search

NCATSTranslator / minihackathons

MIT License
5 stars 5 forks source link

Unsecret no results on Workflow C.1 #37

Open vgardner-renci opened 3 years ago

vgardner-renci commented 3 years ago

@webyrd request for update

vgardner-renci commented 3 years ago

@webyrd @jeffhhk request for update

vgardner-renci commented 3 years ago

@webyrd @jeffhhk request for update

tursynay commented 3 years ago

Either returning error or zero answers. Question from Will: what was going on with the query? Is it very complicated or there was missing data?

Looks like ARS did not send any results when the PK was rerun. David is running the PK again

dkoslicki commented 3 years ago

Fresh submission to the ARS: https://arax.ncats.io/?source=ARS&id=5f15efed-bb8c-4431-a4dd-9cf63286395c image

colleenXu commented 3 years ago

Note: it looks like the ARS's PK was https://ars-dev.transltr.io/ars/api/messages/9434d84a-0977-41db-8fd4-94292b866b97?trace=y. One can see that some ARAs returned results, and there was an "error" for Unsecret.

vgardner-renci commented 3 years ago 

{
  "callback": "http://0.0.0.0:8000/ars/api/messages/4cd7d331-d806-492e-9fe9-c601fb81ff8f",
  "max_results": 100,
  "message": {
    "query_graph": {
      "edges": {
        "e00": {
          "object": "n01",
          "predicates": [
            "biolink:related_to"
          ],
          "subject": "n00"
        }
      },
      "nodes": {
        "n00": {
          "categories": [
            "biolink:ChemicalSubstance"
          ]
        },
        "n01": {
          "categories": [
            "biolink:Disease"
          ],
          "ids": [
            "MONDO:0005301"
          ]
        }
      }
    }
  },
  "validation_result": {
    "message": "",
    "size": "1 kB",
    "status": "PASS",
    "version": "1.1.1"
  }
}
vgardner-renci commented 3 years ago

@webyrd timeline for resolution?

tursynay commented 3 years ago

Two version of the server running, and sometimes (50%), the wrong server is hit, will continue fixing the issue

webyrd commented 3 years ago

We worked with ITRB to fix the deployment issue on our new endpoint. Will triage by August 12, 2021.

vgardner-renci commented 3 years ago

More recent ARAX results: https://arax.ncats.io/index.html?source=ARS&id=27fe1767-60fd-4ac5-a4ce-a85ca96a2fdc

image


{
  "callback": "http://0.0.0.0:8000/ars/api/messages/ce3d5066-c4b1-4c64-8f79-fcf69791770b",
  "logs": [
    {
      "level": "INFO",
      "message": "ARS info: <html>\r\n<head><title>504 Gateway Time-out</title></head>\r\n<body>\r\n<center><h1>504 Gateway Time-out</h1></center>\r\n</body>\r\n</html>\r\n"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Server: awselb/2.0"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Date: Wed, 18 Aug 2021 14:36:59 GMT"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Content-Type: text/html"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Content-Length: 132"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Connection: keep-alive"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.reason: Gateway Time-out"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.url: https://medikanren-trapi.ci.transltr.io/query"
    }
  ],
  "message": {
    "query_graph": {
      "edges": {
        "e00": {
          "object": "n01",
          "predicates": [
            "biolink:has_real_world_evidence_of_association_with"
          ],
          "subject": "n00",
          "id": "e00",
          "parentdivnum": 99999,
          "trapiversion": "1.1 (presumed)",
          "source": "n00",
          "target": "n01",
          "type": "biolink:has_real_world_evidence_of_association_with"
        }
      },
      "nodes": {
        "n00": {
          "categories": [
            "biolink:ChemicalEntity"
          ],
          "parentdivnum": 99999,
          "trapiversion": "1.1 (presumed)",
          "fulltextname": "n00",
          "id": "n00",
          "name": "biolink:ChemicalEntitys?"
        },
        "n01": {
          "categories": [
            "biolink:Disease"
          ],
          "ids": [
            "MONDO:0005301"
          ],
          "parentdivnum": 99999,
          "trapiversion": "1.1 (presumed)",
          "fulltextname": "n01",
          "id": "n01",
          "name": "MONDO:0005301"
        }
      }
    }
  },
  "validation_result": {
    "message": "Returned response is not TRAPI: <html>\r\n<head><title>504 Gateway Time-out</title></head>\r\n<body>\r\n<center><h1>504 Gateway Time-out</h1></center>\r\n</body>\r\n</html>\r\n",
    "size": "2 kB",
    "status": "NA",
    "version": "1.1.1"
  },
  "araxui_provider": "ARS",
  "araxui_response": "ce3d5066-c4b1-4c64-8f79-fcf69791770b",
  "schema_version": "1.1 (presumed)"
}
vgardner-renci commented 3 years ago

https://arax.ncats.io/index.html?source=ARS&id=f1a57d6e-f372-401f-90d3-1b1023ed9d44


{
  "description": "Success. 0 results.",
  "logs": [
    {
      "level": "INFO",
      "message": "Query time: 119ms"
    },
    {
      "level": "INFO",
      "message": "MolePro results: 0"
    },
    {
      "level": "INFO",
      "message": "MolePro response status: #\"HTTP/1.1 200 OK\""
    }
  ],
  "message": {
    "knowledge_graph": {
      "edges": {},
      "nodes": {}
    },
    "results": []
  },
  "query_graph": {
    "edges": {
      "e00": {
        "object": "n01",
        "predicates": [
          "biolink:has_real_world_evidence_of_association_with"
        ],
        "subject": "n00"
      }
    },
    "nodes": {
      "n00": {
        "categories": [
          "biolink:ChemicalEntity"
        ]
      },
      "n01": {
        "categories": [
          "biolink:Disease"
        ],
        "ids": [
          "MONDO:0005301"
        ]
      }
    }
  },
  "status": "Success",
  "validation_result": {
    "message": "",
    "n_edges": 0,
    "n_nodes": 0,
    "provenance_summary": {
      "n_sources": 0,
      "predicate_counts": {},
      "provenance_counts": {}
    },
    "size": "1 kB",
    "status": "PASS",
    "version": "1.1.1"
  },
  "araxui_provider": "ARS",
  "araxui_response": "2862c503-69b2-488a-a1ea-1d5a39132bad",
  "schema_version": "1.1 (presumed)"
}
webyrd commented 3 years ago

Still tracking down the cause.

Will fix before relay.

jh111 commented 3 years ago

@webyrd The current results are returning 0 instead of an error. We expect results to be returned by Unsecret Agent from (Multiomics) EHR Risk KP or (COHD) Clinical Data Provider and possibly by Connections Hypothesis Provider (depending on how you rank those results).