Delete orphaned attachments

api/src/org/labkey/api/attachments/AttachmentService.java

@@ -140,7 +140,9 @@ static AttachmentService get()
 
     HttpView<?> getFindAttachmentParentsView();
 
-    void detectOrphans();
+    void logOrphanedAttachments();
+
+    void deleteOrphanedAttachments();
 
     class DuplicateFilenameException extends IOException implements SkipMothershipLogging
     {

api/src/org/labkey/api/data/ContainerManager.java

@@ -1944,7 +1944,7 @@ private static boolean delete(final Container c, User user, @Nullable String com
                 setContainerTabDeleted(c.getParent(), c.getName(), c.getParent().getFolderType().getName());
             }
 
-            AttachmentService.get().detectOrphans();
+            AttachmentService.get().logOrphanedAttachments();
 
             fireDeleteContainer(c, user);
 

core/module.properties

@@ -1,6 +1,6 @@
 Name: Core
 ModuleClass: org.labkey.core.CoreModule
-SchemaVersion: 26.002
+SchemaVersion: 26.003
 Label: Administration and Essential Services
 Description: The Core module provides central services such as login, \
     security, administration, folder management, user management, \

core/resources/schemas/dbscripts/postgresql/core-26.002-26.003.sql

@@ -0,0 +1 @@
+SELECT core.executeJavaUpgradeCode('deleteOrphanedAttachments');

core/resources/schemas/dbscripts/sqlserver/core-26.002-26.003.sql

@@ -0,0 +1 @@
+EXEC core.executeJavaUpgradeCode 'deleteOrphanedAttachments';

core/src/org/labkey/core/CoreUpgradeCode.java

@@ -71,6 +71,7 @@ public static void migrateAllowedExternalConnectionHosts(ModuleContext context)
         if (context.isNewInstall())
             return;
 
+        // TODO: Remove getExternalSourceHosts() method when this upgrade code is deleted
         List<String> hosts = AppProps.getInstance().getExternalSourceHosts();
         List<AllowedHost> allowedHosts = hosts.stream()
             .map(host -> new AllowedHost(Directive.Connection, host))
@@ -106,4 +107,22 @@ public static void populateAttachmentParentTypeColumn(ModuleContext context)
             new SqlExecutor(CoreSchema.getInstance().getSchema()).execute(updateSql);
         }
     }
+
+    /**
+     * Called from core-26.002-26.003.sql
+     */
+    @DeferredUpgrade // Need to execute this after AttachmentTypes are registered
+    @SuppressWarnings("unused")
+    public static void deleteOrphanedAttachments(ModuleContext context)
+    {
+        if (context.isNewInstall())
+            return;
+
+        AttachmentService svc = AttachmentService.get();
+
+        if (svc != null)
+        {
+            svc.deleteOrphanedAttachments();
+        }
+    }
 }

core/src/org/labkey/core/attachment/AttachmentServiceImpl.java

@@ -45,6 +45,7 @@
 import org.labkey.api.data.ColumnRenderProperties;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.ContainerFilter.AllFolders;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.CoreSchema;
@@ -1098,7 +1099,7 @@ public int available()
     private record Orphan(String documentName, String parentType){}
 
     @Override
-    public void detectOrphans()
+    public void logOrphanedAttachments()
     {
         // Log orphaned attachments in this server, but in dev mode only, since this is for our testing. Also, we
         // don't yet offer a way to delete orphaned attachments via the UI, so it's not helpful to inform admins.
@@ -1135,6 +1136,54 @@ public void detectOrphans()
         }
     }
 
+    record OrphanedAttachment(String container, String parent, String documentName)
+    {
+        AttachmentParent getAttachmentParent()
+        {
+            return new AttachmentParent()
+            {
+                @Override
+                public String getEntityId()
+                {
+                    return parent;
+                }
+
+                @Override
+                public String getContainerId()
+                {
+                    return container;
+                }
+
+                @Override
+                public @NotNull AttachmentParentType getAttachmentParentType()
+                {
+                    return AttachmentParentType.UNKNOWN;
+                }
+            };
+        }
+    }
+
+    @Override
+    public void deleteOrphanedAttachments()
+    {
+        User user = ElevatedUser.getElevatedUser(User.getSearchUser(), TroubleshooterRole.class);
+        UserSchema core = DefaultSchema.get(user, ContainerManager.getRoot()).getUserSchema(CoreQuerySchema.NAME);
+        if (core != null)
+        {
+            // Use "unsafe everything" container filter because it's possible that orphaned attachments have a container
+            // that no longer exists.
+            TableInfo documents = core.getTable(CoreQuerySchema.DOCUMENTS_TABLE_NAME, ContainerFilter.getUnsafeEverythingFilter());
+            if (null != documents)
+            {
+                SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("Orphaned"), true);
+                new TableSelector(documents, new CsvSet("Container, Parent, DocumentName"), filter, null).forEach(OrphanedAttachment.class, orphan -> {
+                    LOG.info("Deleting orphaned attachment: {}", orphan);
+                    deleteAttachment(orphan.getAttachmentParent(), orphan.documentName(), user);
+                });
+            }
+        }
+    }
+
     private CoreSchema coreTables()
     {
         return CoreSchema.getInstance();