Add auditing of what method was used for data imports, updates, deletes

api/src/org/labkey/api/action/BaseViewAction.java

@@ -28,13 +28,16 @@
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.attachments.AttachmentFile;
 import org.labkey.api.attachments.SpringAttachmentFile;
+import org.labkey.api.audit.TransactionAuditProvider;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ConvertHelper;
 import org.labkey.api.security.User;
 import org.labkey.api.util.HelpTopic;
+import org.labkey.api.util.HttpUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.HttpView;
+import org.labkey.api.view.ViewContext;
 import org.labkey.api.view.template.PageConfig;
 import org.labkey.api.writer.ContainerUser;
 import org.springframework.beans.AbstractPropertyAccessor;
@@ -71,6 +74,7 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.function.Predicate;
@@ -535,6 +539,31 @@ public boolean supports(Class clazz)
         return getCommandClass().isAssignableFrom(clazz);
     }
 
+    public Map<TransactionAuditProvider.TransactionDetail, Object> getTransactionAuditDetails()
+    {
+        return getTransactionAuditDetails(getViewContext());
+    }
+
+    public static Map<TransactionAuditProvider.TransactionDetail, Object> getTransactionAuditDetails(ViewContext viewContext)
+    {
+        Map<TransactionAuditProvider.TransactionDetail, Object> map = new HashMap<>();
+        map.put(TransactionAuditProvider.TransactionDetail.Action, viewContext.getActionURL().getController() + "-" + viewContext.getActionURL().getAction());
+        String clientLibrary = HttpUtil.getClientLibrary(viewContext.getRequest());
+        if (null != clientLibrary)
+            map.put(TransactionAuditProvider.TransactionDetail.ClientLibrary, clientLibrary);
+        else
+        {
+            String productName = HttpUtil.getProductNameFromReferer(viewContext.getRequest()); // app
+            if (null != productName)
+                map.put(TransactionAuditProvider.TransactionDetail.Product, productName);
+            else // LKS
+            {
+                String refererRelativeURL = HttpUtil.getRefererRelativeURL(viewContext.getRequest());
+                map.put(TransactionAuditProvider.TransactionDetail.RequestSource, refererRelativeURL);
+            }
+        }
+        return map;
+    }
 
     /* for TableViewForm, uses BeanUtils to work with DynaBeans */
     static public class BeanUtilsPropertyBindingResult extends BeanPropertyBindingResult

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

@@ -2,6 +2,7 @@
 
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.audit.AuditLogService;
+import org.labkey.api.audit.TransactionAuditProvider;
 import org.labkey.api.audit.provider.FileSystemAuditProvider;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
@@ -59,7 +60,7 @@ public static void cleanupPostedFiles(Container container, Set<FileLike> files,
         }
     }
 
-    public CaseInsensitiveHashMap<FileLike> savePostedFiles(Container container, User user, Map<String, MultipartFile> filePropertyMap, Long auditTransactionId, String auditComment) throws ExperimentException
+    public CaseInsensitiveHashMap<FileLike> savePostedFiles(Container container, User user, Map<String, MultipartFile> filePropertyMap, TransactionAuditProvider.TransactionAuditEvent auditTransactionEvent, String auditComment) throws ExperimentException
     {
         FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(container);
         CaseInsensitiveHashMap<FileLike> properties = new CaseInsensitiveHashMap<>();
@@ -87,7 +88,7 @@ public CaseInsensitiveHashMap<FileLike> savePostedFiles(Container container, Use
                 event.setProvidedFileName(originalName);
                 event.setFile(file.getName());
                 event.setDirectory(file.getParent());
-                event.setTransactionId(auditTransactionId);
+                event.setTransactionEvent(auditTransactionEvent, FileSystemAuditProvider.EVENT_TYPE);
                 event.setFieldName(entry.getKey());
                 AuditLogService.get().addEvent(user, event);
 

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

@@ -16,12 +16,15 @@
 package org.labkey.api.assay;
 
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.audit.TransactionAuditProvider;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpExperiment;
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.util.Pair;
 
+import java.util.Map;
+
 /**
  * An AssayRunCreator does the actual work of constructing an assay run and saving it to the database. It gets
  * data about the run to be created from a AssayRunUploadContext and translates it into objects in the Experiment
@@ -40,14 +43,17 @@ public interface AssayRunCreator<ProviderType extends AssayProvider>
      * @param batchId if not null, the run group that's already created for this batch. If null, a new one will be created.
      * @return Pair of batch and run that were inserted.  ExpBatch will not be null, but ExpRun may be null when inserting the run async.
      */
-    Pair<ExpExperiment, ExpRun> saveExperimentRun(AssayRunUploadContext<ProviderType> context, @Nullable Long batchId)
-            throws ExperimentException, ValidationException;
+    default Pair<ExpExperiment, ExpRun> saveExperimentRun(AssayRunUploadContext<ProviderType> context, @Nullable Long batchId)
+            throws ExperimentException, ValidationException
+    {
+        return saveExperimentRun(context, batchId, false, null);
+    }
 
