Open CaseyTa opened 3 months ago
@micheldumontier This issue is ongoing, and I believe is the cause of the following issue created by @isbluis (ARAX) https://github.com/NCATSTranslator/Feedback/issues/946
From their example, the query they're sending is:
{
"message": {
"query_graph": {
"edges": {
"e0": {
"knowledge_type": "inferred",
"object": "un",
"predicates": [
"biolink:related_to"
],
"subject": "sn"
}
},
"nodes": {
"sn": {
"categories": [
"biolink:DiseaseOrPhenotypicFeature",
"biolink:PhenotypicFeature",
"biolink:Disease"
],
"ids": [
"MONDO:0005180"
],
"is_set": false,
"set_interpretation": "BATCH"
},
"un": {
"categories": [
"biolink:NamedThing"
],
"is_set": true,
"set_interpretation": "BATCH"
}
}
}
},
"submitter": "infores:arax"
}
i tried these queries on our locally deployed services, and i don't get the error. without access to the docker containers to see the errors, i can't fix this.
@micheldumontier This seems to be better, but not fully resolved yet.
This query still produces the 500 error, but at least it does so within a couple seconds (not 30 seconds anymore):
{
"message": {
"query_graph": {
"edges": {
"t_edge": {
"knowledge_type": "lookup",
"object": "on",
"predicates": [
"biolink:treats"
],
"subject": "sn"
}
},
"nodes": {
"on": {
"categories": [
"biolink:DiseaseOrPhenotypicFeature"
],
"ids": [
"MONDO:0008383"
]
},
"sn": {
"categories": [
"biolink:ChemicalEntity"
]
}
}
}
},
"submitter": "infores:arax"
}
The same query with ID MONDO:0005180
now returns 200 OK status response.
Will message you with the log file in Slack
I ran a query in UI-Test for what drugs may treat rheuamtoid arthritis to check ARAX's interaction with Knowledge Collaboratory.
Test run from UI: https://ui.test.transltr.io/main/results?l=Rheumatoid%20Arthritis&i=MONDO:0008383&t=0&r=0&q=6909142a-5150-42e9-aeef-523ee7cf6d10
Here are the specific results from ARAX: https://arax.ncats.io/?r=7a6a3b30-78e6-4a6a-8f9b-a2a5ae1ba613
Results from ARAX UI show that Knowledge Collab responded with HTTP error 500.
ARAX UI says this is the query sent to Knowledge Collab:
I sent that query directly to Knowledge Collab in ITRB-Test and can replicate the 500 error.
After testing several variations of the query, it seems like it's the inclusion of
biolink:DiseaseOrPhenotypicFeature
that induces the 500 error. Removing justbiolink:DiseaseOrPhenotypicFeature
allows Knowledge Collab to return a successful response, e.g.,:Conversely, having only
biolink:DiseaesOrPhenotypicFeature
causes the error.