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Update ror.py
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Lines changed: 6 additions & 14 deletions

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src/pyobo/sources/ror.py

Lines changed: 6 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -7,17 +7,9 @@
77
from typing import Any
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import bioregistry
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import ror_downloader
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from pydantic import ValidationError
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from ror_downloader import (
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OrganizationType,
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get_description,
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)
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from ror_downloader import (
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get_organizations as get_ror_records,
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)
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from ror_downloader import (
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get_version_info as get_ror_status,
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)
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from ror_downloader import OrganizationType
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from tqdm.auto import tqdm
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from pyobo.struct import Obo, Reference, Term
@@ -33,7 +25,7 @@
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)
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__all__ = [
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"get_ror_records",
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"RORGetter",
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"get_ror_to_country_geonames",
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]
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@@ -70,7 +62,7 @@ class RORGetter(Obo):
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root_terms = [CITY_CLASS, ORG_CLASS]
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def __post_init__(self):
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self.data_version, _url, _path = get_ror_status()
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self.data_version, _url, _path = ror_downloader.get_version_info()
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super().__post_init__()
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def iter_terms(self, force: bool = False) -> Iterable[Term]:
@@ -105,7 +97,7 @@ def iter_terms(self, force: bool = False) -> Iterable[Term]:
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def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
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"""Iterate over terms in ROR."""
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status, records = get_ror_records(force=force)
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status, records = ror_downloader.get_organizations(force=force)
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unhandled_xref_prefixes: set[str] = set()
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seen_geonames_references = set()
@@ -119,7 +111,7 @@ def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
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term = Term(
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reference=Reference(prefix=PREFIX, identifier=identifier, name=primary_name),
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type="Instance",
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definition=get_description(record),
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definition=record.get_description(),
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)
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for organization_type in record.types:
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if organization_type in ROR_ORGANIZATION_TYPE_TO_OBI:

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