fix swagger page validation errors

[jfkonecn]

Fix #9414

Testing Questions

Do you want me to add a python script to check for regression errors?

Maybe something similar to the code in the issue?

#! /bin/python3
from bravado.client import SwaggerClient
# fix exception is thrown then fail the test
SwaggerClient.from_url('http://localhost:8080/api/v2/api-docs?group=default')

If so, where should I add it?

PR changes

Describe changes proposed in this pull request:

• Hid the Authentication object in the swagger pages in the StudyController
  • It seems like something that should be passed in the body of a POST request. Swagger was confused by it and so I removed it. For context I was getting this error below when running my test script.

jsonschema.exceptions.ValidationError: {'name': 'credentials', 'in': 'query', 'required': False, 'type': 'object'} is not valid under any of the given schemas

Failed validating 'oneOf' in schema['properties']['paths']['patternProperties']['^/']['properties']['get']['properties']['parameters']['items']:
    {'oneOf': [{'$ref': '#/definitions/parameter'},
               {'$ref': '#/definitions/jsonReference'}]}

On instance['paths']['/studies']['get']['parameters'][2]:
    {'in': 'query',
     'name': 'credentials',
     'required': False,
     'type': 'object'}

• Changed default value values for tier parameters for the TreatmentController from Treatment to Agent since Treatment is not a valid value for ClinicalEventKeyCode

Checks

• Runs on heroku
• Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
• The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
• Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

@ersinciftci @inodb

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[haynescd]

Yea, good idea to add testing for our swagger api.

For the place to add it I would suggest creating a new github workflow (ex: sanity-check.yml)

Here is a potential solution for validating Swagger API if you didn't
https://swagger.io/blog/api-design/validate-openapi-definitions-swagger-editor/

[inodb]

@jfkonecn filed a separate ticket to add testing: cBioPortal/icebox#513. We don't really have a recommended place for adding these types of tests yet and there's a lot of ways one might do this, so prolly warrants further discussion

[jfkonecn]

@jfkonecn filed a separate ticket to add testing: cBioPortal/icebox#513. We don't really have a recommended place for adding these types of tests yet and there's a lot of ways one might do this, so prolly warrants further discussion

Sounds good. If you want to include me in the conversation feel free to add me to a meeting.