Show Plate Samples on Sample Assays Page

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

@@ -93,6 +93,7 @@
 import org.labkey.api.study.StudyService;
 import org.labkey.api.study.assay.ParticipantVisitResolver;
 import org.labkey.api.study.publish.StudyPublishService;
+import org.labkey.api.util.IntegerUtils;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.ResultSetUtil;
 import org.labkey.api.util.UnexpectedException;
@@ -517,7 +518,7 @@ public boolean next() throws BatchValidationException
             }
             Map<ExpMaterial, String> rowBasedInputMaterials = new LinkedHashMap<>();
 
-            DataIterator fileData = checkData(container, user, dataTable, dataDomain, iter, settings, resolver, protocolInputMaterials, cf, rowBasedInputMaterials);
+            DataIterator fileData = checkData(container, user, provider, protocol, dataTable, dataDomain, iter, settings, resolver, protocolInputMaterials, cf, rowBasedInputMaterials);
             fileData = convertPropertyNamesToURIs(fileData, dataDomain);
 
             OntologyManager.RowCallback rowCallback = NO_OP_ROW_CALLBACK;
@@ -682,16 +683,18 @@ private void checkColumns(Domain dataDomain, DataIterator rawData) throws BatchV
      * @param rowBasedInputMaterials the map of materials that are inputs to this run based on the data rows
      */
     private DataIterator checkData(
-        Container container,
-        User user,
-        TableInfo dataTable,
-        Domain dataDomain,
-        DataIterator rawData,
-        DataLoaderSettings settings,
-        ParticipantVisitResolver resolver,
-        Map<String, ExpMaterial> inputMaterials,
-        ContainerFilter containerFilter,
-        Map<ExpMaterial, String> rowBasedInputMaterials
+            Container container,
+            User user,
+            AssayProvider provider,
+            ExpProtocol protocol,
+            TableInfo dataTable,
+            Domain dataDomain,
+            DataIterator rawData,
+            DataLoaderSettings settings,
+            ParticipantVisitResolver resolver,
+            Map<String, ExpMaterial> inputMaterials,
+            ContainerFilter containerFilter,
+            Map<ExpMaterial, String> rowBasedInputMaterials
     ) throws BatchValidationException
     {
         final ExperimentService exp = ExperimentService.get();
@@ -705,10 +708,14 @@ private DataIterator checkData(
         DomainProperty visitPropFinder = null;
         DomainProperty datePropFinder = null;
         DomainProperty targetStudyPropFinder = null;
+        DomainProperty platePropFinder = null;
+        DomainProperty wellLocationPropFinder = null;
+        DomainProperty wellLsidPropFinder = null;
 
         RemapCache cache = new RemapCache();
         Map<DomainProperty, TableInfo> remappableLookup = new HashMap<>();
         Map<Long, ExpMaterial> materialCache = new LongHashMap<>();
+        Map<Long, Map<String, Long>> plateWellCache = new LongHashMap<>();
 
         Map<DomainProperty, ExpSampleType> lookupToSampleTypeByName = new HashMap<>();
         Map<DomainProperty, ExpSampleType> lookupToSampleTypeById = new HashMap<>();
@@ -717,6 +724,7 @@ private DataIterator checkData(
 
         List<? extends DomainProperty> columns = dataDomain.getProperties();
         Map<DomainProperty, List<ColumnValidator>> validatorMap = new HashMap<>();
+        boolean isPlateMetadataEnabled = provider.isPlateMetadataEnabled(protocol);
 
         for (DomainProperty pd : columns)
         {
@@ -748,6 +756,25 @@ else if (pd.getName().equalsIgnoreCase(AbstractAssayProvider.TARGET_STUDY_PROPER
             {
                 targetStudyPropFinder = pd;
             }
+            else if (isPlateMetadataEnabled &&
+                    pd.getName().equalsIgnoreCase("WellLocation") &&
+                    pd.getPropertyDescriptor().getPropertyType() == PropertyType.STRING)
+            {
+                wellLocationPropFinder = pd;
+            }
+            else if (isPlateMetadataEnabled &&
+                    pd.getName().equalsIgnoreCase("WellLsid") &&
+                    pd.getPropertyDescriptor().getPropertyType() == PropertyType.STRING)
+            {
+                wellLsidPropFinder = pd;
+            }
+            else if (isPlateMetadataEnabled &&
+                    pd.getName().equalsIgnoreCase("Plate") &&
+                    pd.getPropertyDescriptor().isLookup())
+            {
+                platePropFinder = pd;
+            }
+
             else
             {
                 var sampleLookup = AssaySampleLookupContext.checkSampleLookup(container, user, pd);
@@ -794,6 +821,11 @@ else if (sampleLookup.isLookup())
         DomainProperty visitPD = visitPropFinder;
         DomainProperty datePD = datePropFinder;
         DomainProperty targetStudyPD = targetStudyPropFinder;
+        DomainProperty platePD = platePropFinder;
+        DomainProperty wellLocationPD = wellLocationPropFinder;
+        DomainProperty wellLsidPD = wellLsidPropFinder;
+
+        boolean resolvePlateSamples = isPlateMetadataEnabled && platePD != null && wellLocationPD != null && wellLsidPD != null;
 
         return DataIteratorUtil.mapTransformer(rawData, inputCols ->
         {
@@ -1042,6 +1074,34 @@ else if (validatorMap.containsKey(pd))
                     }
                 }
 
