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Enable passing a custom Gilda grounder class #120

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merged 4 commits into from
Nov 12, 2021
Merged

Enable passing a custom Gilda grounder class #120

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eb9ac21
Update gilda_utils.py
cthoyt Oct 5, 2021
23e115d
Update gilda_utils.py
cthoyt Nov 12, 2021
004c153
Merge branch 'master' into enable-custom-grounder
cthoyt Nov 12, 2021
c33110c
Update gilda_utils.py
cthoyt Nov 12, 2021
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11 changes: 8 additions & 3 deletions src/pyobo/gilda_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

"""PyOBO's Gilda utilities."""

from typing import Iterable, Optional, Tuple, Union
from typing import Iterable, Optional, Tuple, Type, Union

import bioregistry
import gilda.api
Expand Down Expand Up @@ -84,7 +84,9 @@ def normalize_identifier(prefix: str, identifier: str) -> str:


def get_grounder(
prefix: Union[str, Iterable[str]], unnamed: Optional[Iterable[str]] = None
prefix: Union[str, Iterable[str]],
unnamed: Optional[Iterable[str]] = None,
grounder_cls: Optional[Type[Grounder]] = None,
) -> Grounder:
"""Get a Gilda grounder for the given namespace."""
unnamed = set() if unnamed is None else set(unnamed)
Expand All @@ -101,7 +103,10 @@ def get_grounder(
terms.extend(p_terms)
terms = filter_out_duplicates(terms)
terms = multidict((term.norm_text, term) for term in terms)
return Grounder(terms)
if grounder_cls is None:
return Grounder(terms)
else:
return grounder_cls(terms)


def get_gilda_terms(prefix: str, identifiers_are_names: bool = False) -> Iterable[gilda.term.Term]:
Expand Down