diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/metadata.py | 147 |
1 files changed, 83 insertions, 64 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index f023e17..435199b 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -445,72 +445,91 @@ CONSTRUCT { return jsonify({}) -@metadata.route("/genewiki/<symbol>", methods=["GET"]) -def get_genewiki_entries(symbol): +@metadata.route("/genewikis/gn/<symbol>", methods=["GET"]) +def get_gn_genewiki_entries(symbol): """Fetch the GN and NCBI GeneRIF entries""" try: - gn_entries = sparql_query( - sparql_conn=SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), - query=Template(""" -$rdf_prefixes + args = request.args + page = args.get("page", 0) + page_size = args.get("limit", 10) + sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) + sparql.setQuery(Template(""" +$prefix -SELECT ?author ?geneCategory (STR(?gnEntry) AS ?entry) - (STR(?createdOn) AS ?created) - (GROUP_CONCAT(DISTINCT ?pmid; SEPARATOR=',') AS ?PubMedId) - ?weburl -WHERE { - ?generif gn:symbol ?symbol . - ?generif gn:geneWikiEntryOfGn _:gnEntry . - _:gnEntry gn:geneWikiEntry ?gnEntry; - dct:creator ?author; - dct:created ?createdOn . - OPTIONAL { _:gnEntry gn:geneCategory ?geneCategory } . - OPTIONAL { _:gnEntry foaf:homepage ?weburl } . - OPTIONAL { _:gnEntry dct:source ?pmid} . - OPTIONAL { - ?generif gn:wikiEntryOfSpecies ?speciesName . - ?species gn:name ?speciesName ; - gn:binomialName ?speciesBinomialName . - } . - FILTER( lcase(?symbol) = '$symbol' ) -} GROUP BY ?author ?createdOn ?gnEntry - ?generif ?symbol ?weburl - ?geneCategory -ORDER BY ASC(?createdOn)""").substitute(rdf_prefixes=RDF_PREFIXES, - symbol=str(symbol).lower())) - ncbi_entries = sparql_query( - sparql_conn=SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")), - query=Template(""" -$rdf_prefixes +CONSTRUCT { + ?symbol ex:entries [ + rdfs:comment ?comment ; + ex:species ?species_ ; + dct:created ?createTime ; + dct:references ?pmids ; + dct:creator ?creator ; + gnt:belongsToCategory ?categories ; + ] . + ?symbol rdf:type gnc:GNWikiEntry ; + ex:totalCount ?totalCount ; + ex:currentPage $offset . +} WHERE { +{ + SELECT ?symbol ?comment (GROUP_CONCAT(DISTINCT ?speciesName; SEPARATOR='; ') AS ?species_) + ?createTime ?creator + (GROUP_CONCAT(DISTINCT ?pubmed; SEPARATOR='; ') AS ?pmids) + (GROUP_CONCAT(DISTINCT ?category; SEPARATOR='; ') AS ?categories) + WHERE { + ?symbol rdfs:label ?label ; + rdfs:comment _:entry . + ?label bif:contains "'$symbol'" . + _:entry rdf:type gnc:GNWikiEntry ; + rdfs:comment ?comment . + OPTIONAL { + ?species ^xkos:classifiedUnder _:entry ; + ^skos:member gnc:Species ; + skos:prefLabel ?speciesName . + } . + OPTIONAL { _:entry dct:created ?createTime . } . + OPTIONAL { _:entry dct:references ?pubmed . } . + OPTIONAL { + ?investigator foaf:name ?creator ; + ^dct:creator _:entry . + } . + OPTIONAL { _:entry gnt:belongsToCategory ?category . } . + } GROUP BY ?comment ?symbol ?createTime ?creator ORDER BY ?createTime LIMIT $limit OFFSET $offset +} -SELECT ?speciesBinomialName (STR(?gnEntry) AS ?entry) - (STR(?createdOn) AS ?createdOn) - (GROUP_CONCAT(DISTINCT REPLACE(STR(?pmid), pubmed:, ''); SEPARATOR=',') AS ?PubMedId) - ?generif -WHERE { - ?generif gn:symbol ?symbol . - ?generif gn:geneWikiEntryOfNCBI [ - gn:geneWikiEntry ?gnEntry ; - dct:created ?createdOn ; - dct:source ?pmid - ] . - OPTIONAL { - ?generif gn:wikiEntryOfSpecies ?speciesName . - ?species gn:name ?speciesName ; - gn:binomialName ?speciesBinomialName . - } . - FILTER( lcase(?symbol) = '$symbol' ) -} GROUP BY ?createdOn ?gnEntry - ?generif ?symbol - ?speciesBinomialName -ORDER BY ASC(?createdOn)""").substitute(rdf_prefixes=RDF_PREFIXES, - symbol=str(symbol).lower())) - return jsonify({ - "gn_entries": list(map(lambda x: x.data, gn_entries)), - "ncbi_entries": list(map(lambda x: x.data, ncbi_entries)), - }) +{ + SELECT (COUNT(DISTINCT ?comment)/$limit+1 AS ?totalCount) WHERE { + ?symbol rdfs:comment _:entry ; + rdfs:label ?label . + _:entry rdfs:comment ?comment ; + rdf:type gnc:GNWikiEntry . + ?label bif:contains "'$symbol'" . + } +} +} +""").substitute(prefix=RDF_PREFIXES, symbol=symbol, + limit=page_size, offset=page)) + results = sparql.queryAndConvert() + results = json.loads(results.serialize(format="json-ld")) + context = { + "@context": PREFIXES | { + "data": "@graph", + "type": "@type", + "id": "@id", + "entries": "ex:entries", + "comment": "rdfs:comment", + "category": 'gnt:belongsToCategory', + "author": "dct:creator", + "pubmed": "dct:references", + "currentPage": "ex:currentPage", + "pages": "ex:totalCount", + "created": { + "@id": "dct:created", + "@type": "xsd:datetime" + }, + }, + "type": "gnc:GNWikiEntry" + } + return jsonld.compact( + jsonld.frame(results, context), + context) except (RemoteDisconnected, URLError): - return jsonify({ - "gn_entries": {}, - "ncbi_entries": {}, - }) + return jsonify({}) |