fix: close session before doing long latency operation

[Colstuwjx]

Important

1. Make sure you have read our contribution guidelines
2. Ensure there is an associated issue and you have been assigned to it
3. Use the correct syntax to link this PR: Fixes #<issue number>.

Summary

Fixes #21939 .

Screenshots

Local benchmark script:

run-perf-test.txt

Test workflow would be something like:

Start -> Parse Data (Code Block A) -> Iteration Loop( Code Block B -> KB node Query -> LLM node -> Code Block C ) -> Handle Result (Code Block D) -> End

Local Deployment Version dify-api v1.6.0:

0e7efaaeade6   langgenius/dify-api:1.6.0                   "/bin/bash /entrypoi…"   34 hours ago   Up 15 minutes         5001/tcp                                   docker-api-1

Before:

Exception in thread Thread-460 (_retriever):
Traceback (most recent call last):
  File "/usr/local/lib/python3.12/threading.py", line 1075, in _bootstrap_inner
    self.run()
  File "/usr/local/lib/python3.12/threading.py", line 1012, in run
    self._target(*self._args, **self._kwargs)
  File "/app/api/core/rag/retrieval/dataset_retrieval.py", line 601, in _retriever
    dataset = db.session.query(Dataset).filter(Dataset.id == dataset_id).first()
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/query.py", line 2759, in first
    return self.limit(1)._iter().first()  # type: ignore
           ^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/query.py", line 2857, in _iter
    result: Union[ScalarResult[_T], Result[_T]] = self.session.execute(
                                                  ^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2365, in execute
    return self._execute_internal(
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2241, in _execute_internal
    conn = self._connection_for_bind(bind)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2110, in _connection_for_bind
    return trans._connection_for_bind(engine, execution_options)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 2, in _connection_for_bind
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1189, in _connection_for_bind
    conn = bind.connect()
           ^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 3273, in connect
    return self._connection_cls(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 145, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 3297, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 1264, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 713, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/impl.py", line 168, in _do_get
    raise exc.TimeoutError(
sqlalchemy.exc.TimeoutError: QueuePool limit of size 30 overflow 10 reached, connection timed out, timeout 30.00 (Background on this error at: https://sqlalche.me/e/20/3o7r)

2025-07-12 05:30:27.249 ERROR [ThreadPoolExecutor-205_9] [node.py:289] - error while executing llm node
Traceback (most recent call last):
  File "/app/api/core/workflow/nodes/llm/node.py", line 210, in _run
    prompt_messages, stop = self._fetch_prompt_messages(
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/workflow/nodes/llm/node.py", line 733, in _fetch_prompt_messages
    model = ModelManager().get_model_instance(
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/model_manager.py", line 430, in get_model_instance
    provider_model_bundle = self._provider_manager.get_provider_model_bundle(
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/provider_manager.py", line 253, in get_provider_model_bundle
    provider_configurations = self.get_configurations(tenant_id)
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/provider_manager.py", line 98, in get_configurations
    provider_name_to_provider_records_dict = self._get_all_providers(tenant_id)
                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/provider_manager.py", line 401, in _get_all_providers
    providers = session.scalars(stmt)
                ^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2473, in scalars
    return self._execute_internal(
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2241, in _execute_internal
    conn = self._connection_for_bind(bind)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2110, in _connection_for_bind
    return trans._connection_for_bind(engine, execution_options)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 2, in _connection_for_bind
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1189, in _connection_for_bind
    conn = bind.connect()
           ^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 3273, in connect
    return self._connection_cls(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 145, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 3297, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 1264, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 713, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/impl.py", line 168, in _do_get
    raise exc.TimeoutError(
sqlalchemy.exc.TimeoutError: QueuePool limit of size 30 overflow 10 reached, connection timed out, timeout 30.00 (Background on this error at: https://sqlalche.me/e/20/3o7r)

2025-07-12 05:30:26.906 ERROR [Dummy-442] [app.py:875] - Exception on /v1/workflows/run [POST]
Traceback (most recent call last):
  File "/app/api/controllers/service_api/app/workflow.py", line 89, in post
    response = AppGenerateService.generate(
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/services/app_generate_service.py", line 107, in generate
    WorkflowAppGenerator().generate(
  File "/app/api/core/app/apps/workflow/app_generator.py", line 173, in generate
    return self._generate(
           ^^^^^^^^^^^^^^^
  File "/app/api/core/app/apps/workflow/app_generator.py", line 245, in _generate
    response = self._handle_response(
               ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/app/apps/workflow/app_generator.py", line 509, in _handle_response
    return generate_task_pipeline.process()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/app/apps/workflow/generate_task_pipeline.py", line 148, in process
    return self._to_blocking_response(generator)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/app/apps/workflow/generate_task_pipeline.py", line 155, in _to_blocking_response
    for stream_response in generator:
                           ^^^^^^^^^
  File "/app/api/core/app/apps/workflow/generate_task_pipeline.py", line 221, in _wrapper_process_stream_response
    for response in self._process_stream_response(tts_publisher=tts_publisher, trace_manager=trace_manager):
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/app/apps/workflow/generate_task_pipeline.py", line 320, in _process_stream_response
    workflow_node_execution = self._workflow_cycle_manager.handle_workflow_node_execution_success(
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/workflow/workflow_cycle_manager.py", line 268, in handle_workflow_node_execution_success
    self._workflow_node_execution_repository.save(domain_execution)
  File "/app/api/core/repositories/sqlalchemy_workflow_node_execution_repository.py", line 212, in save
    session.merge(db_model)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 3959, in merge
    return self._merge(
           ^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4037, in _merge
    merged = self.get(
             ^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 3694, in get
    return self._get_impl(
           ^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 3873, in _get_impl
    return db_load_fn(
           ^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/loading.py", line 694, in load_on_pk_identity
    session.execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2365, in execute
    return self._execute_internal(
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2241, in _execute_internal
    conn = self._connection_for_bind(bind)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2110, in _connection_for_bind
    return trans._connection_for_bind(engine, execution_options)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 2, in _connection_for_bind
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1189, in _connection_for_bind
    conn = bind.connect()
           ^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 3273, in connect
    return self._connection_cls(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 145, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 3297, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 1264, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/base.py", line 713, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/pool/impl.py", line 168, in _do_get
    raise exc.TimeoutError(
sqlalchemy.exc.TimeoutError: QueuePool limit of size 30 overflow 10 reached, connection timed out, timeout 30.00 (Background on this error at: https://sqlalche.me/e/20/3o7r)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/api/.venv/lib/python3.12/site-packages/flask/app.py", line 917, in full_dispatch_request
    rv = self.dispatch_request()
         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/flask/app.py", line 902, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/flask_restful/__init__.py", line 489, in wrapper
    resp = resource(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/flask/views.py", line 110, in view
    return current_app.ensure_sync(self.dispatch_request)(**kwargs)  # type: ignore[no-any-return]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/flask_restful/__init__.py", line 604, in dispatch_request
    resp = meth(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/controllers/service_api/wraps.py", line 109, in decorated_view
    return view_func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/controllers/service_api/app/workflow.py", line 108, in post
    raise InternalServerError()
werkzeug.exceptions.InternalServerError: 500 Internal Server Error: The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.

After:

# normal output logs, no QueuePool limit issue any more
...

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 dev/reformat(backend) and cd web && npx lint-staged(frontend) to appease the lint gods