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monarch-initiative / biolink-api

API for linked biological knowledge
https://api.monarchinitiative.org/api/
BSD 3-Clause "New" or "Revised" License
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Add scigraph annotator routes #317

Closed deepakunni3 closed 4 years ago

deepakunni3 commented 4 years ago

This PR implements two new routes:

Both GET and POST are implemented for these routes.

See https://github.com/biolink/biolink-api/issues/223 for related discussion.

deepakunni3 commented 4 years ago

@kshefchek Fixed the Behave tests but Travis is failing because biolink-api:master now relies on ontobio:master instead of a stable release of Ontobio, which is what requirements.txt specifies.

kshefchek commented 4 years ago

Maybe we should have travis test the master version of ontobio? Is there a reason to have biolink coupled to an older version of ontobio?

deepakunni3 commented 4 years ago

Ontobio is actively being developed as part of Gene Ontology and Monarch. Locking the requirements.txt was to avoid any issues that might be introduced with new changes to Ontobio.

Are you suggesting we just have two requirements.txt,

kshefchek commented 4 years ago

@deepakunni3 whatever you think is best. I develop biolink against the master branch of ontobio, and in Monarch we test both master versions of ontobio and biolink on api-dev, and then update production when this is stable.

kshefchek commented 4 years ago

I've bumped the ontobio version if you'd like to pull from master and see if the tests pass

kshefchek commented 4 years ago

there are still 4 behave tests failing, but let's merge and fix these in the next PR

monicacecilia commented 4 years ago

Does this address and close #223 now? Or do we need to wait for the updated PR?

kshefchek commented 4 years ago

partially -- we'll need to update the UI to use biolink instead of scigraph