[BIOMAGE-2016] Cleanup api v1 code from the api

[StefanBabukov]

Description

Details

URL to issue

https://biomage.atlassian.net/browse/BIOMAGE-2016

Link to staging deployment URL (or set N/A)

https://ui-grasp6-hazy-moose.scp-staging.biomage.net/

Links to any PRs or resources related to this PR

Integration test branch

master

Merge checklist

Your changes will be ready for merging after all of the steps below have been completed.

Code updates

Have best practices and ongoing refactors being observed in this PR

• Migrated any selector / reducer used to the new format.

Manual/unit testing

• Tested changes using InfraMock locally or no tests required for change, e.g. Kubernetes chart updates.
• Validated that current unit tests for code work as expected and are sufficient for code coverage or no unit tests required for change, e.g. documentation update.
• Unit tests written or no unit tests required for change, e.g. documentation update.

Integration testing

You must check the box below to run integration tests on the latest commit on your PR branch.
Integration tests have to pass before the PR can be merged. Without checking the box, your PR
will not pass the required status checks for merging.

• Started end-to-end tests on the latest commit.

Documentation updates

• Relevant Github READMEs updated or no GitHub README updates required.
• Relevant Wiki pages created/updated or no Wiki updates required.

Optional

• Staging environment is unstaged before merging.
• Photo of a cute animal attached to this PR.

[codecov]

Codecov Report

Merging #392 (11c1244) into master (63a5778) will decrease coverage by 2.03%.
The diff coverage is 57.40%.

@@            Coverage Diff             @@
##           master     #392      +/-   ##
==========================================
- Coverage   88.78%   86.75%   -2.04%     
==========================================
  Files         168      123      -45     
  Lines        4603     2876    -1727     
  Branches      497      323     -174     
==========================================
- Hits         4087     2495    -1592     
+ Misses        483      362     -121     
+ Partials       33       19      -14     

Impacted Files	Coverage Δ
src/app.js	0.00% <ø> (ø)
src/api.v2/middlewares/authMiddlewares.js	57.28% <46.51%> (-7.72%)	⬇️
src/api.v2/helpers/pipeline/gem2s.js	97.36% <100.00%> (ø)
src/api.v2/helpers/pipeline/handleQCResponse.js	96.92% <100.00%> (+0.04%)	⬆️
...i.v2/helpers/pipeline/hooks/assignPodToPipeline.js	84.09% <100.00%> (ø)
src/loaders/express.js	88.13% <100.00%> (-0.39%)	⬇️
...ils/emailTemplates/buildPipelineStatusEmailBody.js	100.00% <100.00%> (ø)
tests/test-utils/mockAWSServices.js	29.23% <0.00%> (-70.77%)	⬇️
src/utils/parse-sns-message.js	23.07% <0.00%> (-66.67%)	⬇️

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[aerlaut]

I think it looks good. Do you have a staged environment? Can you do integration tests?

[kafkasl]

I think we should remove the api.v2 paths and just make them the default api. Not sure whether it's best to do it here or in another PR. Opinions @cosa65 @aerlaut etc... ?

[aerlaut]

I think we should remove the api.v2 paths and just make them the default api. Not sure whether it's best to do it here or in another PR. Opinions @cosa65 @aerlaut etc... ?

I agree with Pol, that we should make this the default API. I think there will be a lot of little work involved over the various repos (UI, pipeline and workers). Might be worth having it in a separate PR, just to divide up the work and make checking easy. Otherwise, I think there will be a lot of changes over the repos.