Do not save cases/samples into the sql database and work uniquely with stats runned on d4 files on the fly

[northwestwitch]

THIS IS A MAJOR CHANGE,

but with the refactoring of the computation of the coverage completeness (upcoming PR), why can't we release a mayor? It's good timing.

Description

Changed

• Do not save cases/samples into the sql database and work uniquely with stats runned on d4 files on the fly (closes Simplify app by not saving cases and samples into the database #329 )

Currently chanjo2 supports saving cases and samples (including paths to local d4 files) data into the database for later use. Later use being the following endpoints:

• Gene coverage/completeness from case name or sample name
• Transcripts coverage/completeness from case name or sample name
• Exons coverage/completeness from case name or sample name

None of the functionalities are used by us or our collaborators, so I want to simplify chanjo2 by removing them.

How to test

• All automatic tests should run as expected
• Deploy on stage and use a scout case to retrieve coverage report

Expected outcome

• Case report from scout case should work as expected

Review

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

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

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.18%. Comparing base (c65c670) to head (719f1b8).
Report is 5 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #330   +/-   ##
=======================================
  Coverage   90.18%   90.18%           
=======================================
  Files          30       30           
  Lines        1457     1457           
=======================================
  Hits         1314     1314           
  Misses        143      143           

Flag	Coverage Δ
unittests	90.18% <100.00%> (ø)

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[northwestwitch]

Hi @Jakob37, I was wondering if you have some time to give this PR a review? It's not adding any new feature, only removing stuff we are not using (see PR description) thus simplifying the whole thing. Thanks!

[Jakob37]

Hi @Jakob37, I was wondering if you have some time to give this PR a review? It's not adding any new feature, only removing stuff we are not using (see PR description) thus simplifying the whole thing. Thanks!

Yes, I can take a look before the end of this week!

[Jakob37]

I ran this locally together with the Scout stack. The latest main branch of Scout.

I needed to mount in the Scout demo data folder to get it working - before that Chanjo2 couldn't access the d4 file. But that is probably as expected.

Looks good!

[Jakob37]

I eyed through the code as well. Didn't find anything to comment on there. This seems to simplify the code a lot, nice 😄

[northwestwitch]

I eyed through the code as well. Didn't find anything to comment on there. This seems to simplify the code a lot, nice 😄

Thank you! Let's go for this and a new major release when we have the new faster completeness stats in place!

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud