Tests fail because I can't get the snakemake test2.out file #40
Description
When running tests, I get this error:
botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://127.0.0.1:9000/snakemake-c2c3961107fc4a8e880eca3b4653c2aa/test2.out" and snakemake_interface_common.exceptions.WorkflowError: Failed to check existence of s3://snakemake-d7b2bd98f3ad49778f8c0029ed68ea02/test2.1.out
I have logged in with azure-cli v2.45.0 and correctly set SNAKEMAKE_AZURE_BATCH_ACCOUNT_URL, SNAKEMAKE_AZURE_BATCH_SUBSCRIPTION_ID, SNAKEMAKE_AZURE_BATCH_RESOURCE_GROUP_NAME.
Full output:
root@4a5152c455ff:/code# poetry run coverage run -m pytest tests/tests_mocked_api.py
=========================================================================================================================== test session starts ============================================================================================================================
platform linux -- Python 3.11.12, pytest-8.4.2, pluggy-1.6.0
rootdir: /code
configfile: pyproject.toml
collected 2 items
tests/tests_mocked_api.py FF [100%]
================================================================================================================================= FAILURES =================================================================================================================================
_________________________________________________________________________________________________________________ TestWorkflowsMocked.test_simple_workflow _________________________________________________________________________________________________________________
+ Exception Group Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/tests/__init__.py", line 23, in wrapper
| return func(self, tmp_path)
| ^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/tests/__init__.py", line 148, in test_simple_workflow
| self.run_workflow("simple", tmp_path)
| File "/usr/local/lib/python3.11/unittest/mock.py", line 1378, in patched
| return func(*newargs, **newkeywargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/code/tests/tests_mocked_api.py", line 49, in run_workflow
| super().run_workflow(*args, **kwargs)
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/tests/__init__.py", line 137, in run_workflow
| dag_api.execute_workflow(
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/api.py", line 597, in execute_workflow
| workflow.execute(
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/workflow.py", line 1142, in execute
| self._build_dag()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/workflow.py", line 1090, in _build_dag
| async_run(self.dag.init())
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/__init__.py", line 99, in async_run
| return asyncio.run(coroutine)
| ^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/asyncio/runners.py", line 190, in run
| return runner.run(main)
| ^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/asyncio/runners.py", line 118, in run
| return self._loop.run_until_complete(task)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
| return future.result()
| ^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/dag.py", line 225, in init
| await self.check_incomplete()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/dag.py", line 496, in check_incomplete
| incomplete = await self.incomplete_files()
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/dag.py", line 596, in incomplete_files
| is_incomplete = await self.workflow.persistence.incomplete(job)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/persistence.py", line 385, in incomplete
| async with asyncio.TaskGroup() as tg:
| File "/usr/local/lib/python3.11/asyncio/taskgroups.py", line 145, in __aexit__
| raise me from None
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 198, in _new_conn
| sock = connection.create_connection(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/connection.py", line 85, in create_connection
| raise err
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/connection.py", line 73, in create_connection
| sock.connect(sa)
| ConnectionRefusedError: [Errno 111] Connection refused
|
| The above exception was the direct cause of the following exception:
|
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/httpsession.py", line 465, in send
| urllib_response = conn.urlopen(
| ^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 841, in urlopen
| retries = retries.increment(
| ^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/retry.py", line 449, in increment
| raise reraise(type(error), error, _stacktrace)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/util.py", line 39, in reraise
| raise value
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 787, in urlopen
| response = self._make_request(
| ^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 493, in _make_request
| conn.request(
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/awsrequest.py", line 96, in request
| rval = super().request(method, url, body, headers, *args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 494, in request
| self.endheaders()
| File "/usr/local/lib/python3.11/http/client.py", line 1298, in endheaders
| self._send_output(message_body, encode_chunked=encode_chunked)
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/awsrequest.py", line 123, in _send_output
| self.send(msg)
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/awsrequest.py", line 223, in send
| return super().send(str)
| ^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/http/client.py", line 996, in send
| self.connect()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 325, in connect
| self.sock = self._new_conn()
| ^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 213, in _new_conn
| raise NewConnectionError(
| urllib3.exceptions.NewConnectionError: <botocore.awsrequest.AWSHTTPConnection object at 0x719658a3c5d0>: Failed to establish a new connection: [Errno 111] Connection refused
|
| During handling of the above exception, another exception occurred:
|
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake_interface_storage_plugins/storage_object.py", line 159, in managed_exists
| return self.exists()
| ^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake_storage_plugin_s3/__init__.py", line 258, in exists
