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

Merged

mvdbeek merged 110 commits into galaxyproject:dev from heisner-tillman:jobs

Nov 22, 2023

Contributor

heisner-tillman commented Oct 3, 2023 •

edited

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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

License

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

heisner-tillman marked this pull request as draft

October 3, 2023 15:50

github-actions bot added the area/API label

github-actions bot added this to the 23.2 milestone

heisner-tillman force-pushed the jobs branch 5 times, most recently from 0c57bb9 to 3532d00 Compare

October 9, 2023 18:26

heisner-tillman force-pushed the jobs branch 5 times, most recently from a96bd90 to 01c0e20 Compare

October 20, 2023 16:47

heisner-tillman force-pushed the jobs branch 5 times, most recently from 3a439cb to 0275657 Compare

October 30, 2023 09:02

davelopez reviewed

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heisner-tillman force-pushed the jobs branch from 565f0d6 to cad8dcc Compare

November 4, 2023 14:51

heisner-tillman commented

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Member

mvdbeek commented Nov 8, 2023

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

heisner-tillman force-pushed the jobs branch 2 times, most recently from 816e6d3 to fd7263b Compare

November 11, 2023 17:46

mvdbeek reviewed

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heisner-tillman and others added 21 commits

November 21, 2023 19:18


          Follow up on previous deprecation and refactor create operation

a48ebf1


          Remove mapping to some legacy routes

75def35


          Regenerate client schema

92559ef


          Divide JobAssociation into Input and Output model

6571f08


          Regenerate the client schema

543a7a4


          Use validator to load job search inputs

899608c


          Remove accidental code insertion in test_jobs.py

d38b8db


          Set Ids of JobBaseModel to encoded and undo previous model split

19c06a9


          Refine EncodedHdacaSourceId model

ec606f8


          Regenerate client schema


          Fix codestyle issue

e4824b2


          Remove completed TODOs and clarify some path parameters

66001b7


          Remove outdated TODO

a8a4b91


          Add test for delete operation

832ecd8


          Regenerate the client schema

c2ca0a6


          Add expetion in case of missing parameter

d925527


          Refine the JobDestinationParams model

78fc912


          Regenerate the client schema

05edd51


          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.


          Update description of '/api/jobs/{job_id}/parameters_display'

f18a33b


          Drop BaseModel docstring

4c4f949

mvdbeek force-pushed the jobs branch from 1aca151 to 4c4f949 Compare

November 21, 2023 18:20

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mvdbeek left a comment

Very nice work, thanks so much @heisner-tillman!

mvdbeek merged commit e95e60a into galaxyproject:dev

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github-actions bot commented Nov 22, 2023

This PR was merged without a "kind/" label, please correct.

davelopez added the kind/refactoring label

nsoranzo reviewed

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nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request


          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 mentioned this pull request

[23.2] Fix job search when command_version is None #17129

Merged

4 tasks

heisner-tillman mentioned this pull request

Create pydantic model for the return of show operation - get: /api/jobs/{job_id} #17153

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4 tasks

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area/API kind/refactoring