1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
|
"""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"""
# FIXME: Get the latest VersionId of a comment.
query = Template("""
$prefix
CONSTRUCT {
_:node rdfs:label '$symbol';
gnt:reason ?reason ;
gnt:species ?species ;
dct:references ?pmid ;
foaf:homepage ?weburl ;
rdfs:comment ?wikientry ;
foaf:mbox ?email ;
gnt:initial ?usercode ;
gnt:belongsToCategory ?category ;
gnt:hasVersion ?versionId
} WHERE {
?symbolId rdfs:comment _:node ;
rdfs:label '$symbol' .
_:node rdf:type gnc:GNWikiEntry ;
dct:hasVersion "0"^^xsd:int ;
dct:hasVersion ?version ;
rdfs:comment ?wikientry .
OPTIONAL { _:node gnt:reason ?reason } .
OPTIONAL {
_:node gnt:belongsToSpecies ?speciesId .
?speciesId gnt:shortName ?species .
} .
OPTIONAL { _:node dct:references ?pubmedId . } .
OPTIONAL { _:node foaf:homepage ?weburl . } .
OPTIONAL { _:node gnt:initial ?usercode . } .
OPTIONAL { _:node gnt:mbox ?email . } .
OPTIONAL { _:node gnt:belongsToCategory ?category . }
BIND (str(?version) AS ?versionId) .
BIND (str(?pubmedId) AS ?pmid)
}
""").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"
}
results = query_frame_and_compact(
query, context,
sparql_uri
)
data = results.get("data")
if not data:
return results
for result in data:
if result.get("categories"):
result["categories"] = [
x.strip() for x in result.get("categories").split(";")]
return results
|
