diff options
| -rw-r--r-- | gn3/api/metadata.py | 125 |
1 files changed, 1 insertions, 124 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 91dc115..9d82dba 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -16,8 +16,7 @@ from gn3.db.datasets import (retrieve_metadata, get_history) from gn3.db.rdf import RDF_PREFIXES from gn3.db.rdf import (query_frame_and_compact, - query_and_compact, - query_and_frame) + query_and_compact) BASE_CONTEXT = { @@ -348,69 +347,6 @@ def edit_dataset(): lambda x: ("Edit successfull", 201) ) -@metadata.route("/datasets/search/<term>", methods=["GET"]) -def search_datasets(term): - """Search datasets""" - args = request.args - page = args.get("page", 0) - page_size = args.get("per-page", 10) - _query = Template(""" -$prefix - -CONSTRUCT { - ex:result rdf:type ex:resultType ; - ex:pages ?pages ; - ex:hits ?hits ; - ex:currentPage $offset ; - ex:items [ - rdfs:label ?label ; - dct:title ?title ; - ex:belongsToInbredSet ?inbredSetName ; - xkos:classifiedUnder ?datasetType ; - ] -} WHERE { -{ - SELECT DISTINCT ?dataset ?label ?inbredSetName ?datasetType ?title - WHERE { - ?dataset rdf:type dcat:Dataset ; - rdfs:label ?label ; - ?datasetPredicate ?datasetObject ; - xkos:classifiedUnder ?inbredSet . - ?inbredSet ^skos:member gnc:Set ; - rdfs:label ?inbredSetName . - ?datasetObject bif:contains "'$term'" . - OPTIONAL { - ?dataset dct:title ?title . - } . - OPTIONAL { - ?classification ^xkos:classifiedUnder ?dataset ; - ^skos:member gnc:DatasetType ; - ?typePredicate ?typeName ; - skos:prefLabel ?datasetType . - } - } ORDER BY ?dataset LIMIT $limit OFFSET $offset -} - -{ - SELECT (COUNT(DISTINCT ?dataset)/$limit+1 AS ?pages) - (COUNT(DISTINCT ?dataset) AS ?hits) WHERE { - ?dataset rdf:type dcat:Dataset ; - ?p ?o . - ?o bif:contains "'$term'" . - } -} - -} -""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page) - _context = { - "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT, - "type": "resultItem", - } - return query_frame_and_compact( - _query, _context, - current_app.config.get("SPARQL_ENDPOINT") - ) - @metadata.route("/publications/<name>", methods=["GET"]) def publications(name): @@ -436,65 +372,6 @@ CONSTRUCT { ) -@metadata.route("/publications/search/<term>", methods=["GET"]) -def search_publications(term): - """Search publications""" - args = request.args - page = args.get("page", 0) - page_size = args.get("per-page", 10) - _query = Template(""" -$prefix - -CONSTRUCT { - ex:result rdf:type ex:resultType ; - ex:totalCount ?totalCount ; - ex:currentPage $offset ; - ex:items [ - rdfs:label ?publication ; - dct:title ?title ; - ] -} WHERE { -{ - SELECT ?publication ?title ?pmid WHERE { - ?pub rdf:type fabio:ResearchPaper ; - ?predicate ?object ; - dct:title ?title . - ?object bif:contains "'$term'" . - BIND( STR(?pub) AS ?publication ) . - } ORDER BY ?title LIMIT $limit OFFSET $offset - } -{ - SELECT (COUNT(*)/$limit+1 AS ?totalCount) WHERE { - ?publication rdf:type fabio:ResearchPaper ; - ?predicate ?object . - ?object bif:contains "'$term'" . - } -} -} -""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page) - _context = { - "@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", - "url": "rdfs:label", - }, - "type": "resultItem", - "paper": { - "@type": "fabio:ResearchPaper", - "@container": "@index" - } - } - return query_and_frame( - _query, _context, - current_app.config.get("SPARQL_ENDPOINT") - ) - - @metadata.route("/phenotypes/<name>", methods=["GET"]) @metadata.route("/phenotypes/<group>/<name>", methods=["GET"]) def phenotypes(name, group=None): |