> rows = pair.first; + List roles = pair.second; + + TableInfo table = createTable(); + QueryUpdateService qus = table.getUpdateService(); + if (qus == null) + throw new IllegalStateException(); + + Map configParams = new HashMap<>(); + // Skip derivation during insert -- DeriveAction will call ExperimentService.get().derive() after samples are inserted + configParams.put(SampleTypeUpdateServiceDI.Options.SkipDerivation, true); + + BatchValidationException qusErrors = new BatchValidationException(); + List> insertedRows = qus.insertRows(getUser(), getContainer(), rows, qusErrors, configParams, null); + if (qusErrors.hasErrors()) + throw qusErrors; + + if (insertedRows.size() != roles.size()) + throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); + + List outputs = getExpObject(insertedRows); + if (outputs.size() != roles.size()) + throw new IllegalStateException("Expected to create " + roles.size() + " new exp objects for derivation"); + + Map outputMap = new HashMap<>(); + for (int i = 0; i < outputs.size(); i++) + { + String role = roles.get(i); + T data = outputs.get(i); + outputMap.put(data, role); + } + + return outputMap; + } + } + } + + public static class CreateExperimentForm extends ExperimentForm implements DataRegionSelection.DataSelectionKeyForm + { + private boolean _addSelectedRuns; + private String _dataRegionSelectionKey; + + public boolean isAddSelectedRuns() + { + return _addSelectedRuns; + } + + public void setAddSelectedRuns(boolean addSelectedRuns) + { + _addSelectedRuns = addSelectedRuns; + } + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String dataRegionSelectionKey) + { + _dataRegionSelectionKey = dataRegionSelectionKey; + } + } + + @RequiresPermission(InsertPermission.class) + @ActionNames("createRunGroup, createExperiment") + public class CreateRunGroupAction extends FormViewAction + { + @Override + public ModelAndView getView(CreateExperimentForm form, boolean reshow, BindException errors) + { + // HACK - convert ExperimentForm to not be a BeanViewForm + form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); + form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + + DataRegion drg = new DataRegion(); + + drg.addHiddenFormField(ActionURL.Param.returnUrl, getViewContext().getRequest().getParameter(ActionURL.Param.returnUrl.name())); + drg.addHiddenFormField("addSelectedRuns", Boolean.toString("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns")))); + form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + // Fix issue 27562 - include session-stored selection + if (form.getDataRegionSelectionKey() != null) + { + for (String rowId : DataRegionSelection.getSelected(getViewContext(), form.getDataRegionSelectionKey(), false)) + { + drg.addHiddenFormField(DataRegion.SELECT_CHECKBOX_NAME, rowId); + } + } + drg.addHiddenFormField(DataRegionSelection.DATA_REGION_SELECTION_KEY, getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + + drg.addColumns(ExperimentServiceImpl.get().getTinfoExperiment(), "RowId,Name,LSID,ContactId,ExperimentDescriptionURL,Hypothesis,Comments,Created"); + + DisplayColumn col = drg.getDisplayColumn("RowId"); + col.setVisible(false); + drg.getDisplayColumn("LSID").setVisible(false); + drg.getDisplayColumn("Created").setVisible(false); + + ButtonBar bb = new ButtonBar(); + bb.setStyle(ButtonBar.Style.separateButtons); + ActionButton insertButton = new ActionButton(new ActionURL(CreateRunGroupAction.class, getContainer()), "Submit", ActionButton.Action.POST); + bb.add(insertButton); + + drg.setButtonBar(bb); + + return new InsertView(drg, errors); + } + + + @Override + public boolean handlePost(CreateExperimentForm form, BindException errors) throws Exception + { + // This is strange... but the "Create new run group..." menu item on the run grid always POSTs, probably to + // allow for long lists of run IDs. This "noPost" parameter on the initial POST is used to inform the action + // that it wants to display the form, not try to save anything yet. + if (!"true".equals(getViewContext().getRequest().getParameter("noPost"))) + { + form.setAddSelectedRuns("true".equals(getViewContext().getRequest().getParameter("addSelectedRuns"))); + form.setDataRegionSelectionKey(getViewContext().getRequest().getParameter(DataRegionSelection.DATA_REGION_SELECTION_KEY)); + + Experiment exp = form.getBean(); + if (exp.getName() == null || exp.getName().trim().isEmpty()) + { + errors.reject(ERROR_MSG, "You must specify a name for the experiment"); + } + else + { + int maxNameLength = ExperimentService.get().getTinfoExperimentRun().getColumn("Name").getScale(); + if (exp.getName().length() > maxNameLength) + { + errors.reject(ERROR_MSG, "Name of the experiment must be " + maxNameLength + " characters or less."); + } + } + + String lsid; + int suffix = 1; + do + { + String template = "urn:lsid:" + XarContext.LSID_AUTHORITY_SUBSTITUTION + ":Experiment.Folder-" + XarContext.CONTAINER_ID_SUBSTITUTION + ":" + exp.getName(); + if (suffix > 1) + { + template = template + suffix; + } + suffix++; + lsid = LsidUtils.resolveLsidFromTemplate(template, new XarContext("Experiment Creation", getContainer(), getUser()), ExpExperiment.DEFAULT_CPAS_TYPE); + } + while (ExperimentService.get().getExpExperiment(lsid) != null); + exp.setLSID(lsid); + exp.setContainer(getContainer()); + + if (errors.getErrorCount() == 0) + { + ExpExperimentImpl wrapper = new ExpExperimentImpl(exp); + wrapper.save(getUser()); + + if (form.isAddSelectedRuns()) + { + addSelectedRunsToExperiment(wrapper, form.getDataRegionSelectionKey()); + } + + if (form.getReturnUrl() != null) + { + throw new RedirectException(form.getReturnUrl()); + } + throw new RedirectException(ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer())); + } + } + return true; + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("runGroups"); + root.addChild("Create Run Group"); + } + + @Override + public URLHelper getSuccessURL(CreateExperimentForm createExperimentForm) + { + return null; // null is used to show the form in the case where IDs are POSTed from the grid + } + + @Override + public void validateCommand(CreateExperimentForm target, Errors errors) { } + } + + public static class MoveRunsForm implements DataRegionSelection.DataSelectionKeyForm + { + private String _targetContainerId; + private String _dataRegionSelectionKey; + + @Override + public String getDataRegionSelectionKey() + { + return _dataRegionSelectionKey; + } + + @Override + public void setDataRegionSelectionKey(String key) + { + _dataRegionSelectionKey = key; + } + + public String getTargetContainerId() + { + return _targetContainerId; + } + + public void setTargetContainerId(String targetContainerId) + { + _targetContainerId = targetContainerId; + } + } + + @RequiresPermission(DeletePermission.class) + public class MoveRunsLocationAction extends SimpleViewAction + { + @Override + public ModelAndView getView(MoveRunsForm form, BindException errors) + { + ActionURL moveURL = new ActionURL(MoveRunsAction.class, getContainer()); + PipelineRootContainerTree ct = new PipelineRootContainerTree(getUser(), moveURL) + { + private boolean _clickHandlerRegistered = false; + + @Override + protected void renderCellContents(StringBuilder html, Container c, ActionURL url, boolean hasRoot) + { + boolean renderLink = hasRoot && !c.equals(getContainer()); + + if (renderLink) + { + html.append(""); + } + html.append(PageFlowUtil.filter(c.getName())); + if (renderLink) + { + html.append(""); + } + + if (!