Unsecret error Workflow A.5

[vgardner-renci]

https://arax.ncats.io/?source=ARS&id=df3f226a-571a-4219-ba5e-a37b7040ee18

No predicates or categories, CURIE on subject

[vgardner-renci]

{
  "callback": "http://0.0.0.0:8000/ars/api/messages/4d831953-06d0-475f-836a-ebf1293fe968",
  "logs": [
    {
      "level": "INFO",
      "message": "ARS info: Field: 'QNode/categories' must be array of CURIESs (TRAPI 1.1)."
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Server: nginx"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Date: Thu, 15 Jul 2021 16:16:38 GMT"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Content-Type: text/plain;charset=utf-8"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Content-Length: 63"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Connection: keep-alive"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.Last-Modified: Thu, 15 Jul 2021 16:16:38 GMT"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.reason: Bad Request"
    },
    {
      "level": "INFO",
      "message": "ARS info: tr_ars.url: https://unsecret.ncats.io/query"
    }
  ],
  "max_results": 100,
  "message": {
    "query_graph": {
      "edges": {
        "e01": {
          "object": "n1",
          "subject": "n0"
        }
      },
      "nodes": {
        "n0": {
          "categories": [
            "biolink:Gene"
          ],
          "ids": [
            "NCBIGene:23221"
          ]
        },
        "n1": {}
      }
    }
  },
  "validation_result": {
    "message": "Returned response is not TRAPI: Field: 'QNode/categories' must be array of CURIESs (TRAPI 1.1).",
    "size": "1 kB",
    "status": "NA",
    "version": "1.1.1"
  }
}

[tursynay]

Current TRAPI server expects array of CURIEs but it gets a single CURIEs. TRAPI allows single CURIEs, Will need to update the code to accommodate for that. There maybe parsing issue as well. Revisit next week.

[webyrd]

I was able to get the error trace, below. Looks like our TRAPI server is treating '#f' (the 'false' value in Racket) as an array of CURIEs. I need to track down why #f is coming from, and also ensure the code checks for extraneous '#f' values.

(base) webyrd@Williams-MBP medikanren2 % racket server.rkt
loading configuration defaults: /Users/webyrd/github/mediKanren/medikanren2/config.defaults.scm
loading configuration overrides: /Users/webyrd/github/mediKanren/medikanren2/config.scm
checking for index /Users/webyrd/github/mediKanren/medikanren2/data/semmed/cprop/concept-name-index.bytes
checking for index /Users/webyrd/github/mediKanren/medikanren2/data/rtx2/20210204/cprop/concept-name-index.bytes
loading configuration defaults: /Users/webyrd/github/mediKanren/medikanren2/config.defaults.scm
loading configuration overrides: /Users/webyrd/github/mediKanren/medikanren2/config.scm
Your Web application is running at http://localhost:8384.
Stop this program at any time to terminate the Web Server.
cpu time: 9 real time: 36374 gc time: 0
cpu time: 6 real time: 97 gc time: 0
cpu time: 19 real time: 36476 gc time: 0
2021-07-22T11:44:37    1626968641    INFO       Broad response:
#"HTTP/1.1 200 OK"

2021-07-22T11:44:37    1626968641    INFO       Headers: (#"Server: nginx" #"Date: Thu, 22 Jul 2021 15:44:37 GMT" #"Content-Type: application/json" #"Content-Length: 98869" #"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")

2021-07-22T11:44:37    1626968641    INFO       Broad result size: 101

2021-07-22T11:44:37    1626968641    INFO       Query received: {"query_graph":{"edges":{"e01":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:Gene"],"ids":["NCBIGene:23221"]},"n1":{}}}}
2021-07-22T11:44:38    1626968641    INFO       Subclasses/synonyms of ("NCBIGene:23221") [cpu time: 813 real time: 822]: ("NCBIGene:23221" "ENSEMBL:ENSG00000008853" "OMIM:607352" "UniProtKB:Q9BYZ6" "HGNC:18756")
Field: 'QNode/categories' must be array of CURIESs (TRAPI 1.1).
Given #f

  context...:
   /Users/webyrd/github/mediKanren/medikanren2/trapi.rkt:125:4: loop
   /Users/webyrd/github/mediKanren/medikanren2/dbk/dbk/syntax.rkt:75:33
   /Users/webyrd/github/mediKanren/medikanren2/dbk/dbk/constraint.rkt:792:19
   /Users/webyrd/github/mediKanren/medikanren2/dbk/dbk/constraint.rkt:783:0: bis:bind
   /Users/webyrd/github/mediKanren/medikanren2/dbk/dbk/constraint.rkt:785:24
   /Users/webyrd/github/mediKanren/medikanren2/dbk/dbk/stream.rkt:79:19
   /Users/webyrd/github/mediKanren/medikanren2/dbk/dbk/stream.rkt:52:19
   /Users/webyrd/github/mediKanren/medikanren2/dbk/dbk/stream.rkt:35:0: s-take/steps
   /Users/webyrd/github/mediKanren/medikanren2/trapi.rkt:80:0: trapi-response
   /Users/webyrd/github/mediKanren/medikanren2/server.rkt:309:6

[webyrd]

Traced the error to an unhandled case in which neither categories nor ids (CURIEs) are specified for a node. Working on implementing the missing case.

[webyrd]

I added the missing case, tested it locally on my machine, checked in the code, and pushed the updated code to our new ITRB CI/CD endpoint:

https://medikanren-trapi.ci.transltr.io

We should now handle this workflow, and probably others that were returning errors.

[webyrd]

Hmmm...I'm running into an intermittent error on the ITRB CI/CD endpoint, but not locally. Investigating...

[webyrd]

Got ITRB to fix the problem of multiple Kubernetes pods with different versions of code being run at the same time. Our new endpoint's code should fix this problem:

https://medikanren-trapi.ci.transltr.io

[webyrd]

Returns answers cleanly when I run the query now.