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

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mugitty
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@mugitty mugitty commented Feb 8, 2024

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

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Has test, so I'm good. I'll leave merge to @dustine32

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Linking to geneontology/go-site#2064

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

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mugitty commented Feb 8, 2024

@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
},

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@mugitty Thanks for confirming. Just wanted to make sure the go-site tests would run successfully.

@mugitty mugitty merged commit 57adf9c into master Feb 8, 2024
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@mugitty mugitty deleted the go-site-2064-gorule-0000001-pipes-not-allowed-in-gene-symbol branch May 6, 2024 17:45
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3 participants