diff options
| -rw-r--r-- | gn3/api/metadata.py | 506 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 13 |
2 files changed, 212 insertions, 307 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 7292549..53aa87d 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -1,6 +1,4 @@ """API for fetching metadata using an API""" -import json - from string import Template from http.client import RemoteDisconnected from urllib.error import URLError @@ -10,10 +8,112 @@ from flask import request from flask import current_app from pyld import jsonld -from SPARQLWrapper import SPARQLWrapper -from gn3.db.rdf import RDF_PREFIXES, PREFIXES +from gn3.db.rdf import RDF_PREFIXES +from gn3.db.rdf import sparql_construct_query + + +BASE_CONTEXT = { + "data": "@graph", + "id": "@id", + "type": "@type", +} + +DATASET_CONTEXT = { + "accessRights": "dct:accessRights", + "accessionId": "dct:identifier", + "acknowledgement": "gnt:hasAcknowledgement", + "altLabel": "skos:altLabel", + "caseInfo": "gnt:hasCaseInfo", + "classifiedUnder": "xkos:classifiedUnder", + "contactPoint": "dcat:contactPoint", + "created": "dct:created", + "dcat": "http://www.w3.org/ns/dcat#", + "dct": "http://purl.org/dc/terms/", + "description": "dct:description", + "ex": "http://example.org/stuff/1.0/", + "experimentDesignInfo": "gnt:hasExperimentDesignInfo", + "foaf": "http://xmlns.com/foaf/0.1/", + "geoSeriesId": "gnt:hasGeoSeriesId", + "gnt": "http://genenetwork.org/term/", + "inbredSet": "ex:belongsToInbredSet", + "info": "ex:info", + "label": "rdfs:label", + "normalization": "gnt:usesNormalization", + "notes": "gnt:hasNotes", + "organization": "foaf:Organization", + "platform": "ex:platform", + "prefLabel": "skos:prefLabel", + "processingInfo": "gnt:hasDataProcessingInfo", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "tissue": "ex:tissue", + "title": "dct:title", + "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", +} + +SEARCH_CONTEXT = { + "pages": "ex:totalCount", + "result": "ex:result", + "results": "ex:items", + "resultItem": "ex:resultType", + "currentPage": "ex:currentPage", +} + +DATASET_SEARCH_CONTEXT = SEARCH_CONTEXT | { + "classifiedUnder": "xkos:classifiedUnder", + "created": "dct:created", + "dct": "http://purl.org/dc/terms/", + "ex": "http://example.org/stuff/1.0/", + "title": "dct:title", + "name": "rdfs:label", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "type": "@type", + "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", +} + +PUBLICATION_CONTEXT = { + "dct": "http://purl.org/dc/terms/", + "fabio": "http://purl.org/spar/fabio/", + "prism": "http://prismstandard.org/namespaces/basic/2.0/", + "xsd": "http://www.w3.org/2001/XMLSchema#", + "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" + }, +} +PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | { + "skos": "http://www.w3.org/2004/02/skos/core#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "gnt": "http://genenetwork.org/term/", + "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", +} metadata = Blueprint("metadata", __name__) @@ -22,8 +122,8 @@ metadata = Blueprint("metadata", __name__) def datasets(name): """Fetch a dataset's metadata given it's ACCESSION_ID or NAME""" try: - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + Template(""" $prefix CONSTRUCT { @@ -69,59 +169,19 @@ CONSTRUCT { ?platform ^gnt:usesPlatform ?dataset ; ?platformPred ?platformObject . } . - OPTIONAL { - ?dataset gnt:hasPlatformInfo ?platformInfo . - } . - OPTIONAL { - ?dataset gnt:hasTissueInfo ?tissueInfo . - } . + 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") +}""").substitute(prefix=RDF_PREFIXES, name=name), + endpoint=current_app.config.get("SPARQL_ENDPOINT") ) frame = { - "@context": { - "accessRights": "dct:accessRights", - "accessionId": "dct:identifier", - "acknowledgement": "gnt:hasAcknowledgement", - "altLabel": "skos:altLabel", - "caseInfo": "gnt:hasCaseInfo", - "classifiedUnder": "xkos:classifiedUnder", - "contactPoint": "dcat:contactPoint", - "created": "dct:created", - "data": "@graph", - "dcat": "http://www.w3.org/ns/dcat#", - "dct": "http://purl.org/dc/terms/", - "description": "dct:description", - "ex": "http://example.org/stuff/1.0/", - "experimentDesignInfo": "gnt:hasExperimentDesignInfo", - "foaf": "http://xmlns.com/foaf/0.1/", - "geoSeriesId": "gnt:hasGeoSeriesId", - "gnt": "http://genenetwork.org/term/", - "id": "@id", - "inbredSet": "ex:belongsToInbredSet", - "info": "ex:info", - "label": "rdfs:label", - "normalization": "gnt:usesNormalization", - "notes": "gnt:hasNotes", - "organization": "foaf:Organization", - "platform": "ex:platform", - "prefLabel": "skos:prefLabel", - "processingInfo": "gnt:hasDataProcessingInfo", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "skos": "http://www.w3.org/2004/02/skos/core#", - "tissue": "ex:tissue", - "title": "dct:title", - "type": "@type", - "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", - }, + "@context": BASE_CONTEXT | DATASET_CONTEXT, "type": "dcat:Dataset", } return jsonld.compact(jsonld.frame(results, frame), frame) @@ -137,8 +197,8 @@ def list_datasets_by_group(group): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -178,31 +238,12 @@ CONSTRUCT { } } } -""").substitute(prefix=RDF_PREFIXES, group=group, limit=page_size, offset=page)) - results = sparql.queryAndConvert() - results = json.loads( - results.serialize(format="json-ld") +""").substitute(prefix=RDF_PREFIXES, group=group, limit=page_size, offset=page), + endpoint=current_app.config.get("SPARQL_ENDPOINT") ) frame = { - "@context": { - "classifiedUnder": "xkos:classifiedUnder", - "created": "dct:created", - "data": "@graph", - "dct": "http://purl.org/dc/terms/", - "ex": "http://example.org/stuff/1.0/", - "id": "@id", - "title": "dct:title", - "name": "rdfs:label", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "type": "@type", - "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", - "pages": "ex:totalCount", - "result": "ex:result", - "results": "ex:items", - "resultItem": "ex:resultType", - "currentPage": "ex:currentPage", - }, -"type": "resultItem", + "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT, + "type": "resultItem", } return jsonld.compact( jsonld.frame(results, frame), @@ -219,8 +260,8 @@ def search_datasets(term): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -264,29 +305,12 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page)) +""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) return jsonld.frame( - json.loads( - sparql.queryAndConvert().serialize(format="json-ld")), - { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", - "ex": "http://example.org/stuff/1.0/", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "dct": "http://purl.org/dc/terms/", - "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", - "inbredSet": "ex:belongsToInbredSet", - "classifiedUnder": "xkos:classifiedUnder", - "dataset": "rdfs:label", - "title": "dct:title", - "currentPage": "ex:currentPage", - "result": "ex:result", - "results": "ex:items", - "resultItem": "ex:resultType", - "pages": "ex:totalCount" - }, + results, { + "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT, "type": "resultItem", } ) @@ -303,8 +327,8 @@ def publications(name): name = f"gn:unpublished{name}" else: name = f"pubmed:{name}" - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -314,33 +338,12 @@ CONSTRUCT { ?predicate ?object . FILTER (!regex(str(?predicate), '(hasPubMedId)', 'i')) . } -""").substitute(name=name, prefix=RDF_PREFIXES)) +""").substitute(name=name, prefix=RDF_PREFIXES), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) return jsonld.compact( - json.loads(sparql.queryAndConvert().serialize(format="json-ld")), - { - "@context": { - "type": "@type", - "id": "@id", - "dct": "http://purl.org/dc/terms/", - "fabio": "http://purl.org/spar/fabio/", - "prism": "http://prismstandard.org/namespaces/basic/2.0/", - "xsd": "http://www.w3.org/2001/XMLSchema#", - "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" - }, - }, - }) + results, {"@context": BASE_CONTEXT | PUBLICATION_CONTEXT} + ) # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) @@ -353,8 +356,8 @@ def search_publications(term): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -383,21 +386,18 @@ CONSTRUCT { } } } -""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page)) - results = sparql.queryAndConvert() - results = json.loads(results.serialize(format="json-ld")) +""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) frame = { - "@context": PREFIXES | { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | SEARCH_CONTEXT | { + "dct": "http://purl.org/dc/terms/", + "ex": "http://example.org/stuff/1.0/", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "fabio": "http://purl.org/spar/fabio/", "title": "dct:title", "pubmed": "fabio:hasPubMedId", "currentPage": "ex:currentPage", - "result": "ex:result", - "results": "ex:items", - "resultItem": "ex:resultType", - "pages": "ex:totalCount", "url": "rdfs:label", }, "type": "resultItem", @@ -417,8 +417,8 @@ def phenotypes(name): try: args = request.args dataset = args.get("dataset", "") - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -452,66 +452,28 @@ CONSTRUCT { } } """).substitute(prefix=RDF_PREFIXES, name=name, - dataset=dataset)) - results = json.loads(sparql.queryAndConvert().serialize(format="json-ld")) + dataset=dataset), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) 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" - }, - }, + "@context": PHENOTYPE_CONTEXT, "type": "gnc:Phenotype", } return jsonld.compact(jsonld.frame(results, frame), frame) 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(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -547,52 +509,13 @@ CONSTRUCT { """).substitute(prefix=RDF_PREFIXES, group=group, name=name, - dataset=dataset)) - results = json.loads(sparql.queryAndConvert().serialize(format="json-ld")) + dataset=dataset), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) 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" - }, - }, + "@context": PHENOTYPE_CONTEXT, "type": "gnc:Phenotype", } return jsonld.compact(jsonld.frame(results, frame), frame) @@ -604,8 +527,8 @@ CONSTRUCT { def genotypes(name): """Fetch a genotype's metadata given it's name""" try: - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -620,15 +543,13 @@ CONSTRUCT { rdfs:label ?speciesName . } } -""").substitute(prefix=RDF_PREFIXES, name=name)) - results = json.loads(sparql.queryAndConvert().serialize(format="json-ld")) +""").substitute(prefix=RDF_PREFIXES, name=name), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) if not results: return jsonify({}) frame = { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "gnt": "http://genenetwork.org/term/", "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", @@ -663,8 +584,8 @@ def get_gn_genewiki_entries(symbol): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -717,14 +638,11 @@ CONSTRUCT { } } """).substitute(prefix=RDF_PREFIXES, symbol=symbol, - limit=page_size, offset=page)) - results = sparql.queryAndConvert() - results = json.loads(results.serialize(format="json-ld")) + limit=page_size, offset=page), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) context = { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "ex": "http://example.org/stuff/1.0/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "gnt": "http://genenetwork.org/term/", @@ -757,10 +675,9 @@ def get_ncbi_genewiki_entries(symbol): """Fetch the NCBI GeneRIF entries""" try: args = request.args - page = args.get("page", 0) - page_size = args.get("per-page", 10) - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + page, page_size = args.get("page", 0), args.get("per-page", 10) + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -812,14 +729,11 @@ CONSTRUCT { } } """).substitute(prefix=RDF_PREFIXES, symbol=symbol, - limit=page_size, offset=page)) - results = sparql.queryAndConvert() - results = json.loads(results.serialize(format="json-ld")) + limit=page_size, offset=page), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) context = { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "ex": "http://example.org/stuff/1.0/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "gnt": "http://genenetwork.org/term/", @@ -853,8 +767,8 @@ CONSTRUCT { def