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NCATSTranslator / minihackathons

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Unsecret no results in Workflow D.4 query #119

Open vgardner-renci opened 3 years ago

vgardner-renci commented 3 years ago

https://arax.ncats.io/?source=ARS&id=66cf5381-18cc-4756-8cd6-232500d7db8e

image

vgardner-renci commented 3 years ago 

{
  "description": "Success. 0 results.",
  "logs": [
    {
      "level": "INFO",
      "message": "Query time: 54156ms"
    },
    {
      "level": "WARNING",
      "message": "MolePro error: \"Multi-edges queries not yet implemented\""
    },
    {
      "level": "INFO",
      "message": "MolePro response status: #\"HTTP/1.1 501 NOT IMPLEMENTED\""
    }
  ],
  "message": {
    "knowledge_graph": {
      "edges": {},
      "nodes": {}
    },
    "results": []
  },
  "query_graph": {
    "edges": {
      "e00": {
        "object": "n01",
        "subject": "n00"
      },
      "e01": {
        "object": "n02",
        "subject": "n01"
      },
      "e02": {
        "object": "n03",
        "subject": "n02"
      },
      "e03": {
        "object": "n04",
        "subject": "n03"
      }
    },
    "nodes": {
      "n00": {
        "categories": [
          "biolink:ChemicalSubstance"
        ],
        "ids": [
          "DRUGBANK:DB00150"
        ]
      },
      "n01": {
        "categories": [
          "biolink:Protein"
        ]
      },
      "n02": {
        "categories": [
          "biolink:MolecularActivity"
        ]
      },
      "n03": {
        "categories": [
          "biolink:MolecularActivity"
        ]
      },
      "n04": {
        "categories": [
          "biolink:ChemicalSubstance"
        ],
        "ids": [
          "KEGG.COMPOUND:C02700"
        ]
      }
    }
  },
  "status": "Success",
  "validation_result": {
    "message": "",
    "n_edges": 0,
    "n_nodes": 0,
    "size": "2 kB",
    "status": "PASS",
    "version": "1.1.1"
  }
}
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

Is this a legal TRAPI query? Does the query graph not need to appear inside the message?

Our TRAPI server seems to expect query_graph to occur inside of message. Perhaps this is why other ARAs were also having trouble with this query?

hash-ref: no value found for key key: query_graph context...: /local/medikanren2/trapi.rkt:81:0: trapi-response /local/medikanren2/server.rkt:312:6

making api-query call to url:

"https://translator.broadinstitute.org/molepro/trapi/v1.1/query" cpu time: 7 real time: 75 gc time: 0 cpu time: 0 real time: 0 gc time: 0 status:

"HTTP/1.1 500 INTERNAL SERVER ERROR"

!!!!!! unexpected non-OK status returned from "https://translator.broadinstitute.org/molepro/trapi/v1.1/query": (#"HTTP/1.1 500 INTERNAL SERVER ERROR" (#"Server: nginx"

"Date: Thu, 26 Aug 2021 08:39:23 GMT"

"Content-Type: application/problem+json"

"Content-Length: 251"

"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\": \"The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.\",\n \"status\": 500,\n \"title\": \"Internal Server Error\",\n \"type\": \"about:blank\"\n}\n") cpu time: 8 real time: 76 gc time: 0 "Broad response:\n#\"HTTP/1.1 500 INTERNAL SERVER ERROR\"\n" 2021-08-26T08:39:23 1629967163 INFO Broad response:

"HTTP/1.1 500 INTERNAL SERVER ERROR"

"Headers: (#\"Server: nginx\" #\"Date: Thu, 26 Aug 2021 08:39:23 GMT\" #\"Content-Type: application/problem+json\" #\"Content-Length: 251\" #\"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" 2021-08-26T08:39:23 1629967163 INFO Headers: (#"Server: nginx" #"Date: Thu, 26 Aug 2021 08:39:23 GMT" #"Content-Type: application/problem+json" #"Content-Length: 251" #"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" 2021-08-26T08:39:23 1629967163 INFO Broad result size: 0

"Query received: {\"knowledge_graph\":{\"edges\":{},\"nodes\":{}},\"results\":[]}" 2021-08-26T08:39:23 1629967163 INFO Query received: {"knowledge_graph":{"edges":{},"nodes":{}},"results":[]}

tursynay commented 3 years ago

@webyrd will rerun the original query.

vgardner-renci commented 3 years ago

https://arax.ncats.io/?source=ARS&id=f2886569-5ebb-49c3-aa35-a047d40f6d9b


{
  "callback": "http://localhost:8000/ars/api/messages/6fa441d6-83fd-4bc5-b0f1-f8830be55e67",
  "logs": [
    {
      "level": "INFO",
      "message": "ARS info: HTTPSConnectionPool(host='unsecret.ncats.io', port=443): Max retries exceeded with url: /query (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f83af7367b8>: Failed to establish a new connection: [Errno 111] Connection refused',))"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.url: https://unsecret.ncats.io/query"
    }
  ],
  "message": {
    "query_graph": {
      "edges": {
        "e00": {
          "object": "n01",
          "subject": "n00"
        },
        "e01": {
          "object": "n02",
          "subject": "n01"
        },
        "e02": {
          "object": "n03",
          "subject": "n02"
        },
        "e03": {
          "object": "n04",
          "subject": "n03"
        }
      },
      "nodes": {
        "n00": {
          "categories": [
            "biolink:SmallMolecule"
          ],
          "ids": [
            "DRUGBANK:DB00150"
          ]
        },
        "n01": {
          "categories": [
            "biolink:Protein"
          ]
        },
        "n02": {
          "categories": [
            "biolink:MolecularActivity"
          ]
        },
        "n03": {
          "categories": [
            "biolink:MolecularActivity"
          ]
        },
        "n04": {
          "categories": [
            "biolink:SmallMolecule"
          ],
          "ids": [
            "KEGG.COMPOUND:C02700"
          ]
        }
      }
    }
  },
  "validation_result": {
    "message": "Returned response is not TRAPI: HTTPSConnectionPool(host='unsecret.ncats.io', port=443): Max retries exceeded with url: /query (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f83af7367b8>: Failed to establish a new connection: [Errno 111] Connection refused',))",
    "size": "2 kB",
    "status": "NA",
    "version": "1.1.1"
  },
  "araxui_provider": "ARS",
  "araxui_response": "6fa441d6-83fd-4bc5-b0f1-f8830be55e67"
}
vgardner-renci commented 3 years ago

https://arax.ncats.io/?source=ARS&id=d80a01b8-d3e9-4699-b248-b7e1c2c01fa2

tursynay commented 3 years ago

Will said these tickets are being worked on currently