elixir-cloud-aai / cwl-WES

Trigger CWL workflows via GA4GH WES and TES
Apache License 2.0
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Unable to launch the latest version from GitHub w/ ImportError: cannot import name 'escape' from 'jinja2' #242

Open superbsky opened 2 years ago

superbsky commented 2 years ago

Describe the bug Unable to launch the latest version from GitHub w/ ImportError: cannot import name 'escape' from 'jinja2'

To Reproduce Steps to reproduce the behavior:

  1. mkdir -p data/cwl_wes/db data/cwl_wes/output data/cwl_wes/tmp
  2. git clone https://github.com/elixir-cloud-aai/cwl-WES.git app && cd app
  3. docker-compose up -d --build

docker-compose ps Name Command State Ports

app_flower_1 flower flower --broker=amq ... Up 0.0.0.0:5555->5555/tcp,:::5555->5555/tcp
app_mongodb_1 docker-entrypoint.sh mongod Up 0.0.0.0:27017->27017/tcp,:::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,:::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

Expected behavior Successfully launched service listening on 8080

Software uname -a Linux 5.13.0-1031-azure #37~20.04.1-Ubuntu SMP Mon Jun 13 22:51:01 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

docker-compose --version docker-compose version 1.25.0, build unknown

Additional context wes_1 | from jinja2 import escape wes_1 | ImportError: cannot import name 'escape' from 'jinja2' (/usr/local/lib/python3.7/site-packages/jinja2/init.py) wes_1 | Failed to read config file: config.py wes_1 | Traceback (most recent call last): wes_1 | File "/usr/local/lib/python3.7/site-packages/gunicorn/app/base.py", line 106, in get_config_from_filename wes1 | execfile(filename, cfg, cfg) wes_1 | File "/usr/local/lib/python3.7/site-packages/gunicorn/compat.py", line 72, in execfile wes1 | return six.exec(code, *args) wes_1 | File "config.py", line 3, in wes_1 | from foca.config.config_parser import get_conf wes_1 | File "/usr/local/lib/python3.7/site-packages/foca/config/config_parser.py", line 10, in wes_1 | from foca.models.config import (Config, LogConfig) wes_1 | File "/usr/local/lib/python3.7/site-packages/foca/models/config.py", line 1097, in wes_1 | class Config(FOCABaseConfig): wes_1 | File "/usr/local/lib/python3.7/site-packages/foca/models/config.py", line 1155, in Config wes_1 | exceptions: ExceptionConfig = ExceptionConfig() wes_1 | File "pydantic/main.py", line 404, in pydantic.main.BaseModel.init wes_1 | File "pydantic/main.py", line 1040, in pydantic.main.validate_model wes_1 | File "pydantic/fields.py", line 716, in pydantic.fields.ModelField.validate wes_1 | File "pydantic/fields.py", line 913, in pydantic.fields.ModelField._apply_validators wes_1 | File "pydantic/class_validators.py", line 279, in pydantic.class_validators._generic_validator_cls.lambda4 wes_1 | File "/usr/local/lib/python3.7/site-packages/foca/models/config.py", line 328, in validate_mapping wes_1 | mod = importlib.import_module(module_path) wes_1 | File "/usr/local/lib/python3.7/importlib/init.py", line 127, in import_module wes_1 | return _bootstrap._gcd_import(name[level:], package, level) wes_1 | File "/usr/local/lib/python3.7/site-packages/foca/errors/exceptions.py", line 15, in wes_1 | from flask import (current_app, Response) wes_1 | File "/usr/local/lib/python3.7/site-packages/flask/init.py", line 14, in wes_1 | from jinja2 import escape wes_1 | ImportError: cannot import name 'escape' from 'jinja2' (/usr/local/lib/python3.7/site-packages/jinja2/init.py)