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biolink / ontobio

python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Default rule_set in validate.py produce is parsed as list ['a', 'l', 'l'] #564

Closed dustine32 closed 3 years ago

dustine32 commented 3 years ago

This new line in validate.py -v produce has the default meant to trigger ALL GORULES to run: https://github.com/biolink/ontobio/blob/aa1346c9ca92bb5a647d1c94008fb3d85c242985/bin/validate.py#L482 However, the RuleSet.ALL str is split by the click multiple option handling into ['a', 'l', 'l'] instead of the intended ['all']. Because of this, no GORULES run by default. This default value should instead be in a list:

default=[assocparser.RuleSet.ALL]
dustine32 commented 3 years ago

Also needed to handle default rule_set in function since list [assocparser.RuleSet.ALL] is converted to tuple (assocparser.RuleSet.ALL,) by click.

dustine32 commented 3 years ago

Closing as this appears to be fixed, given that the GO rules have been running in the last few snapshot releases.