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NCATSTranslator / minihackathons

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Unsecret error on Workflow D.1 query #88

Open vgardner-renci opened 3 years ago

vgardner-renci commented 3 years ago

https://arax.ncats.io/?source=ARS&id=580dfdb6-9e6c-4ac0-a937-ef184363f04f

image

vgardner-renci commented 3 years ago 

{
  "callback": "http://localhost:8000/ars/api/messages/79388b74-1229-4fa9-ba09-13f6d5fbd103",
  "message": {
    "query_graph": {
      "edges": {
        "e00": {
          "object": "n01",
          "subject": "n00"
        },
        "e01": {
          "object": "n02",
          "subject": "n01"
        }
      },
      "nodes": {
        "n00": {
          "categories": [
            "biolink:Disease"
          ],
          "ids": [
            "DOID:14330"
          ]
        },
        "n01": {
          "categories": [
            "biolink:NamedThing"
          ]
        },
        "n02": {
          "categories": [
            "biolink:Disease"
          ],
          "ids": [
            "DOID:8778"
          ]
        }
      }
    }
  },
  "validation_result": {
    "message": "",
    "size": "1 kB",
    "status": "PASS",
    "version": "1.1.1"
  }
}```
tursynay commented 3 years ago

Will will treat this as a bug

vgardner-renci commented 3 years ago

@webyrd request for update

webyrd commented 3 years ago

Will triage by August 12, 2021.

webyrd commented 3 years ago

Still tracking this error down. I'm not sure what is causing it.

I will track it down and fix it by the relay.

2021-08-26T09:15:17 1629968717 ERROR Error: #(struct:exn:fail:resource with-limit: out of time # ...)

making api-query call to url:

"https://translator.broadinstitute.org/molepro/trapi/v1.1/query" cpu time: 8 real time: 82 gc time: 0 cpu time: 0 real time: 0 gc time: 0 status:

"HTTP/1.1 501 NOT IMPLEMENTED"

!!!!!! unexpected non-OK status returned from "https://translator.broadinstitute.org/molepro/trapi/v1.1/query": (#"HTTP/1.1 501 NOT IMPLEMENTED" (#"Server: nginx"

"Date: Thu, 26 Aug 2021 09:15:17 GMT"

"Content-Type: application/json"

"Content-Length: 130"

"Connection: close"

"Access-Control-Allow-Origin: *"

"Access-Control-Allow-Methods: GET, POST, OPTIONS"

"Access-Control-Allow-Headers: DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range"

"Access-Control-Expose-Headers: Content-Length,Content-Range")

"{\n \"detail\": \"Multi-edges queries not yet implemented\",\n \"status\": 501,\n \"title\": \"Not Implemented\",\n \"type\": \"about:blank\"\n}\n") cpu time: 9 real time: 82 gc time: 0 "Broad response:\n#\"HTTP/1.1 501 NOT IMPLEMENTED\"\n" 2021-08-26T09:15:17 1629969317 INFO Broad response:

"HTTP/1.1 501 NOT IMPLEMENTED"

"Headers: (#\"Server: nginx\" #\"Date: Thu, 26 Aug 2021 09:15:17 GMT\" #\"Content-Type: application/json\" #\"Content-Length: 130\" #\"Connection: close\" #\"Access-Control-Allow-Origin: \" #\"Access-Control-Allow-Methods: GET, POST, OPTIONS\" #\"Access-Control-Allow-Headers: DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range\" #\"Access-Control-Expose-Headers: Content-Length,Content-Range\")\n" 2021-08-26T09:15:17 1629969317 INFO Headers: (#"Server: nginx" #"Date: Thu, 26 Aug 2021 09:15:17 GMT" #"Content-Type: application/json" #"Content-Length: 130" #"Connection: close" #"Access-Control-Allow-Origin: " #"Access-Control-Allow-Methods: GET, POST, OPTIONS" #"Access-Control-Allow-Headers: DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range" #"Access-Control-Expose-Headers: Content-Length,Content-Range")

"Broad result size: 0\n" 2021-08-26T09:15:17 1629969317 INFO Broad result size: 0