| self.s3obj().load()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/boto3/resources/factory.py", line 565, in do_action
| response = action(self, *args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/boto3/resources/action.py", line 88, in __call__
| response = getattr(parent.meta.client, operation_name)(*args, **params)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/client.py", line 602, in _api_call
| return self._make_api_call(operation_name, kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/context.py", line 123, in wrapper
| return func(*args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/client.py", line 1060, in _make_api_call
| http, parsed_response = self._make_request(
| ^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/client.py", line 1084, in _make_request
| return self._endpoint.make_request(operation_model, request_dict)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 119, in make_request
| return self._send_request(request_dict, operation_model)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 229, in _send_request
| raise exception
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 279, in _do_get_response
| http_response = self._send(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 383, in _send
| return self.http_session.send(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/httpsession.py", line 494, in send
| raise EndpointConnectionError(endpoint_url=request.url, error=e)
| botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://127.0.0.1:9000/snakemake-c2c3961107fc4a8e880eca3b4653c2aa/test2.out"
|
| The above exception was the direct cause of the following exception:
|
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/persistence.py", line 381, in is_incomplete
| exists = await f.exists()
| ^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/io.py", line 452, in exists
| return await self.exists_in_storage()
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/io.py", line 210, in wrapper
| v = await func(self, *args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/io.py", line 471, in exists_in_storage
| return await self.storage_object.managed_exists()
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake_interface_storage_plugins/storage_object.py", line 161, in managed_exists
| raise WorkflowError(
| snakemake_interface_common.exceptions.WorkflowError: Failed to check existence of s3://snakemake-c2c3961107fc4a8e880eca3b4653c2aa/test2.out
+------------------------------------
--------------------------------------------------------------------------------------------------------------------------- Captured stderr call ---------------------------------------------------------------------------------------------------------------------------
host: 4a5152c455ff
Building DAG of jobs...
---------------------------------------------------------------------------------------------------------------------------- Captured log call -----------------------------------------------------------------------------------------------------------------------------
INFO snakemake.logging:logging.py:540 host: 4a5152c455ff
WARNING snakemake.logging:logging.py:625 Building DAG of jobs...
_________________________________________________________________________________________________________________ TestWorkflowsMocked.test_group_workflow __________________________________________________________________________________________________________________
+ Exception Group Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/tests/__init__.py", line 23, in wrapper
| return func(self, tmp_path)
| ^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/tests/__init__.py", line 152, in test_group_workflow
| self.run_workflow("groups", tmp_path)
| File "/usr/local/lib/python3.11/unittest/mock.py", line 1378, in patched
| return func(*newargs, **newkeywargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/code/tests/tests_mocked_api.py", line 49, in run_workflow
| super().run_workflow(*args, **kwargs)
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/tests/__init__.py", line 137, in run_workflow
| dag_api.execute_workflow(
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/api.py", line 597, in execute_workflow
| workflow.execute(
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/workflow.py", line 1142, in execute
| self._build_dag()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/workflow.py", line 1090, in _build_dag
| async_run(self.dag.init())
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/common/__init__.py", line 99, in async_run
| return asyncio.run(coroutine)
| ^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/asyncio/runners.py", line 190, in run
| return runner.run(main)
| ^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/asyncio/runners.py", line 118, in run
| return self._loop.run_until_complete(task)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
| return future.result()
| ^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/dag.py", line 225, in init
| await self.check_incomplete()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/dag.py", line 496, in check_incomplete
| incomplete = await self.incomplete_files()
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/dag.py", line 596, in incomplete_files
| is_incomplete = await self.workflow.persistence.incomplete(job)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/persistence.py", line 385, in incomplete
| async with asyncio.TaskGroup() as tg:
| File "/usr/local/lib/python3.11/asyncio/taskgroups.py", line 145, in __aexit__
| raise me from None
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 198, in _new_conn
| sock = connection.create_connection(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/connection.py", line 85, in create_connection
| raise err
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/connection.py", line 73, in create_connection
| sock.connect(sa)
| ConnectionRefusedError: [Errno 111] Connection refused
|
| The above exception was the direct cause of the following exception:
|
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/httpsession.py", line 465, in send
| urllib_response = conn.urlopen(
| ^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 841, in urlopen