list_species(): """List all species""" try: - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -869,16 +783,11 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES)) - results = sparql.queryAndConvert() - results = json.loads( - results.serialize(format="json-ld") +""").substitute(prefix=RDF_PREFIXES), + endpoint=current_app.config.get("SPARQL_ENDPOINT") ) return jsonld.compact(results, { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "skos": "http://www.w3.org/2004/02/skos/core#", "gnt": "http://genenetwork.org/term/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", @@ -897,8 +806,8 @@ CONSTRUCT { def fetch_species(name): """Fetch a Single species information""" try: - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -914,16 +823,11 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES, name=name)) - results = sparql.queryAndConvert() - results = json.loads( - results.serialize(format="json-ld") +""").substitute(prefix=RDF_PREFIXES, name=name), + endpoint=current_app.config.get("SPARQL_ENDPOINT") ) return jsonld.compact(results, { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "skos": "http://www.w3.org/2004/02/skos/core#", "gnt": "http://genenetwork.org/term/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", @@ -943,8 +847,8 @@ CONSTRUCT { def groups(): """Fetch the list of groups""" try: - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -959,16 +863,11 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES)) - results = sparql.queryAndConvert() - results = json.loads( - results.serialize(format="json-ld") +""").substitute(prefix=RDF_PREFIXES), + endpoint=current_app.config.get("SPARQL_ENDPOINT") ) return jsonld.compact(results, { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "skos": "http://www.w3.org/2004/02/skos/core#", "gnt": "http://genenetwork.org/term/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", @@ -989,8 +888,8 @@ CONSTRUCT { def fetch_group_by_species(name): """Fetch the list of groups""" try: - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -1008,16 +907,11 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES, name=name)) - results = sparql.queryAndConvert() - results = json.loads( - results.serialize(format="json-ld") +""").substitute(prefix=RDF_PREFIXES, name=name), + endpoint=current_app.config.get("SPARQL_ENDPOINT") ) return jsonld.compact(results, { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "skos": "http://www.w3.org/2004/02/skos/core#", "gnt": "http://genenetwork.org/term/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", @@ -1037,8 +931,8 @@ CONSTRUCT { def probesets(name): """Fetch a probesets's metadata given it's name""" try: - sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) - sparql.setQuery(Template(""" + results = sparql_construct_query( + query=Template(""" $prefix CONSTRUCT { @@ -1054,15 +948,13 @@ CONSTRUCT { ?chip rdfs:label ?chipName . } . } -""").substitute(prefix=RDF_PREFIXES, name=name)) - results = json.loads(sparql.queryAndConvert().serialize(format="json-ld")) +""").substitute(prefix=RDF_PREFIXES, name=name), + endpoint=current_app.config.get("SPARQL_ENDPOINT") + ) if not results: return jsonify({}) frame = { - "@context": { - "data": "@graph", - "type": "@type", - "id": "@id", + "@context": BASE_CONTEXT | { "gnt": "http://genenetwork.org/term/", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index 54458ac..017e687 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -3,6 +3,11 @@ This module is a collection of functions that handle SPARQL queries. """ +import json + +from SPARQLWrapper import SPARQLWrapper + + PREFIXES = { "dcat": "http://www.w3.org/ns/dcat#", "dct": "http://purl.org/dc/terms/", @@ -30,3 +35,11 @@ PREFIXES = { RDF_PREFIXES = "\n".join([f"PREFIX {key}: <{value}>"for key, value in PREFIXES.items()]) + + +def sparql_construct_query(query: str, endpoint: str) -> dict: + """Query virtuoso using a CONSTRUCT query and return a json-ld dictionary""" + sparql = SPARQLWrapper(endpoint) + sparql.setQuery(query) + results = sparql.queryAndConvert() + return json.loads(results.serialize(format="json-ld")) |