8080 port error

[karafecho]

This issue is to suggest that we prioritize fixing the 8080 port error that seems to show up somewhat randomly, somewhat consistently.

Here's the (fleeting) error message:

And here's an example query, but note that I can provide others:

{
  "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:Gene"
          ],
          "name": "Gene"
        },
        "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"
          ]
        }
      }
    }
  }
}

I think it would be good to fix this issue prior to any upcoming presentations/demos/workshops, e.g., the planned meeting with Scott Auerbach (NIEHS DTT) and his team.

[karafecho]

Also see #195 and #181.

[EvanDietzMorris]

We might want to consolidate these issues. This is essentially the same as #195 and #181

As mentioned in #181 there are really two issues: the error message should be improved for timeouts, and we should try to find the cause of timeouts for queries that we would expect to be faster, but there are a number of reasons why we might see performance variability, and we may not be able to recreate the issue.

This has never had anything to do with the port, that's just part of the aragorn endpoint the UI communicates with.

[karafecho]

Closing, see consolidated issue in #215.