-    Pair<ExpExperiment, ExpRun> saveExperimentRun(AssayRunUploadContext<ProviderType> context, @Nullable Long batchId, boolean forceAsync)
+    Pair<ExpExperiment, ExpRun> saveExperimentRun(AssayRunUploadContext<ProviderType> context, @Nullable Long batchId, boolean forceAsync, Map<TransactionAuditProvider.TransactionDetail, Object> transactionDetails)
             throws ExperimentException, ValidationException;
     /**
      * @return the batch to which the run has been assigned
      */
-    ExpExperiment saveExperimentRun(AssayRunUploadContext<ProviderType> context, @Nullable ExpExperiment batch, ExpRun run, boolean forceSaveBatchProps)
+    ExpExperiment saveExperimentRun(AssayRunUploadContext<ProviderType> context, @Nullable ExpExperiment batch, ExpRun run, boolean forceSaveBatchProps, @Nullable Map<TransactionAuditProvider.TransactionDetail, Object> transactionDetails)
         throws ExperimentException, ValidationException;
 }

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

@@ -123,13 +123,6 @@ public TransformResult transform(AssayRunUploadContext<ProviderType> context, Ex
     {
         return DataTransformService.get().transformAndValidate(context, run, DataTransformService.TransformOperation.INSERT);
     }
-
-    @Override
-    public Pair<ExpExperiment, ExpRun> saveExperimentRun(AssayRunUploadContext<ProviderType> context, @Nullable Long batchId) throws ExperimentException, ValidationException
-    {
-        return saveExperimentRun(context, batchId, false);
-    }
-
     /**
      * Create and save an experiment run synchronously or asynchronously in a background job depending upon the assay design.
      *
@@ -141,7 +134,8 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(AssayRunUploadContext<Provi
     public Pair<ExpExperiment, ExpRun> saveExperimentRun(
             AssayRunUploadContext<ProviderType> context,
             @Nullable Long batchId,
-            boolean forceAsync
+            boolean forceAsync,
+            Map<TransactionAuditProvider.TransactionDetail, Object> transactionDetails
     ) throws ExperimentException, ValidationException
     {
         ExpExperiment exp = null;
@@ -156,9 +150,10 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(
 
         try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction(ExperimentService.get().getProtocolImportLock()))
         {
-            if (transaction.getAuditId() == null)
+            TransactionAuditProvider.TransactionAuditEvent auditEvent = transaction.getAuditEvent();
+            if (auditEvent == null)
             {
-                TransactionAuditProvider.TransactionAuditEvent auditEvent = AbstractQueryUpdateService.createTransactionAuditEvent(context.getContainer(), context.getReRunId() == null ? QueryService.AuditAction.UPDATE : QueryService.AuditAction.INSERT);
+                auditEvent = AbstractQueryUpdateService.createTransactionAuditEvent(context.getContainer(), context.getReRunId() == null ? QueryService.AuditAction.UPDATE : QueryService.AuditAction.INSERT, transactionDetails);
                 AbstractQueryUpdateService.addTransactionAuditEvent(transaction, context.getUser(), auditEvent);
             }
             context.init();
@@ -172,11 +167,13 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(
                     throw new ClassCastException("FileLike expected: " + errFile + " context: " + context.getClass() + " " + context);
                 }
                 FileLike primaryFile = context.getUploadedData().get(AssayDataCollector.PRIMARY_FILE);
+                if (primaryFile != null)
+                    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());
 
-                exp = saveExperimentRun(context, exp, run, false);
+                exp = saveExperimentRun(context, exp, run, false, transactionDetails);
 
