Plate Set Auditing

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

@@ -22,7 +22,6 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
-import org.labkey.api.action.ApiUsageException;
 import org.labkey.api.assay.plate.AssayPlateMetadataService;
 import org.labkey.api.assay.sample.AssaySampleLookupContext;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
@@ -598,14 +597,11 @@ protected void insertRowData(
         OntologyManager.UpdateableTableImportHelper importHelper = new SimpleAssayDataImportHelper(data, protocol, provider);
         if (provider.isPlateMetadataEnabled(protocol))
         {
-            if (context.getReRunId() != null)
+            // check if we are merging the re-imported data
+            if (context != null && context.getReRunId() != null && context.getReImportOption() == MERGE_DATA)
             {
-                // check if we are merging the re-imported data
-                if (context.getReImportOption() == MERGE_DATA)
-                {
-                    DataIteratorBuilder mergedData = AssayPlateMetadataService.get().mergeReRunData(container, user, context, fileData, provider, protocol, data);
-                    fileData = DataIteratorUtil.wrapMap(mergedData.getDataIterator(new DataIteratorContext()), false);
-                }
+                DataIteratorBuilder mergedData = AssayPlateMetadataService.get().mergeReRunData(container, user, context, fileData, provider, protocol, data);
+                fileData = DataIteratorUtil.wrapMap(mergedData.getDataIterator(new DataIteratorContext()), false);
             }
 
             importHelper = AssayPlateMetadataService.get().getImportHelper(container, user, run, data, protocol, provider, context);

api/src/org/labkey/api/audit/AbstractAuditTypeProvider.java

@@ -222,20 +222,11 @@ private void ensureProperties(User user, Domain domain)
         }
     }
 
-    // #26311  We want to trigger a save if the scale has changed
+    // Issue 26311: We want to trigger a save if the scale has changed
     // CONSIDER: check for other differences here as well.
     private boolean differ(PropertyDescriptor pd, DomainProperty dp, Container c)
     {
-        return dp.getScale() != pd.getScale()
-                || !dp.getRangeURI().equals(pd.getRangeURI())
-//                || !dp.getLabel().equals(pd.getLabel())
-//                || dp.isRequired() != pd.isRequired()
-//                || dp.isHidden() != pd.isHidden()
-//                || dp.isMvEnabled() != pd.isMvEnabled()
-//                || dp.getDefaultValueTypeEnum() != pd.getDefaultValueTypeEnum()
-                ;
-
-
+        return dp.getScale() != pd.getScale() || !dp.getRangeURI().equals(pd.getRangeURI());
     }
 
     private void copyTo(DomainProperty dp, PropertyDescriptor pd, Container c)
@@ -321,7 +312,7 @@ protected void appendValueMapColumns(AbstractTableInfo table, String eventName,
         MutableColumnInfo oldCol = table.getMutableColumn(FieldKey.fromString(OLD_RECORD_PROP_NAME));
         MutableColumnInfo newCol = table.getMutableColumn(FieldKey.fromString(NEW_RECORD_PROP_NAME));
 
-        if(oldCol != null)
+        if (oldCol != null)
         {
             var added = table.addColumn(new AliasedColumn(table, "OldValues", oldCol));
             added.setDisplayColumnFactory(DataMapColumn::new);
@@ -330,7 +321,7 @@ protected void appendValueMapColumns(AbstractTableInfo table, String eventName,
             oldCol.setHidden(true);
         }
 
-        if(newCol != null)
+        if (newCol != null)
         {
             var added = table.addColumn(new AliasedColumn(table, "NewValues", newCol));
             added.setDisplayColumnFactory(DataMapColumn::new);
@@ -390,16 +381,16 @@ public static String encodeForDataMap(Map<String, ?> properties)
                 entry.getKey().equals(ExperimentService.ALIASCOLUMNALIAS))
                 continue;
             Object value = entry.getValue();
-            if (value instanceof Time)
+            if (value instanceof Time time)
             {
-                String formatted = DateUtil.formatIsoLongTime((Time)value);
+                String formatted = DateUtil.formatIsoLongTime(time);
                 stringMap.put(entry.getKey(), formatted);
             }
-            else if (value instanceof Date)
+            else if (value instanceof Date date)
             {
-                // issue: 35002 - normalize Date values to avoid Timestamp/Date toString differences
-                // issue: 36472 - use iso format to show date-time values
-                String formatted = DateUtil.toISO((Date)value);
+                // Issue 35002 - normalize Date values to avoid Timestamp/Date toString differences
+                // Issue 36472 - use iso format to show date-time values
+                String formatted = DateUtil.toISO(date);
                 stringMap.put(entry.getKey(), formatted);
             }
             else

