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Fom MANE overview, link out to gene overview #368

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merged 3 commits into from
Oct 8, 2024

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@northwestwitch northwestwitch commented Oct 8, 2024

Description

Added/Changed/Fixed

image

How to test

  • Deploy on stage server and make sure gene links on MANE page work

Review

  • Tests executed by CR
  • "Merge and deploy" approved by

This version is a

  • MAJOR - when you make incompatible API changes
  • MINOR - when you add functionality in a backwards compatible manner
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

@northwestwitch northwestwitch marked this pull request as draft October 8, 2024 06:51
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codecov-commenter commented Oct 8, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.13%. Comparing base (719f1b8) to head (9682a04).
Report is 97 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #368      +/-   ##
==========================================
+ Coverage   90.18%   93.13%   +2.95%     
==========================================
  Files          30       31       +1     
  Lines        1457     1501      +44     
==========================================
+ Hits         1314     1398      +84     
+ Misses        143      103      -40     
Flag Coverage Δ
unittests 93.13% <ø> (+2.95%) ⬆️

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sonarqubecloud bot commented Oct 8, 2024

@northwestwitch northwestwitch marked this pull request as ready for review October 8, 2024 08:22
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I've got one small PR that adds gene links to the MANE report. It should work but you could give it a try if you want @Jakob37 . As a final step for this release I was thinking to address #366.

@@ -27,6 +27,8 @@ <h2 class="accordion-header" id="flush-headingOne">
<!-- hidden fields passed from previous query -->
<form name="customizeForm" action="{{url_for('mane_overview')}}" method="post">
<input type="hidden" name="build" value="GRCh38"/>
<input type="hidden" name="default_level" id="defaultLevel" value="{{extras.default_level}}"/>
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Default level is not used in the MANE overview report, but in the gene overview, and this is a way to pass along the value

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Jakob37 commented Oct 8, 2024

I've got one small PR that adds gene links to the MANE report. It should work but you could give it a try if you want @Jakob37 . As a final step for this release I was thinking to address #366.

I'll try it out!

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Jakob37 commented Oct 8, 2024

Looks like it is working!

pr_1

pr_2

On the gene page. Would it be possible to show what transcript is MANE as well? As the ID type differs, the users will not immediately see which one was "NM_001101.5" in the example above.

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On the gene page. Would it be possible to show what transcript is MANE as well? As the ID type differs, the users will not immediately see which one was "NM_001101.5" in the example above.

Yes, I'll add it, but on my new PR, the one adding also exons. It will be easier

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Merging this one. Thanks @Jakob37!

@northwestwitch northwestwitch merged commit 9ea5313 into main Oct 8, 2024
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@northwestwitch northwestwitch deleted the mane_links_to_genes branch October 8, 2024 08:48
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Link out to gene overview from MANE genes overview
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