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Migrate a part of the jobs API to Fast API #16778

Merged
merged 110 commits into from Nov 22, 2023
Merged

Migrate a part of the jobs API to Fast API #16778

merged 110 commits into from Nov 22, 2023

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heisner-tillman
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@heisner-tillman heisner-tillman commented Oct 3, 2023 •
edited

This is a part of #10889.

Summary

  • Refactored API routes
  • Added pydantic models
  • Operations now return pydanctic models
  • Removed the mapping to the legacy routes

How to test the changes?

  • This is a refactoring of components with existing test coverage.
  • I added automated tests for the operations missing tests
  • Instructions for manual testing are as follows:
    You can find the interactive API documentation here: http://127.0.0.1:8080/api/docs#/jobs

image

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@heisner-tillman heisner-tillman marked this pull request as draft October 3, 2023 15:50
@github-actions github-actions bot added this to the 23.2 milestone Oct 3, 2023
davelopez
davelopez reviewed Nov 1, 2023
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mvdbeek
mvdbeek reviewed Nov 8, 2023
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@mvdbeek
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mvdbeek commented Nov 8, 2023

Thanks a lot @heisner-tillman, this is shaping up very nicely!

heisner-tillman and others added 21 commits November 21, 2023 19:18
@heisner-tillman @mvdbeek
Follow up on previous deprecation and refactor create operation
a48ebf1
@heisner-tillman @mvdbeek
Remove mapping to some legacy routes
75def35
@heisner-tillman @mvdbeek
Regenerate client schema
92559ef
@heisner-tillman @mvdbeek
Divide JobAssociation into Input and Output model
6571f08
@heisner-tillman @mvdbeek
Regenerate the client schema
543a7a4
@mvdbeek
Use validator to load job search inputs
899608c
@heisner-tillman @mvdbeek
Remove accidental code insertion in test_jobs.py
d38b8db
@heisner-tillman @mvdbeek
Set Ids of JobBaseModel to encoded and undo previous model split
19c06a9
@heisner-tillman @mvdbeek
Refine EncodedHdacaSourceId model
ec606f8
@heisner-tillman @mvdbeek
Regenerate client schema
1405391
@heisner-tillman @mvdbeek
Fix codestyle issue
e4824b2
@heisner-tillman @mvdbeek
Remove completed TODOs and clarify some path parameters
66001b7
@heisner-tillman @mvdbeek
Remove outdated TODO
a8a4b91
@heisner-tillman @mvdbeek
Add test for delete operation
832ecd8
@heisner-tillman @mvdbeek
Regenerate the client schema
c2ca0a6
@heisner-tillman @mvdbeek
Add expetion in case of missing parameter
d925527
@heisner-tillman @mvdbeek
Refine the JobDestinationParams model
78fc912
@heisner-tillman @mvdbeek
Regenerate the client schema
05edd51
@mvdbeek
Drop POST /api/jobs
c0d43cf 
This is a remnant from the old routes setup that would automatically
create thr CRUD methods ... much better to just drop this.
@mvdbeek
Update description of '/api/jobs/{job_id}/parameters_display'
f18a33b
@mvdbeek
Drop BaseModel docstring
4c4f949
mvdbeek
mvdbeek approved these changes Nov 21, 2023
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Very nice work, thanks so much @heisner-tillman!

@mvdbeek mvdbeek merged commit e95e60a into galaxyproject:dev Nov 22, 2023
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This PR was merged without a "kind/" label, please correct.

@davelopez davelopez added the kind/refactoring cleanup or refactoring of existing code, no functional changes label Nov 22, 2023
nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Dec 4, 2023
@nsoranzo
Fix job search when command_version is None
06a5d2e 
Fix 500 response when searching jobs via API as seen in BioBlend
tests on release_23.2 and dev, e.g.:

https://github.com/galaxyproject/bioblend/actions/runs/7090125691/job/19296402084#step:10:3256

Broken in galaxyproject#16778 .
@nsoranzo nsoranzo mentioned this pull request Dec 4, 2023
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@heisner-tillman heisner-tillman mentioned this pull request Dec 8, 2023
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@mvdbeek mvdbeek mvdbeek approved these changes

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