+                // Wire up well samples as materials inputs
+                if (resolvePlateSamples)
+                {
+                    Long plateId = IntegerUtils.asLong(map.get(platePD.getName()));
+                    String wellLocation = (String) map.get(wellLocationPD.getName());
+                    Long sampleId = null;
+                    ExpMaterial material = null;
+
+                    if (plateId != null && wellLocation != null)
+                    {
+                        Map<String, Long> wellSampleCache = plateWellCache.computeIfAbsent(plateId, (id) -> AssayPlateMetadataService.get().getWellLocationToSampleIdMap(container, user, plateId));
+                        sampleId = wellSampleCache.get(wellLocation);
+                    }
+
+                    if (sampleId != null)
+                    {
+                        material = materialCache.computeIfAbsent(sampleId, (id) -> exp.getExpMaterial(id, containerFilter));
+                    }
+
+                    if (material != null)
+                    {
+                        // Note: we have to use the wellLsidPD as the Property Input Lineage Role because we resolve
+                        // the material inputs for a plate assay based on WellLsid during delete.
+                        rowBasedInputMaterials.putIfAbsent(material, AssayService.get().getPropertyInputLineageRole(wellLsidPD));
+                        rowInputLSIDs.add(material.getLSID());
+                    }
+                }
+
                 if (!errors.isEmpty())
                     throw new RuntimeValidationException(new ValidationException(errors, rowNum));
 

api/src/org/labkey/api/assay/plate/AssayPlateMetadataService.java

@@ -4,6 +4,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayRunUploadContext;
+import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.TableInfo;
@@ -183,6 +184,13 @@ void applyHitSelectionCriteria(
         List<Long> runIds
     ) throws ValidationException;
 
+    /**
+     * Returns a Map of Well Location to Sample RowID for a given Plate ID.
+     */
+    Map<String, Long> getWellLocationToSampleIdMap(Container container, User user, Long plateId);
+
+    boolean isWellLookup(ColumnInfo col);
+
     /**
      * Should only be used to get a local instance of a plate schema where a contextual role might be involved. Schemas created this way are not cached,
      * and all other usages should retrieve schemas from the QueryService.

api/src/org/labkey/api/assay/sample/AssaySampleLookupContext.java

@@ -2,15 +2,18 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.assay.AssayProtocolSchema;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayService;
+import org.labkey.api.assay.plate.AssayPlateMetadataService;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
+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.ExpSampleType;
@@ -93,6 +96,33 @@ public void trackSampleLookupChange(Container container, User user, TableInfo ta
         }
     }
 
+    /**
+     * Keeps track of experiment runs for assays that have columns with a sample lookup, including plate metadata
+     * enabled assays. Useful in data updates of assay run/result domains where sample lookups are subsequently
+     * reflected as material inputs to  an experiment run.
+     * @param container Container from which to resolve sample lookup information.
+     * @param user User to utilize to resolve sample lookup information.
+     * @param table The table to utilize to resole sample lookup information.
+     * @param schema The AssayProtocolSchema associated with the run.
+     * @param run The experiment run to track.
+     */
+    public void trackSampleLookupChange(Container container, User user, TableInfo table, AssayProtocolSchema schema, ExpRun run)
+    {
+        if (table.getDomain() == null) return;
+
+        for (DomainProperty dp : table.getDomain().getNonBaseProperties())
+            trackSampleLookupChange(container, user, table, table.getColumn(dp.getName()), run);
+
+        if (_runIds.contains(run.getRowId()))
+            return;
+
+        AssayProvider provider = schema.getProvider();
+        ExpProtocol protocol = schema.getProtocol();
+
+        if (provider.isPlateMetadataEnabled(protocol))
+            _runIds.add(run.getRowId());
+    }
+
     /**
      * Check if a domain property is considered a valid sample lookup.
      * @param container Container from which to resolve sample lookup information.
@@ -112,8 +142,9 @@ private static SampleLookup checkSampleLookup(Container container, User user, @N
 
         ExpSampleType sampleType = ExperimentService.get().getLookupSampleType(dp, container, user);
         boolean isSampleLookup = sampleType != null || ExperimentService.get().isLookupToMaterials(dp);
+        boolean isWellLookup = dp.getName().equalsIgnoreCase("WellLsid") && col != null && AssayPlateMetadataService.get().isWellLookup(col);
 
