"""RDF utilities This module is a collection of functions that handle SPARQL queries. """ import json from string import Template from SPARQLWrapper import SPARQLWrapper from pyld import jsonld # type: ignore from gn3.db.constants import ( RDF_PREFIXES, BASE_CONTEXT ) 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")) # type: ignore def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict: """Frame and then compact the results given a context""" results = sparql_construct_query(query, endpoint) return jsonld.compact(jsonld.frame(results, context), context) def query_and_compact(query: str, context: dict, endpoint: str) -> dict: """Compact the results given a context""" results = sparql_construct_query(query, endpoint) return jsonld.compact(results, context) def query_and_frame(query: str, context: dict, endpoint: str) -> dict: """Frame the results given a context""" results = sparql_construct_query(query, endpoint) return jsonld.frame(results, context) def get_wiki_entries_by_symbol(symbol: str, sparql_uri: str) -> dict: """Fetch all the Wiki entries using the symbol""" # This query uses a sub-query to fetch the latest comment by the # version id. query = Template(""" $prefix CONSTRUCT { ?uid rdfs:label ?symbolName; gnt:reason ?reason ; gnt:species ?species ; dct:references ?pmid ; foaf:homepage ?weburl ; rdfs:comment ?comment ; foaf:mbox ?email ; gnt:initial ?usercode ; gnt:belongsToCategory ?category ; gnt:hasVersion ?versionId ; dct:created ?created ; dct:identifier ?identifier . } WHERE { ?symbolId rdfs:label ?symbolName . ?uid rdfs:comment ?comment ; gnt:symbol ?symbolId ; rdf:type gnc:GNWikiEntry ; dct:created ?createTime . FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) . { SELECT (MAX(?vers) AS ?max) ?id_ WHERE { ?symbolId rdfs:label ?symbolName . ?uid dct:identifier ?id_ ; dct:hasVersion ?vers ; dct:identifier ?id_ ; gnt:symbol ?symbolId . FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) . } } ?uid dct:hasVersion ?max ; dct:identifier ?id_ . OPTIONAL { ?uid gnt:reason ?reason } . OPTIONAL { ?uid gnt:belongsToSpecies ?speciesId . ?speciesId gnt:shortName ?species . } . OPTIONAL { ?uid dct:references ?pubmedId . } . OPTIONAL { ?uid foaf:homepage ?weburl . } . OPTIONAL { ?uid gnt:initial ?usercode . } . OPTIONAL { ?uid gnt:mbox ?email . } . OPTIONAL { ?uid gnt:belongsToCategory ?category . } . BIND (str(?version) AS ?versionId) . BIND (str(?id_) AS ?identifier) . BIND (str(?pubmedId) AS ?pmid) . BIND (str(?createTime) AS ?created) . } """).substitute(prefix=RDF_PREFIXES, symbol=symbol,) context = BASE_CONTEXT | { "foaf": "http://xmlns.com/foaf/0.1/", "dct": "http://purl.org/dc/terms/", "categories": "gnt:belongsToCategory", "web_url": "foaf:homepage", "version": "gnt:hasVersion", "symbol": "rdfs:label", "reason": "gnt:reason", "species": "gnt:species", "pubmed_id": "dct:references", "email": "foaf:mbox", "initial": "gnt:initial", "comment": "rdfs:comment", "created": "dct:created", "id": "dct:identifier", # This points to the RDF Node which is the unique identifier # for this triplet. It's constructed using the comment-id and # the comment-versionId "wiki_identifier": "@id", } results = query_frame_and_compact( query, context, sparql_uri ) data = results.get("data") if not data: return results return results