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"""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
|
