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ValueSetExpander is too eager in using sqlite:obo as a default resolver #718

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cmungall opened this issue Mar 15, 2024 · 0 comments
Open

ValueSetExpander is too eager in using sqlite:obo as a default resolver #718

cmungall opened this issue Mar 15, 2024 · 0 comments

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@cmungall
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If you create a ValueSetExpander without specifying a configuration, it will include a default config:

DEFAULT_CONFIG = ValueSetConfiguration(default_resolver=Resolver("", shorthand_prefix="sqlite:obo"))

...
    configuration: ValueSetConfiguration = field(default_factory=lambda: DEFAULT_CONFIG)

This is handy for OBO ontologies but is too magical. Instead it should only match this when the user specified obo: as the prefix.

Also it's probably best if this is not the default resolver but instead something the user has to opt in to

See also monarch-initiative/ontogpt#346
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@cmungall