Job Source Actions

api/src/org/labkey/api/workflow/Action.java

@@ -295,7 +295,9 @@ else if (_type == WorkflowService.ActionType.AliquotSamples)
 
             return messages;
         }
-        else if (_type == WorkflowService.ActionType.DeriveSamples || _type == WorkflowService.ActionType.PoolSamples)
+        else if (_type == WorkflowService.ActionType.DeriveSamples
+                || _type == WorkflowService.ActionType.PoolSamples
+                || _type == WorkflowService.ActionType.DeriveSamplesFromSources)
         {
             String emptyMessage = prefix + "data about sample types and sample counts per parent is required for action of type " + _type + ".";
 
@@ -358,9 +360,14 @@ else if (countObj instanceof Integer count)
 
             if (hasAnySampleStatusKey())
             {
-                String statusMessage = validateStatus(container, prefix, true);
+                if (_type == WorkflowService.ActionType.DeriveSamplesFromSources)
+                    messages.add(prefix + "data about updating parent status not allowed for action of type " + _type + ".");
+                else
+                {
+                    String statusMessage = validateStatus(container, prefix, true);
 
-                if (statusMessage != null) messages.add(statusMessage);
+                    if (statusMessage != null) messages.add(statusMessage);
+                }
             }
 
             return messages;
@@ -377,6 +384,67 @@ else if (_type == WorkflowService.ActionType.RemoveFromStorage || _type == Workf
 
             return Collections.emptyList();
         }
+        else if (_type == WorkflowService.ActionType.DeriveSources)
+        {
+            String emptyMessage = prefix + "data about source types and source counts per parent is required for action of type " + _type + ".";
+
+            if (_inputParameters == null) return List.of(emptyMessage);
+
+            // We can't just check _inputParameters size because it may include sample status keys, so we extract the
+            // source type IDs and validate against those.
+            List<String> sourceTypeIds = new ArrayList<>();
+            _inputParameters.keys().forEachRemaining(id -> {
+                if (isSampleStatusKey(id)) return;
+                sourceTypeIds.add(id);
+            });
+
+            if (sourceTypeIds.isEmpty())
+                return List.of(emptyMessage);
+
+            // don't allow more than one target source type
+            if (sourceTypeIds.size() > 1)
+                return List.of(prefix + "only one source type can be specified for action of type " + _type + ".");
+
+            List<String> messages = new ArrayList<>();
+            String sourceTypeId = sourceTypeIds.get(0);
+            boolean invalidId;
+            try
+            {
+                invalidId = ExperimentService.get().getDataClass(container, Long.parseLong(sourceTypeId), true) == null;
+            }
+            catch (NumberFormatException e)
+            {
+                invalidId = true;
+            }
+            if (invalidId)
+                messages.add(prefix + "invalid source type ID " + sourceTypeId + ".");
+
+            Object countObj = _inputParameters.get(sourceTypeId);
+            boolean invalidCount;
+            if (countObj instanceof String countStr)
+            {
+                try
+                {
+                    invalidCount = Integer.parseInt(countStr) < 0;
+                }
+                catch (NumberFormatException e)
+                {
+                    invalidCount = true;
+                }
+            }
+            else if (countObj instanceof Integer count)
+                invalidCount = count < 0;
+            else
+                invalidCount = true;
+
+            if (invalidCount)
+                messages.add(prefix + "invalid source count value " + countObj + ".");
+
+            if (hasAnySampleStatusKey())
+                messages.add(prefix + "data about updating parent status not allowed for action of type " + _type + ".");
+
+            return messages;
+        }
         else
         {
             if (_inputParameters != null && !_inputParameters.isEmpty())

api/src/org/labkey/api/workflow/Task.java

@@ -43,6 +43,7 @@ public abstract class Task extends CreatedModified implements Comparable<Task>
 
     protected String _description;
     protected String _entityFilter;
+    protected WorkEntity.EntityType _inputEntityType;
     protected Integer _status;
     protected Date _startDate;
     protected Date _endDate;
@@ -93,6 +94,16 @@ public void setEntityFilter(String entityFilter)
         _entityFilter = entityFilter;
     }
 
