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Missing category for FET expand

Open dkoslicki opened this issue 2 years ago • 15 comments

For this query:

add_qnode(ids=[UMLS:C0220914,CHEMBL.COMPOUND:CHEMBL2108117,HMDB:HMDB0304735], categories=[biolink:ChemicalEntity], key=n0)
add_qnode(key=n1)
add_qedge(key=e0,subject=n0,object=n1,predicates=biolink:affects)
expand()
overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=n0, object_qnode_key=n1)
overlay(action=fisher_exact_test,subject_qnode_key=n0,virtual_relation_label=F1,object_qnode_key=n1)
resultify()
filter_results(action=limit_number_of_results, max_results=100)

I am getting the following error: Object node with qnode key n1 was set to None in Query Graph. Please specify the node type. This is likely the FET step in expand not liking the generic middle node. Would be nice to find some way around this (say, for each returned n1, when FET is used, take the category of that current n1).

dkoslicki avatar Apr 05 '22 16:04 dkoslicki