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Add improved export for curies #631

Merged
merged 26 commits into from
Oct 20, 2022
Merged

Add improved export for curies #631

merged 26 commits into from
Oct 20, 2022

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cthoyt
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@cthoyt cthoyt commented Oct 18, 2022

This PR does the following:

  • implements a more fully-featured generation of a curies.Converter class from the Bioregistry
  • creates an output for loading the Bioregstry extended prefix map in curies
  • reimplement reverse prefix map generation
  • Rename reverse prefix map (requires updating curies package)

CC @caufieldjh

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Follow-up

  • create a workflow for generating extended prefix maps for other contexts (notably, the OBO one, but this should be general)

@caufieldjh
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Great!

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codecov-commenter commented Oct 19, 2022

Codecov Report

Base: 38.86% // Head: 39.70% // Increases project coverage by +0.84% 🎉

Coverage data is based on head (67372c4) compared to base (2e4d01a).
Patch coverage: 73.42% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #631      +/-   ##
==========================================
+ Coverage   38.86%   39.70%   +0.84%     
==========================================
  Files         118      119       +1     
  Lines        6775     6941     +166     
  Branches     1359     1410      +51     
==========================================
+ Hits         2633     2756     +123     
- Misses       3967     4002      +35     
- Partials      175      183       +8     
Impacted Files Coverage Δ
src/bioregistry/export/prefix_maps.py 0.00% <0.00%> (ø)
src/bioregistry/export/tables_export.py 0.00% <ø> (ø)
src/bioregistry/external/miriam.py 33.92% <ø> (ø)
src/bioregistry/external/prefixcommons.py 30.18% <0.00%> (ø)
src/bioregistry/external/uniprot.py 27.58% <0.00%> (-1.51%) ⬇️
src/bioregistry/resource_manager.py 75.98% <40.00%> (-0.63%) ⬇️
src/bioregistry/schema/struct.py 86.38% <70.37%> (-0.72%) ⬇️
src/bioregistry/record_accumulator.py 86.75% <86.75%> (ø)
src/bioregistry/parse_iri.py 38.02% <100.00%> (ø)
src/bioregistry/uri_format.py 91.66% <100.00%> (+5.95%) ⬆️
... and 2 more

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@cthoyt cthoyt marked this pull request as ready for review October 19, 2022 10:35
@cthoyt cthoyt merged commit 0e0219c into main Oct 20, 2022
@cthoyt cthoyt deleted the record-export branch October 20, 2022 09:05
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3 participants