db connection error when embedding task takes a long time

[liuky74]

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Dify version

1.9.2

Cloud or Self Hosted

Self Hosted (Docker)

Steps to reproduce

When I submitted a large document (58.2k words) using the knowledge base and embedded it with ollama, a timeout occurred.
I checked the relevant components and found that the small file(30k words) could be executed normally.
The error report is as follows:

7-27bc-4873-b7c9-ac0da24d3715/dispatch/text_embedding/invoke "HTTP/1.1 200 OK"
2025-10-25 04:18:02.056 INFO [ThreadPoolExecutor-19_0] [_client.py:1038] - HTTP Request: POST http://plugin_daemon:5002/plugin/63dcd377-27bc-4873-b7c9-ac0da24d3715/dispatch/text_embedding/invoke "HTTP/1.1 200 OK"
2025-10-25 04:18:02.154 INFO [ThreadPoolExecutor-19_0] [_client.py:1038] - HTTP Request: POST http://plugin_daemon:5002/plugin/63dcd377-27bc-4873-b7c9-ac0da24d3715/dispatch/text_embedding/invoke "HTTP/1.1 200 OK"
2025-10-25 04:18:02.251 INFO [ThreadPoolExecutor-19_0] [_client.py:1038] - HTTP Request: POST http://plugin_daemon:5002/plugin/63dcd377-27bc-4873-b7c9-ac0da24d3715/dispatch/text_embedding/invoke "HTTP/1.1 200 OK"
2025-10-25 04:18:02.349 INFO [ThreadPoolExecutor-19_0] [_client.py:1038] - HTTP Request: POST http://plugin_daemon:5002/plugin/63dcd377-27bc-4873-b7c9-ac0da24d3715/dispatch/text_embedding/invoke "HTTP/1.1 200 OK"
2025-10-25 04:18:02.455 INFO [ThreadPoolExecutor-19_0] [_client.py:1038] - HTTP Request: POST http://plugin_daemon:5002/plugin/63dcd377-27bc-4873-b7c9-ac0da24d3715/dispatch/text_embedding/invoke "HTTP/1.1 200 OK"
2025-10-25 04:18:02.563 INFO [ThreadPoolExecutor-19_0] [_client.py:1038] - HTTP Request: POST http://plugin_daemon:5002/plugin/63dcd377-27bc-4873-b7c9-ac0da24d3715/dispatch/text_embedding/invoke "HTTP/1.1 200 OK"
2025-10-25 04:18:02.712 ERROR [ThreadPoolExecutor-19_0] [cached_embedding.py:101] - Failed to embed documents
Traceback (most recent call last):
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2118, in _exec_insertmany_context
    dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
psycopg2.OperationalError: FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/app/api/core/rag/embedding/cached_embedding.py", line 96, in embed_documents
    db.session.commit()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2030, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1311, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1286, in _prepare_impl
    self.session.flush()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4331, in flush
    self._flush(objects)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4466, in _flush
    with util.safe_reraise():
         ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/util/langhelpers.py", line 224, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4427, in _flush
    flush_context.execute()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 466, in execute
    rec.execute(self)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 642, in execute
    util.preloaded.orm_persistence.save_obj(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 93, in save_obj
    _emit_insert_statements(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 1143, in _emit_insert_statements
    result = connection.execute(
             ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1419, in execute
    return meth(
           ^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/sql/elements.py", line 526, in _execute_on_connection
    return connection._execute_clauseelement(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1641, in _execute_clauseelement
    ret = self._execute_context(
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1844, in _execute_context
    return self._exec_insertmany_context(dialect, context)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2126, in _exec_insertmany_context
    self._handle_dbapi_exception(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2355, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2118, in _exec_insertmany_context
    dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.

