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Refactor the route POST: /api/tools to FastAPI #17295

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Refactor the route POST: /api/tools to FastAPI #17295

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heisner-tillman
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@heisner-tillman heisner-tillman commented Jan 15, 2024 •
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This is a part of #10889.

Summary

  • Refactored API route
    • POST: /api/tools
  • Added pydantic model to input
  • Added pydantic model to return
  • Removed the mapping to the legacy route

How to test the changes?

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 January 15, 2024 11:13
@github-actions github-actions bot added this to the 24.0 milestone Jan 15, 2024
@heisner-tillman heisner-tillman force-pushed the tools branch 8 times, most recently from f0c50aa to 05629e6 Compare January 25, 2024 09:57
@heisner-tillman heisner-tillman marked this pull request as ready for review February 8, 2024 14:53
@heisner-tillman heisner-tillman force-pushed the tools branch 3 times, most recently from 41a4b5e to abd26a3 Compare February 18, 2024 09:45
@davelopez
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@heisner-tillman can you fix the conflict? You might resolve it just by regenerating the schema again.

@mvdbeek mvdbeek modified the milestones: 24.0, 24.1 Mar 5, 2024
@heisner-tillman heisner-tillman force-pushed the tools branch 2 times, most recently from b644a37 to 3afc2fd Compare March 28, 2024 11:02
@heisner-tillman
Remove json keyword from interactor method, when posting to /api/tools
00ce35e
@heisner-tillman
Regenerate the client schema
ecd3a48
@heisner-tillman
Regenerate the client schema
37e5a41
@heisner-tillman
Add typing to input of service methods used in execute operation
6826dbf
@heisner-tillman
Type collections in return model of execute oerpation
ae36dfe
@heisner-tillman
Type tool_id with str in payload of execute operation
b272fd5
@heisner-tillman
Remove unused typing
4379464
@heisner-tillman
Do not encode id's in method, as it is handled by the return model
9be481d
@heisner-tillman
Type outputs field in model ToolResponse with extended HDA models
e8133c6
@heisner-tillman
Rename ToolResponse model and only use it in execute operation of the…
95c02d4 
… tool API
@heisner-tillman
Rename the class FetchTools to FastAPITools as it covers more endpoin…
8a44ea0 
…ts now
@heisner-tillman
Type field tool_uuid with UUID4 in ExecuteToolPayload model
a3ba4a7
@heisner-tillman
Cast tool_uuid to string - if present in the payload - after validati…
0d0ada3 
…on as uuid via the pydantic model, as it is expected to be of this type further down the line
@heisner-tillman
Apply code suggestions
d125e30
@heisner-tillman
Remove invalid parameter when creating payload to run a tool
8d97c50
@heisner-tillman
Add an optional tool version field to the JobBaseModel
60a5bbf
@heisner-tillman
Narrow down the HDA, HDCA and Jobmodels used in the response model of…
b033aa4 
… the execute operation
@heisner-tillman
Apply code suggestions
71f7bfc
@heisner-tillman
Add missing field state to payload model of the execute operation
a10088a
@heisner-tillman
Add validator for extra fields to payload model of the execute operat…
54448e5 
…ion from the tools API
@heisner-tillman
Adjust error type that get raised by model validator
3d803d3
@heisner-tillman
Add missing field in payload model of execute operation
2d65739
@heisner-tillman
Add missing field in payload model of execute operation
dc03471
@heisner-tillman
Regenerate the client schema
3d6c325
@heisner-tillman
Add umask-friendly permissions fixing, when creating a temporary file
34fe594
@heisner-tillman
Regenerate the client schema
d7833d3
@heisner-tillman heisner-tillman marked this pull request as draft September 6, 2024 11:51
@jdavcs jdavcs modified the milestones: 24.2, 25.0 Nov 20, 2024
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@mvdbeek mvdbeek Awaiting requested review from mvdbeek

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@heisner-tillman @davelopez @jdavcs @mvdbeek