"Query received: {\"query_graph\":{\"edges\":{\"e00\":{\"object\":\"n01\",\"subject\":\"n00\"},\"e01\":{\"object\":\"n02\",\"subject\":\"n01\"}},\"nodes\":{\"n00\":{\"categories\":[\"biolink:Disease\"],\"ids\":[\"DOID:14330\"]},\"n01\":{\"categories\":[\"biolink:NamedThing\"]},\"n02\":{\"categories\":[\"biolink:Disease\"],\"ids\":[\"DOID:8778\"]}}}}" 2021-08-26T09:15:17 1629969317 INFO Query received: {"query_graph":{"edges":{"e00":{"object":"n01","subject":"n00"},"e01":{"object":"n02","subject":"n01"}},"nodes":{"n00":{"categories":["biolink:Disease"],"ids":["DOID:14330"]},"n01":{"categories":["biolink:NamedThing"]},"n02":{"categories":["biolink:Disease"],"ids":["DOID:8778"]}}}} entering trapi-nodes loop...

id: n01 n: #hasheq((categories . ("biolink:NamedThing"))) curie (deprecated): #f curies: #f category (deprecated): #f categories: ("biolink:NamedThing") constraints: () is-set?: #f reasoning?: #f

2021-08-26T09:15:17 1629969317 INFO Subclasses of ("biolink:NamedThing") [cpu time: 0 real time: 0]: ("biolink:GeneFamily" "biolink:BiologicalProcessOrActivity" "biolink:EpidemiologicalOutcome" "biolink:OrganismTaxon" "biolink:GenomicEntity" "biolink:Genotype" "biolink:AnatomicalEntity" "biolink:Cell" "biolink:PlanetaryEntity" "biolink:Haplotype" "biolink:EnvironmentalExposure" "biolink:DataSet" "biolink:MacromolecularComplex" "biolink:ChemicalExposure" "biolink:EnvironmentalFeature" "biolink:CellLine" "biolink:DataFile" "biolink:Exon" "biolink:BioticExposure" "biolink:MacromolecularMachine" "biolink:CodingSequence" "biolink:IndividualOrganism" "biolink:SocioeconomicOutcome" "biolink:DrugExposure" "biolink:ClinicalEntity" "biolink:LifeStage" "biolink:Device" "biolink:GeneOrGeneProduct" "biolink:ClinicalTrial" "biolink:EvidenceType" "biolink:MolecularActivity" "biolink:DataSetSummary" "biolink:PathologicalProcess" "biolink:Behavior" "biolink:MaterialSample" "biolink:PopulationOfIndividualOrganisms" "biolink:BehavioralOutcome" "biolink:StudyPopulation" "biolink:BiologicalProcess" "biolink:ChemicalSubstance" "biolink:SequenceVariant" "biolink:RNAProduct" "biolink:ClinicalIntervention" "biolink:ComplexChemicalExposure" "biolink:GeographicExposure" "biolink:PhysicalEntity" "biolink:PhysiologicalProcess" "biolink:MortalityOutcome" "biolink:Metabolite" "biolink:ProcessedMaterial" "biolink:Treatment" "biolink:Transcript" "biolink:GeographicLocationAtTime" "biolink:GeneProduct" "biolink:DiseaseOrPhenotypicFeature" "biolink:MolecularEntity" "biolink:InformationContentEntity" "biolink:DiseaseOrPhenotypicFeatureExposure" "biolink:BehavioralExposure" "biolink:Book" "biolink:CellularComponent" "biolink:Carbohydrate" "biolink:OntologyClass" "biolink:AdministrativeEntity" "biolink:TaxonomicRank" "biolink:BiologicalEntity" "biolink:Article" "biolink:PhenotypicFeature" "biolink:Procedure" "biolink:SiRNA" "biolink:OrganismalEntity" "biolink:NoncodingRNAProduct" "biolink:Hospitalization" "biolink:DrugToGeneInteractionExposure" "biolink:Phenomenon" "biolink:Cohort" "biolink:Drug" "biolink:ProteinIsoform" "biolink:DistributionLevel" "biolink:Snv" "biolink:SourceFile" "biolink:Genome" "biolink:MicroRNA" "biolink:ClinicalFinding" "biolink:Death" "biolink:RNAProductIsoform" "biolink:Agent" "biolink:SocioeconomicExposure" "biolink:Publication" "biolink:GrossAnatomicalStructure" "biolink:DataSetVersion" "biolink:Disease" "biolink:EnvironmentalProcess" "biolink:RelationshipType" "biolink:GeneOntologyClass" "biolink:GenomicBackgroundExposure" "biolink:Food" "biolink:NamedThing" "biolink:Pathway" "biolink:Protein" "biolink:ConfidenceLevel" "biolink:Gene" "biolink:BookChapter" "biolink:DiseaseOrPhenotypicFeatureOutcome" "biolink:Activity" "biolink:GeographicLocation" "biolink:ReagentTargetedGene" "biolink:HospitalizationOutcome" "biolink:Serial" "biolink:Case")

id: n00 n: #hasheq((categories . ("biolink:Disease")) (ids . ("DOID:14330"))) curie (deprecated): #f curies: ("DOID:14330") category (deprecated): #f categories: ("biolink:Disease") constraints: () is-set?: #f reasoning?: #f

