Add support for sample creation actions in workflow jobs

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

@@ -1,13 +1,27 @@
 package org.labkey.api.workflow;
 
+import jakarta.servlet.http.HttpServletRequest;
 import org.jetbrains.annotations.NotNull;
-import org.labkey.api.data.Container;import org.labkey.api.security.User;import org.labkey.api.services.ServiceRegistry;
+import org.labkey.api.data.Container;
+import org.labkey.api.dataiterator.DataIteratorBuilder;
+import org.labkey.api.security.User;import org.labkey.api.services.ServiceRegistry;
+
+import java.util.Map;
 
 public interface WorkflowService
 {
+    enum WorkflowConfigs
+    {
+        ActionId,
+        JobId,
+    }
+
     enum ActionType
     {
-        AssayImport("assay types", "Imported assay data");
+        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");
 
         private final String _inputDescription;
         private final String _auditMessage;
@@ -39,6 +53,13 @@ static WorkflowService get()
         return ServiceRegistry.get().getService(WorkflowService.class);
     }
 
+    void populateConfigParams(Map<String, Object> provided, Map<Enum, Object> configParameters);
+
+    void populateConfigParams(HttpServletRequest request, Map<Enum, Object> configParameters);
     void onActionComplete(@NotNull Container container, @NotNull User user, @NotNull Long actionId);
     void onActionComplete(@NotNull Container container, @NotNull User user, @NotNull Long taskId, @NotNull ActionType actionType);
+
+    DataIteratorBuilder getSampleCreationDataIteratorBuilder(DataIteratorBuilder data, Container container, User user);
+
+    DataIteratorBuilder getActionAuditDataIteratorBuilder(DataIteratorBuilder data, Container container, User user);
 }

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

@@ -108,6 +108,7 @@
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.UnauthorizedException;
+import org.labkey.api.workflow.WorkflowService;
 import org.labkey.experiment.ExpDataIterators;
 import org.labkey.experiment.SampleTypeAuditProvider;
 
@@ -416,6 +417,14 @@ public DataIteratorBuilder createImportDIB(User user, Container container, DataI
 
             if (sampleType.getAutoLinkTargetContainer() != null && StudyPublishService.get() != null && !context.getInsertOption().updateOnly/* TODO support link to study on update? */)
                 dib = LoggingDataIterator.wrap(new ExpDataIterators.AutoLinkToStudyDataIteratorBuilder(dib, getSchema(), userSchema.getContainer(), userSchema.getUser(), sampleType));
+            if (WorkflowService.get() != null)
+            {
+                if (context.getConfigParameter(WorkflowService.WorkflowConfigs.ActionId) != null)
+                {
+                    dib = WorkflowService.get().getSampleCreationDataIteratorBuilder(dib, userSchema.getContainer(), userSchema.getUser());
+                    dib = WorkflowService.get().getActionAuditDataIteratorBuilder(dib, userSchema.getContainer(), userSchema.getUser());
+                }
+            }
         }
         return dib;
     }

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

@@ -252,6 +252,7 @@
 import org.labkey.api.view.WebPartView;
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.api.view.template.PageConfig;
+import org.labkey.api.workflow.WorkflowService;
 import org.labkey.experiment.ChooseExperimentTypeBean;
 import org.labkey.experiment.ConfirmDeleteView;
 import org.labkey.experiment.CustomPropertiesView;
@@ -4448,6 +4449,8 @@ protected int importData(
                 tInfo = ExperimentService.get().createMaterialTable(new SamplesSchema(getUser(), getContainer()), ContainerFilter.current(this), null);
                 updateService = tInfo.getUpdateService();
             }
+            if (WorkflowService.get() != null)
+                WorkflowService.get().populateConfigParams(getViewContext().getRequest(), _context.getConfigParameters());
 
             int count = importData(dl, tInfo, updateService, _context, auditEvent, getUser(), getContainer());
 

query/src/org/labkey/query/controllers/QueryController.java

@@ -267,6 +267,7 @@
 import org.labkey.api.view.ViewServlet;
 import org.labkey.api.view.WebPartView;
 import org.labkey.api.view.template.PageConfig;
+import org.labkey.api.workflow.WorkflowService;
 import org.labkey.api.writer.HtmlWriter;
 import org.labkey.api.writer.ZipFile;
 import org.labkey.data.xml.ColumnType;
@@ -4659,11 +4660,13 @@ protected JSONObject executeJson(JSONObject json, CommandType commandType, boole
                 }
             }
 
-            Map<String, Object> extraContext = json.has("extraContext") ? json.getJSONObject("extraContext").toMap() : new CaseInsensitiveHashMap<>();
+            Map<String, Object> extraContext = json.has("extraContext") ? new CaseInsensitiveHashMap(json.getJSONObject("extraContext").toMap()) : new CaseInsensitiveHashMap<>();
 
             Map<String, Object> auditDetails = json.has("auditDetails") ? json.getJSONObject("auditDetails").toMap() : new CaseInsensitiveHashMap<>();
 
             Map<Enum, Object> configParameters = new HashMap<>();
+            if (WorkflowService.get() != null)
+                WorkflowService.get().populateConfigParams(extraContext, configParameters);
 
             // Check first if the audit behavior has been defined for the table either in code or through XML.
             // If not defined there, check for the audit behavior defined in the action form (json).