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-rw-r--r--gn3/api/metadata.py95
1 files changed, 95 insertions, 0 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index fd4de69..d18fff9 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -505,6 +505,101 @@ CONSTRUCT {
except (RemoteDisconnected, URLError):
return jsonify({})
+@metadata.route("/phenotypes/<group>/<name>", methods=["GET"])
+def fetch_phenotype_by_group(group, name):
+ """Fetch a phenotype's metadata given it's name"""
+ try:
+ args = request.args
+ dataset = args.get("dataset", "")
+ sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
+ sparql.setQuery(Template("""
+$prefix
+
+CONSTRUCT {
+ ?phenotype ?predicate ?object ;
+ ?pubPredicate ?pubObject ;
+ ex:species ?speciesName ;
+ ex:inbredSet ?inbredSetName ;
+ ex:dataset ?datasetName .
+} WHERE {
+ ?phenotype rdfs:label "$name" ;
+ xkos:classifiedUnder ?inbredSet ;
+ ?predicate ?object .
+ ?inbredSet ^xkos:classifiedUnder ?phenotype ;
+ (rdfs:label|skos:prefLabel|gnt:code) "$group" ;
+ xkos:generalizes ?species .
+ ?species skos:prefLabel ?speciesName .
+ FILTER (!regex(str(?predicate), '(classifiedUnder)', 'i')) .
+ OPTIONAL {
+ ?publication ^dct:isReferencedBy ?phenotype ;
+ rdf:type fabio:ResearchPaper ;
+ ?pubPredicate ?pubObject .
+ FILTER (!regex(str(?pubPredicate), '(hasPubMedId|type)', 'i')) .
+ } .
+ OPTIONAL {
+ ?dataset rdf:type dcat:Dataset ;
+ xkos:classifiedUnder ?type;
+ rdfs:label "$dataset" ;
+ skos:prefLabel ?datasetName .
+ ?type ^skos:member gnc:DatasetType .
+ FILTER(?type = gnc:Phenotype) .
+ }
+}
+""").substitute(prefix=RDF_PREFIXES,
+ group=group,
+ name=name,
+ dataset=dataset))
+ results = json.loads(sparql.queryAndConvert().serialize(format="json-ld"))
+ if not results:
+ return jsonify({})
+ frame = {
+ "@context": {
+ "data": "@graph",
+ "type": "@type",
+ "id": "@id",
+ "skos": "http://www.w3.org/2004/02/skos/core#",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "dct": "http://purl.org/dc/terms/",
+ "gnt": "http://genenetwork.org/term/",
+ "fabio": "http://purl.org/spar/fabio/",
+ "xsd": "http://www.w3.org/2001/XMLSchema#",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "gnc": "http://genenetwork.org/category/",
+ "traitName": "skos:altLabel",
+ "trait": "rdfs:label",
+ "altName": "rdfs:altLabel",
+ "description": "dct:description",
+ "abbreviation": "dct:abbreviation",
+ "labCode": "gnt:labCode",
+ "submitter": "gnt:submitter",
+ "contributor": "dct:contributor",
+ "mean": "gnt:mean",
+ "locus": "gnt:locus",
+ "LRS": "gnt:LRS",
+ "references": "dct:isReferencedBy",
+ "additive": "gnt:additive",
+ "sequence": "gnt:sequence",
+ "title": "dct:title",
+ "journal": "fabio:Journal",
+ "volume": "prism:volume",
+ "page": "fabio:page",
+ "creator": "dct:creator",
+ "abstract": "dct:abstract",
+ "year": {
+ "@id": "fabio:hasPublicationYear",
+ "@type": "xsd:gYear",
+ },
+ "month": {
+ "@id": "prism:publicationDate",
+ "@type": "xsd:gMonth"
+ },
+ },
+ "type": "gnc:Phenotype",
+ }
+ return jsonld.compact(jsonld.frame(results, frame), frame)
+ except (RemoteDisconnected, URLError):
+ return jsonify({})
+
@metadata.route("/genotypes/<name>", methods=["GET"])
def genotypes(name):