Weird FET warning in message output. Possible bug.

[finnagin]

In this query: https://arax.ncats.io/?r=38025

We get the following message:
2022-03-10T21:45:07.679701 WARNING: Most of edges between the subject node with qnode key n00 and object node with qnode key n01 are from RTX-KG2 rather than RTX-KG2. But we can't access the total number of nodes with specific node type from RTX-KG2, so RTX-KG2 was still used to calcualte Fisher's exact test.

Seems like FET may not be noticing that RTX-KG2 is the same as RTX-KG2. Maybe there is white space in the string?

[finnagin]

The original input json is as follows:

{
  "workflow": [
    {
      "id": "fill"
    },
    {
      "id": "overlay_compute_ngd",
      "parameters": {
        "virtual_relation_label": "NGD1",
        "qnode_keys": [
          "n00",
          "n01"
        ]
      }
    },
    {
      "id": "overlay_compute_ngd",
      "parameters": {
        "virtual_relation_label": "NGD2",
        "qnode_keys": [
          "n01",
          "n02"
        ]
      }
    },
    {
      "id": "overlay_fisher_exact_test",
      "parameters": {
        "subject_qnode_key": "n00",
        "object_qnode_key": "n01",
        "virtual_relation_label": "FET1"
      }
    },
    {
      "id": "overlay_fisher_exact_test",
      "parameters": {
        "subject_qnode_key": "n01",
        "object_qnode_key": "n02",
        "virtual_relation_label": "FET2"
      }
    },
    {
      "id": "complete_results"
    },
    {
      "id": "score"
    },
    {
      "id": "sort_results_score",
      "parameters": {
        "ascending_or_descending": "descending"
      }
    }
  ],
  "message": {
    "query_graph": {
      "edges": {
        "e00": {
          "subject": "n00",
          "object": "n01",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e01": {
          "subject": "n01",
          "object": "n02",
          "predicates": [
            "biolink:related_to"
          ]
        }
      },
      "nodes": {
        "n00": {
          "ids": [
            "PUBCHEM.COMPOUND:644073"
          ],
          "categories": [
            "biolink:ChemicalEntity"
          ]
        },
        "n01": {
          "categories": [
            "biolink:NamedThing"
          ]
        },
        "n02": {
          "ids": [
            "HP:0000217"
          ],
          "categories": [
            "biolink:DiseaseOrPhenotypicFeature"
          ]
        }
      }
    }
  }
}

[chunyuma]

Hi @finnagin, this should not be a bug. I let the FET script print out this warning to make us realize that there is more than one knowledge source between n00 and n01. However, most of the edges are still from RTX-KG2c so it should be fine to use infores:rtx-kg2 was still used to calculate Fisher's exact test.

This warning message might make people feel confused. I have changed it to There is more than one knowledge source for the edges between the subject node with qnode key {subject_qnode_key} and object node with qnode key {object_qnode_key} and most of them are from {kp}. The infores:rtx-kg2 is still used to calculate Fisher's exact test.

[finnagin]

Ah that makes sense. Thanks @chunyuma !