Skip to content

Minor changes to the API #347

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gaurav wants to merge 2 commits into
base: master
Choose a base branch
from
+6 −6
Open

Minor changes to the API #347

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7ac4452
Add 'NCBIGene:1756' to GET/POST examples, turn DrugChemical conflate on.
gaurav Nov 30, 2025
f6dde40
Remove leading/trailing whitespace on CURIEs before normalization.
gaurav Nov 30, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions node_normalizer/model/input.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,10 +44,10 @@ class CurieList(BaseModel):
class Config:
schema_extra = {
"example": {
"curies": ['MESH:D014867', 'NCIT:C34373'],
"curies": ['MESH:D014867', 'NCIT:C34373', 'NCBIGene:1756'],
"conflate": True,
"description": False,
"drug_chemical_conflate": False,
"drug_chemical_conflate": True,
}
}

Expand Down Expand Up @@ -88,4 +88,4 @@ class SetIDs(BaseModel):
""" Query for Set IDs. You can provide a set of named CURIE sets, and we return a response for each one. """
sets: Dict[str, SetIDQuery] = Field(
description="A list of ",
)
)
2 changes: 1 addition & 1 deletion node_normalizer/normalizer.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -551,7 +551,7 @@ async def get_normalized_nodes(
# conflation_types = {"biolink:Gene", "biolink:Protein"}
# conflation_redis = 5

upper_curies = [c.upper() for c in curies]
upper_curies = [c.strip().upper() for c in curies]
canonical_ids = await app.state.eq_id_to_id_db.mget(*upper_curies, encoding='utf-8')
canonical_nonan = [canonical_id for canonical_id in canonical_ids if canonical_id is not None]
info_contents = {}
Expand Down
4 changes: 2 additions & 2 deletions node_normalizer/server.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -257,11 +257,11 @@ async def get_normalized_node_handler(
curie: List[str] = fastapi.Query(
[],
description="List of curies to normalize",
example=["MESH:D014867", "NCIT:C34373"],
example=["MESH:D014867", "NCIT:C34373", "NCBIGene:1756"],
min_items=1,
),
conflate: bool = fastapi.Query(True, description="Whether to apply gene/protein conflation"),
drug_chemical_conflate: bool = fastapi.Query(False, description="Whether to apply drug/chemical conflation"),
drug_chemical_conflate: bool = fastapi.Query(True, description="Whether to apply drug/chemical conflation"),
description: bool = fastapi.Query(False, description="Whether to return curie descriptions when possible"),
individual_types: bool = fastapi.Query(False, description="Whether to return individual types for equivalent identifiers"),
include_taxa: bool = fastapi.Query(True, description="Whether to return taxa for equivalent identifiers"),
Expand Down