_clickHandlerRegistered) + { + HttpView.currentPageConfig().addHandlerForQuerySelector("a.move-target-container", "click", "moveTo(this.attributes.getNamedItem('data-objectid').value);" ); + _clickHandlerRegistered = true; + } + } + }; + ct.setInitialLevel(1); + + MoveRunsBean bean = new MoveRunsBean(ct, form.getDataRegionSelectionKey()); + JspView result = new JspView<>("/org/labkey/experiment/moveRunsLocation.jsp", bean); + result.setTitle("Choose Destination Folder"); + result.setFrame(WebPartView.FrameType.PORTAL); + return result; + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild("Move Runs"); + } + } + + + @RequiresPermission(DeletePermission.class) + public class MoveRunsAction extends FormHandlerAction + { + private Container _targetContainer; + + @Override + public void validateCommand(MoveRunsForm target, Errors errors) + { + } + + @Override + public boolean handlePost(MoveRunsForm form, BindException errors) + { + _targetContainer = ContainerManager.getForId(form.getTargetContainerId()); + if (_targetContainer == null || !_targetContainer.hasPermission(getUser(), InsertPermission.class)) + { + throw new UnauthorizedException(); + } + + Set runIds = DataRegionSelection.getSelectedIntegers(getViewContext(), form.getDataRegionSelectionKey(), false); + List runs = new ArrayList<>(); + for (Long runId : runIds) + { + ExpRun run = ExperimentService.get().getExpRun(runId); + if (run != null) + { + runs.add(run); + } + } + + ViewBackgroundInfo info = getViewBackgroundInfo(); + info.setContainer(_targetContainer); + + try + { + ExperimentService.get().moveRuns(info, getContainer(), runs); + if (form.getDataRegionSelectionKey() != null) + DataRegionSelection.clearAll(getViewContext(), form.getDataRegionSelectionKey()); + } + catch (IOException e) + { + throw new NotFoundException("Failed to initialize move. Check that the pipeline root is configured correctly. " + e); + } + return true; + } + + @Override + public ActionURL getSuccessURL(MoveRunsForm form) + { + return urlProvider(PipelineUrls.class).urlBegin(_targetContainer); + } + } + + public static class ShowExternalDocsForm + { + private String _objectURI; + private String _propertyURI; + + public String getObjectURI() + { + return _objectURI; + } + + public void setObjectURI(String objectURI) + { + _objectURI = objectURI; + } + + public String getPropertyURI() + { + return _propertyURI; + } + + public void setPropertyURI(String propertyURI) + { + _propertyURI = propertyURI; + } + } + + @RequiresPermission(ReadPermission.class) + public static class ShowExternalDocsAction extends SimpleViewAction + { + @Override + public ModelAndView getView(ShowExternalDocsForm form, BindException errors) throws Exception + { + Map props = OntologyManager.getPropertyObjects(getContainer(), form.getObjectURI()); + ObjectProperty prop = props.get(form.getPropertyURI()); + if (prop == null || !getContainer().equals(prop.getContainer())) + { + throw new NotFoundException(); + } + URI uri = new URI(prop.getStringValue()); + File f = new File(uri); + if (!f.exists()) + { + throw new NotFoundException(); + } + + PageFlowUtil.streamFile(getViewContext().getResponse(), new File(f.getAbsolutePath()), false); + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + } + } + + + // TODO: DotGraph has been adding a "runId" parameter, but ShowGraphMoreListAction + public static ActionURL getShowGraphMoreListURL(Container c, @Nullable Long runId, @NotNull String objtype) + { + ActionURL url = new ActionURL(ShowGraphMoreListAction.class, c); + + if (null != runId) + url.addParameter("runId", runId); + + url.addParameter("objtype", objtype); + + return url; + } + + + @RequiresPermission(ReadPermission.class) + public static class ShowGraphMoreListAction extends SimpleViewAction + { + private ExperimentRunForm _form; + + @Override + public ModelAndView getView(ExperimentRunForm form, BindException errors) + { + _form = form; + return new GraphMoreGrid(getContainer(), errors, getViewContext().getActionURL()); + } + + @Override + public void addNavTrail(NavTree root) + { + root.addChild(new NavTree("Experiments", ExperimentUrlsImpl.get().getShowExperimentsURL(getContainer()))); + ExpRun run = ExperimentService.get().getExpRun(_form.getRowId()); + if (run != null) + { + root.addChild(new NavTree("Experiment Run", ExperimentUrlsImpl.get().getRunGraphURL(_form.lookupRun()))); + } + root.addChild(new NavTree("Selected Protocol Applications")); + } + } + + @RequiresPermission(DesignAssayPermission.class) + public class AssayXarFileAction extends MutatingApiAction + { + + @Override + public Object execute(Object o, BindException errors) throws Exception + { + ApiSimpleResponse response = new ApiSimpleResponse(); + + if (!(getViewContext().getRequest() instanceof MultipartHttpServletRequest)) + throw new BadRequestException("Expected MultipartHttpServletRequest when posting files."); + + if (!PipelineService.get().hasValidPipelineRoot(getContainer())) + { + return false; + } + + MultipartFile formFile = getFileMap().get("file"); + if (formFile == null) + { + errors.reject(ERROR_MSG, "No file was posted by the browser."); + return false; + } + + byte[] bytes = formFile.getBytes(); + if (bytes.length == 0) + { + errors.reject(ERROR_MSG, "No file was posted by the browser."); + return false; + } + + PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer()); + FileLike systemDir = pipeRoot.ensureSystemDirectory(); + FileLike uploadDir = systemDir.resolveChild("UploadedXARs"); + FileUtil.createDirectories(uploadDir); + if (!uploadDir.isDirectory()) + { + errors.reject(ERROR_MSG, "Unable to create a 'system/UploadedXARs' directory under the pipeline root"); + return false; + } + String userDirName = getUser().getEmail(); + if (userDirName == null || userDirName.isEmpty()) + { + userDirName = GUEST_DIRECTORY_NAME; + } + FileLike userDir = uploadDir.resolveChild(userDirName); + FileUtil.createDirectories(userDir); + if (!userDir.isDirectory()) + { + errors.reject(ERROR_MSG, "Unable to create an 'UploadedXARs/" + userDirName + "' directory under the pipeline root"); + return false; + } + + FileLike xarFile = userDir.resolveChild(formFile.getOriginalFilename()); + + // As this is multi-part will need to use finally to close, to prevent a stream closure exception + try (OutputStream out = new BufferedOutputStream(xarFile.openOutputStream())) + { + out.write(bytes); + } + catch (IOException e) + { + errors.reject(ERROR_MSG, "Unable to write uploaded XAR file to " + xarFile); + return false; + } + //noinspection EmptyCatchBlock + + ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), xarFile, + "Uploaded file", true, pipeRoot); + PipelineService.get().queueJob(job); + + response.put("success", true); + return response; + } + } + + @RequiresPermission(InsertPermission.class) + public class ImportXarFileAction extends FormHandlerAction + { + @Override + public void validateCommand(ImportXarForm target, Errors errors) + { + } + + @Override + public boolean handlePost(ImportXarForm form, BindException errors) throws Exception + { + for (FileLike f : form.getValidatedFiles(getContainer())) + { + if (f.isFile()) + { + ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); + + // TODO: Configure module resources with the appropriate log location per container + if (form.getModule() != null) + { + FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); + job.setLogFile(logFile); + } + + PipelineService.get().queueJob(job); + } + else + { + throw new NotFoundException("Expected a file but found a directory: " + f.getName()); + } + } + + return true; + } + + @Override + public URLHelper getSuccessURL(ImportXarForm importXarForm) + { + return getContainer().getStartURL(getUser()); + } + } + + + @RequiresPermission(InsertPermission.class) + public class ImportXarAction extends MutatingApiAction + { + @Override + public Object execute(ImportXarForm form, BindException errors) throws Exception + { + ApiSimpleResponse response = new ApiSimpleResponse(); + + List> archives = new ArrayList<>(); + for (FileLike f : form.getValidatedFiles(getContainer())) + { + Map archive = new HashMap<>(); + ExperimentPipelineJob job = new ExperimentPipelineJob(getViewBackgroundInfo(), f, "Experiment Import", false, form.getPipeRoot(getContainer())); + + // TODO: Configure module resources with the appropriate log location per container + if (form.getModule() != null) + { + FileLike logFile = form.getPipeRoot(getContainer()).getLogDirectoryFileLike(true).resolveChild("module-resource-xar.log"); + job.setLogFile(logFile); + } + + PipelineService.get().queueJob(job); + + archive.put("file", f.getName()); + archive.put("job", job.getJobGUID()); + archive.put("path", form.getPath()); // echo back the public path + + archives.add(archive); + } + + response.put("success", true); + response.put("archives", archives); + + return response; + } + } + + + /** + * User: jeckels + * Date: Jan 27, 2008 + */ + public static class ExperimentUrlsImpl implements ExperimentUrls + { + public ActionURL getOverviewURL(Container c) + { + return new ActionURL(BeginAction.class, c); + } + + @Override + public ActionURL getExperimentDetailsURL(Container c, ExpExperiment expExperiment) + { + return new ActionURL(DetailsAction.class, c).addParameter("rowId", expExperiment.getRowId()); + } + + public ActionURL getShowSampleURL(Container c, ExpMaterial material) + { + return getMaterialDetailsBaseURL(c, null).addParameter("rowId", material.getRowId()); + } + + @Override + public ActionURL getExportProtocolURL(Container container, ExpProtocol protocol) + { + return new ActionURL(ExperimentController.ExportProtocolsAction.class, container). + addParameter("protocolId", protocol.getRowId()). + addParameter("xarFileName", protocol.getName() + ".xar"); + } + + @Override + public ActionURL getMoveRunsLocationURL(Container container) + { + return new ActionURL(ExperimentController.MoveRunsLocationAction.class, container); + } + + @Override + public ActionURL getProtocolDetailsURL(ExpProtocol protocol) + { + return new ActionURL(ProtocolDetailsAction.class, protocol.getContainer()).addParameter("rowId", protocol.getRowId()); + } + + @Override + public ActionURL getProtocolApplicationDetailsURL(ExpProtocolApplication app) + { + return getShowApplicationURL(app.getContainer(), app.getRowId()); + } + + public ActionURL getProtocolGridURL(Container c) + { + return new ActionURL(ShowProtocolGridAction.class, c); + } + + public ActionURL getRunGraphDetailURL(ExpRun run) + { + return getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpData focus) + { + return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_DATA); + } + + public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpMaterial focus) + { + return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_MATERIAL); + } + + public ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpProtocolApplication focus) + { + return getRunGraphDetailURL(run, focus, DotGraph.TYPECODE_PROT_APP); + } + + private ActionURL getRunGraphDetailURL(ExpRun run, @Nullable ExpObject focus, String typeCode) + { + ActionURL result = getShowRunGraphDetailURL(run.getContainer(), run.getRowId()); + result.addParameter("detail", "true"); + if (focus != null) + { + result.addParameter("focus", typeCode + focus.getRowId()); + } + return result; + } + + @Override + public ActionURL getRunGraphURL(Container container, long runId) + { + return ExperimentController.getRunGraphURL(container, runId); + } + + @Override + public ActionURL getRunGraphURL(ExpRun run) + { + return getRunGraphURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getRunTextURL(Container c, long runId) + { + return new ActionURL(ShowRunTextAction.class, c).addParameter("rowId", runId); + } + + @Override + public ActionURL getRunTextURL(ExpRun run) + { + return getRunTextURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getDeleteExperimentsURL(Container container, URLHelper returnUrl) + { + return new ActionURL(DeleteSelectedExperimentsAction.class, container).addReturnUrl(returnUrl); + } + + @Override + public ActionURL getDeleteProtocolURL(@NotNull ExpProtocol protocol, URLHelper returnUrl) + { + ActionURL result = new ActionURL(DeleteProtocolByRowIdsAction.class, protocol.getContainer()); + result.addParameter("singleObjectRowId", protocol.getRowId()); + if (returnUrl != null) + { + result.addReturnUrl(returnUrl); + } + return result; + } + + @Override + public ActionURL getAddRunsToExperimentURL(Container c, ExpExperiment exp) + { + return new ActionURL(AddRunsToExperimentAction.class, c).addParameter("expRowId", exp.getRowId()); + } + + @Override + public ActionURL getShowRunsURL(Container c, ExperimentRunType type) + { + ActionURL result = new ActionURL(ShowRunsAction.class, c); + result.addParameter("experimentRunFilter", type.getDescription()); + return result; + } + + public ActionURL getShowExperimentsURL(Container c) + { + return new ActionURL(ShowRunGroupsAction.class, c); + } + + @Override + public ActionURL getShowSampleTypeListURL(Container c) + { + return getShowSampleTypeListURL(c, null); + } + + @Override + public ActionURL getShowSampleTypeURL(ExpSampleType sampleType) + { + return getShowSampleTypeURL(sampleType, sampleType.getContainer()); + } + + @Override + public ActionURL getShowSampleTypeURL(ExpSampleType sampleType, Container container) + { + return new ActionURL(ShowSampleTypeAction.class, container).addParameter("rowId", sampleType.getRowId()); + } + + public ActionURL getExperimentListURL(Container container) + { + return new ActionURL(ShowRunGroupsAction.class, container); + } + + public ActionURL getShowSampleTypeListURL(Container c, String errorMessage) + { + ActionURL url = new ActionURL(ListSampleTypesAction.class, c); + if (errorMessage != null) + { + url.addParameter("errorMessage", errorMessage); + } + return url; + } + + @Override + public ActionURL getDataClassListURL(Container c) + { + return getDataClassListURL(c, null); + } + + public ActionURL getDataClassListURL(Container c, String errorMessage) + { + ActionURL url = new ActionURL(ListDataClassAction.class, c); + if (errorMessage != null) + { + url.addParameter("errorMessage", errorMessage); + } + return url; + } + + @Override + public ActionURL getDeleteDatasURL(Container c, URLHelper returnUrl) + { + ActionURL url = new ActionURL(DeleteSelectedDataAction.class, c); + if (returnUrl != null) + url.addReturnUrl(returnUrl); + return url; + } + + public ActionURL getDeleteSelectedExperimentsURL(Container c, URLHelper returnUrl) + { + ActionURL result = new ActionURL(DeleteSelectedExperimentsAction.class, c); + if (returnUrl != null) + result.addReturnUrl(returnUrl); + return result; + } + + @Override + public ActionURL getDeleteSelectedExpRunsURL(Container container, URLHelper returnUrl) + { + return new ActionURL(DeleteSelectedExpRunsAction.class, container).addReturnUrl(returnUrl); + } + + public ActionURL getShowUpdateURL(ExpExperiment experiment) + { + return new ActionURL(ShowUpdateAction.class, experiment.getContainer()).addParameter("rowId", experiment.getRowId()); + } + + @Override + public ActionURL getRemoveSelectedExpRunsURL(Container container, URLHelper returnUrl, ExpExperiment exp) + { + return new ActionURL(RemoveSelectedExpRunsAction.class, container).addReturnUrl(returnUrl).addParameter("expRowId", exp.getRowId()); + } + + @Override + public ActionURL getCreateRunGroupURL(Container container, URLHelper returnUrl, boolean addSelectedRuns) + { + ActionURL result = new ActionURL(CreateRunGroupAction.class, container); + if (returnUrl != null) + { + result.addReturnUrl(returnUrl); + } + if (addSelectedRuns) + { + result.addParameter("addSelectedRuns", "true"); + } + return result; + } + + + public static ExperimentUrlsImpl get() + { + return (ExperimentUrlsImpl) urlProvider(ExperimentUrls.class); + } + + public ActionURL getDownloadGraphURL(ExpRun run, boolean detail, String focus, String focusType) + { + ActionURL result = new ActionURL(DownloadGraphAction.class, run.getContainer()); + result.addParameter("rowId", run.getRowId()).addParameter("detail", detail); + if (focus != null) + { + result.addParameter("focus", focus); + } + if (focusType != null) + { + result.addParameter("focusType", focusType); + } + return result; + } + + public ActionURL getBeginURL(Container container) + { + return new ActionURL(BeginAction.class, container); + } + + @Override + public ActionURL getDomainEditorURL(Container container, String domainURI, boolean createOrEdit) + { + Domain domain = PropertyService.get().getDomain(container, domainURI); + if (domain != null) + return getDomainEditorURL(container, domain); + + ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); + url.addParameter("domainURI", domainURI); + if (createOrEdit) + url.addParameter("createOrEdit", true); + return url; + } + + @Override + public ActionURL getDomainEditorURL(Container container, Domain domain) + { + ActionURL url = new ActionURL(PropertyController.EditDomainAction.class, container); + url.addParameter("domainId", domain.getTypeId()); + return url; + } + + @Override + public ActionURL getCreateDataClassURL(Container container) + { + return new ActionURL(EditDataClassAction.class, container); + } + + @Override + public ActionURL getShowDataClassURL(Container container, long rowId) + { + ActionURL url = new ActionURL(ShowDataClassAction.class, container); + url.addParameter("rowId", rowId); + return url; + } + + @Override + public ActionURL getShowFileURL(ExpData data, boolean inline) + { + ActionURL result = getShowFileURL(data.getContainer()).addParameter("rowId", data.getRowId()); + if (inline) + { + result.addParameter("inline", inline); + } + return result; + } + + @Override + public ActionURL getMaterialDetailsURL(ExpMaterial material) + { + return getMaterialDetailsURL(material.getContainer(), material.getRowId()); + } + + @Override + public ActionURL getMaterialDetailsURL(Container c, long materialRowId) + { + return getMaterialDetailsBaseURL(c, null).addParameter("rowId", materialRowId); + } + + @Override + public ActionURL getMaterialDetailsBaseURL(Container c, @Nullable String materialIdFieldKey) + { + return new ActionURL(ShowMaterialAction.class, c); + } + + @Override + public ActionURL getCreateSampleTypeURL(Container container) + { + return new ActionURL(EditSampleTypeAction.class, container); + } + + @Override + public ActionURL getImportSamplesURL(Container container, String sampleTypeName) + { + ActionURL url = new ActionURL(ImportSamplesAction.class, container); + url.addParameter("query.queryName", sampleTypeName); + url.addParameter("schemaName", "exp.materials"); + return url; + } + + @Override + public ActionURL getImportDataURL(Container container, String dataClassName) + { + ActionURL url = new ActionURL(ImportDataAction.class, container); + url.addParameter("query.queryName", dataClassName); + url.addParameter("schemaName", "exp.data"); + return url; + } + + @Override + public ActionURL getDataDetailsURL(ExpData data) + { + return new ActionURL(ShowDataAction.class, data.getContainer()).addParameter("rowId", data.getRowId()); + } + + @Override + public ActionURL getShowFileURL(Container c) + { + return new ActionURL(ShowFileAction.class, c); + } + + @Override + public ActionURL getSetFlagURL(Container container) + { + return new ActionURL(SetFlagAction.class, container); + } + + @Override + public ActionURL getShowRunGraphURL(ExpRun run) + { + return ExperimentController.getRunGraphURL(run.getContainer(), run.getRowId()); + } + + @Override + public ActionURL getRepairTypeURL(Container container) + { + return new ActionURL(TypesController.RepairAction.class, container); + } + + @Override + public ActionURL getUpdateMaterialQueryRowAction(Container c, TableInfo table) + { + ActionURL url = new ActionURL(UpdateMaterialQueryRowAction.class, c); + url.addParameter("schemaName", "samples"); + url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); + + return url; + } + + @Override + public ActionURL getInsertMaterialQueryRowAction(Container c, TableInfo table) + { + ActionURL url = new ActionURL(InsertMaterialQueryRowAction.class, c); + url.addParameter(QueryView.DATAREGIONNAME_DEFAULT + "." + QueryParam.queryName, table.getName()); + + return url; + } + + @Override + public ActionURL getDataClassAttachmentDownloadAction(Container c) + { + return new ActionURL(ExperimentController.DataClassAttachmentDownloadAction.class, c); + } + + } + + private static abstract class BaseResolveLsidApiAction extends ReadOnlyApiAction + { + protected Set _seeds; + + @Override + public void validateForm(F form, Errors errors) + { + if (null != form.getLsids()) + { + _seeds = new LinkedHashSet<>(form.getLsids().size()); + for (String lsid : form.getLsids()) + { + Identifiable id = LsidManager.get().getObject(lsid); + if (id == null) + throw new NotFoundException("Unable to resolve object: " + lsid); + + // ensure the user has read permission in the seed container + if (!getContainer().equals(id.getContainer())) + { + if (!id.