TranslatorSRI / NodeNormalization

Service that produces Translator compliant nodes given a curie
MIT License
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Empty response when query contains only unresolvable curies #113

Closed tokebe closed 2 years ago

tokebe commented 2 years ago

When posting to https://nodenormalization-sri.renci.org/1.2/get_normalized_nodes, a query containing only unresolvable curies will receive an empty response.

Unresolvable only:

{
  "curies": ["NCBIGene:ABCD", "NCBIGene:GENE:1017"]
}

response:

{}

With resolvable curie, response is as expected:

{
  "curies": ["MESH:D014867", "NCBIGene:ABCD", "NCBIGene:GENE:1017"]
}
response ```json { "MESH:D014867": { "id": { "identifier": "PUBCHEM.COMPOUND:962", "label": "Water" }, "equivalent_identifiers": [ { "identifier": "PUBCHEM.COMPOUND:962", "label": "Water" }, { "identifier": "CHEMBL.COMPOUND:CHEMBL1098659", "label": "WATER" }, { "identifier": "UNII:059QF0KO0R", "label": "WATER" }, { "identifier": "CHEBI:15377", "label": "water" }, { "identifier": "DRUGBANK:DB09145" }, { "identifier": "MESH:D014867", "label": "Water" }, { "identifier": "CAS:7732-18-5" }, { "identifier": "HMDB:HMDB0002111", "label": "Water" }, { "identifier": "KEGG.COMPOUND:C00001", "label": "H2O" }, { "identifier": "INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N" }, { "identifier": "UMLS:C0043047", "label": "Water" }, { "identifier": "UMLS:C0991883", "label": "purified water" } ], "type": [ "biolink:SmallMolecule", "biolink:MolecularEntity", "biolink:ChemicalEntity", "biolink:NamedThing", "biolink:Entity", "biolink:PhysicalEssence", "biolink:PhysicalEssenceOrOccurrent", "biolink:ChemicalOrDrugOrTreatment", "biolink:ChemicalEntityOrGeneOrGeneProduct", "biolink:ChemicalEntityOrProteinOrPolypeptide" ], "information_content": 85.7 }, "NCBIGene:ABCD": null, "NCBIGene:GENE:1017": null } ```
gaurav commented 2 years ago

This seems to be working as expected now:

Query:

curl -X 'POST' \
  'https://nodenorm.transltr.io/1.3/get_normalized_nodes' \
  -H 'accept: application/json' \
  -H 'Content-Type: application/json' \
  -d '{
  "curies": ["NCBIGene:ABCD", "NCBIGene:GENE:1017"]
}'

Response:

{
  "NCBIGene:ABCD": null,
  "NCBIGene:GENE:1017": null
}

Closing.