diff --git a/node_normalizer/model/input.py b/node_normalizer/model/input.py index ea7820e..78591b8 100644 --- a/node_normalizer/model/input.py +++ b/node_normalizer/model/input.py @@ -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, } } @@ -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 ", - ) \ No newline at end of file + ) diff --git a/node_normalizer/normalizer.py b/node_normalizer/normalizer.py index 32d9126..b5f3880 100644 --- a/node_normalizer/normalizer.py +++ b/node_normalizer/normalizer.py @@ -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 = {} diff --git a/node_normalizer/server.py b/node_normalizer/server.py index 18ca7ca..0fbc7e7 100644 --- a/node_normalizer/server.py +++ b/node_normalizer/server.py @@ -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"),