+    public WorkEntity.EntityType getInputEntityType()
+    {
+        return _inputEntityType;
+    }
+
+    public void setInputEntityType(WorkEntity.EntityType inputEntityType)
+    {
+        _inputEntityType = inputEntityType;
+    }
+
     @JsonProperty("assignee")
     public JSONObject getAssigneeJSON()
     {
@@ -278,6 +289,8 @@ public Map<String, Object> toAuditDetailMap()
             map.put("dueDate", getDueDate());
         if (getEntityId() != null)
             map.put("entityId", getEntityId().toString());
+        if (getInputEntityType() != null)
+            map.put("inputEntityType", getInputEntityType());
         map.put("ordinal", getOrdinal());
         int actionIndex = 1;
         for (Action action : getActions())

api/src/org/labkey/api/workflow/WorkflowService.java

@@ -36,24 +36,28 @@ enum WorkflowConfigs
 
     enum ActionType
     {
-        AssayImport("assay types", "Imported assay data"),
-        DeriveSamples("derivation sample type parameters", "Derived samples"),
-        AliquotSamples("aliquot sample type parameters", "Aliquot samples"),
-        PoolSamples("pooling sample type parameters", "Pooled samples"),
-        AddToStorage("input parameters", "Added samples to storage"),
-        MoveInStorage("input parameters", "Moved samples in storage"),
-        CheckOut("input parameters", "Checked out samples"),
-        CheckIn("input parameters", "Checked in samples"),
-        RemoveFromStorage("sample status value", "Removed samples from storage"),
-        UpdateSampleStatus("sample status value", "Updated sample status");
+        AssayImport("assay types", "Imported assay data", WorkEntity.EntityType.Sample),
+        DeriveSamples("derivation sample type parameters", "Derived samples", WorkEntity.EntityType.Sample),
+        AliquotSamples("aliquot sample type parameters", "Aliquot samples", WorkEntity.EntityType.Sample),
+        PoolSamples("pooling sample type parameters", "Pooled samples", WorkEntity.EntityType.Sample),
+        AddToStorage("input parameters", "Added samples to storage", WorkEntity.EntityType.Sample),
+        MoveInStorage("input parameters", "Moved samples in storage", WorkEntity.EntityType.Sample),
+        CheckOut("input parameters", "Checked out samples", WorkEntity.EntityType.Sample),
+        CheckIn("input parameters", "Checked in samples", WorkEntity.EntityType.Sample),
+        RemoveFromStorage("sample status value", "Removed samples from storage", WorkEntity.EntityType.Sample),
+        UpdateSampleStatus("sample status value", "Updated sample status", WorkEntity.EntityType.Sample),
+        DeriveSamplesFromSources("derivation source type parameters", "Derived samples from sources", WorkEntity.EntityType.Source),
+        DeriveSources("derivation source type parameters", "Derived sources", WorkEntity.EntityType.Source);
 
         private final String _inputDescription;
         private final String _auditMessage;
+        private final WorkEntity.EntityType _inputEntityType;
 
-        ActionType(String inputDescription, String auditMessage)
+        ActionType(String inputDescription, String auditMessage,  WorkEntity.EntityType inputEntityType)
         {
             _inputDescription = inputDescription;
             _auditMessage = auditMessage;
+            _inputEntityType = inputEntityType;
         }
 
         public String getInputDescription()
@@ -65,6 +69,11 @@ public String getAuditMessage()
         {
             return _auditMessage;
         }
+
+        public WorkEntity.EntityType getInputEntityType()
+        {
+            return _inputEntityType;
+        }
     }
 
     static void setInstance(WorkflowService impl)
@@ -84,9 +93,12 @@ static WorkflowService get()
     void onActionComplete(@NotNull Container container, @NotNull User user, @NotNull Long actionId, @Nullable String userAuditComment);
     void onActionComplete(@NotNull Container container, @NotNull User user, @NotNull Long taskId, @NotNull ActionType actionType);
     boolean actionWillAddSamples(Long actionId);
+    boolean actionWillAddSources(Long actionId);
 
     DataIteratorBuilder getSampleCreationDataIteratorBuilder(DataIteratorBuilder data, Container container, User user);
 
+    DataIteratorBuilder getSourceCreationDataIteratorBuilder(DataIteratorBuilder data, Container container, User user);
+
     DataIteratorBuilder getActionAuditDataIteratorBuilder(DataIteratorBuilder data, Container container, User user);
 
