Identify and reduce code debt

yuanzhou commented 5 months ago

Over the years, ingest-api has become more and more complex with functionalities and features developed by various contributors to be consumed by UI apps and other microservices. It's getting hard to debug and maintain the codebase. It's worth spending some time to:

Identify the existing code debt and prioritize the ones that need immediate attention
Reorganize the code and reduce duplicate functionalities
Reduce unnecessary dependencies including Python modules and files that are no longer being used
Improve code level documentations

Test thoroughly in both local and DEV, with verifications from PSC and Harvard teams.

yuanzhou commented 4 months ago

Will remove https://github.com/hubmapconsortium/ingest-api/blob/db4d8fc13c39239a08f40d059cd6f0dc7ee46c3a/src/app.py#L186-L195

yuanzhou commented 4 months ago

Will disable or remove https://github.com/hubmapconsortium/ingest-api/blob/db4d8fc13c39239a08f40d059cd6f0dc7ee46c3a/src/app.py#L1302 and all related functionalities. The PSC team no longer uses it, instead they update the dataset against entity-api directly.

Also comment out the endpoint in gateway.

yuanzhou commented 1 month ago

src/specimen.py has been deprecated for a while, see if we can remove it completely.

yuanzhou commented 1 month ago

CEDAR_API_KEY configuration is no longer needed. From Juan:

We thought we needed it to perform CEDAR validation but were mistaken

https://github.com/hubmapconsortium/ingest-api/blob/ccbacbb44b280c95f8b9d2e7526450220cfc8389/src/instance/app.cfg.example#L144-L145

hubmapconsortium / ingest-api

Identify and reduce code debt #555