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Replace CURIE inference mechanism with curies.Converter.from_extended_prefix_map #363
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This is a mid-priority refactoring that can be done as a subsequent PR to #396 |
As per discussion in #396, we can replace everything, including the built-in prefix map, with Hwoever, I would like to ensure we have a test in place in the testing framework that ensures that whenever the epm is updated, the built-in prefixes are exactly what we expect them to be (which is what is in sssom context). |
hrshdhgd
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Jul 27, 2023
Part of #363 This PR does the following: 1. Adds a minimum version of `curies` that has the strict compress and expand functions 2. Rewrites the SPARQL utils and RDF utils to use `curies` functionality 3. Updates custom `curie_from_uri` to use `curies` (will make a follow-up PR that replaces this completely) --------- Co-authored-by: Harshad Hegde <[email protected]> Co-authored-by: Nico Matentzoglu <[email protected]>
cthoyt
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Oct 2, 2023
Closes #363 (final nail in the coffin) This provides an alternative to #429 that makes more explicit the chaining operations done on the metadata and prefix maps. This is also a good change to carefully document the way that this is handled, since I might not have captured it accurately. As it is, The priority order for combining prefix maps are: 1. Internal prefix map inside the document 2. Prefix map passed through this function inside the ``meta`` 3. Prefix map passed through this function to ``prefix_map`` 4. Default prefix map (handled with ensure_converter)
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Right now, we are using the bioregistry bimap, and old bioregistry tooling for getting from CU:RIE string to URIs and back.
@cthoyt has now introduced the concept of "extended prefix maps" which are much more powerful for guessing and standardising prefixes then the bimap.
Here is a snippet:
We should replace the old way of doing this with the new one.
For now, I still want to mirror the prefix map as part of the package rather than relying on bioregistry to doing the hosting/versioning.
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