Clinical-Genomics / chanjo-report

Report generator for Chanjo output
MIT License
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cannot import name '_app_ctx_stack' from 'flask' error when launching report #55

Open northwestwitch opened 10 months ago

northwestwitch commented 10 months ago

To reproduce:

make build
make setup
make report
(base) chiararasi@n190-p146 chanjo-report % make report
docker-compose run -p 5000:5000 chanjo-report chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test report --render html
[+] Running 1/0
 ✔ Container mariadb  Running                                              0.0s
Traceback (most recent call last):
  File "/venv/bin/chanjo", line 8, in <module>
    sys.exit(root())
  File "/venv/lib/python3.8/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/venv/lib/python3.8/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/venv/lib/python3.8/site-packages/click/core.py", line 1682, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/venv/lib/python3.8/site-packages/click/core.py", line 1729, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/venv/lib/python3.8/site-packages/chanjo/cli/base.py", line 39, in get_command
    return commands[name].load()
  File "/venv/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2450, in load
    return self.resolve()
  File "/venv/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2456, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/worker/app/chanjo_report/cli/__init__.py", line 2, in <module>
    from .core import report
  File "/home/worker/app/chanjo_report/cli/core.py", line 4, in <module>
    from chanjo_report.interfaces import html, pdf
  File "/home/worker/app/chanjo_report/interfaces/__init__.py", line 2, in <module>
    from .html import render_html
  File "/home/worker/app/chanjo_report/interfaces/html.py", line 4, in <module>
    from chanjo_report.server.app import create_app
  File "/home/worker/app/chanjo_report/server/app.py", line 5, in <module>
    from .config import DefaultConfig
  File "/home/worker/app/chanjo_report/server/config.py", line 2, in <module>
    from .blueprints import report_bp, index_bp
  File "/home/worker/app/chanjo_report/server/blueprints/__init__.py", line 2, in <module>
    from .index import index_bp
  File "/home/worker/app/chanjo_report/server/blueprints/index/__init__.py", line 2, in <module>
    from .views import index_bp
  File "/home/worker/app/chanjo_report/server/blueprints/index/views.py", line 7, in <module>
    from chanjo_report.server.extensions import api
  File "/home/worker/app/chanjo_report/server/extensions.py", line 3, in <module>
    from flask_sqlalchemy import SQLAlchemy
  File "/venv/lib/python3.8/site-packages/flask_sqlalchemy/__init__.py", line 14, in <module>
    from flask import _app_ctx_stack, abort, current_app, request
ImportError: cannot import name '_app_ctx_stack' from 'flask' (/venv/lib/python3.8/site-packages/flask/__init__.py)
make: *** [report] Error 1
(base) chiararasi@n190-p146 chanjo-report %