Reimplement Workflow with its own schema

api/src/org/labkey/api/announcements/EmailOption.java

@@ -38,8 +38,8 @@ public enum EmailOption
     FILES_NONE(512),
     FILES_INDIVIDUAL(513),
     FILES_DAILY_DIGEST(514),
-    SAMPLEMANAGER_NONE(701),
-    SAMPLEMANAGER_ALL(702),
+    WORKFLOW_NONE(701),
+    WORKFLOW_ALL(702),
     LABBOOK_NONE(801),
     LABBOOK_ALL(802);
 

api/src/org/labkey/api/assay/AssayRunDatabaseContext.java

@@ -128,12 +128,9 @@ public String getName()
     }
 
     @Override
-    public @Nullable Long getWorkflowTask()
+    public @Nullable Long getWorkflowTaskId()
     {
-        if (_run.getWorkflowTask() != null)
-            return _run.getWorkflowTask().getRowId();
-
-        return null;
+        return _run.getWorkflowTaskId();
     }
 
     @Override

api/src/org/labkey/api/assay/AssayRunUploadContext.java

@@ -72,7 +72,7 @@ enum ReImportOption
 
     String getName();
 
-    default @Nullable Long getWorkflowTask()
+    default @Nullable Long getWorkflowTaskId()
     {
         return null;
     }
@@ -253,7 +253,7 @@ abstract class Factory<ProviderType extends AssayProvider, FACTORY extends Facto
         protected ViewContext _context;
         protected String _comments;
         protected String _name;
-        protected Long _workflowTask;
+        protected Long _workflowTaskId;
         protected String _targetStudy;
         protected Long _reRunId;
         protected AssayRunUploadContext.ReImportOption _reImportOption;
@@ -318,9 +318,9 @@ public final FACTORY setName(String name)
             return self();
         }
 
-        public final FACTORY setWorkflowTask(Long workflowTask)
+        public final FACTORY setWorkflowTaskId(Long workflowTaskId)
         {
-            _workflowTask = workflowTask;
+            _workflowTaskId = workflowTaskId;
             return self();
         }
 

api/src/org/labkey/api/assay/AssayRunUploadContextImpl.java

@@ -69,7 +69,7 @@ public class AssayRunUploadContextImpl<ProviderType extends AssayProvider> imple
     private final ViewContext _context;
     private final String _comments;
     private final String _name;
-    private final Long _workflowTask;
+    private final Long _workflowTaskId;
     private final String _targetStudy;
     private final Long _reRunId;
     private final ReImportOption _reImportOption;
@@ -114,7 +114,7 @@ private AssayRunUploadContextImpl(Factory<ProviderType> factory)
         _logger = factory._logger;
 
         _name = factory._name;
-        _workflowTask = factory._workflowTask;
+        _workflowTaskId = factory._workflowTaskId;
         _comments = factory._comments;
 
         _rawRunProperties = factory._rawRunProperties == null ? emptyMap() : unmodifiableMap(factory._rawRunProperties);
@@ -279,9 +279,9 @@ public String getName()
     }
 
     @Override
-    public @Nullable Long getWorkflowTask()
+    public @Nullable Long getWorkflowTaskId()
     {
-        return _workflowTask;
+        return _workflowTaskId;
     }
 
     @Override

api/src/org/labkey/api/assay/DefaultAssayRunCreator.java

@@ -171,7 +171,7 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(
                     auditEvent.addDetail(TransactionAuditProvider.TransactionDetail.ImportFileName, primaryFile.getName());
                 run = AssayService.get().createExperimentRun(context.getName(), context.getContainer(), protocol, null == primaryFile ? null : primaryFile.toNioPathForRead().toFile());
                 run.setComments(context.getComments());
-                run.setWorkflowTaskId(context.getWorkflowTask());
+                run.setWorkflowTaskId(context.getWorkflowTaskId());
 
                 exp = saveExperimentRun(context, exp, run, false, transactionDetails);
 

api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java

@@ -90,7 +90,7 @@ public class AssayRunUploadForm<ProviderType extends AssayProvider> extends Prot
     protected Map<DomainProperty, String> _runProperties = null;
     private String _comments;
     private String _name;
-    private Long _workflowTask;
+    private Long _workflowTaskId;
     private String _dataCollectorName;
     private boolean _multiRunUpload;
     private String _uploadStep;
@@ -214,14 +214,14 @@ public void setName(String name)
     }
 
