diff options
| -rw-r--r-- | gn3/api/metadata.py | 49 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 40 |
2 files changed, 38 insertions, 51 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index fd3166c..5ef14ab 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -13,7 +13,6 @@ 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 @@ -201,20 +200,48 @@ CONSTRUCT { return jsonify({}) -@metadata.route("/publication/<name>", methods=["GET"]) -def publication(name): +@metadata.route("/publications/<name>", methods=["GET"]) +def publications(name): """Fetch a publication's metadata given it's ACCESSION_ID""" try: if "unpublished" in name: - name = f"gn:{name}" + name = f"gn:unpublished{name}" else: - name = f"publication:{name}" - return jsonify( - get_publication_metadata( - SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), - name, - ).data - ) + name = f"pubmed:{name}" + sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) + sparql.setQuery(Template(""" +$prefix + +CONSTRUCT { + $name ?predicate ?object . +} WHERE { + $name rdf:type fabio:ResearchPaper ; + ?predicate ?object . + FILTER (!regex(str(?predicate), '(hasPubMedId)', 'i')) . +} +""").substitute(name=name, prefix=RDF_PREFIXES)) + return jsonld.compact( + json.loads(sparql.queryAndConvert().serialize(format="json-ld")), + { + "@context": PREFIXES | { + "type": "@type", + "id": "@id", + "title": "dct:title", + "journal": "fabio:Journal", + "volume": "prism:volume", + "page": "fabio:page", + "creator": "dct:creator", + "abstract": "dct:abstract", + "year": { + "@id": "fabio:hasPublicationYear", + "@type": "xsd:gYear", + }, + "month": { + "@id": "prism:publicationDate", + "@type": "xsd:gMonth" + }, + }, + }) # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index 1d714c1..2f80aa2 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -130,46 +130,6 @@ CONSTRUCT { return response -def get_publication_metadata( - sparql_conn: SPARQLWrapper, name: str -): - """Return info about a publication with a given NAME""" - __metadata_query = """ -$prefix - -CONSTRUCT { - gn:publication ?publicationTerm ?publicationValue . - gn:publication ?predicate ?subject . -} WHERE { - $name ?publicationTerm ?publicationValue . - ?publication ?publicationTerm ?publicationValue . - OPTIONAL { - ?subject ?predicate ?publication . - } . - VALUES ?publicationTerm { - gn:pubMedId gn:title gn:volume - gn:abstract gn:pages gn:month gn:year gn:author - } - VALUES ?predicate { - gn:phenotypeOfPublication - } -} -""" - response: MonadicDict = MonadicDict() - for key, value in sparql_query( - sparql_conn, - Template(__metadata_query) - .substitute( - prefix=RDF_PREFIXES, - name=name - ) - )[0].items(): - response[key] = value - if isinstance(value, str) and not key.endswith("pubMedId"): - response[key] = value.map(get_url_local_name) # type: ignore - return response - - def get_phenotype_metadata( sparql_conn: SPARQLWrapper, name: str ): |