lib/togostanza/stanza/querying.rb in togostanza-2.0.0 vs lib/togostanza/stanza/querying.rb in togostanza-2.1.0

@@ -1,43 +1,29 @@
 require 'sparql/client'
+require 'flavour_saver'
 
 module TogoStanza::Stanza
   module Querying
     MAPPINGS = {
-      togogenome: 'http://ep.dbcls.jp/sparql7',
-      uniprot:    'http://ep.dbcls.jp/sparql7',
-      go:         'http://ep.dbcls.jp/sparql7'
+      togogenome: 'http://togogenome.org/sparql'
     }
 
-    def query(endpoint, sparql)
+    def query(endpoint, text_or_filename)
+      path = File.join(root, 'sparql', text_or_filename)
+
+      if File.exist?(path)
+        data = OpenStruct.new params
+        text_or_filename = Tilt.new(path).render(data)
+      end
+
       client = SPARQL::Client.new(MAPPINGS[endpoint] || endpoint)
 
       #Rails.logger.debug "SPARQL QUERY: \n#{sparql}"
 
-      client.query(sparql).map {|binding|
+      client.query(text_or_filename).map {|binding|
         binding.each_with_object({}) {|(name, term), hash|
           hash[name] = term.to_s
         }
       }
-    end
-
-    def uniprot_url_from_togogenome(gene_id)
-      # refseq の UniProt
-      # slr1311 の時 "http://purl.uniprot.org/refseq/NP_439906.1"
-      query(:togogenome, <<-SPARQL).first[:up]
-      PREFIX insdc: <http://insdc.org/owl/>
-      PREFIX idorg: <http://rdf.identifiers.org/database/>
-
-      SELECT DISTINCT ?up
-      FROM <http://togogenome.org/graph/refseq/>
-      WHERE {
-          ?s insdc:feature_locus_tag "#{gene_id}" .
-          ?s rdfs:seeAlso ?np .
-          ?s rdfs:seeAlso ?xref .
-          ?np rdf:type idorg:Protein .
-          BIND (STRAFTER(STR(?np), "ncbiprotein/") AS ?npid)
-          BIND (IRI(CONCAT("http://purl.uniprot.org/refseq/", ?npid)) AS ?up)
-      }
-      SPARQL
     end
   end
 end