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linkml / prefixmaps

Semantic prefix map registry
https://linkml.io/prefixmaps/
Apache License 2.0
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refresh prefix maps #32

Closed sierra-moxon closed 1 year ago

sierra-moxon commented 1 year ago

I updated the bioregistry ingest to exclude deprecated prefixes. This means that the problematic "gro"/"GRO" prefix is excluded and the tests now pass.

I spent some time in both the bioregistry package and this one, to try and isolate why the alias test was failing for GRO -- and best I could tell, in bioregistry there is a mismatch between the prefix expansion for the preferred prefix and the prefix expansion for the prefix itself. I would submit a ticket upstream, but since this prefix is deprecated anyway, I felt it was better to just exclude it. Happy to revisit if including deprecated prefixes from bioregistry is preferred.

cthoyt commented 1 year ago

we should probably implement canonical ordering to avoid spurious diffs...

This was already done in https://github.com/linkml/prefixmaps/commit/48c9f574c09d3af7d38d0ed6d6cd308497987d46, but the data had not been refreshed since.