     @Override
-    public @Nullable Long getWorkflowTask()
+    public @Nullable Long getWorkflowTaskId()
     {
-        return _workflowTask;
+        return _workflowTaskId;
     }
 
-    public void setWorkflowTask(Long workflowTask)
+    public void setWorkflowTaskId(Long workflowTaskId)
     {
-        _workflowTask = workflowTask;
+        _workflowTaskId = workflowTaskId;
     }
 
     public String getDataCollectorName()

api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java

@@ -63,7 +63,7 @@ public class AssayRunAsyncContext<ProviderType extends AssayProvider> implements
     private String _containerId;
     private String _runName;
     private String _runComments;
-    private Long _runWorkflowTask;
+    private Long _runWorkflowTaskId;
     private ActionURL _actionURL;
     private Map<String, FileLike> _uploadedData;
     private Set<FileLike> _uploadedPropertyFiles;
@@ -111,7 +111,7 @@ public AssayRunAsyncContext(AssayRunUploadContext<ProviderType> originalContext)
         _targetStudy = originalContext.getTargetStudy();
         _runName = originalContext.getName();
         _runComments = originalContext.getComments();
-        _runWorkflowTask = originalContext.getWorkflowTask();
+        _runWorkflowTaskId = originalContext.getWorkflowTaskId();
         _container = originalContext.getContainer();
         if (_container != null)
             _containerId = _container.getId();
@@ -298,9 +298,9 @@ public String getName()
     }
 
     @Override
-    public @Nullable Long getWorkflowTask()
+    public @Nullable Long getWorkflowTaskId()
     {
-        return _runWorkflowTask;
+        return _runWorkflowTaskId;
     }
 
     @Override

api/src/org/labkey/api/assay/pipeline/AssayUploadPipelineJob.java

@@ -140,7 +140,7 @@ public void doWork()
             // Create the basic run
             _run = AssayService.get().createExperimentRun(_context.getName(), getContainer(), _context.getProtocol(), _primaryFile);
             _run.setComments(_context.getComments());
-            _run.setWorkflowTaskId(_context.getWorkflowTask());
+            _run.setWorkflowTaskId(_context.getWorkflowTaskId());
             // remember which job created the run so we can show this run on the job details page
             _run.setJobId(PipelineService.get().getJobId(getUser(), getContainer(), getJobGUID()));
 

api/src/org/labkey/api/data/CreatedModified.java

@@ -5,6 +5,7 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import org.json.JSONObject;
 import org.labkey.api.security.User;
+import org.labkey.api.security.UserManager;
 
 import java.util.Date;
 
@@ -22,6 +23,12 @@ public Long getCreated()
         return _created;
     }
 
+    @JsonIgnore
+    public Date getCreatedDate()
+    {
+        return _created == null ? null : new Date(_created);
+    }
+
     public void setCreated(Long created)
     {
         _created = created;
@@ -42,17 +49,34 @@ public JSONObject getCreatedBy()
         return _createdBy.getUserProps();
     }
 
+    @JsonIgnore
+    public User getCreatedByUser()
+    {
+        return _createdBy;
+    }
+
     public void setCreatedBy(User createdBy)
     {
         _createdBy = createdBy;
     }
 
+    public void setCreatedBy(int createdById)
+    {
+        _createdBy = UserManager.getUser(createdById);
+    }
+
     @JsonProperty("modified")
     public Long getModified()
     {
         return _modified;
     }
 
+    @JsonIgnore
+    public Date getModifiedDate()
+    {
+        return _modified == null ? null : new Date(_modified);
+    }
+
     public void setModified(Long modified)
     {
         _modified = modified;
@@ -73,8 +97,19 @@ public JSONObject getModifiedBy()
         return _modifiedBy.getUserProps();
     }
 
