Navigate to query when clicking on a bar

[heralden]

I added a navigate function to the tool API, which is passed as the 6th argument to the tool main function, which can be used like this navigate('query', myQueryObj);, where you'll want myQueryObj to be similar to the object below.

All the Gene ID's will come from the list (I think they're returned from the enrichment call) and the GO term code will be the one clicked.

{
      "model": {
        "name": "genomic"
      },
      "select": [
        "Gene.secondaryIdentifier",
        "Gene.symbol",
        "Gene.primaryIdentifier",
        "Gene.organism.name",
        "Gene.goAnnotation.ontologyTerm.identifier",
        "Gene.goAnnotation.ontologyTerm.name",
        "Gene.goAnnotation.ontologyTerm.parents.identifier",
        "Gene.goAnnotation.ontologyTerm.parents.name"
      ],
      "where": [
        {
          "path": "Gene",
          "op": "IN",
          "code": "A",
          "ids": [
            1007941,
            1009359,
            1010020,
            1069069,
            1085883,
            1092581,
            1103527,
            1117091,
            1126873,
            1128788,
            1141026,
            1172088,
            1177376,
            1194292,
            1234233,
            1243313,
            1245718,
            1259594,
            1264304,
            1284464
          ]
        },
        {
          "path": "Gene.goAnnotation.ontologyTerm.parents.identifier",
          "op": "ONE OF",
          "values": [
            "GO:0001946"
          ]
        }
      ],
      "title": "GO:0001946"
    }

[heralden]

I'm reopening this issue as it wasn't fixed in #11.
I can see that the navigate function is passed from RootContainer, but it doesn't seem to get called anywhere.

[akshatbhargava123]

Hey @uosl , thanks for pointing this out.
I'm not receiving Gene IDs from enrichment call, could you please suggest a way to get them?

[heralden]

Ah, that's too bad.

You can change the query to take a list name instead of a list of gene ID's, and pass in the list name you get from bluegenes.

{
      "model": {
        "name": "genomic"
      },
      "select": [
        "Gene.secondaryIdentifier",
        "Gene.symbol",
        "Gene.primaryIdentifier",
        "Gene.organism.name",
        "Gene.goAnnotation.ontologyTerm.identifier",
        "Gene.goAnnotation.ontologyTerm.name",
        "Gene.goAnnotation.ontologyTerm.parents.identifier",
        "Gene.goAnnotation.ontologyTerm.parents.name"
      ],
     "where": [
        {
          "path": "Gene",
          "op": "IN",
          "value": "esyN demo list", // <-- your list name
          "code": "A"
        },
        {
          "path": "Gene.goAnnotation.ontologyTerm.parents.identifier",
          "op": "ONE OF",
          "values": [
            "GO:0001946" // <-- GO term clicked
          ]
        }
      ],
      "title": "GO:0001946" // <-- GO term clicked
    }

[akshatbhargava123]

@uosl Thanks for the query :)