-        return new SampleLookup(isSampleLookup, col, dp, sampleType);
+        return new SampleLookup(isSampleLookup || isWellLookup, col, dp, sampleType);
     }
 
     private SampleLookup checkSampleLookup(Container container, User user, TableInfo table, ColumnInfo col)
@@ -384,7 +415,18 @@ private SQLFragment getLookupColumnSql(TableInfoKey tableInfoKey, SampleLookup s
         var role = AssayService.get().getPropertyInputLineageRole(sampleLookup.domainProperty);
         var sql = new SQLFragment();
 
-        if (column.getJdbcType().isInteger())
+        if (AssayPlateMetadataService.get().isWellLookup(column))
+        {
+            // tableSql selects all the Well LSIDs for the given runId, we then select all the SampleIds from the
+            // assay.well table that match those Well LSIDs.
+            tableSql = QueryService.get().getSelectBuilder(table)
+                    .columns(Set.of(column))
+                    .filter(tableFilter)
+                    .buildSqlFragment();
+            sql.append("SELECT WS.SampleId as MaterialRowId, ").appendValue(role).append(" AS MaterialInputRole\n");
+            sql.append("FROM assay.well WS WHERE LSID IN (").append(tableSql).append(")");
+        }
+        else if (column.getJdbcType().isInteger())
         {
             sql.append("SELECT DA.").appendIdentifier(column.getAlias()).append(" AS MaterialRowId");
             sql.append(", ?").add(role).append(" AS MaterialInputRole\n");

assay/api-src/org/labkey/api/assay/AssayResultUpdateService.java

@@ -368,11 +368,7 @@ protected Map<String, Object> deleteRow(
         }
 
         // Issue 51126: need to track and resync run/sample lineage on delete in the same way we do for update
-        if (datatableInfo.getDomain() != null)
-        {
-            for (DomainProperty dp : datatableInfo.getDomain().getNonBaseProperties())
-                _assaySampleLookupContext.trackSampleLookupChange(container, user, datatableInfo, datatableInfo.getColumn(dp.getName()), run);
-        }
+        _assaySampleLookupContext.trackSampleLookupChange(container, user, datatableInfo, _schema, run);
 
         return result;
     }

assay/package.json

@@ -12,7 +12,7 @@
     "clean": "rimraf resources/web/assay/gen && rimraf resources/views/gen && rimraf resources/web/gen"
   },
   "dependencies": {
-    "@labkey/components": "6.63.1"
+    "@labkey/components": "6.64.0"
   },
   "devDependencies": {
     "@labkey/build": "8.6.0",

assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java

@@ -96,6 +96,7 @@
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.assay.TSVProtocolSchema;
+import org.labkey.assay.plate.data.WellData;
 import org.labkey.assay.plate.model.WellBean;
 import org.labkey.assay.plate.query.PlateSchema;
 import org.labkey.assay.plate.query.PlateTable;
@@ -1517,6 +1518,32 @@ public String format(FieldKey fieldKey)
         return new PlateSchema(querySchema, contextualRoles);
     }
 
+    @Override
+    public Map<String, Long> getWellLocationToSampleIdMap(Container container, User user, Long plateId)
+    {
+        Map<String, Long> wellLocationToSampleIdMap = new HashMap<>();
+        List<WellData> wellData = PlateManager.get().getWellData(container, user, plateId, true, false);
+
+        for (WellData data : wellData)
+            wellLocationToSampleIdMap.put(data.getPosition(), data.getSampleId());
+
+        return wellLocationToSampleIdMap;
+    }
+
+    @Override
+    public boolean isWellLookup(ColumnInfo col)
+    {
+        if (col == null) return false;
+
+        if (!col.isLookup()) return false;
+
+        var wellTable = AssayDbSchema.getInstance().getTableInfoWell();
+        var lookupTable = col.getFkTableInfo();
+
+        return lookupTable.getSchema().getName().equalsIgnoreCase(wellTable.getSchema().getName())
+                && lookupTable.getName().equalsIgnoreCase(wellTable.getName());
+    }
+
     private static class PlateMetadataImportHelper extends SimpleAssayDataImportHelper
     {
         private final Map<Long, Map<Position, Lsid>> _wellPositionMap;       // map of plate position to well table

core/package.json

@@ -53,7 +53,7 @@
     }
   },
   "dependencies": {
-    "@labkey/components": "6.63.1",
+    "@labkey/components": "6.64.0",
     "@labkey/themes": "1.4.2"
   },
   "devDependencies": {

experiment/package.json

@@ -13,7 +13,7 @@
     "test-integration": "cross-env NODE_ENV=test jest --ci --runInBand -c test/js/jest.config.integration.js"
   },
   "dependencies": {
-    "@labkey/components": "6.63.1"
+    "@labkey/components": "6.64.0"
   },
   "devDependencies": {
     "@labkey/build": "8.6.0",