api/src/org/labkey/api/audit/AuditTypeEvent.java

@@ -30,8 +30,6 @@
 /**
  * Bean object to capture audit log entries. Will be used to populate the database tables via get/set methods that
  * align with column names in the corresponding provisioned table.
- * User: klum
- * Date: 7/12/13
  */
 public class AuditTypeEvent
 {
@@ -53,7 +51,7 @@ public class AuditTypeEvent
     private User _createdBy;
     private Date _modified;
     private User _modifiedBy;
-    private String userComment;
+    private String _userComment;
     private Long _transactionId;
 
     public AuditTypeEvent(@NotNull String eventType, @NotNull Container container, @Nullable String comment)
@@ -69,7 +67,9 @@ public AuditTypeEvent(@NotNull String eventType, @NotNull Container container, @
     }
 
     /** Important for reflection-based instantiation */
-    public AuditTypeEvent(){}
+    public AuditTypeEvent()
+    {
+    }
 
     public long getRowId()
     {
@@ -173,12 +173,12 @@ public void setModifiedBy(User modifiedBy)
 
     public void setUserComment(String userComment)
     {
-        this.userComment = userComment;
+        _userComment = userComment;
     }
 
     public String getUserComment()
     {
-        return this.userComment;
+        return _userComment;
     }
 
     public Long getTransactionId()

api/src/org/labkey/api/data/triggers/Trigger.java

@@ -32,9 +32,6 @@
 import java.util.stream.Collectors;
 
 /**
- * User: kevink
- * Date: 12/21/15
- *
  * Trigger scripts are invoked before insert/update/delete on many LabKey tables.
  * The Trigger is created by a TriggerFactory added to AbstractTableInfo.
  */

assay/package.json

@@ -12,7 +12,7 @@
     "clean": "rimraf resources/web/assay/gen && rimraf resources/views/gen && rimraf resources/web/gen"
   },
   "dependencies": {
-    "@labkey/components": "6.61.1"
+    "@labkey/components": "6.62.7"
   },
   "devDependencies": {
     "@labkey/build": "8.6.0",

assay/src/org/labkey/assay/AssayModule.java

@@ -34,6 +34,7 @@
 import org.labkey.api.assay.plate.PlateService;
 import org.labkey.api.assay.plate.PlateUtils;
 import org.labkey.api.assay.plate.PositionImpl;
+import org.labkey.api.audit.AuditLogService;
 import org.labkey.api.cache.CacheManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
@@ -87,6 +88,8 @@
 import org.labkey.assay.plate.PlateReplicateStatsDomainKind;
 import org.labkey.assay.plate.PlateSetDocumentProvider;
 import org.labkey.assay.plate.TsvPlateLayoutHandler;
+import org.labkey.assay.plate.audit.PlateAuditProvider;
+import org.labkey.assay.plate.audit.PlateSetAuditProvider;
 import org.labkey.assay.plate.query.PlateSchema;
 import org.labkey.assay.plate.query.PlateSchemaTest;
 import org.labkey.assay.plate.query.PlateTypeTable;
@@ -203,6 +206,8 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
             return result;
         });
         PlateManager.get().registerLsidHandlers();
+        AuditLogService.get().registerAuditType(new PlateSetAuditProvider());
+        AuditLogService.get().registerAuditType(new PlateAuditProvider());
         SearchService ss = SearchService.get();
 
         // ASSAY_CATEGORY

assay/src/org/labkey/assay/PlateController.java

@@ -15,7 +15,6 @@
  */
 package org.labkey.assay;
 
