labkey-jeckels · Oct 23, 2026
diff --git a/api/src/org/labkey/api/assay/AssayFileWriter.java b/api/src/org/labkey/api/assay/AssayFileWriter.java
@@ -262,7 +262,11 @@ public Map<String, FileLike> savePostedFiles(ContextType context, @NotNull Set<S
                                 event.setProvidedFileName(fileName);
                                 event.setFile(file.getName());
                                 event.setDirectory(dir.toURI().getPath());
-                                AuditLogService.get().addEvent(context.getUser(), event);
+                                List<FileSystemAuditProvider.FileSystemAuditEvent> pending = context.getPendingFileAuditEvents();
+                                if (pending != null)
+                                    pending.add(event);
+                                else
+                                    AuditLogService.get().addEvent(context.getUser(), event);
                             }
                             if (!isAfterFirstFile)  // first file gets stored with multipartFile's name
                             {

diff --git a/api/src/org/labkey/api/assay/AssayRunUploadContext.java b/api/src/org/labkey/api/assay/AssayRunUploadContext.java
@@ -20,6 +20,7 @@
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.audit.provider.FileSystemAuditProvider;
 import org.labkey.api.collections.CollectionUtils;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ExpDataFileConverter;
@@ -37,6 +38,7 @@
 import org.labkey.api.writer.ContainerUser;
 import org.labkey.vfs.FileLike;
 
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
@@ -188,6 +190,17 @@ default void setPreparedTransform(@Nullable PreparedTransform prepared)
         throw new UnsupportedOperationException(getClass().getName() + " can't carry a prepared transform");
     }
 
+    /** File audit events held until the import transaction opens, or null to add them as they're created. */
+    default @Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> getPendingFileAuditEvents()
+    {
+        return null;
+    }
+
+    default void setPendingFileAuditEvents(@Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> events)
+    {
+        throw new UnsupportedOperationException(getClass().getName() + " can't hold file audit events");
+    }
+
     /** The RowId for the run that is being deleted and reuploaded, or null if this is a new run */
     Long getReRunId();
 

diff --git a/api/src/org/labkey/api/assay/AssayRunUploadContextImpl.java b/api/src/org/labkey/api/assay/AssayRunUploadContextImpl.java
@@ -34,6 +34,7 @@
 import org.labkey.api.assay.transform.DefaultTransformResult;
 import org.labkey.api.assay.transform.PreparedTransform;
 import org.labkey.api.assay.transform.TransformResult;
+import org.labkey.api.audit.provider.FileSystemAuditProvider;
 import org.labkey.api.security.User;
 import org.labkey.api.util.URIUtil;
 import org.labkey.api.view.ActionURL;
@@ -95,6 +96,7 @@ public class AssayRunUploadContextImpl<ProviderType extends AssayProvider> imple
     // Mutable fields
     private TransformResult _transformResult;
     private @Nullable PreparedTransform _preparedTransform;
+    private @Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> _pendingFileAuditEvents;
 
     // async fields
     protected String _jobDescription;
@@ -453,6 +455,18 @@ public void setPreparedTransform(@Nullable PreparedTransform prepared)
         _preparedTransform = prepared;
     }
 
+    @Override
+    public @Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> getPendingFileAuditEvents()
+    {
+        return _pendingFileAuditEvents;
+    }
+
+    @Override
+    public void setPendingFileAuditEvents(@Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> events)
+    {
+        _pendingFileAuditEvents = events;
+    }
+
     @Override
     public void uploadComplete(ExpRun run)
     {

diff --git a/api/src/org/labkey/api/assay/DefaultAssayRunCreator.java b/api/src/org/labkey/api/assay/DefaultAssayRunCreator.java
@@ -33,7 +33,9 @@
 import org.labkey.api.assay.transform.TransformDataHandler;
 import org.labkey.api.assay.transform.TransformResult;
 import org.labkey.api.collections.LongHashMap;
+import org.labkey.api.audit.AuditLogService;
 import org.labkey.api.audit.TransactionAuditProvider;
+import org.labkey.api.audit.provider.FileSystemAuditProvider;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
@@ -148,6 +150,8 @@ private PreparedTransform prepareTransformAfterInit(AssayRunUploadContext<Provid
         Map<DomainProperty, String> allProperties = new HashMap<>(context.getRunProperties());
         allProperties.putAll(context.getBatchProperties());
 