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new UnauthorizedException("User does not have permission to read object: " + lsid); + } + + _seeds.add(id); + } + } + else + { + throw new ApiUsageException("Starting lsids required"); + } + } + } + + @RequiresPermission(ReadPermission.class) + public static class ResolveAction extends BaseResolveLsidApiAction + { + @Override + public Object execute(ResolveLsidsForm form, BindException errors) + { + var settings = new ExperimentJSONConverter.Settings(form.isIncludeProperties(), form.isIncludeInputsAndOutputs(), form.isIncludeRunSteps()); + var data = _seeds.stream().map(n -> ExperimentJSONConverter.serialize(n, getUser(), settings)).collect(toList()); + return new ApiSimpleResponse("data", data); + } + } + + @RequiresPermission(ReadPermission.class) + public static class LineageAction extends BaseResolveLsidApiAction + { + @Override + public Object execute(ExpLineageOptions options, BindException errors) throws Exception + { + ExpLineageServiceImpl.get().streamLineage(getContainer(), getUser(), getViewContext().getResponse(), _seeds, options); + return null; + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class RebuildEdgesAction extends MutatingApiAction + { + @Override + public Object execute(ExperimentRunForm form, BindException errors) + { + if (form.getRowId() != 0 || form.getLsid() != null) + { + ExpRun run = form.lookupRun(); + if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new UnauthorizedException("Not permitted"); + + ExperimentServiceImpl.get().syncRunEdges(run); + } + else + { + // should this require site admin permissions? + ExperimentServiceImpl.get().rebuildAllRunEdges(); + } + return success(); + } + } + + private static class VerifyEdgesForm extends ExperimentRunForm + { + private Integer _limit; + + public Integer getLimit() + { + return _limit; + } + + public void setLimit(Integer limit) + { + _limit = limit; + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class VerifyEdgesAction extends ReadOnlyApiAction + { + @Override + public Object execute(VerifyEdgesForm form, BindException errors) + { + if (form.getRowId() != 0 || form.getLsid() != null) + { + ExpRun run = form.lookupRun(); + if (!run.getContainer().hasPermission(getUser(), ReadPermission.class)) + throw new UnauthorizedException("Not permitted"); + + ExperimentServiceImpl.get().verifyRunEdges(run); + } + else + { + ExperimentServiceImpl.get().verifyAllEdges(getContainer(), form.getLimit()); + } + return success(); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class RebuildAncestorsAction extends MutatingApiAction + { + @Override + public Object execute(Object form, BindException errors) + { + ClosureQueryHelper.truncateAndRecreate(); + return success(); + } + } + + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class CheckDataClassesIndexedAction extends ReadOnlyApiAction + { + @Override + public Object execute(Object o, BindException errors) throws Exception + { + List> notInIndex = new ArrayList<>(100); + + List list = ExperimentService.get().getDataClasses(getContainer(), getUser(), false); + for (ExpDataClass dc : list) + { + for (ExpData d : dc.getDatas()) + { + String docId = d.getDocumentId(); + if (docId != null) + { + SearchService.SearchHit hit = SearchService.get().find(docId); + if (hit == null) + { + JSONObject props = ExperimentJSONConverter.serializeData(d, getUser(), ExperimentJSONConverter.DEFAULT_SETTINGS); + props.put("docid", docId); + notInIndex.add(props.toMap()); + } + } + } + } + + return success(notInIndex); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(AdminPermission.class) + public static class CheckEdgesAction extends ReadOnlyApiAction + { + @Override + public Object execute(Object o, BindException errors) throws Exception + { + List result; + DbSchema schema = ExperimentService.get().getSchema(); + TableInfo edgeTable = schema.getTable("Edge"); + + if (null != edgeTable.getColumn("fromObjectId")) + { + var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") + .resultSetStream() + .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) + .collect(toList()); + var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); + result = cycles.stream().map(e -> new Integer[]{e.first, e.second}).collect(toList()); + } + else + { + var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromLsid, toLsid FROM exp.Edge") + .resultSetStream() + .map(r -> { try { return new Pair<>(r.getString(1), r.getString(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) + .collect(toList()); + var cycles = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); + result = cycles.stream().map(e -> new String[]{e.first, e.second}).collect(toList()); + } + + JSONObject ret = new JSONObject(); + ret.put("result", result); + ret.put("success", true); + return ret; + } + } + + @RequiresPermission(UpdatePermission.class) + public static class UpdateMaterialQueryRowAction extends UserSchemaAction + { + @Override + protected QueryForm createQueryForm(ViewContext context) + { + QueryForm form = new QueryForm("samples", null); + form.setViewContext(getViewContext()); + form.bindParameters(getViewContext().getBindPropertyValues()); + return form; + } + + @Override + public BindException bindParameters(PropertyValues m) throws Exception + { + BindException bind = super.bindParameters(m); + + QueryUpdateForm tableForm = (QueryUpdateForm)bind.getTarget(); + + int sampleId; + try + { + sampleId = Integer.parseInt((String) tableForm.getPkVal()); + } + catch (NumberFormatException e) + { + throw new NotFoundException("Invalid RowId: " + tableForm.getPkVal()); + } + + ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); + if (material == null) + throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); + + return bind; + } + + @Override + public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) + { + int sampleId = Integer.parseInt((String) tableForm.getPkVal()); + + ExpMaterial material = ExperimentService.get().getExpMaterial(sampleId); + if (material == null) + throw new NotFoundException("Invalid material: " + tableForm.getPkVal()); + + boolean isAliquot = !StringUtils.isEmpty(material.getAliquotedFromLSID()); + + TableInfo tableInfo = tableForm.getTable(); + Map scopedFields = new CaseInsensitiveHashMap<>(); + for (DomainProperty dp : tableInfo.getDomain().getProperties()) + { + if (!ExpSchema.DerivationDataScopeType.All.name().equalsIgnoreCase(dp.getDerivationDataScope())) + scopedFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); + } + + for (var column : tableInfo.getColumns()) + { + String columnName = column.getName(); + if (scopedFields.containsKey(columnName)) + { + boolean isAliquotField = scopedFields.get(columnName); + boolean show = (isAliquot && isAliquotField) || (!isAliquot && !isAliquotField); + ((BaseColumnInfo)column).setUserEditable(show); + ((BaseColumnInfo)column).setHidden(!show); + } + } + + ButtonBar bb = createSubmitCancelButtonBar(tableForm); + UpdateView view = new UpdateView(tableForm, errors); + view.getDataRegion().setButtonBar(bb); + return view; + } + + @Override + public boolean handlePost(QueryUpdateForm tableForm, BindException errors) + { + doInsertUpdate(tableForm, errors, false); + return 0 == errors.getErrorCount(); + } + + @Override + public void addNavTrail(NavTree root) + { + super.addNavTrail(root); + root.addChild("Edit " + _form.getQueryName()); + } + } + + @RequiresPermission(InsertPermission.class) + public static class InsertMaterialQueryRowAction extends UserSchemaAction + { + @Override + protected QueryForm createQueryForm(ViewContext context) + { + QueryForm form = new QueryForm("samples", null); + form.setViewContext(getViewContext()); + form.bindParameters(getViewContext().getBindPropertyValues()); + + return form; + } + + @Override + public ModelAndView getView(QueryUpdateForm tableForm, boolean reshow, BindException errors) + { + TableInfo tableInfo = tableForm.getTable(); + Map propertyFields = new CaseInsensitiveHashMap<>(); + for (DomainProperty dp : tableInfo.getDomain().getProperties()) + { + propertyFields.put(dp.getName(), ExpSchema.DerivationDataScopeType.ChildOnly.name().equalsIgnoreCase(dp.getDerivationDataScope())); + } + + for (var column : tableInfo.getColumns()) + { + String columnName = column.getName(); + if (propertyFields.containsKey(columnName)) + { + boolean isAliquotField = propertyFields.get(columnName); + ((BaseColumnInfo)column).setUserEditable(!isAliquotField); + ((BaseColumnInfo)column).setHidden(isAliquotField); + } + } + + InsertView view = new InsertView(tableForm, errors); + view.getDataRegion().setButtonBar(createSubmitCancelButtonBar(tableForm)); + return view; + } + + @Override + public boolean handlePost(QueryUpdateForm tableForm, BindException errors) + { + doInsertUpdate(tableForm, errors, true); + return 0 == errors.getErrorCount(); + } + + @Override + public void addNavTrail(NavTree root) + { + super.addNavTrail(root); + root.addChild("Insert " + _form.getQueryName()); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class SaveFindIdsAction extends ReadOnlyApiAction + { + + public static final String FIND_BY_IDS_SESSION_KEY_PREFIX = "findByIds"; + + @Override + public Object execute(FindByIdsForm form, BindException errors) throws Exception + { + HttpServletRequest request = getViewContext().getRequest(); + String key = form.getSessionKey(); + boolean removePrevious = false; + + if (key == null) + { + removePrevious = true; + key = FIND_BY_IDS_SESSION_KEY_PREFIX + "_" + UniqueID.getServerSessionScopedUID(); + } + + if (request != null) + { + if (removePrevious) + SessionHelper.clearAttributesWithPrefix(request, FIND_BY_IDS_SESSION_KEY_PREFIX); + HttpSession session = request.getSession(false); + if (session != null) + { + @SuppressWarnings("unchecked") + List existingIds = (List) session.getAttribute(key); + + // deduplicate from existing ids + if (existingIds != null && form.getSessionKey() != null) + { + existingIds.addAll(form.getIds().stream().filter(id -> !existingIds.contains(id)).toList()); + session.setAttribute(key, existingIds); + } + else + { + session.setAttribute(key, form.getIds()); + } + return success("Saved ids to session key", key); + } + } + + return new SimpleResponse<>(false, "Unable to save to session. Session or request may be null."); + } + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class SaveOrderedSamplesQueryAction extends ReadOnlyApiAction + { + private static final String SAMPLE_ID_PREFIX = "s:"; + private static final String UNIQUE_ID_PREFIX = "u:"; + + private List _ids; + private Map> _uniqueIdLsids; + + @Override + public void validateForm(FindByIdsForm form, Errors errors) + { + if (form.getSessionKey() == null) + errors.reject(ERROR_REQUIRED, "sessionKey must be provided"); + else + { + _ids = getFindIdsFromSession(form.getSessionKey()); + if (_ids == null || _ids.isEmpty()) + errors.reject(ERROR_REQUIRED, "No ids found corresponding to session key " + form.getSessionKey()); + } + } + + private void ensureUniqueIdLsids() + { + boolean hasUniqueId = _ids.stream().anyMatch(s -> s.startsWith(UNIQUE_ID_PREFIX)); + if (hasUniqueId && _uniqueIdLsids == null) + { + List uniqueIds = _ids.stream().map(s -> s.substring(UNIQUE_ID_PREFIX.length())).toList(); + _uniqueIdLsids = ExperimentService.get().getUniqueIdLsids(uniqueIds, getUser(), getContainer()); + } + } + + @Override + public Object execute(FindByIdsForm form, BindException errors) throws Exception + { + ensureUniqueIdLsids(); + + SQLFragment select = getOrderedRowsSql(); + // need to set the key field so selections are possible + // need the SampleTypeUnits so we will display using that unit + String metadata = + """ + + + + + true + true + + + true + + + true + + +
+ """; + QueryDefinition def = QueryService.get().saveSessionQuery(getViewContext(), getContainer(), ExperimentServiceImpl.getExpSchema().getName(), select.getSQL(), metadata); + return success("Session query created", Map.of("queryName", def.getName(), "ids", _ids)); + } + + + private List getFindIdsFromSession(String sessionKey) + { + HttpServletRequest request = getViewContext().getRequest(); + List ids = new ArrayList<>(); + if (request != null) + { + HttpSession session = request.getSession(false); + if (session != null) + { + ids = (List) session.getAttribute(sessionKey); + } + } + return ids; + } + + private SQLFragment getOrderedRowsSql() + { + boolean isFMEnabled = InventoryService.isFreezerManagementEnabled(getContainer()); + String samplesTable = isFMEnabled ? "inventory.SampleItems" : "exp.materials"; + List orderedIdCols = new ArrayList<>(Arrays.asList("Id AS ProvidedID", "RowId", "Ordinal")); + List sampleColumns = new ArrayList<>(); + if (!isFMEnabled) + { + sampleColumns.addAll(Arrays.asList( + "S.Name AS SampleID", + "S.MaterialExpDate AS ExpirationDate", + "S.SampleSet as SampleType", + "S.SampleState", + "S.isAliquot", + "S.Created", + "S.CreatedBy" + )); + } + else + { + sampleColumns.addAll(Arrays.asList( + "S.Name AS SampleID", + "S.MaterialExpDate AS ExpirationDate", + "S.LabelColor", + "S.SampleSet", + "S.SampleState", + "S.StoredAmount", + "S.Units", + "S.SampleTypeUnits", + "S.FreezeThawCount", + "S.StorageStatus", + "S.CheckedOutBy", + "S.StorageLocation", + "S.StorageRow", + "S.StorageCol", + "S.StoragePositionNumber", + "S.IsAliquot", + "S.Created", + "S.CreatedBy" + )); + } + + + String sampleIdComma = ""; + String uniqueIdComma = ""; + int index = 1; + SQLFragment sampleIdValuesSql = new SQLFragment(); + SQLFragment uniqueIdValuesSql = new SQLFragment(); + for (String id : _ids) + { + if (id.startsWith(SAMPLE_ID_PREFIX)) + { + sampleIdValuesSql.append(sampleIdComma).append("\t(").appendValue(index); + sampleIdValuesSql.append(", "); + sampleIdValuesSql.append(LabKeySql.quoteString(id.substring(SAMPLE_ID_PREFIX.length()))); + sampleIdValuesSql.append(", "); + sampleIdValuesSql.append(LabKeySql.quoteString("null")); + sampleIdValuesSql.append(")"); + sampleIdComma = "\n,"; + } + else if (id.startsWith(UNIQUE_ID_PREFIX)) + { + String idClean = id.substring(UNIQUE_ID_PREFIX.length()); + + List lsids = _uniqueIdLsids.get(idClean); + if (lsids != null) + { + for (String lsid : lsids) + { + uniqueIdValuesSql.append(uniqueIdComma).append("\t(").appendValue(index); + uniqueIdValuesSql.append(", "); + uniqueIdValuesSql.append(LabKeySql.quoteString(idClean)); + uniqueIdValuesSql.append(", "); + uniqueIdValuesSql.append(LabKeySql.quoteString(lsid)); + uniqueIdValuesSql.append(")"); + uniqueIdComma = "\n,"; + } + } + } + index++; + } + + boolean haveData = !sampleIdValuesSql.isEmpty() || !