+    @JsonIgnore
+    public User getModifiedByUser()
+    {
+        return _modifiedBy;
+    }
+
     public void setModifiedBy(User modifiedBy)
     {
         _modifiedBy = modifiedBy;
     }
+
+    public void setModifiedBy(int modifiedById)
+    {
+        _modifiedBy = UserManager.getUser(modifiedById);
+    }
 }

api/src/org/labkey/api/data/NameGenerator.java

@@ -1658,6 +1658,12 @@ public NameGeneratorState createState(boolean incrementSampleCounts)
         return new NameGeneratorState(this, incrementSampleCounts, _expressionSummary.sampleSummary);
     }
 
+    @NotNull
+    public NameGeneratorState createState(boolean incrementSampleCounts, String nameField)
+    {
+        return new NameGeneratorState(this, incrementSampleCounts, _expressionSummary.sampleSummary, nameField);
+    }
+
     public String generateName(@NotNull NameGeneratorState state, @NotNull Map<String, Object> rowMap) throws NameGenerationException
     {
         return state.nextName(rowMap, null, null, null, null);

api/src/org/labkey/api/data/NameGeneratorState.java

@@ -77,12 +77,19 @@ public class NameGeneratorState implements AutoCloseable
     protected final Map<Long, ExpData> dataCache = new LongHashMap<>();
     protected final RemapCache renameCache;
     private final Map<String, Map<String, Object>> objectPropertiesCache = new HashMap<>();
+    private final String _nameField;
 
     public NameGeneratorState(@NotNull NameGenerator nameGenerator, boolean incrementSampleCounts, NameGenerator.SampleNameExpressionSummary expressionSummary)
+    {
+        this(nameGenerator, incrementSampleCounts, expressionSummary, "Name");
+    }
+
+    public NameGeneratorState(@NotNull NameGenerator nameGenerator, boolean incrementSampleCounts, NameGenerator.SampleNameExpressionSummary expressionSummary, String nameField)
     {
         _nameGenerator = nameGenerator;
         _incrementSampleCounts = incrementSampleCounts;
         _container = nameGenerator.getContainer();
+        _nameField = nameField;
 
         DbSequence sampleCounterSequence;
         DbSequence rootCounterSequence;
@@ -274,7 +281,7 @@ private String genName(@NotNull Map<String, Object> rowMap,
         }
 
         // If a name is already provided, just use it as is
-        Object currNameObj = rowMap.get("Name");
+        Object currNameObj = rowMap.get(_nameField);
         if (currNameObj != null)
         {
             String currName = currNameObj.toString();

api/src/org/labkey/api/dataiterator/NameExpressionDataIterator.java

@@ -38,25 +38,32 @@ public class NameExpressionDataIterator extends WrapperDataIterator
     private final Map<String, Pair<NameGenerator, NameGeneratorState>> _nameGeneratorMap = new HashMap<>();
     private final Map<String, String> _newNames = new HashMap<>();
     private final Integer _nameCol;
+    private final String _nameColName;
     private final Integer _expressionCol;
     private final TableInfo _parentTable;
     private final Container _container;
     private final Function<String, Long> _getNonConflictCountFn;
     private final String _counterSeqPrefix;
     private boolean _allowUserSpecifiedNames = true;        // whether manual names specification is allowed or only name expression generation
     private final List<Supplier<Map<String, Object>>> _extraPropsFns = new ArrayList<>();
-    private Map<String, String> _importAliases;
+    private final Map<String, String> _importAliases;
 
     public NameExpressionDataIterator(DataIterator di, DataIteratorContext context, @Nullable TableInfo parentTable, @Nullable Container container, Function<String, Long> getNonConflictCountFn, String counterSeqPrefix, @Nullable Map<String, String> importAliases)
+    {
+        this(di, context, parentTable, container, getNonConflictCountFn, counterSeqPrefix, importAliases, "name", "nameExpression");
+    }
+
+    public NameExpressionDataIterator(DataIterator di, DataIteratorContext context, @Nullable TableInfo parentTable, @Nullable Container container, Function<String, Long> getNonConflictCountFn, String counterSeqPrefix, @Nullable Map<String, String> importAliases, String nameColName, String expressionColName)
     {
         super(DataIteratorUtil.wrapMap(di, false));
         _context = context;
         _parentTable = parentTable;
         _importAliases = importAliases;
 
