diff options
| -rw-r--r-- | gn3/api/metadata.py | 109 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 42 |
2 files changed, 100 insertions, 51 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index df3c4a9..877ff7c 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -1,4 +1,6 @@ """API for fetching metadata using an API""" +import json + from string import Template from http.client import RemoteDisconnected from urllib.error import URLError @@ -6,29 +8,118 @@ from flask import Blueprint from flask import jsonify from flask import current_app -from SPARQLWrapper import SPARQLWrapper +from pyld import jsonld +from SPARQLWrapper import JSON, JSONLD, 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 +from gn3.db.rdf import RDF_PREFIXES, PREFIXES metadata = Blueprint("metadata", __name__) -@metadata.route("/dataset/<name>", methods=["GET"]) -def dataset(name): +@metadata.route("/datasets/<name>", methods=["GET"]) +def datasets(name): """Fetch a dataset's metadata given it's ACCESSION_ID or NAME""" try: - return jsonify( - get_dataset_metadata( - SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), - name, - ).data + sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) + sparql.setQuery(Template(""" +$prefix + +CONSTRUCT { + ?dataset ?predicate ?term ; + rdf:type dcat:Dataset ; + ex:belongsToInbredSet ?inbredSetName ; + gnt:usesNormalization ?normalizationLabel ; + dcat:contactPoint ?investigatorName ; + xkos:classifiedUnder ?altName ; + ex:platform ?platform ; + ex:tissue ?tissue . + ?platform ?platformPred ?platformObject ; + ex:info ?platformInfo . + ?tissue rdfs:label ?tissueName ; + rdf:type gnc:tissue ; + ex:info ?tissueInfo . +} WHERE { + ?dataset rdf:type dcat:Dataset ; + xkos:classifiedUnder ?inbredSet ; + rdfs:label "$name" . + OPTIONAL { + ?inbredSet ^skos:member gnc:Set ; + rdfs:label ?inbredSetName . + } . + OPTIONAL { + ?type ^xkos:classifiedUnder ?dataset ; + ^skos:member gnc:DatasetType ; + skos:prefLabel ?altName . + } . + OPTIONAL { + ?normalization ^gnt:usesNormalization ?dataset ; + rdfs:label ?normalizationLabel . + } . + OPTIONAL { + ?investigator foaf:name ?investigatorName ; + ^dcat:contactPoint ?dataset . + } . + OPTIONAL { + ?platform ^gnt:usesPlatform ?dataset ; + ?platformPred ?platformObject . + } . + OPTIONAL { + ?dataset gnt:hasPlatformInfo ?platformInfo . + } . + OPTIONAL { + ?dataset gnt:hasTissueInfo ?tissueInfo . + } . + OPTIONAL { + ?dataset gnt:hasTissue ?tissue . + ?tissue rdfs:label ?tissueName . + } . + FILTER (!regex(str(?predicate), '(classifiedUnder|usesNormalization|contactPoint|hasPlatformInfo|tissueInfo)', 'i')) . + FILTER (!regex(str(?platformPred), '(classifiedUnder|geoSeriesId|hasGoTreeValue)', 'i')) . +}""").substitute(prefix=RDF_PREFIXES, name=name)) + results = sparql.queryAndConvert() + results = json.loads( + results.serialize(format="json-ld") ) + frame = { + "@context": PREFIXES | { + "data": "@graph", + "type": "@type", + "id": "@id", + "inbredSet": "ex:belongsToInbredSet", + "description": "dct:description", + "created": "dct:created", + "normalization": "gnt:usesNormalization", + "classifiedUnder": "xkos:classifiedUnder", + "accessRights": "dct:accessRights", + "accessionId": "dct:identifier", + "title": "dct:title", + "label": "rdfs:label", + "altLabel": "skos:altLabel", + "prefLabel": "skos:prefLabel", + "contactPoint": "dcat:contactPoint", + "organization": "foaf:Organization", + "info": "ex:info", + "caseInfo": "gnt:hasCaseInfo", + "geoSeriesId": "gnt:hasGeoSeriesId", + "experimentDesignInfo": "gnt:hasExperimentDesignInfo", + "notes": "gnt:hasNotes", + "processingInfo": "gnt:hasDataProcessingInfo", + "acknowledgement": "gnt:hasAcknowledgement", + "tissue": "ex:tissue", + "platform": "ex:platform", + }, + "type": "dcat:Dataset", + } + return jsonld.compact(jsonld.frame(results, frame), frame) + # The virtuoso server is misconfigured or it isn't running at all + except (RemoteDisconnected, URLError): + return jsonify({}) # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index 472da64..c5a75f2 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -213,45 +213,3 @@ 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 |