1 files changed, 0 insertions, 124 deletions
diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py
deleted file mode 100644
index 5a95683..0000000
--- a/gn3/db/rdf.py
+++ /dev/null
@@ -1,124 +0,0 @@
-"""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