Make sure that it responds correctly to all the integration tests in CAM-KP-API repository

[gaurav]

This issue compares the queries in the CAM-KP-API Integration Tests with the output from Automat-CAM-KP. Just running the test against the new endpoint doesn't work (it returns a 422 Unprocessable Entity error), and I can't immediately figure out why. However, running these queries directly against CAM-KP-API and Automat-CAM-KP using the Swagger endpoint works.

• CAM-KP-API: https://cam-kp-api.transltr.io/1.3.0/docs/index.html?url=docs.yaml#/default/postQuery
• Automat-CAM-KP: https://automat-dev.apps.renci.org/#/cam-kp/reasoner_api_1_3_query_post --

Tests returning results on both CAM-KP-API and Automat-CAM-KP.

{"message":{"query_graph":{"nodes":{"n0":{"categories":["biolink:BiologicalProcessOrActivity"]},"n1":{"ids":["GO:0005737"],"categories":["biolink:AnatomicalEntity"]}},"edges":{"e0":{"predicates":["biolink:occurs_in"],"subject":"n0","object":"n1"}}}}}

{"message":{"query_graph":{"nodes":{"n0":{"categories":["biolink:GeneOrGeneProduct"]},"n1":{"ids":["GO:0005634"],"categories":["biolink:AnatomicalEntity"]}},"edges":{"e0":{"predicates":["biolink:part_of"],"subject":"n0","object":"n1"}}}}}

Tests failing

Here are some queries that currently work on CAM-KP-API but fail on Automat-CAM-KP with an Internal Server Error:

{"message":{"query_graph":{"nodes":{"n0":{"categories":["biolink:BiologicalProcessOrActivity"]},"n1":{"ids":["GO:0004707"]}},"edges":{"e0":{"predicates":["biolink:positively_regulates"],"subject":"n0","object":"n1"}}}}}

• This seems to be because biolink:positively_regulates is no longer in Biolink (although a better error message would be nice). Replacing that with biolink:regulates works, but returns zero results.

{"message":{"query_graph":{"nodes":{"n0":{"categories":["biolink:GeneOrGeneProduct"]},"n1":{"ids":["UniProtKB:Q9HC97"],"categories":["biolink:GeneOrGeneProduct"]},"n2":{"ids":["CL:0000738"],"categories":["biolink:AnatomicalEntity"]}},"edges":{"e0":{"predicates":["biolink:affects_activity_of"],"subject":"n0","object":"n1"},"e1":{"predicates":["biolink:part_of"],"subject":"n1","object":"n2"}}}}}

• Probably because biolink:affects_activity_of is no longer in Biolink; replacing it with biolink:affects works, but returns zero results.
• Note that CAM-KP-API returns an error too.

Tests that return results on CAM-KP-API but return no results on Automat-CAM-KP

{"message":{"query_graph":{"nodes":{"n0":{"ids":["CHEBI:39867"]},"n1":{"categories":["biolink:NamedThing"]}},"edges":{"e0":{"predicates":["biolink:related_to"],"subject":"n0","object":"n1"}}}}}

{"message":{"query_graph":{"nodes":{"n0":{"ids":["CHEBI:15361"]},"n1":{"categories":["biolink:NamedThing"]}},"edges":{"e0":{"predicates":["biolink:related_to"],"subject":"n0","object":"n1"}}}}}

• This query does work if you use the normalized form of CHEBI:15361 -- which is PUBCHEM.COMPOUND:107735 -- instead. So that's probably the only reason it doesn't work.

[gaurav]

The examples tests have been ported over in https://github.com/ExposuresProvider/cam-pipeline/pull/111. The others will take longer to work through, and probably aren't a high priority for us right now.