diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/metadata.py | 2 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 90 |
2 files changed, 27 insertions, 65 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index f21739a..df3c4a9 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -21,7 +21,7 @@ metadata = Blueprint("metadata", __name__) @metadata.route("/dataset/<name>", methods=["GET"]) def dataset(name): - """Fetch a dataset's metadata given it's ACCESSION_ID""" + """Fetch a dataset's metadata given it's ACCESSION_ID or NAME""" try: return jsonify( get_dataset_metadata( diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index 80b32fa..78ddc17 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -89,80 +89,42 @@ def get_dataset_metadata( sparql_conn: SPARQLWrapper, name: str ) -> MonadicDict: """Return info about dataset with a given NAME""" - __metadata_query = """ + response: MonadicDict = MonadicDict() + for key, value in sparql_query( + sparql_conn, + Template(""" $prefix CONSTRUCT { - gn:dataset ?datasetTerm ?datasetValue . - gn:dataset ?platformName ?platform_name . - gn:dataset gn:normalization ?normalization . - gn:dataset gn:investigatorName ?investigatorName . - gn:dataset gn:investigatorWebUrl ?investigatorWebUrl . - gn:dataset gn:tissueName ?tissueName . - gn:dataset gn:organism ?speciesDisplayName . - gn:dataset gn:organismUrl ?ncbiReference . - gn:dataset gn:inbredSetName ?inbredSetName . - gn:dataset gn:geoPlatformUrl ?geoPlatform . - gn:dataset gn:platformName ?platform_name . + ?dataset ?predicate ?term . + ?dataset gnt:classifiedUnder ?inbredSetName . + ?dataset gnt:usesNormalization ?normalizationLabel . + ?typePredicate ex:DatasetType ?typeName . } WHERE { - ?subClass rdf:subClassOf gn:dataset . - ?dataset rdf:type ?subclass ; - gn:name "$name"; - ?datasetTerm ?datasetValue . - OPTIONAL { - ?dataset gn:datasetOfInvestigator ?investigator . - ?investigator foaf:name ?investigatorName . - ?investigator foaf:homepage ?investigatorWebUrl . - } . - OPTIONAL{ - ?dataset gn:normalization ?normalizationType . - ?normalizationType gn:name ?normalization . - } . - OPTIONAL{ - ?dataset gn:datasetOfSpecies ?species . - ?species gn:displayName ?speciesDisplayName . - ?species gn:organism ?ncbiReference . - } . - OPTIONAL { - ?dataset gn:datasetOfInbredSet ?inbredSet . - ?inbredSet gn:binomialName ?inbredSetName . - ?inbredSet gn:inbredSetOfSpecies ?species . - ?species gn:displayName ?speciesDisplayName . - ?species gn:organism ?ncbiReference . - } . - OPTIONAL{ - ?dataset gn:datasetOfPlatform ?platform . - ?platform gn:name ?platform_name . - ?platform gn:geoPlatform ?geoPlatform . - } . - OPTIONAL{ - ?dataset gn:datasetOfTissue ?tissue . - ?tissue gn:name ?tissueName . - } . - VALUES ?datasetTerm { - dct:created gn:aboutCases gn:aboutDataProcessing gn:aboutPlatform - gn:aboutTissue gn:accessionId gn:acknowledgment gn:citation - gn:contributors gn:datasetGroup gn:datasetOfinvestigator - gn:experimentDesign gn:geoSeries gn:name gn:notes - gn:specifics gn:summary gn:title gn:publicationTitle - gn:datasetStatusName gn:datasetOfOrganization - } -} -""" - response: MonadicDict = MonadicDict() - for key, value in sparql_query( - sparql_conn, - Template(__metadata_query) + ?dataset rdf:type dcat:Dataset . + ?dataset ?predicate ?term . + ?dataset xkos:classifiedUnder ?inbredSet . + gnc:Set skos:member ?inbredSet . + ?dataset (rdfs:label|dct:identifier) "$name" . + ?inbredSet rdfs:label ?inbredSetName . + OPTIONAL { + ?dataset xkos:classifiedUnder ?type . + gnc:DatasetType skos:member ?type . + ?type ?typePredicate ?typeName . + ?type (skos:altLabel|skos:prefLabel) ?typeName . + } . + OPTIONAL { + ?dataset gnt:usesNormalization ?normalization . + ?normalization rdfs:label ?normalizationLabel . + } + FILTER (!regex(str(?predicate), '(classifiedUnder|usesNormalization)','i')) . +}""") .substitute( prefix=RDF_PREFIXES, name=name ) )[0].items(): response[key] = value - if isinstance(value, str) and not ( - key.endswith("Url") or key == "geoSeries" - ): - response[key] = value.map(get_url_local_name) # type: ignore return response |