     @Nullable

experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java

@@ -124,6 +124,7 @@
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.api.view.ViewContext;
+import org.labkey.api.workflow.WorkflowService;
 import org.labkey.data.xml.TableType;
 import org.labkey.experiment.ExpDataIterators;
 import org.labkey.experiment.ExpDataIterators.AliasDataIteratorBuilder;
@@ -942,8 +943,24 @@ public DataIteratorBuilder persistRows(DataIteratorBuilder data, DataIteratorCon
 
             }, DbScope.CommitTaskOption.POSTCOMMIT));
 
+
             DataIteratorBuilder builder = LoggingDataIterator.wrap(step0);
-            return LoggingDataIterator.wrap(new AliasDataIteratorBuilder(builder, getUserSchema().getContainer(), getUserSchema().getUser(), ExperimentService.get().getTinfoDataAliasMap(), _dataClass, false));
+            UserSchema userSchema = getUserSchema();
+            builder = LoggingDataIterator.wrap(new AliasDataIteratorBuilder(builder, userSchema.getContainer(), userSchema.getUser(), ExperimentService.get().getTinfoDataAliasMap(), _dataClass, false));
+            WorkflowService workService = WorkflowService.get();
+            if (workService != null && !context.getInsertOption().allowUpdate)
+            {
+                if (context.getConfigParameter(WorkflowService.WorkflowConfigs.ActionId) != null)
+                {
+                    Long actionId = (Long) context.getConfigParameter(WorkflowService.WorkflowConfigs.ActionId);
+
+                    if (workService.actionWillAddSources(actionId))
+                        builder = workService.getSourceCreationDataIteratorBuilder(builder, userSchema.getContainer(), userSchema.getUser());
+
+                    builder = workService.getActionAuditDataIteratorBuilder(builder, userSchema.getContainer(), userSchema.getUser());
+                }
+            }
+            return builder;
         }
         catch (IOException e)
         {

experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java

@@ -429,7 +429,7 @@ public DataIteratorBuilder createImportDIB(User user, Container container, DataI
                 {
                     Long actionId = (Long) context.getConfigParameter(WorkflowService.WorkflowConfigs.ActionId);
 
-                    if (WorkflowService.get().actionWillAddSamples(actionId))
+                    if (workService.actionWillAddSamples(actionId) && !context.getInsertOption().allowUpdate)
                     {
                         dib = workService.getSampleCreationDataIteratorBuilder(dib, userSchema.getContainer(), userSchema.getUser());
                     }

experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java

@@ -4426,17 +4426,6 @@ protected int importData(
                 tInfo = ExperimentService.get().createMaterialTable(new SamplesSchema(getUser(), getContainer()), ContainerFilter.current(this), null);
                 updateService = tInfo.getUpdateService();
             }
-            if (WorkflowService.get() != null)
-            {
-                try
-                {
-                    WorkflowService.get().populateConfigParams(getViewContext().getRequest(), _context.getConfigParameters());
-                }
-                catch (ValidationException e)
-                {
-                    errors.addRowError(e);
-                }
-            }
 
             int count = importData(dl, tInfo, updateService, _context, auditEvent, getUser(), getContainer());
 
@@ -4551,6 +4540,21 @@ protected Set<String> getLineageImportAliases() throws IOException
         protected void initContext(DataLoader dl, BatchValidationException errors, @Nullable AuditBehaviorType auditBehaviorType, @Nullable String auditUserComment)
         {
             _context = createDataIteratorContext(_insertOption, getOptionParamsMap(), getLookupResolutionType(), auditBehaviorType, auditUserComment, errors, null, getContainer());
+
+            // Both samples and data classes can be created via a workflow job action, so the action and job ids need to
+            // be available to the update service for either type. The background import path populates these separately
+            // via AbstractQueryImportAction.getImportContextBuilder().
+            if (WorkflowService.get() != null)
+            {
+                try
+                {
+                    WorkflowService.get().populateConfigParams(getViewContext().getRequest(), _context.getConfigParameters());
+                }
+                catch (ValidationException e)
+                {
+                    errors.addRowError(e);
+                }
+            }
         }
 
         @Override