_uniqueIdLsids.isEmpty(); + SQLFragment sql = new SQLFragment(); + if (!sampleIdValuesSql.isEmpty()) + { + sql.append("WITH _ordered_ids_ AS (\nSELECT * FROM (VALUES\n"); + sql.append(sampleIdValuesSql); + sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter + } + if (!uniqueIdValuesSql.isEmpty()) + { + if (!sampleIdValuesSql.isEmpty()) + sql.append(",\n"); + else + sql.append("WITH "); + + sql.append("_ordered_unique_ids_ AS (\nSELECT * FROM (VALUES\n"); + sql.append(uniqueIdValuesSql); + sql.append("\n) AS _values_ )\n"); // name of the alias here doesn't matter + } + + sql.append("SELECT "); + sql.append("\n\tOID.").append(StringUtils.join(orderedIdCols, ",\n\tOID.")); + sql.append(",\n\t").append(StringUtils.join( sampleColumns, ",\n\t")); + sql.append("\nFROM\n("); + if (!sampleIdValuesSql.isEmpty()) + { + sql.append("SELECT\n\tM.RowId,\n\t_ordered_ids_.column1 as Ordinal,\n\t_ordered_ids_.column2 as Id,\n\t_ordered_ids_.column2 as lsid"); + sql.append("\nFROM _ordered_ids_\n"); + sql.append("INNER JOIN exp.materials M ON _ordered_ids_.column2 = M.Name"); + sql.append("\n"); + } + if (!uniqueIdValuesSql.isEmpty()) + { + if (!sampleIdValuesSql.isEmpty()) + sql.append("\nUNION ALL\n\n"); + + sql.append("SELECT\n\tM.RowId,\n\t_ordered_unique_ids_.column1 as Ordinal,\n\t_ordered_unique_ids_.column2 as Id,\n\t_ordered_unique_ids_.column3 as lsid"); + sql.append("\nFROM _ordered_unique_ids_\n"); + sql.append("INNER JOIN exp.materials M ON _ordered_unique_ids_.column3 = M.lsid"); + sql.append("\n"); + } + if (!haveData) // no data to return but return data in the expected shape. + { + sql = new SQLFragment("SELECT\n"); + sql.append(orderedIdCols.stream() + .map(col -> { + int asIndex = col.indexOf("AS"); + if (asIndex > 0) + return "NULL AS " + col.substring(asIndex+ 3); + else + return "NULL AS " + col; + }) + .collect(Collectors.joining(",\t\n"))); + sql.append(",\t\n").append(StringUtils.join(sampleColumns, ",\t\n")); + sql.append("\nFROM ").append(samplesTable).append(" S WHERE 1 = 2"); + return sql; + } + else + { + sql.append(") OID"); + if (isFMEnabled) + sql.append("\nLEFT JOIN inventory.SampleItems S on S.RowId = OID.RowId"); + else + sql.append("\nINNER JOIN exp.materials S on S.RowId = OID.RowId"); + sql.append("\n\nORDER BY Ordinal"); + return sql; + } + } + } + + public static class FindByIdsForm extends FindSessionKeyForm + { + List _ids; + + public List getIds() + { + return _ids; + } + + public void setIds(List ids) + { + _ids = ids; + } + } + + + public static class FindSessionKeyForm + { + private String _sessionKey; + + public String getSessionKey() + { + return _sessionKey; + } + + public void setSessionKey(String sessionKey) + { + _sessionKey = sessionKey; + } + } + + static void validateEntitySequenceForm(EntitySequenceForm form, Errors errors) + { + String kindName = form.getKindName(); + if (StringUtils.isEmpty(kindName) || form.getSeqType() == null) + { + errors.reject(ERROR_REQUIRED, "KindName and SeqType must be provided"); + return; + } + + if (form.getSeqType() == NameGenerator.EntityCounter.genId) + { + if (form.getRowId() == null) + errors.reject(ERROR_REQUIRED, "Data type RowId must be provided for genId"); + } + else if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName)) + { + errors.reject(ERROR_MSG, form.getSeqType() + " is not supported for " + kindName); + } + + if (!SampleTypeDomainKind.NAME.equalsIgnoreCase(kindName) && !DataClassDomainKind.NAME.equalsIgnoreCase(kindName)) + errors.reject(ERROR_MSG, "Invalid KindName. Should be either " + SampleTypeDomainKind.NAME + " or " + DataClassDomainKind.NAME + "."); + + } + + @RequiresPermission(ReadPermission.class) + public static class GetEntitySequenceAction extends ReadOnlyApiAction + { + @Override + public void validateForm(EntitySequenceForm form, Errors errors) + { + validateEntitySequenceForm(form, errors); + } + + @Override + public Object execute(EntitySequenceForm form, BindException errors) throws Exception + { + long value = -1; + if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + if (form.getSeqType() == NameGenerator.EntityCounter.genId) + { + ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); + if (sampleType != null) + value = sampleType.getCurrentGenId(); + } + else + { + value = SampleTypeService.get().getCurrentCount(form.getSeqType(), getContainer()); + } + + } + else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); + if (dataClass != null) + value = dataClass.getCurrentGenId(); + } + + ApiSimpleResponse resp = new ApiSimpleResponse(); + resp.put("success", value > -1); + resp.put("value", value); + return resp; + } + } + + @RequiresPermission(ReadPermission.class) // actual permission checked later + public static class SetEntitySequenceAction extends MutatingApiAction + { + @Override + public void validateForm(EntitySequenceForm form, Errors errors) + { + validateEntitySequenceForm(form, errors); + + if (form.getNewValue() == null || form.getNewValue() < 0) + errors.reject(ERROR_MSG, "Invalid newValue."); + } + + @Override + public Object execute(EntitySequenceForm form, BindException errors) + { + ApiSimpleResponse resp = new ApiSimpleResponse(); + resp.put("success", true); + + try + { + Domain domain = null; + if (SampleTypeDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + if (form.getSeqType() == NameGenerator.EntityCounter.genId) + { + if (!getContainer().hasPermission(getUser(), DesignSampleTypePermission.class)) + throw new UnauthorizedException("Insufficient permissions."); + + ExpSampleType sampleType = SampleTypeService.get().getSampleType(form.getRowId()); + if (sampleType != null) + { + sampleType.ensureMinGenId(form.getNewValue()); + domain = sampleType.getDomain(); + } + else + { + resp.put("success", false); + resp.put("error", "Sample type does not exist."); + } + } + else + { + if (!getContainer().hasPermission(getUser(), AdminPermission.class)) + throw new UnauthorizedException("Insufficient permissions."); + + SampleTypeService.get().ensureMinSampleCount(form.getNewValue(), form.getSeqType(), getContainer()); + } + } + else if (DataClassDomainKind.NAME.equalsIgnoreCase(form.getKindName())) + { + if (!getContainer().hasPermission(getUser(), DesignDataClassPermission.class)) + throw new BadRequestException("Insufficient permissions."); + + ExpDataClass dataClass = ExperimentService.get().getDataClass(form.getRowId()); + if (dataClass != null) + { + dataClass.ensureMinGenId(form.getNewValue(), getContainer()); + domain = dataClass.getDomain(); + } + else + { + resp.put("success", false); + resp.put("error", "DataClass does not exist."); + } + } + + if (domain != null) + { + DomainAuditProvider.DomainAuditEvent event = new DomainAuditProvider.DomainAuditEvent(getContainer(), "The genId for domain " + domain.getName() + " has been updated to " + form.getNewValue() + "."); + event.setDomainUri(domain.getTypeURI()); + event.setDomainName(domain.getName()); + AuditLogService.get().addEvent(getUser(), event); + } + } + catch (ExperimentException e) + { + resp.put("success", false); + resp.put("error", e.getMessage()); + } + + return resp; + } + } + + public static class EntitySequenceForm + { + private String _kindName; + private NameGenerator.EntityCounter _seqType; + private Integer _rowId; + private Long _newValue; + + public Integer getRowId() + { + return _rowId; + } + + public void setRowId(Integer rowId) + { + _rowId = rowId; + } + + public String getKindName() + { + return _kindName; + } + + public void setKindName(String kindName) + { + _kindName = kindName; + } + + public Long getNewValue() + { + return _newValue; + } + + public void setNewValue(Long newValue) + { + this._newValue = newValue; + } + + public NameGenerator.EntityCounter getSeqType() + { + return _seqType; + } + + public void setSeqType(String seqType) + { + _seqType = NameGenerator.EntityCounter.valueOf(seqType); + } + + } + + @Marshal(Marshaller.Jackson) + @RequiresPermission(ReadPermission.class) + public