-import org.apache.commons.lang3.ArrayUtils;
 import org.apache.logging.log4j.Logger;
 import org.json.JSONArray;
 import org.json.JSONObject;
@@ -278,9 +277,9 @@ public void validateCommand(NameForm target, Errors errors)
         @Override
         public boolean handlePost(NameForm form, BindException errors) throws Exception
         {
-            Plate template = PlateService.get().getPlate(getContainer(), form.getPlateId());
-            if (template != null && template.getRowId() != null)
-                PlateService.get().deletePlate(getContainer(), getUser(), template.getRowId());
+            Plate plate = PlateService.get().getPlate(getContainer(), form.getPlateId());
+            if (plate != null && plate.getRowId() != null)
+                PlateService.get().deletePlate(getContainer(), getUser(), plate.getRowId());
             return true;
         }
 

assay/src/org/labkey/assay/data/generator/PlateSetDataGenerator.java

@@ -284,7 +284,7 @@ private PlateSet createPlateSet(PlateSetType plateSetType, @Nullable PlateSet pa
         _plateSetsCreated++;
         CPUTimer timer = new CPUTimer("Plate");
         timer.start();
-        PlateSet result = PlateManager.get().createPlateSet(getContainer(), getUser(), plateSet, plates, parentPlateSet != null ? parentPlateSet.getRowId() : null);
+        PlateSet result = PlateManager.get().createPlateSet(getContainer(), getUser(), plateSet, plates, parentPlateSet != null ? parentPlateSet.getRowId() : null, null);
         timer.stop();
         _plateTimings.add(Double.valueOf((double) timer.getTotalMilliseconds() / plates.size()));
 

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

@@ -164,7 +164,7 @@ public DataIteratorBuilder mergePlateMetadata(
             @Override
             public Map<String, Object> apply(Map<String, Object> row)
             {
-                // ensure the result data includes a wellLocation field with values like : A1, F12, etc
+                // ensure the result data includes a wellLocation field with position value (e.g., A1, F12, etc.)
                 Object wellLocation = PropertyService.get().getDomainPropertyValueFromRow(wellLocationProperty, row);
                 if (wellLocation == null)
                     throw new RuntimeValidationException("Imported data must contain a WellLocation column to support plate metadata integration.");
@@ -179,11 +179,14 @@ public Map<String, Object> apply(Map<String, Object> row)
                 if (plateIdentifier == null)
                     throw new RuntimeValidationException("Unable to resolve plate identifier for results row (" + rowCounter + ").");
 
-                Plate plate = PlateService.get().getPlate(cf, plateSetId, plateIdentifier);
-                if (plate == null)
-                    throw new RuntimeValidationException("Unable to resolve the plate \"" + plateIdentifier + "\" for the results row (" + rowCounter + ").");
+                plateIdentifierMap.computeIfAbsent(plateIdentifier, k -> {
+                    Plate plate = PlateService.get().getPlate(cf, plateSetId, plateIdentifier);
+                    if (plate == null)
+                        throw new RuntimeValidationException("Unable to resolve the plate \"" + plateIdentifier + "\" for the results row (" + rowCounter + ").");
 
-                plateIdentifierMap.putIfAbsent(plateIdentifier, new Pair<>(plate, new HashMap<>()));
+                    return Pair.of(plate, new HashMap<>());
+                });
+                Plate plate = plateIdentifierMap.get(plateIdentifier).first;
 
                 // if the plate identifier is the plate name, we need to make sure it resolves during importRows
                 // so replace it with the plateId (which will be unique)
@@ -205,12 +208,14 @@ public Map<String, Object> apply(Map<String, Object> row)
                     }
 
                     if (!wellSamples.isEmpty())
+                    {
                         // stash away any samples associated with the plate
                         ExperimentService.get().getExpMaterials(wellSamples).forEach(s -> sampleMap.put(s.getRowId(), s));
+                    }
                 }
 
                 PositionImpl well = new PositionImpl(null, String.valueOf(wellLocation));
-                // need to adjust the column value to be 0 based to match the template locations
+                // need to adjust the column value to be 0-based to match the template locations
                 well.setColumn(well.getColumn() - 1);
 
                 if (!positionToWell.containsKey(well))
@@ -386,7 +391,7 @@ public DataIteratorBuilder mergeReRunData(
             throw new ExperimentException(String.format("Unable to query the assay results for protocol : %s", protocol.getName()));
 