         Map<String, Integer> map = DataIteratorUtil.createColumnNameMap(di);
-        _nameCol = map.get("name");
-        _expressionCol = map.get("nameExpression");
+        _nameColName = nameColName;
+        _nameCol = map.get(nameColName);
+        _expressionCol = map.get(expressionColName);
         assert _nameCol != null;
         assert _expressionCol != null;
 
@@ -90,7 +97,7 @@ private BatchValidationException getErrors()
     private void addNameGenerator(String nameExpression)
     {
         NameGenerator nameGen = new NameGenerator(nameExpression, _parentTable, false, _importAliases, _container, _getNonConflictCountFn, _counterSeqPrefix);
-        NameGeneratorState state = nameGen.createState(false);
+        NameGeneratorState state = nameGen.createState(false, _nameColName);
         _nameGeneratorMap.put(nameExpression, Pair.of(nameGen, state));
     }
 

api/src/org/labkey/api/dataiterator/NameExpressionDataIteratorBuilder.java

@@ -21,17 +21,26 @@ public class NameExpressionDataIteratorBuilder implements DataIteratorBuilder
 {
     final DataIteratorBuilder _pre;
     private final TableInfo _parentTable;
+    private final String _nameColumnName;
+    private final String _nameExpressionColumnName;
 
     public NameExpressionDataIteratorBuilder(DataIteratorBuilder pre, TableInfo parentTable)
+    {
+        this(pre, parentTable, "name", "nameExpression");
+    }
+
+    public NameExpressionDataIteratorBuilder(DataIteratorBuilder pre, TableInfo parentTable, String nameColumn, String nameExpressionColumn)
     {
         _pre = pre;
         _parentTable = parentTable;
+        _nameColumnName = nameColumn;
+        _nameExpressionColumnName = nameExpressionColumn;
     }
 
     @Override
     public DataIterator getDataIterator(DataIteratorContext context)
     {
         DataIterator pre = _pre.getDataIterator(context);
-        return LoggingDataIterator.wrap(new NameExpressionDataIterator(pre, context, _parentTable, null, null, null, null));
+        return LoggingDataIterator.wrap(new NameExpressionDataIterator(pre, context, _parentTable, null, null, null, null, _nameColumnName, _nameExpressionColumnName));
     }
 }

assay/src/org/labkey/assay/plate/query/NamePlusIdDataIterator.java → api/src/org/labkey/api/dataiterator/NamePlusIdDataIterator.java

@@ -1,16 +1,11 @@
-package org.labkey.assay.plate.query;
+package org.labkey.api.dataiterator;
 
 import org.apache.commons.lang3.StringUtils;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.NameGenerator;
 import org.labkey.api.data.NameGeneratorState;
 import org.labkey.api.data.TableInfo;
-import org.labkey.api.dataiterator.DataIterator;
-import org.labkey.api.dataiterator.DataIteratorContext;
-import org.labkey.api.dataiterator.DataIteratorUtil;
-import org.labkey.api.dataiterator.MapDataIterator;
-import org.labkey.api.dataiterator.WrapperDataIterator;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.ValidationException;
 

api/src/org/labkey/api/exp/api/ExpObject.java

@@ -70,8 +70,10 @@ default void setComment(User user, String comment, boolean index) throws Validat
     }
 
     User getCreatedBy();
+    Integer getCreatedById();
     Date getCreated();
     User getModifiedBy();
+    Integer getModifiedById();
     Date getModified();
 
     void save(User user) throws BatchValidationException;

api/src/org/labkey/api/exp/api/ExpProtocol.java

@@ -175,6 +175,7 @@ static boolean isSampleWorkflowTaskProtocol(String lsid)
         return lsid.contains(ExperimentService.SAMPLE_MANAGEMENT_TASK_PROTOCOL_PREFIX);
     }
 
+    // TODO remove this and its relatives once the workflow folder import/export rewrite has happened.
     static boolean isSampleWorkflowProtocol(String lsid)
     {
         return isSampleWorkflowTaskProtocol(lsid) || isSampleWorkflowJobProtocol(lsid);