[SQL: INSERT INTO embeddings (model_name, hash, embedding, provider_name) VALUES (%(model_name)s, %(hash)s, %(embedding)s, %(provider_name)s) RETURNING embeddings.id, embeddings.created_at]
[parameters: {'model_name': 'quentinz/bge-large-zh-v1.5:latest', 'hash': '9b5e5be952b9f6706f15530aa7d3acf7370dbdfe5f917f51916de0b1cf647b76', 'embedding': <psycopg2.extensions.Binary object at 0x71407a5b0d50>, 'provider_name': 'langgenius/ollama/ollama'}]
(Background on this error at: https://sqlalche.me/e/20/e3q8)
2025-10-25 04:18:02.720 ERROR [Dummy-88] [indexing_runner.py:54] - consume document failed
Traceback (most recent call last):
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2118, in _exec_insertmany_context
    dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
psycopg2.OperationalError: FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/app/api/core/indexing_runner.py", line 232, in run_in_indexing_status
    self._load(
  File "/app/api/core/indexing_runner.py", line 591, in _load
    tokens += future.result()
              ^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 456, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/usr/local/lib/python3.12/concurrent/futures/thread.py", line 59, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/indexing_runner.py", line 650, in _process_chunk
    index_processor.load(dataset, chunk_documents, with_keywords=False)
  File "/app/api/core/rag/index_processor/processor/parent_child_index_processor.py", line 116, in load
    vector.create(formatted_child_documents)
  File "/app/api/core/rag/datasource/vdb/vector_factory.py", line 199, in create
    batch_embeddings = self._embeddings.embed_documents([document.page_content for document in batch])
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/rag/embedding/cached_embedding.py", line 102, in embed_documents
    raise ex
  File "/app/api/core/rag/embedding/cached_embedding.py", line 96, in embed_documents
    db.session.commit()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2030, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1311, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1286, in _prepare_impl
    self.session.flush()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4331, in flush
    self._flush(objects)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4466, in _flush
    with util.safe_reraise():
         ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/util/langhelpers.py", line 224, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4427, in _flush
    flush_context.execute()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 466, in execute
    rec.execute(self)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 642, in execute
    util.preloaded.orm_persistence.save_obj(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 93, in save_obj
    _emit_insert_statements(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 1143, in _emit_insert_statements
    result = connection.execute(
             ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1419, in execute
    return meth(
           ^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/sql/elements.py", line 526, in _execute_on_connection
    return connection._execute_clauseelement(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1641, in _execute_clauseelement
    ret = self._execute_context(
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1844, in _execute_context
    return self._exec_insertmany_context(dialect, context)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2126, in _exec_insertmany_context
    self._handle_dbapi_exception(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2355, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2118, in _exec_insertmany_context
    dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.

[SQL: INSERT INTO embeddings (model_name, hash, embedding, provider_name) VALUES (%(model_name)s, %(hash)s, %(embedding)s, %(provider_name)s) RETURNING embeddings.id, embeddings.created_at]
[parameters: {'model_name': 'quentinz/bge-large-zh-v1.5:latest', 'hash': '9b5e5be952b9f6706f15530aa7d3acf7370dbdfe5f917f51916de0b1cf647b76', 'embedding': <psycopg2.extensions.Binary object at 0x71407a5b0d50>, 'provider_name': 'langgenius/ollama/ollama'}]
(Background on this error at: https://sqlalche.me/e/20/e3q8)
2025-10-25 04:18:02.745 ERROR [Dummy-88] [recover_document_indexing_task.py:46] - recover_document_indexing_task failed, document_id: 0a2ea213-206a-4b23-b86c-9399ea23d24b
Traceback (most recent call last):
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2118, in _exec_insertmany_context
    dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
psycopg2.OperationalError: FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/app/api/core/indexing_runner.py", line 232, in run_in_indexing_status
    self._load(
  File "/app/api/core/indexing_runner.py", line 591, in _load
    tokens += future.result()
              ^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 456, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/usr/local/lib/python3.12/concurrent/futures/thread.py", line 59, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/indexing_runner.py", line 650, in _process_chunk
    index_processor.load(dataset, chunk_documents, with_keywords=False)
  File "/app/api/core/rag/index_processor/processor/parent_child_index_processor.py", line 116, in load
    vector.create(formatted_child_documents)
  File "/app/api/core/rag/datasource/vdb/vector_factory.py", line 199, in create
    batch_embeddings = self._embeddings.embed_documents([document.page_content for document in batch])
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/core/rag/embedding/cached_embedding.py", line 102, in embed_documents
    raise ex
  File "/app/api/core/rag/embedding/cached_embedding.py", line 96, in embed_documents
    db.session.commit()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2030, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1311, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1286, in _prepare_impl
    self.session.flush()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4331, in flush
    self._flush(objects)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4466, in _flush
    with util.safe_reraise():
         ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/util/langhelpers.py", line 224, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4427, in _flush
    flush_context.execute()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 466, in execute
    rec.execute(self)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 642, in execute
    util.preloaded.orm_persistence.save_obj(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 93, in save_obj
    _emit_insert_statements(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 1143, in _emit_insert_statements
    result = connection.execute(
             ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1419, in execute
    return meth(
           ^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/sql/elements.py", line 526, in _execute_on_connection
    return connection._execute_clauseelement(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1641, in _execute_clauseelement
    ret = self._execute_context(
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1844, in _execute_context
    return self._exec_insertmany_context(dialect, context)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2126, in _exec_insertmany_context
    self._handle_dbapi_exception(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2355, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2118, in _exec_insertmany_context
    dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.

