feat: PUT for manifest files

[ivirshup]

Reason for Change

• A curator can start the ingestion of an anndata and/or fragment file using the Discovery PUT manifest endpoint single-cell#738
• If the reason for this PR's code changes are not clear in the issue, state value/impact

TODO

• Tests
  • Test submission of dataset with ATAC fragments
  • Fill out tests for errors at new endpoint
• Features
  • [ ] Submit ATAC to SFN
• Open questions
  • Do we need to handle file sizes for ATAC fragments? No

I think it would be better if ingest_dataset ONLY took a manifest, and that the routing layer above it had to account for transforming the JSON. But the method is called in really a lot of tests, so changing it would touch a lot of code.

Changes

• Added a PUT endpoint for manifest files

Testing steps

Checklist 🛎️

Notes for Reviewer

[github-actions]

Deployment Summary

• backend_url: https://pr-7431-backend.rdev.single-cell.czi.technology
• backend_de_url: https://pr-7431-backend-de.rdev.single-cell.czi.technology
• backend_wmg_url: https://pr-7431-backend-wmg.rdev.single-cell.czi.technology
• frontend_url: https://pr-7431-frontend.rdev.single-cell.czi.technology
• delete_db_task_definition_arn: arn:aws:ecs:us-west-2:***:task-definition/dp-rdev-pr-7431-deletion:1
• migrate_db_task_definition_arn: arn:aws:ecs:us-west-2:***:task-definition/dp-rdev-pr-7431-migration:1

[codecov]

Codecov Report

Attention: Patch coverage is 87.20930% with 11 lines in your changes missing coverage. Please review.

Please upload report for BASE (feature/schema-5-3@07a6435). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
...lection_id/datasets/dataset_id/manifest/actions.py	66.66%	9 Missing ⚠️
backend/layers/business/business.py	80.00%	2 Missing ⚠️

Additional details and impacted files

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##             feature/schema-5-3    #7431   +/-   ##
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Flag	Coverage Δ
unittests	92.99% <87.20%> (?)

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[Bento007]

One nit, otherwise it looks good.