Migrate Library Contents API to FastAPI

[arash77]

What did you do?

• Include an API test under lib/galaxy_test/api/
• Refactor the legacy library_contents API logic so all the logic is contained in the LibraryContentsService class
• Create pydantic models for the responses and payloads
• Create the FastAPI routes that will replace the old ones

related to #10889

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

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

[davelopez]

At least some of the test failures are due to wrong Library Folder ID decoding.

Looks like LibraryFolderDatabaseIdField is not stripping the initial "F" before decoding here:

galaxy/lib/galaxy/schema/fields.py

Line 81 in 5e332f0

BeforeValidator(lambda database_id: Security.security.decode_id(database_id)),

[arash77]

At least some of the test failures are due to wrong Library Folder ID decoding.

Looks like LibraryFolderDatabaseIdField is not stripping the initial "F" before decoding here:

galaxy/lib/galaxy/schema/fields.py

Line 81 in 5e332f0

BeforeValidator(lambda database_id: Security.security.decode_id(database_id)),

I think the test failures are because I forgot to add the model for the folder ids on library_id! I have added them to the new commit.

[arash77]

I noticed test failures that I believe are caused by files being sent to the create endpoint (here and here). This results in the payload being sent as data instead of JSON, which leads to issues. Do you have any suggestions for handling file uploads in this case?

[davelopez]

I noticed test failures that I believe are caused by files being sent to the create endpoint (here and here). This results in the payload being sent as data instead of JSON, which leads to issues. Do you have any suggestions for handling file uploads in this case?

Have a look at other endpoints that upload files, for example this one:

galaxy/lib/galaxy/webapps/galaxy/api/tools.py

Line 93 in 5e332f0

payload: FetchDataFormPayload = Depends(FetchDataForm.as_form),