diff options
Diffstat (limited to 'gn3/db')
-rw-r--r-- | gn3/db/rdf.py | 47 |
1 files changed, 0 insertions, 47 deletions
diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index ae0ec29..c8a5017 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -85,50 +85,3 @@ def get_url_local_name(string: str) -> str: url = urlparse(string) return unquote(url.path).rpartition("/")[-1] return string - - -def get_phenotype_metadata( - sparql_conn: SPARQLWrapper, name: str -): - """Return info about a phenotype with a given NAME""" - __metadata_query = """ -$prefix - -CONSTRUCT { - ?phenotype ?pPredicate ?pValue . - ?phenotype ?publicationTerm ?publicationValue . - ?phenotype gn:speciesName ?speciesName . - ?phenotype gn:inbredSetName ?inbredSetBinomialName . - ?phenotype gn:datasetName ?datasetFullName . -} WHERE { - ?phenotype ?pPredicate ?pValue . - OPTIONAL { - ?phenotype gn:phenotypeOfPublication ?publication . - ?publication ?publicationTerm ?publicationValue . - } . - OPTIONAL { - ?phenotype gn:phenotypeOfDataset ?dataset . - ?dataset gn:name ?datasetFullName . - ?dataset gn:datasetOfInbredSet ?inbredSet . - ?inbredSet gn:binomialName ?inbredSetBinomialName . - ?inbredSet gn:inbredSetOfSpecies ?species . - ?species gn:displayName ?speciesName . - } . - FILTER( ?phenotype = phenotype:$name ) . - MINUS { - ?phenotype rdf:type ?pValue . - } - MINUS { - ?publication rdf:type ?publicationValue . - } -} -""" - 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 |