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refactor: remove unnecessary .lower() call when creating concept mapping #387

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Dec 28, 2024
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refactor: remove unnecessary .lower() call when creating concept mapping #387

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10 changes: 7 additions & 3 deletions src/gene/query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -396,6 +396,8 @@ def _add_gene(
:param record: Gene record
:param match_type: query's match type
:param possible_concepts: List of other normalized concepts found
:raises ValueError: If source of record's concept ID or xrefs/associated with
sources is not a valid ``NamespacePrefix``
:return: Response with core Gene
"""

Expand All @@ -404,16 +406,18 @@ def _create_concept_mapping(
) -> ConceptMapping:
"""Create concept mapping for identifier

:param concept_id: Concept identifier represented as a curie
:param concept_id: A lowercase concept identifier represented as a curie
:param relation: SKOS mapping relationship, default is relatedMatch
:raises ValueError: If source of concept ID is not a valid
``NamespacePrefix``
:return: Concept mapping for identifier
"""
source, source_id = concept_id.split(":")

try:
source = NamespacePrefix(source.lower())
source = NamespacePrefix(source)
except ValueError as e:
err_msg = f"Namespace prefix not supported: {source.lower()}"
err_msg = f"Namespace prefix not supported: {source}"
raise ValueError(err_msg) from e

system = NAMESPACE_TO_SYSTEM_URI.get(source, source)
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