| retries = retries.increment(
| ^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/retry.py", line 449, in increment
| raise reraise(type(error), error, _stacktrace)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/util/util.py", line 39, in reraise
| raise value
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 787, in urlopen
| response = self._make_request(
| ^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 493, in _make_request
| conn.request(
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/awsrequest.py", line 96, in request
| rval = super().request(method, url, body, headers, *args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 494, in request
| self.endheaders()
| File "/usr/local/lib/python3.11/http/client.py", line 1298, in endheaders
| self._send_output(message_body, encode_chunked=encode_chunked)
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/awsrequest.py", line 123, in _send_output
| self.send(msg)
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/awsrequest.py", line 223, in send
| return super().send(str)
| ^^^^^^^^^^^^^^^^^
| File "/usr/local/lib/python3.11/http/client.py", line 996, in send
| self.connect()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 325, in connect
| self.sock = self._new_conn()
| ^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/urllib3/connection.py", line 213, in _new_conn
| raise NewConnectionError(
| urllib3.exceptions.NewConnectionError: <botocore.awsrequest.AWSHTTPConnection object at 0x71965873f2d0>: Failed to establish a new connection: [Errno 111] Connection refused
|
| During handling of the above exception, another exception occurred:
|
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake_interface_storage_plugins/storage_object.py", line 159, in managed_exists
| return self.exists()
| ^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake_storage_plugin_s3/__init__.py", line 258, in exists
| self.s3obj().load()
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/boto3/resources/factory.py", line 565, in do_action
| response = action(self, *args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/boto3/resources/action.py", line 88, in __call__
| response = getattr(parent.meta.client, operation_name)(*args, **params)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/client.py", line 602, in _api_call
| return self._make_api_call(operation_name, kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/context.py", line 123, in wrapper
| return func(*args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/client.py", line 1060, in _make_api_call
| http, parsed_response = self._make_request(
| ^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/client.py", line 1084, in _make_request
| return self._endpoint.make_request(operation_model, request_dict)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 119, in make_request
| return self._send_request(request_dict, operation_model)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 229, in _send_request
| raise exception
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 279, in _do_get_response
| http_response = self._send(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/endpoint.py", line 383, in _send
| return self.http_session.send(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/botocore/httpsession.py", line 494, in send
| raise EndpointConnectionError(endpoint_url=request.url, error=e)
| botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://127.0.0.1:9000/snakemake-d7b2bd98f3ad49778f8c0029ed68ea02/test2.1.out"
|
| The above exception was the direct cause of the following exception:
|
| Traceback (most recent call last):
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/persistence.py", line 381, in is_incomplete
| exists = await f.exists()
| ^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/io.py", line 452, in exists
| return await self.exists_in_storage()
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/io.py", line 210, in wrapper
| v = await func(self, *args, **kwargs)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake/io.py", line 471, in exists_in_storage
| return await self.storage_object.managed_exists()
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/root/.cache/pypoetry/virtualenvs/snakemake-executor-plugin-azure-batch-MATOk_fk-py3.11/lib/python3.11/site-packages/snakemake_interface_storage_plugins/storage_object.py", line 161, in managed_exists
| raise WorkflowError(
| snakemake_interface_common.exceptions.WorkflowError: Failed to check existence of s3://snakemake-d7b2bd98f3ad49778f8c0029ed68ea02/test2.1.out
+------------------------------------
--------------------------------------------------------------------------------------------------------------------------- Captured stderr call ---------------------------------------------------------------------------------------------------------------------------
host: 4a5152c455ff
Building DAG of jobs...
---------------------------------------------------------------------------------------------------------------------------- Captured log call -----------------------------------------------------------------------------------------------------------------------------
INFO snakemake.logging:logging.py:540 host: 4a5152c455ff
WARNING snakemake.logging:logging.py:625 Building DAG of jobs...
========================================================================================================================= short test summary info ==========================================================================================================================
FAILED tests/tests_mocked_api.py::TestWorkflowsMocked::test_simple_workflow - WorkflowError('Failed to check existence of s3://snakemake-c2c3961107fc4a8e880eca3b4653c2aa/test2.out') [single exception in ExceptionGroup]
FAILED tests/tests_mocked_api.py::TestWorkflowsMocked::test_group_workflow - WorkflowError('Failed to check existence of s3://snakemake-d7b2bd98f3ad49778f8c0029ed68ea02/test2.1.out') [single exception in ExceptionGroup]
======================================================================================================================= 2 failed in 99.07s (0:01:39) =================================================================================