codecov[bot]
commented
10 months ago Codecov Report
Attention: 25 lines in your changes are missing coverage. Please review.
| Files | Coverage Δ | |
|---|---|---|
| src/bioregistry/__init__.py | 100.00% <ø> (ø) |
|
| src/bioregistry/record_accumulator.py | 91.41% <100.00%> (+0.27%) |
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| src/bioregistry/uri_format.py | 91.66% <100.00%> (+5.00%) |
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| src/bioregistry/resource_manager.py | 75.15% <66.66%> (-0.08%) |
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| src/bioregistry/external/prefixcommons.py | 21.35% <14.28%> (+0.14%) |
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| src/bioregistry/external/miriam.py | 31.34% <12.50%> (-1.45%) |
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| src/bioregistry/external/n2t.py | 43.90% <22.22%> (-6.10%) |
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This PR gets rid of code that focuses on lists of
curies.Recordobjects and instead works directly withcuries.Converterobjects.Along the way, this also identified issues with the data integrity on MIRIAM, N2T, and Prefix Commons with respect to the TAIR resources (
tair.geneandtair.protein) which all used non-specific, overlapping URLs. Therefore, these needed to get cleaned out before being import.Why do this? If we work directly with converters, we can make use of the CURIE prefix reconciliation tooling to more cleanly refactor the Bioregistry to Converter pipeline (which is causing issues when adding prefix casing variants in a related PR #969)