static class GetCrossFolderDataSelectionAction extends ReadOnlyApiAction + { + @Override + public void validateForm(CrossFolderSelectionForm form, Errors errors) + { + if (form.getDataRegionSelectionKey() == null && form.getRowIds() == null) + errors.reject(ERROR_REQUIRED, "You must provide either a set of rowIds or a dataRegionSelectionKey."); + if (!"samples".equalsIgnoreCase(form.getDataType()) && !"exp.data".equalsIgnoreCase(form.getDataType())&& !"assay".equalsIgnoreCase(form.getDataType())) + errors.reject(ERROR_REQUIRED, "Data type (sample, data or assayrun) must be specified."); + } + + @Override + public Object execute(CrossFolderSelectionForm form, BindException errors) + { + Pair result = ExperimentServiceImpl.getCurrentAndCrossFolderDataCount(form.getIds(false), form.getDataType(), getContainer()); + + ApiSimpleResponse resp = new ApiSimpleResponse(); + resp.put("success", true); + resp.put("currentFolderSelectionCount", result.first); + resp.put("crossFolderSelectionCount", result.second); + + return success(resp); + } + } + + public static class CrossFolderSelectionForm extends DataViewSnapshotSelectionForm + { + private String _dataType; + private String _picklistName; + + public String getDataType() + { + return _dataType; + } + + public void setDataType(String dataType) + { + _dataType = dataType; + } + + public String getPicklistName() + { + return _picklistName; + } + + public void setPicklistName(String picklistName) + { + _picklistName = picklistName; + } + + @Override + public Set getIds(boolean clear) + { + Set selectedIds; + + if (_rowIds != null) + selectedIds = _rowIds; + else if (isUseSnapshotSelection()) + selectedIds = new HashSet<>(DataRegionSelection.getSnapshotSelectedIntegers(getViewContext(), getDataRegionSelectionKey())); + else + selectedIds = DataRegionSelection.getSelectedIntegers(getViewContext(), getDataRegionSelectionKey(), clear); + + if (_picklistName != null) + { + User user = getViewContext().getUser(); + Container container = getViewContext().getContainer(); + UserSchema schema = ListService.get().getUserSchema(user, container); + TableInfo tInfo = schema.getTable(_picklistName); + if (tInfo != null) + { + SimpleFilter filter = SimpleFilter.createContainerFilter(container); + filter.addInClause(FieldKey.fromParts("id"), selectedIds); + TableSelector selector = new TableSelector(tInfo, Collections.singleton("SampleID"), filter, null); + return new HashSet<>(selector.getArrayList(Long.class)); + } + } + return selectedIds; + } + } + + @RequiresPermission(AdminPermission.class) + public static class RecomputeAliquotRollup extends SimpleViewAction + { + @Override + public void addNavTrail(NavTree root) + { + } + + @Override + public ModelAndView getView(Object o, BindException errors) throws SQLException + { + try (var ignore = SpringActionController.ignoreSqlUpdates()) + { + Container container = getContainer(); + User user = getUser(); + + List sampleTypes = SampleTypeService.get() + .getSampleTypes(container, user, true); + + HtmlStringBuilder builder = HtmlStringBuilder.of(); + builder.unsafeAppend(""); + + SampleTypeService service = SampleTypeService.get(); + for (ExpSampleType sampleType : sampleTypes) + { + int updatedCount; + updatedCount = service.recomputeSampleTypeRollup(sampleType, container); + // we could check "if (0 < updatedCount) refresh(rollup)", but since this is a "manual" usage lets just always refresh + SampleTypeServiceImpl.get().refreshSampleTypeMaterializedView(sampleType, update); + builder.unsafeAppend(""); + } + + builder.unsafeAppend("
Sample Type#Recomputed
") + .append(sampleType.getName()) + .unsafeAppend("") + .append(updatedCount) + .unsafeAppend("
"); + return new HtmlView("Aliquot Rollup Recalculation Result", builder); + } + } + } + + /* Also see API CheckEdgesAction */ + @RequiresPermission(TroubleshooterPermission.class) + public static class CycleCheckAction extends FormViewAction + { + List cycleObjectIds = null; + + @Override + public void validateCommand(Object target, Errors errors) + { + + } + + @Override + public ModelAndView getView(Object o, boolean reshow, BindException errors) + { + if (!reshow) + { + return new HtmlView( + DIV("This operation can use a lot of memory.", + LK.FORM(at(method,"POST"), + PageFlowUtil.button("Continue").submit(true))) + ); + } + + if (null == cycleObjectIds) + return new HtmlView(HtmlString.of("No cycles found")); + + Map map = new LongHashMap<>(); + var cf = new ContainerFilter.AllFolders(getUser()); + var materials = ExperimentServiceImpl.get().getExpMaterialsByObjectId(cf, cycleObjectIds); + materials.forEach( (m) -> map.put(m.getObjectId(), m)); + var datas = ExperimentServiceImpl.get().getExpDatasByObjectId(cf, cycleObjectIds); + datas.forEach( (d) -> map.put(d.getObjectId(), d)); + var runs = ExperimentServiceImpl.get().getRunsByObjectId(cf, cycleObjectIds); + runs.forEach( (r) -> map.put(r.getObjectId(), r)); + + ExperimentUrls urls = ExperimentUrls.get(); + return new HtmlView( + DIV("Cycle found involving these objects.", + UL(cycleObjectIds.stream().map((objectid) -> + { + ExpObject exp = map.get(objectid); + if (exp instanceof ExpMaterial mat) + return LI(A(at(target, "_blank", href, urls.getMaterialDetailsURL(mat)), objectid + " : material - " + mat.getName())); + else if (exp instanceof ExpRun run) + return LI(A(at(target, "_blank", href, urls.getRunTextURL(run)), objectid + " : run - " + run.getName())); + else if (exp instanceof ExpData data) + return LI(A(at(target, "_blank", href, urls.getDataDetailsURL(data)), objectid + " : run - " + data.getName())); + else + return LI(String.valueOf(objectid)); + })) + ) + ); + } + + @Override + public boolean handlePost(Object o, BindException errors) + { + var edges = new SqlSelector(ExperimentService.get().getSchema(), "SELECT fromObjectId, toObjectId FROM exp.Edge") + .resultSetStream() + .map(r -> { try { return new Pair<>(r.getInt(1), r.getInt(2)); } catch (SQLException x) { throw new RuntimeException(x); } }) + .collect(toList()); + var cyclesEdges = (new GraphAlgorithms()).detectCycleInDirectedGraph(edges); + + var set = new LinkedHashSet(); + cyclesEdges.forEach( (edge) -> { + set.add(edge.first); + set.add(edge.second); + }); + cycleObjectIds = set.stream().toList(); + return false; + } + + @Override + public URLHelper getSuccessURL(Object o) + { + return null; + } + + @Override + public void addNavTrail(NavTree root) + { + + } + } + + @RequiresPermission(AdminPermission.class) + public static class MissingFilesCheckAction extends ReadOnlyApiAction + { + @Override + public Object execute(Object o, BindException errors) throws Exception + { + Map> info = ExperimentServiceImpl.get().doMissingFilesCheck(getUser(), getContainer(), true); + JSONObject results = new JSONObject(); + for (String containerId : info.keySet()) + { + JSONObject containerResults = new JSONObject(); + for (String sourceName : info.get(containerId).keySet()) + containerResults.put(sourceName, info.get(containerId).get(sourceName).toJSON()); + results.put(containerId, containerResults); + } + + ApiSimpleResponse response = new ApiSimpleResponse(); + response.put("success", true); + response.put("result", results); + return response; + } + } + +}