feat(Search samples) Modify samples endpoint to allow for searching.

[Vince-janv]

Description

Adds a sample search functionality.

Added

• Function for querying samples based on substring

Changed

• Added a enquiry parameter to the samples endpoint to allow for sample searches

Steps to consider while deploying

• Configuration changes: N/A
• Documentation updates: N/A
• Inform users by email: N/A

Review:

• Code approved by
• Tests executed on stage by: (Document the test done with screen shots and description.)
• "Merge and deploy" approved by

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[Vince-janv]

Test on the genotype stage swagger:

[elevu]

Approving the PR, just some tiny comments :)

• The endpoints returns 500 when making some calls like https://genotype-stage.scilifelab.se/api/v2/samples/?skip=0&limit=2&enquiry=ACC&plate_id=ID127&incomplete=true&commented=true&status_missing=true but I guess it is not relevant to this PR.
• The search by plate id seems also not to work, but maybe I am wrong and just searching for non existing combination (commented true and so on).
• No tests? :D

[Vince-janv]

Approving the PR, just some tiny comments :)

• The endpoints returns 500 when making some calls like https://genotype-stage.scilifelab.se/api/v2/samples/?skip=0&limit=2&enquiry=ACC&plate_id=ID127&incomplete=true&commented=true&status_missing=true but I guess it is not relevant to this PR.
• The search by plate id seems also not to work, but maybe I am wrong and just searching for non existing combination (commented true and so on).
• No tests? :D

Thanks for the review @elevu! 😊

• I played around a bit with the swagger UI and it seems that incomplete=true in combination with some other options returns 500. Probably not related to anything I changed, but I can take a look.
• hmm, plate id works for me 🤔
• That's why I wanted your review. How would you suggest to test these kind of PRs except via the swagger UI. There are no pytests in the genotype-api repo 😨

[henrikstranneheim]

👍

[henrikstranneheim]

@Vince-janv For API endpoint testing there is a framework in fastAPI to use. See https://github.com/Clinical-Genomics/atlas/tree/master/tests/api for inspiration

[Vince-janv]

@henrikstranneheim Should I spend time starting to write tests here or should I merge this and prioritise something else?

[henrikstranneheim]

@Vince-janv I think it is no worse then when you arrived. I think we should not spend time on this technical debt now, as this code seem to be of poor standards and would require some work. We should make a project out of it and work on it in a team in a more focused way.