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Make return properties on basic vocab functions configurable #122

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Merged
elewis2 merged 3 commits into from
Oct 2, 2026
Merged

Make return properties on basic vocab functions configurable #122

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71b2248
Make return properties on basic vocab functions configurable
creisle Sep 21, 2026
31bb7f1
Merge branch 'develop' into feature/configurable-return-props
elewis2 Sep 29, 2026
5c24487
Merge branch 'develop' into feature/configurable-return-props
creisle Oct 2, 2026
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19 changes: 9 additions & 10 deletions pori_python/graphkb/vocab.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
from typing import Callable, Dict, Iterable, List, Set, cast, Union
from typing import Callable, Dict, Iterable, List, Set, Union, cast

from pori_python.types import Ontology

from . import GraphKBConnection
from .util import convert_to_rid_list

DEFAULT_RETURN_PROPERTIES = ['sourceId', 'sourceIdVersion', 'deprecated', 'name', '@rid']


def query_by_name(ontology_class: str, base_term_name: Union[str, list[str]]) -> Dict:
return {'target': ontology_class, 'filters': {'name': base_term_name}}
Expand All @@ -17,6 +19,7 @@ def get_equivalent_terms(
ontology_class: str = 'Vocabulary',
ignore_cache: bool = False,
build_base_query: Callable = query_by_name,
return_properties=DEFAULT_RETURN_PROPERTIES,
) -> List[Ontology]:
"""
Get a list of terms equivalent to the current term up to the root term
Expand All @@ -35,7 +38,7 @@ def get_equivalent_terms(
'target': {'target': base_records, 'queryType': 'descendants'},
'queryType': 'similarTo',
'treeEdges': [],
'returnProperties': ['sourceId', 'sourceIdVersion', 'deprecated', 'name', '@rid'],
'returnProperties': return_properties,
},
ignore_cache=ignore_cache,
),
Expand All @@ -54,13 +57,7 @@ def get_equivalent_terms(
'target': {'target': root_records, 'queryType': 'descendants'},
'queryType': 'similarTo',
'treeEdges': [],
'returnProperties': [
'sourceId',
'sourceIdVersion',
'deprecated',
'name',
'@rid',
],
'returnProperties': ['@rid'],
},
ignore_cache=ignore_cache,
)
Expand All @@ -78,6 +75,7 @@ def get_term_tree(
include_superclasses: bool = True,
ignore_cache: bool = False,
build_base_query: Callable = query_by_name,
return_properties=DEFAULT_RETURN_PROPERTIES,
) -> List[Ontology]:
"""
Get terms equivalent to the base term by traversing the subclassOf tree and expanding related
Expand Down Expand Up @@ -105,7 +103,7 @@ def get_term_tree(
'target': {'target': base_records, 'queryType': 'ancestors'},
'queryType': 'similarTo',
'treeEdges': [],
'returnProperties': ['sourceId', 'sourceIdVersion', 'deprecated', 'name', '@rid'],
'returnProperties': return_properties,
},
ignore_cache=ignore_cache,
),
Expand All @@ -119,6 +117,7 @@ def get_term_tree(
ontology_class=ontology_class,
ignore_cache=ignore_cache,
build_base_query=build_base_query,
return_properties=return_properties,
)
else:
parent_terms = []
Expand Down
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