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biocodellc / ontology-data-pipeline

A high-throughput ontology-based pipeline for data integration
BSD 3-Clause "New" or "Revised" License
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Strange quoting causes reasoner to crash #43

Open jdeck88 opened 5 years ago

jdeck88 commented 5 years ago

Incoming records with scientificName like: """Hippo"" sp." technically is a valid # of quotes but reasoner chokes on these with:

java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: org.semanticweb.owlapi.formats.OBODocumentFormat is not a PrefixDocumentFormat

Changing the above to: "Hippo sp." makes the reasoning work again.... so, we need a check in validator.py to check for this quoting issue and punt it to invalid data.