fix(api): isolate side-effect session writes in multimodal and RAG handlers

[agarwalpranav0711]

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Summary

Fixes #38176

Extends the session isolation fix from #37895 to two files that were missed: base_app_runner.py and index_tool_callback_handler.py.

Both files used db.session.commit() on the shared Flask request-scoped session to persist side-effect writes (a MessageFile during multimodal LLM streaming, and DatasetQuery audit logs / hit_count updates during RAG retrieval). This flushed all pending ORM changes in the request transaction, not just the intended record, risking premature commits and DetachedInstanceError under concurrency.

Changes:

• base_app_runner.py: _handle_multimodal_image_content() now persists the MessageFile through an independent sessionmaker session instead of the shared session.
• index_tool_callback_handler.py: on_query() and on_tool_end() now persist audit/analytics writes through an independent session, following the same pattern as fix(api): isolate side-effect database writes #37895.
• Added/updated unit tests in both corresponding test files to cover the new session isolation behavior.

Screenshots

N/A - backend transaction/session fix

Checklist

• This change requires a documentation update, included: Dify Document
• I understand that this PR may be closed in case there was no previous discussion or issues. (This doesn't apply to typos!)
• I've added a test for each change that was introduced, and I tried as much as possible to make a single atomic change.
• I've updated the documentation accordingly.
• I ran make lint && make type-check (backend) and cd web && pnpm exec vp staged (frontend) to appease the lint gods

[github-actions]

Pyrefly Diff

base → PR

--- /tmp/pyrefly_base.txt	2026-06-30 13:45:52.202826908 +0000
+++ /tmp/pyrefly_pr.txt	2026-06-30 13:45:43.870745082 +0000
@@ -4226,17 +4226,17 @@
 ERROR Object of class `NoneType` has no attribute `status` [missing-attribute]
    --> tests/unit_tests/core/base/test_app_generator_tts_publisher.py:188:16
 ERROR Argument `None` is not assignable to parameter `app_id` with type `str` in function `core.callback_handler.index_tool_callback_handler.DatasetIndexToolCallbackHandler.__init__` [bad-argument-type]
-  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:66:20
+  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:84:20
 ERROR Argument `None` is not assignable to parameter `message_id` with type `str` in function `core.callback_handler.index_tool_callback_handler.DatasetIndexToolCallbackHandler.__init__` [bad-argument-type]
-  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:67:24
+  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:85:24
 ERROR Argument `None` is not assignable to parameter `user_id` with type `str` in function `core.callback_handler.index_tool_callback_handler.DatasetIndexToolCallbackHandler.__init__` [bad-argument-type]
-  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:68:21
+  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:86:21
 ERROR Argument `None` is not assignable to parameter `invoke_from` with type `InvokeFrom` in function `core.callback_handler.index_tool_callback_handler.DatasetIndexToolCallbackHandler.__init__` [bad-argument-type]
-  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:69:25
+  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:87:25
 ERROR Argument `None` is not assignable to parameter `query` with type `str` in function `core.callback_handler.index_tool_callback_handler.DatasetIndexToolCallbackHandler.on_query` [bad-argument-type]
-  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:72:26
+  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:90:26
 ERROR Argument `None` is not assignable to parameter `dataset_id` with type `str` in function `core.callback_handler.index_tool_callback_handler.DatasetIndexToolCallbackHandler.on_query` [bad-argument-type]
-  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:72:32
+  --> tests/unit_tests/core/callback_handler/test_index_tool_callback_handler.py:90:32
 ERROR Argument `list[DummyToolInvokeMessage]` is not assignable to parameter `tool_outputs` with type `Iterable[ToolInvokeMessage]` in function `core.callback_handler.workflow_tool_callback_handler.DifyWorkflowCallbackHandler.on_tool_execution` [bad-argument-type]
   --> tests/unit_tests/core/callback_handler/test_workflow_tool_callback_handler.py:55:30
 ERROR Argument `list[DummyToolInvokeMessage]` is not assignable to parameter `tool_outputs` with type `Iterable[ToolInvokeMessage]` in function `core.callback_handler.workflow_tool_callback_handler.DifyWorkflowCallbackHandler.on_tool_execution` [bad-argument-type]
@@ -4581,7 +4581,7 @@
 ERROR Argument `SimpleNamespace` is not assignable to parameter `tenant` with type `Tenant` in function `core.plugin.backwards_invocation.model.PluginModelBackwardsInvocation.invoke_summary` [bad-argument-type]
   --> tests/unit_tests/core/plugin/test_backwards_invocation_model.py:54:72
 ERROR Generator function should return `Generator` [bad-return]
-  --> tests/unit_tests/core/plugin/test_model_runtime_adapter.py:72:51
+  --> tests/unit_tests/core/plugin/test_model_runtime_adapter.py:49:51
 ERROR Class member `_BadString.__str__` overrides a member in a parent class but is missing an `@override` decorator [missing-override-decorator]
    --> tests/unit_tests/core/plugin/test_plugin_entities.py:238:17
 ERROR Argument `TestPluginDaemonEntities.test_credential_type_helpers._FakeCredential` is not assignable to parameter `self` with type `CredentialType` in function `core.plugin.entities.plugin_daemon.CredentialType.get_name` [bad-argument-type]

[github-actions]

Pyrefly Type Coverage

Metric	Base	PR	Delta
Type coverage	51.58%	51.57%	-0.01%
Strict coverage	51.10%	51.08%	-0.01%
Typed symbols	31,008	30,993	-15
Untyped symbols	29,384	29,384	0
Modules	2935	2935	0