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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 facet_fields parameter to all Bioentity routes #315

Closed deepakunni3 closed 5 years ago

deepakunni3 commented 5 years ago

@kshefchek This PR basically adds facet_fields parameter to all Bioentity routes.

And when facet_fields is None, the default subject_taxon_label and object_closure is used. This is to ensure that we don't break any existing implementations that might assume that these fields are faceted. But this default behavior may be removed in a future release.

This PR is related to https://github.com/monarch-initiative/monarch-ui/issues/168

deepakunni3 commented 5 years ago

Travis failing due to api.mi.org being down

kshefchek commented 5 years ago

I reran the travis tests now that all of our services are stable, but same results. Odd, I had similar logs on my recent PR

deepakunni3 commented 5 years ago

@kshefchek It looks like a lot of the behave tests are failing, mostly due to change in the data. Routes that yielded results before now return empty.

Ex: /api/bioentity/publication/PMID:20220848/genotypes should return an association with object being MONARCH:FBgeno426941, but now there are no associations.

Is this expected?

kshefchek commented 5 years ago

This is expected, we removed fly genotypes in this release

deepakunni3 commented 5 years ago

@kshefchek Thanks for merging the PR.

I'll fix the behave tests in a separate PR. I made some assumptions regarding the data which is likely to change from one release to another.