[SQL: INSERT INTO embeddings (model_name, hash, embedding, provider_name) VALUES (%(model_name)s, %(hash)s, %(embedding)s, %(provider_name)s) RETURNING embeddings.id, embeddings.created_at]
[parameters: {'model_name': 'quentinz/bge-large-zh-v1.5:latest', 'hash': '9b5e5be952b9f6706f15530aa7d3acf7370dbdfe5f917f51916de0b1cf647b76', 'embedding': <psycopg2.extensions.Binary object at 0x71407a5b0d50>, 'provider_name': 'langgenius/ollama/ollama'}]
(Background on this error at: https://sqlalche.me/e/20/e3q8)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
    self.dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
psycopg2.OperationalError: FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/app/api/tasks/recover_document_indexing_task.py", line 40, in recover_document_indexing_task
    indexing_runner.run_in_indexing_status(document)
  File "/app/api/core/indexing_runner.py", line 243, in run_in_indexing_status
    self._handle_indexing_error(document_id, e)
  File "/app/api/core/indexing_runner.py", line 61, in _handle_indexing_error
    db.session.commit()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2030, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1311, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 1286, in _prepare_impl
    self.session.flush()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4331, in flush
    self._flush(objects)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4466, in _flush
    with util.safe_reraise():
         ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/util/langhelpers.py", line 224, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 4427, in _flush
    flush_context.execute()
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 466, in execute
    rec.execute(self)
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py", line 642, in execute
    util.preloaded.orm_persistence.save_obj(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 85, in save_obj
    _emit_update_statements(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/orm/persistence.py", line 912, in _emit_update_statements
    c = connection.execute(
        ^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1419, in execute
    return meth(
           ^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/sql/elements.py", line 526, in _execute_on_connection
    return connection._execute_clauseelement(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1641, in _execute_clauseelement
    ret = self._execute_context(
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1846, in _execute_context
    return self._exec_single_context(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1986, in _exec_single_context
    self._handle_dbapi_exception(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2355, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
    self.dialect.do_execute(
  File "/app/api/.venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 951, in do_execute
    cursor.execute(statement, parameters)
  File "/app/api/.venv/lib/python3.12/site-packages/psycogreen/gevent.py", line 32, in gevent_wait_callback
    state = conn.poll()
            ^^^^^^^^^^^
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL:  terminating connection due to idle-in-transaction timeout
server closed the connection unexpectedly
        This probably means the server terminated abnormally
        before or while processing the request.

[SQL: UPDATE documents SET error=%(error)s, stopped_at=%(stopped_at)s, indexing_status=%(indexing_status)s WHERE documents.id = %(documents_id)s::UUID]
[parameters: {'error': "(psycopg2.OperationalError) FATAL:  terminating connection due to idle-in-transaction timeout\nserver closed the connection unexpectedly\n\tThis prob ... (448 characters truncated) ... ensions.Binary object at 0x71407a5b0d50>, 'provider_name': 'langgenius/ollama/ollama'}]\n(Background on this error at: https://sqlalche.me/e/20/e3q8)", 'stopped_at': datetime.datetime(2025, 10, 25, 4, 18, 2, 724818), 'indexing_status': 'error', 'documents_id': '0a2ea213-206a-4b23-b86c-9399ea23d24b'}]
(Background on this error at: https://sqlalche.me/e/20/e3q8)
2025-10-25 04:18:02.786 INFO [Dummy-88] [trace.py:128] - Task tasks.recover_document_indexing_task.recover_document_indexing_task[7a39f181-022c-4a34-8adc-cf51ed632bee] succeeded in 87.00235312298173s: None

I checked the relevant issues and attempted to modify the timeout period. I added/modified the following parameters in the docker-compose.yaml file:

POSTGRES_STATEMENT_TIMEOUT
POSTGRES_STATEMENT_TIMEOUT
MODEL_EMBEDDING_REQUEST_TIMEOUT
SSRF_DEFAULT_READ_TIME_OUT
PLUGIN_MAX_EXECUTION_TIMEOUT

But all of this is of no avail. May I ask what solutions there are?

✔️ Expected Behavior

The word embedding can be completed normally

❌ Actual Behavior

Embedding processing...

[dosubot]

This issue is caused by long-held database transactions during large embedding tasks, which can trigger PostgreSQL's idle-in-transaction timeout. Modifying timeout parameters alone doesn't resolve it because the transaction itself remains open while embeddings are processed.

Recent updates to Dify have addressed this by releasing the database connection before starting long-running embedding operations. Specifically, the fix involves calling db.session.close() before invoking the embedding model, which prevents the database connection from being held idle during lengthy computations and avoids the timeout error. You can see the relevant change in this pull request.

If you're running Dify v1.9.2, consider updating to the latest version where this fix is included, or manually apply the change to your codebase. This should allow large document embeddings to complete without database connection errors.

To reply, just mention @dosu.

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[liuky74]

Thank you very much. It has been successfully resolved