diff options
| -rw-r--r-- | gn3/api/metadata.py | 16 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 43 |
2 files changed, 59 insertions, 0 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index a2eff05..f21739a 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -11,6 +11,7 @@ from SPARQLWrapper import SPARQLWrapper from gn3.db.rdf import get_dataset_metadata from gn3.db.rdf import get_publication_metadata from gn3.db.rdf import get_phenotype_metadata +from gn3.db.rdf import get_genotype_metadata from gn3.db.rdf import sparql_query from gn3.db.rdf import RDF_PREFIXES @@ -67,6 +68,21 @@ def phenotype(name): return jsonify({}) +@metadata.route("/genotype/<name>", methods=["GET"]) +def genotype(name): + """Fetch a genotype's metadata given it's name""" + try: + return jsonify( + get_genotype_metadata( + SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), + name, + ).data + ) + # The virtuoso server is misconfigured or it isn't running at all + except (RemoteDisconnected, URLError): + return jsonify({}) + + @metadata.route("/genewiki/<symbol>", methods=["GET"]) def get_genewiki_entries(symbol): """Fetch the GN and NCBI GeneRIF entries""" diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index 83bc46b..ad2e3be 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -26,6 +26,7 @@ PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX publication: <http://genenetwork.org/publication/> PREFIX phenotype: <http://genenetwork.org/phenotype/> +PREFIX genotype: <http://genenetwork.org/genotype/> """ @@ -243,3 +244,45 @@ CONSTRUCT { )[0].items(): result[key] = value return result + + +def get_genotype_metadata( + sparql_conn: SPARQLWrapper, name: str +): + """Return info about a phenotype with a given NAME""" + __metadata_query = """ +$prefix + +CONSTRUCT { + ?genotype ?pPredicate ?pValue . + ?genotype gn:speciesName ?speciesName . + ?genotype gn:inbredSetName ?inbredSetBinomialName . + ?genotype gn:datasetName ?datasetFullName . +} WHERE { + ?genotype ?pPredicate ?pValue . + OPTIONAL { + ?genotype gn:genotypeOfDataset ?dataset . + ?dataset gn:fullName ?datasetFullName . + }. + OPTIONAL { + ?genotype gn:genotypeOfDataset ?dataset . + ?dataset gn:datasetOfInbredSet ?inbredSet . + ?inbredSet gn:binomialName ?inbredSetBinomialName . + ?inbredSet gn:inbredSetOfSpecies ?species . + ?species gn:displayName ?speciesName . + } . + FILTER( ?genotype = genotype:$name ) . + MINUS { + ?genotype rdf:type ?pValue . + } +} +""" + result: MonadicDict = MonadicDict() + for key, value in sparql_query( + sparql_conn, + Template(__metadata_query) + .substitute(name=name, + prefix=RDF_PREFIXES) + )[0].items(): + result[key] = value + return result |