Public Release of API

[inodb]

Before the official 1.0 release of the API we should do the following:

• Create User Friendly API Documentation. Current API auto generated docs are not easy to read. Give general overview of API (#7469)
• Deprecation message (Add Deprecation Text to Top of Web API Page cbioportal#2967)
• Go over all API endpoints and check consistency
  • In particular generic assay endpoints: change endpoint path of GENERIC_ASSAY cbioportal#6955, API Documentation of Generic Assay API #200
• Address issues identified while going over all endpoints: https://docs.google.com/document/d/1KC07Rl_oD6jYUyYahv4UrS-GIuLWnr4biaWop826U1Y
• Only use public API endpoints (Public API clients should only connects to the public client cbioportal#3289)
• Jupyter Notebooks
  • Python (can use a lot from https://github.com/mskcc/cbsp-hackathon)
  • R (Deprecate cgdsr in favor of cBioPortalData and rapiclient if endpoint is not supported)
• Document other clients
  • JavaScript (fix Difficult to only import API clients for cbioportal-frontend-commons cbioportal#6716)
  • Java
• Remove A/B/C etc from endpoint names (find another way to sort endpoints)
• Styling/navigation of API page. Should it live inside docs.cbioportal.org and/or inside cBioPortal shell, or should we expand swagger page with more custom look (related: Embed the Swagger API Page into the larger cBioPortal shell cbioportal#2969)
• Move treatments to internal (move treatments endpoint to internal #561)
• Move Clinical_Events endpoint to default (Move Clinical_Events endpoint to default #562)
• Move Structural_Variants endpoint to default (Move Structural_Variants endpoint to default #563)
• Add more notebooks to codebook repo (http://github.com/cbioportal/codebook)
• Describe API at a higher level. Explain what molecular profiles are, generic assays, gene panels, etc
• Decide how we manage versioning of the API and document the process of endpoint updates (API specific version - github action to keep version up to date #267)
• Swagger issues: Swagger Validation Issues cbioportal#9414
• Should we expose the Session endpoint?

For auth enabled portals:

• For each of the client docs include how to connect to an authenticated portal

Would be nice (requires db migration):

• Remove Category from Sample List API (Remove category from Sample List API cbioportal#4933). (Decided not to follow up on because of potential future case list changes)

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.