2021-08-26T09:15:17 1629969317 INFO Subclasses/synonyms of ("DOID:14330") [cpu time: 0 real time: 0]: ("DOID:0060367" "DOID:0060368" "DOID:0060369" "DOID:0060370" "DOID:0060372" "DOID:0060371" "DOID:0111251" "DOID:0111250" "DOID:0060898" "DOID:0060897" "DOID:0060896" "DOID:0080504" "DOID:0060891" "DOID:0060895" "DOID:0060894" "DOID:0060893" "DOID:0060892" "DOID:14330" "DOID:0060900" "DOID:0060556" "MESH:C566823" "OMIM:168601" "UMLS:C3489791" "MONDO:0008200" "OMIM:600116" "UMLS:C1868675" "MONDO:0010820" "MESH:C565276" "OMIM:605909" "MONDO:0011613" "MESH:C565238" "OMIM:606324" "UMLS:C1853445" "MONDO:0011658" "MESH:C538104" "OMIM:260300" "ORPHANET:171695" "SNOMEDCT:783012006" "UMLS:C1850100" "MONDO:0009830" "OMIM:607060" "UMLS:C1846862" "MONDO:0011764" "OMIM:615530" "UMLS:C3809824" "MONDO:0014233" "OMIM:614203" "UMLS:C3280133" "MONDO:0013625" "OMIM:616840" "UMLS:C4225186" "MONDO:0014796" "OMIM:615528" "UMLS:C3809811" "MONDO:0014231" "MESH:C565324" "OMIM:605543" "UMLS:C1854182" "MONDO:0011562" "ORPHANET:2828" "SNOMEDCT:715345007" "UMLS:C4275179" "MONDO:0017279" "MONDO:0000828" "ORPHANET:411602" "SNOMEDCT:716662004" "UMLS:C4274355" "MONDO:0018466" "EFO:0002508" "MEDDRA:10061536" "MESH:D010300" "NCIT:C26845" "SNOMEDCT:49049000" "UMLS:C0030567" "UMLS:C0853008" "UMLS:C4049471" "MONDO:0005180" "MESH:C567844" "OMIM:612953" "ORPHANET:199351" "SNOMEDCT:720466001" "UMLS:C2751842" "MONDO:0013060" "MESH:C537177" "OMIM:606693" "ORPHANET:306674" "SNOMEDCT:723992000" "UMLS:C1847640" "MONDO:0011706")

id: n02 n: #hasheq((categories . ("biolink:Disease")) (ids . ("DOID:8778"))) curie (deprecated): #f curies: ("DOID:8778") category (deprecated): #f categories: ("biolink:Disease") constraints: () is-set?: #f reasoning?: #f

2021-08-26T09:15:17 1629969317 INFO Subclasses/synonyms of ("DOID:8778") [cpu time: 0 real time: 0]: ("DOID:0060192" "DOID:0060191" "DOID:0060190" "DOID:0060188" "DOID:0060189" "DOID:8778" "EFO:0005622" "NCIT:C35211" "MONDO:0005532" "MONDO:0000710" "EFO:0005624" "UMLS:C0949272" "MONDO:0005534" "MONDO:0000708" "MEDDRA:10014866" "MESH:D007079" "NCIT:C35329" "NCIT:C78613" "SNOMEDCT:38106008" "SNOMEDCT:52457000" "SNOMEDCT:80805005" "UMLS:C0020877" "UMLS:C0235775" "UMLS:C0267380" "UMLS:C0341276" "UMLS:C0860173" "UMLS:C0860257" "UMLS:C1698626" "UMLS:C4524144" "MONDO:0000709" "EFO:0000384" "NCIT:C2965" "SNOMEDCT:7620006" "UMLS:CN043071" "MONDO:0005011")

webyrd commented 3 years ago

This query is a true server-side timeout after 10 minutes. On production, the client will currently timeout after 60 seconds, due to a Kubernetes configuration problem that we are trying to track down with ITRB.

We are investigating how to make this query faster.