This issue is to report that both @xu-hao and I cannot run direct three-hop ARAGORN queries for Workflow B. I initially thought the error was on my end, but if Hao is encountering issues, then I think there's something not quite right on the ARAGORN side.
The TRAPI query can be found here. Note that Hao tested both e01 biolink:has_real_world_evidence_of_association_with and e01 biolink_correlated_with. I only tested the latter predicate, as that's the one I used when testing direct three-hop ARAX queries.
Here's the command:
curl -XPOST https://aragorn.renci.org/1.1/query -d '{
"message": {
"query_graph": {
"nodes": {
"n0": {
"ids": ["MESH:D056487"],
"categories": ["biolink:DiseaseOrPhenotypicFeature"]
},
"n1": {
"categories": ["biolink:DiseaseOrPhenotypicFeature"]
},
"n2": {
"categories": ["biolink:Gene"]
},
"n3": {
"categories": ["biolink:ChemicalEntity"]
}
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:correlated_with"]
},
"e02": {
"subject": "n2",
"object": "n1",
"predicates": ["biolink:gene_associated_with_condition"]
},
"e03": {
"subject": "n2",
"object": "n3",
"predicates": ["biolink:related_to"]
}
}
}
}
}' -H "Content-Type: application/json"
Here's the error message that Hao received from e01 biolink:has_real_world_evidence_of_association_with:
{"message":{"query_graph":{"nodes":{"n0":{"ids":["MESH:D056487"],"categories":["biolink:DiseaseOrPhenotypicFeature"],"is_set":false,"constraints":null},"n1":{"ids":null,"categories":["biolink:DiseaseOrPhenotypicFeature"],"is_set":false,"constraints":null},"n2":{"ids":null,"categories":["biolink:Gene"],"is_set":false,"constraints":null},"n3":{"ids":null,"categories":["biolink:ChemicalEntity"],"is_set":false,"constraints":null}},"edges":{"e01":{"subject":"n0","object":"n1","predicates":["biolink:has_real_world_evidence_of_association_with"],"relation":null,"constraints":null},"e02":{"subject":"n2","object":"n1","predicates":["biolink:gene_associated_with_condition"],"relation":null,"constraints":null},"e03":{"subject":"n2","object":"n3","predicates":["biolink:related_to"],"relation":null,"constraints":null}}},"knowledge_graph":{"nodes":{},"edges":{}},"results":[]},"logs":[{"timestamp":"2021-08-24T22:13:34.599883","level":"WARNING","code":null,"message":"warning: empty returned"},{"timestamp":"2021-08-24T22:13:34.648997","level":"ERROR","code":null,"message":"No results to coalesce"},{"timestamp":"2021-08-24T22:13:34.653174","level":"ERROR","code":null,"message":"answer_coalesce error: HTML error status code 422 returned."},{"timestamp":"2021-08-24T22:13:34.785124","level":"WARNING","code":null,"message":"warning: empty returned"},{"timestamp":"2021-08-24T22:13:34.836039","level":"WARNING","code":null,"message":"warning: empty returned"},{"timestamp":"2021-08-24T22:13:34.882219","level":"WARNING","code":null,"message":"warning: empty returned"}],"status":null,"workflow":["lookup","enrich_results","connect_knodes","score"]}
And here's the error message that was returned with e01 biolink:correlated_with:
{"message":{"query_graph":{"nodes":{"n0":{"ids":["MESH:D056487"],"categories":["biolink:DiseaseOrPhenotypicFeature"],"is_set":false,"constraints":null},"n1":{"ids":null,"categories":["biolink:DiseaseOrPhenotypicFeature"],"is_set":false,"constraints":null},"n2":{"ids":null,"categories":["biolink:Gene"],"is_set":false,"constraints":null},"n3":{"ids":null,"categories":["biolink:ChemicalEntity"],"is_set":false,"constraints":null}},"edges":{"e01":{"subject":"n0","object":"n1","predicates":["biolink:correlated_with"],"relation":null,"constraints":null},"e02":{"subject":"n2","object":"n1","predicates":["biolink:gene_associated_with_condition"],"relation":null,"constraints":null},"e03":{"subject":"n2","object":"n3","predicates":["biolink:related_to"],"relation":null,"constraints":null}}},"knowledge_graph":null,"results":null},"logs":[{"timestamp":"2021-08-24 22:36:29.878473","level":"ERROR","message":"Exception 'logs'","code":null}],"status":null}
Any chance you all can work on this query and send me/Hao both the executable query and the associated JSON output, so that Hao and I can figure out what we did wrong and (importantly) I can review the answers? I honestly think this might be the more efficient testing approach.
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