diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/rdf.py | 69 |
1 files changed, 67 insertions, 2 deletions
diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index c5a8d7f..9d6346b 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -4,11 +4,11 @@ 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 + RDF_PREFIXES, BASE_CONTEXT ) @@ -43,3 +43,68 @@ def query_and_frame(query: str, context: dict, endpoint: str) -> dict: if not results: return {} 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", + "web_url": "foaf:homepage", + "email": "foaf:mbox", + "initial": "gnt:initial", + "comment": "rdfs:comment" + } + results = query_frame_and_compact( + query, context, + sparql_uri + ) + if data := results.get("data"): + for result in data: + if result.get("categories"): + result["categories"] = list(map(str.strip, + result.get("categories").split(";"))) + return results |