Managed variant csv file verification

[dnil]

This PR adds a functionality and updates documentation.

How to test:

1. how to test it, possibly with real cases/data:

• try loading a managed variants file with a faulty line, e.g.

## Managed variants from some reliable source
#chromosome;position;end;reference;alternative;category;sub_category;description
14;76548781;76548781;CTGGACC;G;snv;indel;IFT43 indel test
17;48696925;48696925;G;T;snv;snv;CACNA1G intronic test
;;;T;C;snv;snv;silly
7;124491972;124491972;C;A;snv;snv;POT1 test snv

• ensure uploading a normal example still works

Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.

Review:

• code approved by
• tests executed by

[coveralls]

Coverage decreased (-0.04%) to 83.578% when pulling f01214a on fix_managed_variant_verif into b5917b7 on main.

[codecov-commenter]

Codecov Report

Merging #3060 (54e9934) into main (cea95ac) will increase coverage by 0.04%.
The diff coverage is 80.00%.

@@            Coverage Diff             @@
##             main    #3060      +/-   ##
==========================================
+ Coverage   83.71%   83.76%   +0.04%     
==========================================
  Files         286      286              
  Lines       16480    16490      +10     
==========================================
+ Hits        13797    13813      +16     
+ Misses       2683     2677       -6     

Impacted Files	Coverage Δ
.../server/blueprints/managed_variants/controllers.py	77.63% <72.72%> (+12.48%)	⬆️
scout/adapter/mongo/managed_variant.py	79.71% <100.00%> (ø)
scout/server/blueprints/managed_variants/forms.py	100.00% <100.00%> (ø)
scout/server/blueprints/cases/controllers.py	77.58% <0.00%> (ø)

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[northwestwitch]

Check out my suggestion!

[northwestwitch]

🏅

[northwestwitch]

Works perfectly! 🥇

I have a few suggestions:

• Since we are touching the functionality: improving the looks of this form by placing all elements on one line, with the right spacing and vertical padding.

• In the form above replace CSV file with text file, since it's either tab or semicolon-separated text file

• Add required to the required fields in the other form, when you add a single variant, since it's crashing as well whenever the right fields are not found
  

[dnil]

Thank you for the review!
I fixed the upload button layout, added the same file-name-updater as for gene panels, and made mandatory fields required on both add and edit forms.

[dnil]

Meh, but now the edit is partially broken. I'll check, but perhaps after dinner. 😅

[dnil]

Ok, it was just a small thing, broken with an earlier update..