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elixir-cloud-aai / cwl-WES

Trigger CWL workflows via GA4GH WES and TES
Apache License 2.0
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docker-compose failed to start app_wes-worker_1 and app_wes_1 #217

Closed superbsky closed 2 years ago

superbsky commented 3 years ago

Describe the bug cwl-WES does not work after docker-compose up with multiple issues

docker logs -f app_flower_1:

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/tornado/gen.py", line 828, in callback
    result_list.append(f.result())
  File "/usr/local/lib/python3.6/concurrent/futures/_base.py", line 398, in result
    return self.__get_result()
  File "/usr/local/lib/python3.6/concurrent/futures/_base.py", line 357, in __get_result
    raise self._exception
  File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 55, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/usr/local/lib/python3.6/site-packages/celery/app/control.py", line 126, in conf
    return self._request('conf', with_defaults=with_defaults)
  File "/usr/local/lib/python3.6/site-packages/celery/app/control.py", line 81, in _request
    timeout=self.timeout, reply=True,
  File "/usr/local/lib/python3.6/site-packages/celery/app/control.py", line 436, in broadcast
    limit, callback, channel=channel,
  File "/usr/local/lib/python3.6/site-packages/kombu/pidbox.py", line 304, in _broadcast
    chan = channel or self.connection.default_channel
  File "/usr/local/lib/python3.6/site-packages/kombu/connection.py", line 819, in default_channel
    self.connection
  File "/usr/local/lib/python3.6/site-packages/kombu/connection.py", line 802, in connection
    self._connection = self._establish_connection()
  File "/usr/local/lib/python3.6/site-packages/kombu/connection.py", line 757, in _establish_connection
    conn = self.transport.establish_connection()
  File "/usr/local/lib/python3.6/site-packages/kombu/transport/pyamqp.py", line 130, in establish_connection
    conn.connect()
  File "/usr/local/lib/python3.6/site-packages/amqp/connection.py", line 294, in connect
    self.transport.connect()
  File "/usr/local/lib/python3.6/site-packages/amqp/transport.py", line 120, in connect
    self._connect(self.host, self.port, self.connect_timeout)
  File "/usr/local/lib/python3.6/site-packages/amqp/transport.py", line 161, in _connect
    self.sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused

[[E 210329 14:39:53 events:123] Failed to capture events: '[Errno 111] Connection refused', trying again in 4 seconds. [[E 210329 14:39:57 events:123] Failed to capture events: '[Errno 111] Connection refused', trying again in 8 seconds. [[I 210329 14:40:05 mixins:224] Connected to amqp://guest:**@rabbitmq:5672//

docker logs -f app_wes-worker_1:

Traceback (most recent call last): File "/usr/local/bin/celery", line 8, in sys.exit(main()) File "/usr/local/lib/python3.6/site-packages/celery/main.py", line 16, in main _main() File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 322, in main cmd.execute_from_commandline(argv) File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 484, in execute_from_commandline super(CeleryCommand, self).execute_from_commandline(argv))) File "/usr/local/lib/python3.6/site-packages/celery/bin/base.py", line 275, in execute_from_commandline return self.handle_argv(self.prog_name, argv[1:]) File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 476, in handle_argv return self.execute(command, argv) File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 408, in execute ).run_from_argv(self.prog_name, argv[1:], command=argv[0]) File "/usr/local/lib/python3.6/site-packages/celery/bin/worker.py", line 223, in run_from_argv return self(*args, *options) File "/usr/local/lib/python3.6/site-packages/celery/bin/base.py", line 238, in call ret = self.run(args, kwargs) File "/usr/local/lib/python3.6/site-packages/celery/bin/worker.py", line 257, in run kwargs) File "/usr/local/lib/python3.6/site-packages/celery/worker/worker.py", line 96, in init self.app.loader.init_worker() File "/usr/local/lib/python3.6/site-packages/celery/loaders/base.py", line 114, in init_worker self.import_default_modules() File "/usr/local/lib/python3.6/site-packages/celery/loaders/base.py", line 109, in import_default_modules return [self.import_task_module(m) for m in self.default_modules] File "/usr/local/lib/python3.6/site-packages/celery/loaders/base.py", line 109, in return [self.import_task_module(m) for m in self.default_modules] File "/usr/local/lib/python3.6/site-packages/celery/loaders/base.py", line 95, in import_task_module return self.import_from_cwd(module) File "/usr/local/lib/python3.6/site-packages/celery/loaders/base.py", line 104, in import_from_cwd package=package, File "/usr/local/lib/python3.6/site-packages/celery/utils/imports.py", line 104, in import_from_cwd return imp(module, package=package) File "/usr/local/lib/python3.6/site-packages/celery/loaders/base.py", line 98, in import_module return importlib.import_module(module, package=package) File "/usr/local/lib/python3.6/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 955, in _find_and_load_unlocked File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "/app/cwl_wes/tasks/tasks/cancel_run.py", line 11, in from pymongo import collection as Collection File "/usr/local/lib/python3.6/site-packages/pymongo/init.py", line 77, in from pymongo.collection import ReturnDocument File "/usr/local/lib/python3.6/site-packages/pymongo/collection.py", line 20, in from bson.code import Code File "/usr/local/lib/python3.6/site-packages/bson/code.py", line 18, in from bson.py3compat import abc, string_type, PY3, text_type ImportError: cannot import name 'abc'

docker-compose ps:

  Name                    Command                 State                                                    Ports

app_flower_1 flower flower --broker=amq ... Up 0.0.0.0:5555->5555/tcp
app_mongodb_1 docker-entrypoint.sh mongod Up 0.0.0.0:27017->27017/tcp
app_rabbitmq_1 docker-entrypoint.sh rabbi ... Up 15671/tcp, 15672/tcp, 15691/tcp, 15692/tcp, 25672/tcp, 4369/tcp, 5671/tcp, 0.0.0.0:5672->5672/tcp app_wes-worker_1 bash -c cd /app/cwl_wes; c ... Restarting
app_wes_1 bash -c cd /app/cwl_wes; g ... Restarting

Both services app_wes-worker_1 and app_wes_1 are always in Restarting state.

To Reproduce I tried the latest git version as described in the documentation:

Create dirs: Clone the repo: git clone https://github.com/elixir-cloud-aai/cwl-WES.git app Modify the config with local TES settings: vi cwl_wes/config/app_config.yaml Start the services: docker-compose up -d --build

I also tried the version from the release https://github.com/elixir-cloud-aai/cwl-WES/releases/tag/v0.1.1-dev but with same outcome.

Expected behavior I expect all services up and running with WES API accessible via http://0.0.0.0:8080/ga4gh/wes/v1/ui

Software Azure Ubuntu VM as uname -a Linux genx 5.4.0-1023-azure #23~18.04.1-Ubuntu SMP Thu Aug 20 14:46:48 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

docker -v Docker version 19.03.6, build 369ce74a3c

docker-compose -v docker-compose version 1.28.6, build 5db8d86f

Additional context I am working on linking together TRS+RDS->WES->TES use case

superbsky commented 3 years ago

@uniqueg seems that the issue was related to https://github.com/py-bson/bson/issues/82 in short, you don't need a py-bson if you installing pymongo too I simply commented out py-bson from the requirements.txt and re-build the container

uniqueg commented 2 years ago

Thanks so much