TemplateNotFound

[koellerMC]

Dear HistoQC Team, I just pulled the latest docker image and let histoQC run on a file, without errors. However, when starting the UI I get the following error:

The CMD output is:

/opt/HistoQC/venv/lib/python3.8/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/opt/HistoQC/venv/lib/python3.8/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/opt/HistoQC/venv/lib/python3.8/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/opt/HistoQC/venv/lib/python3.8/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
 * Serving Flask app '__main__'
 * Debug mode: on
WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.
 * Running on all addresses (0.0.0.0)
 * Running on http://127.0.0.1:5000
 * Running on http://172.17.0.2:5000
Press CTRL+C to quit
 * Restarting with stat
/opt/HistoQC/venv/lib/python3.8/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/opt/HistoQC/venv/lib/python3.8/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/opt/HistoQC/venv/lib/python3.8/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/opt/HistoQC/venv/lib/python3.8/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
 * Debugger is active!
 * Debugger PIN: 143-466-257
172.17.0.1 - - [12/Jun/2024 15:26:57] "GET / HTTP/1.1" 500 -
Traceback (most recent call last):
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/app.py", line 2213, in __call__
    return self.wsgi_app(environ, start_response)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/app.py", line 2193, in wsgi_app
    response = self.handle_exception(e)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/app.py", line 2190, in wsgi_app
    response = self.full_dispatch_request()
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/app.py", line 1486, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/app.py", line 1484, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/app.py", line 1469, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/histoqc/ui/HQC_html.py", line 16, in index
    return render_template('index.html')
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/templating.py", line 150, in render_template
    template = app.jinja_env.get_or_select_template(template_name_or_list)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/jinja2/environment.py", line 1084, in get_or_select_template
    return self.get_template(template_name_or_list, parent, globals)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/jinja2/environment.py", line 1013, in get_template
    return self._load_template(name, globals)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/jinja2/environment.py", line 972, in _load_template
    template = self.loader.load(self, name, self.make_globals(globals))
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/jinja2/loaders.py", line 126, in load
    source, filename, uptodate = self.get_source(environment, name)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/templating.py", line 64, in get_source
    return self._get_source_fast(environment, template)
  File "/opt/HistoQC/venv/lib/python3.8/site-packages/flask/templating.py", line 98, in _get_source_fast
    raise TemplateNotFound(template)
jinja2.exceptions.TemplateNotFound: index.html
172.17.0.1 - - [12/Jun/2024 15:26:57] "GET /?__debugger__=yes&cmd=resource&f=style.css HTTP/1.1" 200 -
172.17.0.1 - - [12/Jun/2024 15:26:57] "GET /?__debugger__=yes&cmd=resource&f=debugger.js HTTP/1.1" 200 -
172.17.0.1 - - [12/Jun/2024 15:26:57] "GET /?__debugger__=yes&cmd=resource&f=console.png HTTP/1.1" 200 -
172.17.0.1 - - [12/Jun/2024 15:26:57] "GET /?__debugger__=yes&cmd=resource&f=console.png HTTP/1.1" 304 -

If I understand correctly there seems to be some problem with the 'Index.html' of the flask app?

Do you have an idea how i can resolve this?

Thank you in advance!

Best MK

[koellerMC]

A ok I fugured it out. One has to:

cd /opt/HistoQC

Then it works just fine.

Potentially, this could be added to the readme.md. Or the ui.CLI could be independent of the directory it is called.

Thanks again for the amazing tool. Best MK

[jacksonjacobs1]

Hi @koellerMC,

Thanks for reporting this issue. This is indeed a bug; the user's current directory should not affect HistoQC's behavior.

I've reproduced the problematic behavior on my side and am working on a fix. Will get back to you soon.

[jacksonjacobs1]

Update: This bug was fixed in commit 6f0bacd6f5dc12f5fe3052addd85b198904d95df

Thanks again for reporting the issue. Please let me know if you have any further issues

[koellerMC]

Hi @jacksonjacobs1 Thank you very much for the fast fix! We will try it out ASAP.

KR MK