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Fisher exact test doesn't infer node category

Open dkoslicki opened this issue 3 years ago • 17 comments

For this query:

add_qnode(id=MONDO:0001475, key=n0)
add_qnode(category=biolink:Protein, key=n1, is_set=true)
add_qedge(subject=n0, object=n1, key=e0)
add_qnode(category=[biolink:Drug], key=n2)
add_qedge(subject=n1, object=n2, key=e1)
expand(edge_key=e0)
expand(edge_key=e1)
overlay(action=fisher_exact_test,subject_qnode_key=n0,virtual_relation_label=F1,object_qnode_key=n1,filter_type=top_n,value=50)
overlay(action=fisher_exact_test,subject_qnode_key=n1,virtual_relation_label=F2,object_qnode_key=n2,filter_type=top_n,value=50)
overlay(action=compute_ngd, virtual_relation_label=N2, subject_qnode_key=n0, object_qnode_key=n2)
overlay(action=predict_drug_treats_disease, virtual_relation_label=P1, subject_qnode_key=n2, object_qnode_key=n0)
resultify()
filter_results(action=limit_number_of_results, max_results=30)

I get the following error: 2021-04-21T21:00:21.421021 INFO: Performing Fisher's Exact Test to add p-value to edge attribute of virtual edge 2021-04-21T21:00:21.843015 ERROR: [UnknownError] Subject node with qnode key n0 was set to None in Query Graph. Please specify the node type

Even though the category wasn't specified, it really should infer it from the preferred category.

dkoslicki avatar Apr 21 '21 21:04 dkoslicki