+        // Collecting the inputs saves the primary file, whose audit event belongs to the import transaction that isn't open yet
+        context.setPendingFileAuditEvents(new ArrayList<>());
         Map<ExpData, String> inputDatas = new HashMap<>();
         addRunDataInputs(context, null, findResolverType(allProperties), inputDatas);
         PreparedTransform prepared = runTransformBeforeRun(context, inputDatas.keySet());
@@ -206,6 +210,19 @@ private PreparedTransform runTransformBeforeRun(AssayRunUploadContext<ProviderTy
         return prepared;
     }
 
+    private static void addPendingFileAuditEvents(AssayRunUploadContext<?> context, TransactionAuditProvider.TransactionAuditEvent auditEvent)
+    {
+        List<FileSystemAuditProvider.FileSystemAuditEvent> pending = context.getPendingFileAuditEvents();
+        if (pending == null)
+            return;
+        context.setPendingFileAuditEvents(null);
+        for (FileSystemAuditProvider.FileSystemAuditEvent event : pending)
+        {
+            event.setTransactionEvent(auditEvent, FileSystemAuditProvider.EVENT_TYPE);
+            AuditLogService.get().addEvent(context.getUser(), event);
+        }
+    }
+
     /** Issue 26811: If we don't have a view, assume that we are on a background job thread already. */
     public static boolean isBackgroundImport(AssayProvider provider, ExpProtocol protocol, boolean forceAsync)
     {
@@ -263,6 +280,7 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(
                 auditEvent = AbstractQueryUpdateService.createTransactionAuditEvent(context.getContainer(), context.getReRunId() == null ? QueryService.AuditAction.UPDATE : QueryService.AuditAction.INSERT, transactionDetails);
                 AbstractQueryUpdateService.addTransactionAuditEvent(transaction, context.getUser(), auditEvent);
             }
+            addPendingFileAuditEvents(context, auditEvent);
             if (!importInBackground)
             {
                 if ((Object) context.getUploadedData().get(AssayDataCollector.PRIMARY_FILE) instanceof File errFile)

diff --git a/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java b/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java
@@ -51,6 +51,7 @@
 import org.labkey.api.assay.transform.DefaultTransformResult;
 import org.labkey.api.assay.transform.PreparedTransform;
 import org.labkey.api.assay.transform.TransformResult;
+import org.labkey.api.audit.provider.FileSystemAuditProvider;
 import org.labkey.api.qc.TsvDataExchangeHandler;
 import org.labkey.api.query.DefaultSchema;
 import org.labkey.api.query.PdLookupForeignKey;
@@ -108,6 +109,7 @@ public class AssayRunUploadForm<ProviderType extends AssayProvider> extends Prot
     private List<AssayDataCollector> _collectors;
     private TransformResult _transformResult = DefaultTransformResult.createEmptyResult();
     private @Nullable PreparedTransform _preparedTransform;
+    private @Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> _pendingFileAuditEvents;
     private ExpRun _reRun;
     private boolean _allowCrossRunFileInputs;
 
@@ -727,6 +729,18 @@ public void setPreparedTransform(@Nullable PreparedTransform prepared)
         _preparedTransform = prepared;
     }
 
+    @Override
+    public @Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> getPendingFileAuditEvents()
+    {
+        return _pendingFileAuditEvents;
+    }
+
+    @Override
+    public void setPendingFileAuditEvents(@Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> events)
+    {
+        _pendingFileAuditEvents = events;
+    }
+
     @Override
     public Long getReRunId()
     {

diff --git a/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java b/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java
@@ -36,6 +36,7 @@
 import org.labkey.api.assay.transform.DefaultTransformResult;
 import org.labkey.api.assay.transform.PreparedTransform;
 import org.labkey.api.assay.transform.TransformResult;
+import org.labkey.api.audit.provider.FileSystemAuditProvider;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.view.ActionURL;
@@ -47,6 +48,7 @@
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
@@ -90,6 +92,7 @@ public class AssayRunAsyncContext<ProviderType extends AssayProvider> implements
     private transient Set<Domain> _domains;
     private transient TransformResult _transformResult;
     private transient @Nullable PreparedTransform _preparedTransform;
+    private transient @Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> _pendingFileAuditEvents;
     private transient Logger _logger;
 
     // async fields
@@ -404,6 +407,18 @@ public void setPreparedTransform(@Nullable PreparedTransform prepared)
         _preparedTransform = prepared;
     }
 
+    @Override
+    public @Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> getPendingFileAuditEvents()
+    {
+        return _pendingFileAuditEvents;
+    }
+
+    @Override
+    public void setPendingFileAuditEvents(@Nullable List<FileSystemAuditProvider.FileSystemAuditEvent> events)
+    {
+        _pendingFileAuditEvents = events;
+    }
+
     @Override
     public Long getReRunId()
     {