                 // re-fetch the run after it has been fully constructed
                 run = ExperimentService.get().getExpRun(run.getRowId());
@@ -187,6 +184,10 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(
             {
                 context.uploadComplete(null);
                 context.setTransactionAuditId(transaction.getAuditId());
+                FileLike primaryFile = context.getUploadedData().get(AssayDataCollector.PRIMARY_FILE);
+                if (primaryFile != null)
+                    auditEvent.addDetail(TransactionAuditProvider.TransactionDetail.ImportFileName, primaryFile.getName());
+                auditEvent.addDetail(TransactionAuditProvider.TransactionDetail.ImportOptions, "BackgroundImport");
                 exp = saveExperimentRunAsync(context, exp);
             }
             transaction.commit();
@@ -267,7 +268,8 @@ public ExpExperiment saveExperimentRun(
         final AssayRunUploadContext<ProviderType> context,
         @Nullable ExpExperiment batch,
         @NotNull ExpRun run,
-        boolean forceSaveBatchProps
+        boolean forceSaveBatchProps,
+        @Nullable Map<TransactionAuditProvider.TransactionDetail, Object> transactionDetails
     ) throws ExperimentException, ValidationException
     {
         context.setAutoFillDefaultResultColumns(run.getRowId() > 0); // need to setAutoFillDefaultResultColumns before run is saved
@@ -327,7 +329,7 @@ public ExpExperiment saveExperimentRun(
                 }
                 else
                 {
-                    var auditEvent = AbstractQueryUpdateService.createTransactionAuditEvent(container, auditAction);
+                    var auditEvent = AbstractQueryUpdateService.createTransactionAuditEvent(container, auditAction, transactionDetails);
                     AbstractQueryUpdateService.addTransactionAuditEvent(transaction, context.getUser(), auditEvent);
                 }
             }

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

@@ -1027,7 +1027,7 @@ public class RunStepHandler extends StepHandler<FormType>
 
         public final ExpRun saveExperimentRun(FormType form) throws ExperimentException, ValidationException
         {
-            Pair<ExpExperiment, ExpRun> pair = form.getProvider().getRunCreator().saveExperimentRun(form, form.getBatchId());
+            Pair<ExpExperiment, ExpRun> pair = form.getProvider().getRunCreator().saveExperimentRun(form, form.getBatchId(), false, getTransactionAuditDetails());
             assert pair != null && pair.first != null;
             ExpExperiment exp = pair.first;
             ExpRun run = pair.second;

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

@@ -22,6 +22,7 @@
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayService;
 import org.labkey.api.assay.AssayUrls;
+import org.labkey.api.audit.TransactionAuditProvider;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpExperiment;
 import org.labkey.api.exp.api.ExpRun;
@@ -155,8 +156,13 @@ public void doWork()
                 _forceSaveBatchProps = true;
             }
 
+            Map<TransactionAuditProvider.TransactionDetail, Object> transactionDetails = new HashMap<>();
+            transactionDetails.put(TransactionAuditProvider.TransactionDetail.ImportFileName, _primaryFile.getName());
+            transactionDetails.put(TransactionAuditProvider.TransactionDetail.ImportOptions, "BackgroundImport");
+            transactionDetails.put(TransactionAuditProvider.TransactionDetail.Action, "AssayUploadPipelineJob");
+
             // Do all the real work of the import
-            ExpExperiment result = _context.getProvider().getRunCreator().saveExperimentRun(_context, batch, _run, _forceSaveBatchProps);
+            ExpExperiment result = _context.getProvider().getRunCreator().saveExperimentRun(_context, batch, _run, _forceSaveBatchProps, transactionDetails);
             setStatus(TaskStatus.complete);
             getLogger().info("Finished assay upload");
 

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

@@ -191,6 +191,15 @@ public void setTransactionId(Long transactionId)
         _transactionId = transactionId;
     }
 
+    public void setTransactionEvent(@Nullable TransactionAuditProvider.TransactionAuditEvent transactionEvent, String auditEventType)
+    {
+        if (transactionEvent == null)
+            return;
+
+        _transactionId = transactionEvent.getRowId();
+        transactionEvent.addDetail(TransactionAuditProvider.TransactionDetail.AuditEvents, auditEventType);
+    }
+
     protected String getContainerMessageElement(@NotNull Container container)
     {
         String value = " (" + container.getId() + ")";

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

@@ -21,13 +21,12 @@ public class ExperimentAuditEvent extends AuditTypeEvent
     public ExperimentAuditEvent()
     {
         super();
-        setTransactionId(TransactionAuditProvider.getCurrentTransactionAuditId());
     }
 
     public ExperimentAuditEvent(Container container, String comment)
     {
         super(EVENT_TYPE, container, comment);
-        setTransactionId(TransactionAuditProvider.getCurrentTransactionAuditId());
+        setTransactionEvent(TransactionAuditProvider.getCurrentTransactionAuditEvent(), EVENT_TYPE);
     }
 
     public String getProtocolLsid()

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

@@ -104,13 +104,12 @@ public static SampleTimelineEventType getTypeFromName(@Nullable String name)
     public SampleTimelineAuditEvent()
     {
         super();
-        setTransactionId(TransactionAuditProvider.getCurrentTransactionAuditId());
     }
 
     public SampleTimelineAuditEvent(Container container, String comment)
     {
         super(EVENT_TYPE, container, comment);
-        setTransactionId(TransactionAuditProvider.getCurrentTransactionAuditId());
+        setTransactionEvent(TransactionAuditProvider.getCurrentTransactionAuditEvent(), EVENT_TYPE);
     }
 
     public String getSampleLsid()