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Clinical-Genomics-Lund / bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen
https://bonsai-wgs.readthedocs.io/en/latest/
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Accessing resistance report link from sample page triggers an internal server error #93

Closed alkc closed 8 months ago

alkc commented 11 months ago

Describe the bug

Accessing the resistance report link from the /samples/ view triggers a 500 error in the client:

[2023-10-23 12:45:31 +0000] [8] [ERROR] Exception on /samples/11MT0500103/resistance_report [GET]
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/site-packages/flask/app.py", line 2190, in wsgi_app
    response = self.full_dispatch_request()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/flask/app.py", line 1486, in full_dispatch_request
    rv = self.handle_user_exception(e)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/flask/app.py", line 1484, in full_dispatch_request
    rv = self.dispatch_request()
         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/flask/app.py", line 1469, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/flask_login/utils.py", line 290, in decorated_view
    return current_app.ensure_sync(func)(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/app/blueprints/sample/views.py", line 289, in resistance_report
    return render_template(
           ^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/flask/templating.py", line 151, in render_template
    return _render(app, template, context)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/flask/templating.py", line 132, in _render
    rv = template.render(context)
         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/jinja2/environment.py", line 1301, in render
    self.environment.handle_exception()
  File "/usr/local/lib/python3.11/site-packages/jinja2/environment.py", line 936, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/home/worker/app/app/blueprints/sample/templates/resistance_report.html", line 3, in top-level template code
    {% from "cards.html" import resistance_card, virulence_card %}
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/app/templates/layout.html", line 2, in top-level template code
    {% from "navbar.html" import navbar %}
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/app/templates/bootstrap_base.html", line 56, in top-level template code
    {% block body %}
  File "/home/worker/app/app/templates/bootstrap_base.html", line 57, in block 'body'
    {% block content %}
  File "/home/worker/app/app/blueprints/sample/templates/resistance_report.html", line 15, in block 'content'
    {{ sidebar(sample, navigation=False) }}
    ^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: macro 'sidebar' takes no keyword argument 'navigation'

To Reproduce

Open http://mtlucmds1.lund.skane.se/bonsai/samples/11MT0500103/resistance_report