bioregistry 0.13.15__py3-none-any.whl → 0.13.17__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- bioregistry/app/impl.py +1 -1
- bioregistry/curation/bulk_import.py +2 -3
- bioregistry/data/bioregistry.json +311 -85
- bioregistry/data/curated_papers.tsv +2 -0
- bioregistry/external/aberowl/processed.json +24 -10
- bioregistry/external/bartoc/processed.json +21 -13
- bioregistry/external/bioportal/agroportal.json +206 -12
- bioregistry/external/bioportal/bioportal.json +155 -56
- bioregistry/external/fairsharing/processed.json +58 -43
- bioregistry/external/integbio/__init__.py +3 -3
- bioregistry/external/integbio/processed.json +130 -0
- bioregistry/external/lov/processed.json +37 -0
- bioregistry/external/ols/processed.json +29 -98
- bioregistry/external/re3data/processed.json +35 -2
- bioregistry/version.py +1 -1
- {bioregistry-0.13.15.dist-info → bioregistry-0.13.17.dist-info}/METADATA +1 -1
- {bioregistry-0.13.15.dist-info → bioregistry-0.13.17.dist-info}/RECORD +19 -20
- {bioregistry-0.13.15.dist-info → bioregistry-0.13.17.dist-info}/WHEEL +1 -1
- bioregistry/curation/add_descriptions_from_gs.py +0 -38
- {bioregistry-0.13.15.dist-info → bioregistry-0.13.17.dist-info}/entry_points.txt +0 -0
bioregistry/app/impl.py
CHANGED
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@@ -68,7 +68,7 @@ BIOREGISTRY_FOOTER_DEFAULT = dedent(f"""\
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<p class="small text-center text-muted">
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Developed with ❤️ by the
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<a href="https://www.iac.rwth-aachen.de">Institute
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<a href="https://www.iac.rwth-aachen.de">Institute of Inorganic Chemistry</a> at RWTH Aachen University
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</br> and the
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<a href="https://gyorilab.github.io">Gyori Lab for Computational Biomedicine</a>
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at Northeastern University.<br/>
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@@ -19,7 +19,6 @@ from __future__ import annotations
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import sys
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from collections import defaultdict
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-
from collections.abc import Mapping
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from typing import Any
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import click
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@@ -32,7 +31,7 @@ from bioregistry.utils import norm
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NESTED = {"contact", "contributor"}
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def _resource_from_row(row:
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def _resource_from_row(row: dict[str, Any]) -> Resource:
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kwargs = {}
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nested: defaultdict[str, dict[str, str]] = defaultdict(dict)
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for key, value in row.items():
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@@ -60,7 +59,7 @@ def _resource_from_row(row: Mapping[str, Any]) -> Resource:
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def _bulk_import_df(df: pd.DataFrame) -> None:
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for _, row in df.iterrows():
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resource = _resource_from_row(row.to_dict())
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resource = _resource_from_row(row.to_dict()) # type:ignore[arg-type]
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try:
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add_resource(resource)
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except KeyError as e:
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