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

northwestwitch commented 3 months ago

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 #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:

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

How to test

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

Expected outcome

Case report from scout case should work as expected

Review

[x] Tests executed by CR, JW
[x] "Merge and deploy" approved by JW

This version is a

[x] 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 commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #330 +/- ## ======================================= Coverage 90.18% 90.18% ======================================= Files 30 30 Lines 1457 1457 ======================================= Hits 1314 1314 Misses 143 143 ``` | [Flag](https://app.codecov.io/gh/Clinical-Genomics/chanjo2/pull/330/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/Clinical-Genomics/chanjo2/pull/330/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics) | `90.18% <100.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics#carryforward-flags-in-the-pull-request-comment) to find out more.

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northwestwitch commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

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!

new_chanjo2