For #2064 - Added check for pipe in gene symbol

biolink / ontobio

python library for working with ontologies and ontology associations

https://ontobio.readthedocs.io/en/latest/

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For #2064 - Added check for pipe in gene symbol #666

Closed mugitty closed 4 months ago

mugitty commented 4 months ago

For #2064 - gorule-0000001 check for pipe in gene symbol

dustine32 commented 4 months ago

Linking to https://github.com/geneontology/go-site/issues/2064

dustine32 commented 4 months ago

Yep @mugitty this looks good to me. Have you confirmed it works with @pgaudet's new test line here?: https://github.com/geneontology/go-site/pull/2174

mugitty commented 4 months ago

@dustine32 , Thanks for checking. I ran it against the errors.gaf file. Output in errors json file for pipe in gene symbol is as follows: { "level": "ERROR", "line": "UniProtKB\tA1B2F4\tazt|D\tacts_upstream_of_or_within_negative_effect\tGO:0005634\tPMID:26468286\tIDA\t\tC\tGORULE_TEST:0000001-18\t\tprotein\ttaxon:318586\t20230427\tPomBase\t", "type": "Invalid symbol", "message": "Pipes are not allowed in gene symbol", "obj": "GO:0005634", "taxon": "taxon:318586", "rule": 1 },