         // The plate identifier is either a row ID or plate ID on incoming data, need to match that when merging existing data.
-        FieldKey plateFieldKey = FieldKey.fromParts(AssayResultDomainKind.Column.Plate.name());
+        FieldKey plateFieldKey = AssayResultDomainKind.Column.Plate.fieldKey();
         // Note that in the case where there is a transform script on the assay design, the LK data parsing might not have
         // found any rows, and we might be deferring to the transform script to do that parsing. This block of code should
         // be able to proceed in that case by just passing through all run results to the transform script for the run being replaced.
@@ -1507,7 +1512,7 @@ public String format(FieldKey fieldKey)
     }
 
     @Override
-    public UserSchema getPlateSchema(QuerySchema querySchema, Set<Role> contextualRoles)
+    public @NotNull UserSchema getPlateSchema(QuerySchema querySchema, Set<Role> contextualRoles)
     {
         return new PlateSchema(querySchema, contextualRoles);
     }
@@ -1524,7 +1529,6 @@ private static class PlateMetadataImportHelper extends SimpleAssayDataImportHelp
         private final ExpProtocol _protocol;
         private final AssayProvider _provider;
         private final AssayRunUploadContext<?> _context;
-        private DomainProperty _stateProp;
 
         public PlateMetadataImportHelper(
             ExpData data,
@@ -1556,7 +1560,7 @@ public void bindAdditionalParameters(Map<String, Object> map, ParameterMapStatem
 
             Domain runDomain = _provider.getRunDomain(_protocol);
             Domain resultDomain = _provider.getResultsDomain(_protocol);
-            _stateProp = AssayPlateMetadataServiceImpl.getAssayStateProp(resultDomain);
+            DomainProperty stateProp = AssayPlateMetadataServiceImpl.getAssayStateProp(resultDomain);
             DomainProperty plateSetProperty = runDomain.getPropertyByName(AssayPlateMetadataService.PLATE_SET_COLUMN_NAME);
             DomainProperty plateProperty = resultDomain.getPropertyByName(AssayResultDomainKind.Column.Plate.name());
             DomainProperty wellLocationProperty = resultDomain.getPropertyByName(AssayResultDomainKind.Column.WellLocation.name());
@@ -1629,7 +1633,7 @@ public void bindAdditionalParameters(Map<String, Object> map, ParameterMapStatem
             // Validate any data state values on the row. No hit selection / data state processing is done on import
             // because at this time transform script hit selection is not supported nor is there any intersection
             // in the re-import case yet.
-            validateRowDataStates(_container, map, _stateProp);
+            validateRowDataStates(_container, map, stateProp);
         }
 
         /**
@@ -1650,11 +1654,12 @@ public void afterBatchInsert(int rowCount)
 
                 AssayProtocolSchema schema = _provider.createProtocolSchema(_user, _container, _protocol, null);
                 TableInfo resultsTable = schema.createDataTable(null, false);
+                boolean isReimport = isExistingRun();
 
                 // Re-select any hits that were present in the previous run, this works in conjunction with the code in
                 // mergeReRunData where previous hits are removed for any data unchanged by the new incoming data. At this
                 // point any remaining hits should represent selections we plan to move forward to the new run
-                if (isExistingRun())
+                if (isReimport)
                 {
                     ExpRun prevRun = ExperimentService.get().getExpRun(_context.getReRunId());
                     if (prevRun != null)
@@ -1677,6 +1682,8 @@ public void afterBatchInsert(int rowCount)
 
                 AssayPlateMetadataService.get().applyHitSelectionCriteria(_container, _user, _protocol, resultsTable, List.of(_run.getRowId()));
 
+                PlateManager.get().addPlateImportAuditEvents(_container, _user, tx, _plateIdentifierMap.values().stream().toList(), _run, isReimport);
+
                 tx.commit();
             }
             catch (Throwable e)
@@ -1711,7 +1718,7 @@ public void testGridAnnotations() throws Exception
                     new PlateManager.PlateData(null, plateType.getRowId(), null, null, Collections.emptyList())
             );
 
-            PlateSet plateSet = PlateManager.get().createPlateSet(container, user, new PlateSetImpl(), plates, null);
+            PlateSet plateSet = PlateManager.get().createPlateSet(container, user, new PlateSetImpl(), plates, null, null);
             List<Plate> plateSetPlates = PlateManager.get().getPlatesForPlateSet(plateSet);
             assertEquals("Expected two plates to be created.", 2, plateSetPlates.size());
             Plate plate = plateSetPlates.get(0);