Query ran forever and failed

[karafecho]

This issue is to report that the following query ran forever (well, at least 30 min) and then failed. Note that I was attempting to replicate results from David W., so I wouldn't have expected a failed response.

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "name": "PPARA",
          "categories": [
            "biolink:Gene",
            "biolink:BiologicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:GeneOrGeneProduct",
            "biolink:GenomicEntity",
            "biolink:ChemicalEntityOrGeneOrGeneProduct",
            "biolink:PhysicalEssence",
            "biolink:OntologyClass",
            "biolink:ThingWithTaxon",
            "biolink:PhysicalEssenceOrOccurrent",
            "biolink:MacromolecularMachineMixin",
            "biolink:Protein",
            "biolink:Polypeptide",
            "biolink:GeneProductMixin",
            "biolink:ChemicalEntityOrProteinOrPolypeptide"
          ],
          "ids": [
            "NCBIGene:5465"
          ]
        },
        "n1": {
          "categories": [
            "biolink:Gene"
          ],
          "name": "Gene"
        },
        "n2": {
          "name": "Hepatic fibrosis",
          "categories": [
            "biolink:PhenotypicFeature",
            "biolink:DiseaseOrPhenotypicFeature",
            "biolink:BiologicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:ThingWithTaxon"
          ],
          "ids": [
            "HP:0001395"
          ]
        },
        "n3": {
          "categories": [
            "biolink:DiseaseOrPhenotypicFeature"
          ],
          "name": "Disease Or Phenotypic Feature"
        }
      },
      "edges": {
        "e0": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e1": {
          "subject": "n1",
          "object": "n2",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e2": {
          "subject": "n1",
          "object": "n3",
          "predicates": [
            "biolink:related_to"
          ]
        }
      }
    }
  }
}

[karafecho]

I'll add that I did not receive any sort of error message; rather, the query just stopped running and returned to the "submit query" state. I believe I posted a ticket about this issue a while back.

[karafecho]

Same behavior with this query, which ran for hours and then failed without any sort of error message:

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "name": "Clofibric acid",
          "categories": [
            "biolink:SmallMolecule",
            "biolink:MolecularEntity",
            "biolink:ChemicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:PhysicalEssence",
            "biolink:ChemicalOrDrugOrTreatment",
            "biolink:ChemicalEntityOrGeneOrGeneProduct",
            "biolink:ChemicalEntityOrProteinOrPolypeptide",
            "biolink:PhysicalEssenceOrOccurrent"
          ],
          "ids": [
            "PUBCHEM.COMPOUND:2797"
          ]
        },
        "n1": {
          "name": "PPARA",
          "categories": [
            "biolink:Gene",
            "biolink:BiologicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:GeneOrGeneProduct",
            "biolink:GenomicEntity",
            "biolink:ChemicalEntityOrGeneOrGeneProduct",
            "biolink:PhysicalEssence",
            "biolink:OntologyClass",
            "biolink:ThingWithTaxon",
            "biolink:PhysicalEssenceOrOccurrent",
            "biolink:MacromolecularMachineMixin",
            "biolink:Protein",
            "biolink:Polypeptide",
            "biolink:GeneProductMixin",
            "biolink:ChemicalEntityOrProteinOrPolypeptide"
          ],
          "ids": [
            "NCBIGene:5465"
          ]
        },
        "n2": {
          "categories": [
            "biolink:NamedThing"
          ],
          "name": "Named Thing"
        },
        "n3": {
          "name": "Hepatic fibrosis",
          "categories": [
            "biolink:PhenotypicFeature",
            "biolink:DiseaseOrPhenotypicFeature",
            "biolink:BiologicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:ThingWithTaxon"
          ],
          "ids": [
            "HP:0001395"
          ]
        }
      },
      "edges": {
        "e0": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e1": {
          "subject": "n1",
          "object": "n2",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e2": {
          "subject": "n2",
          "object": "n3",
          "predicates": [
            "biolink:related_to"
          ]
        }
      }
    }
  }
}

[cbizon]

@karafecho we made some updates towards the end of 2023. I wonder if you've continued to see this kind of problem in the last few months?

[karafecho]

This issue is due to the issue noted in #184; it's just that users do not always see the error as it pops up only briefly. I feel like I've seen the issue recently, but I will monitor and post an update if and when the issue arises again.

[EvanDietzMorris]

I think we have two issues when this occurs: 1 - the error message stinks, this is almost certainly just a time out 2 - why are we timing out?

for 1 it would probably be fairly straightforward for the UI to give a better error message, but there's currently not a great way to tell (in the UI) if the time out occured in neo4j, plater, or robokop-ara

[karafecho]

Closing, see consolidated issue in #215.