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NCATSTranslator / minihackathons

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Textmining error on Workflow A.9 #161

Closed vgardner-renci closed 3 years ago

vgardner-renci commented 3 years ago

https://arax.ncats.io/?source=ARS&id=1bb22918-c6f3-4aa8-bfcd-b82af2c310ef

EGFR

image

vgardner-renci commented 3 years ago 

{
  "callback": "http://0.0.0.0:8000/ars/api/messages/8477f662-bdbf-4090-a6f5-2558f9c113fe",
  "max_results": 100,
  "message": {
    "query_graph": {
      "edges": {
        "e0": {
          "object": "n1",
          "predicates": [
            "biolink:negatively_regulates_entity_to_entity",
            "biolink:entity_negatively_regulates_entity"
          ],
          "subject": "n0"
        }
      },
      "nodes": {
        "n0": {
          "categories": [
            "biolink:ChemicalSubstance"
          ],
          "name": "Chemical Substance"
        },
        "n1": {
          "ids": [
            "PR:000006933"
          ],
          "name": "EGFR"
        }
      }
    }
  },
  "validation_result": {
    "message": "",
    "size": "1 kB",
    "status": "PASS",
    "version": "1.1.1"
  }
}
bill-baumgartner commented 3 years ago

This error would be better classified as a timeout. There was an issue last week with BTE timeouts, and since Text Mining Provider is hosted by Service Provider I think the timeouts affected our service as well. They appear to be resolved at this point.

Question: would it be worth having the ARS report timeouts as something different than an error?

I believe this same comment should also apply to the other Text Mining Provider issues from last week:

tursynay commented 3 years ago

Need to differentiate between different 400 and 500 errors, and timeouts, more text on what type of errors occuring

vgardner-renci commented 3 years ago

@bill-baumgartner rerunning the same ARAX a week later yields same result on TextMining.

bill-baumgartner commented 3 years ago

@vgardner-renci Is there a PK for the most recent run? Thanks!

vgardner-renci commented 3 years ago

I'm using the PK embedded in the ARAX link in the first comment. 1bb22918-c6f3-4aa8-bfcd-b82af2c310ef

bill-baumgartner commented 3 years ago

Ok, thanks. I could be wrong but I think there should be a new PK each time a query is run. Also, I think the ARS is down for maintenance today so I'm not sure we can run queries.

vgardner-renci commented 3 years ago

Textmining returning results

https://arax.ncats.io/index.html?source=ARS&id=f96dd2dc-4f43-4115-8d35-f826be6f07d6

image