togostanza 2.0.0 → 2.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a3a84fadcce286880cf1905ef4ba2468e9ab0838
-  data.tar.gz: 20df3090d324e8a82b9aafb556eb6cd9b0844e6f
+  metadata.gz: 0379c6310562da1453a679c51d90c6496ae83095
+  data.tar.gz: 1073dd02b8261acf5780349581f07243523d2182
 SHA512:
-  metadata.gz: 671db4dce5c8235e401c5e0b40014f5eafb3172133a729d05ca2a80197c2332f3a90dfc4456eb4801048031762d539d21ddb2ad2ed0261cd76dd9aa0384306e0
-  data.tar.gz: 34f60db878f722079c567fe7f510829ba226dfac48dd3359694d579638b2a6fe3ae10db9f63eab5af0e1e52b14a9c33edca53f90475fe6a17f2e5a066354115a
+  metadata.gz: 0d4292ab3bff30defb01f8fbe94aaf37c3f2d9a1e9388d21b4188df4ed11d171baec65efa474e14c97c6738c590b9b06ddc7fc84ac2f82bbb73a5dc697955c6c
+  data.tar.gz: a7839f24738a41d013e1650bbd9e3704dd08baa8b41e64c8016e32813100e99dfcc8cb90adf1d20d17adda90ec15ed8bc3739361c7601d83e04ae26aa15c733f

data/lib/togostanza/cli.rb

@@ -48,6 +48,7 @@ module TogoStanza
         template 'template.hbs.erb',  "#{file_name}/template.hbs"
         template 'metadata.json.erb', "#{file_name}/metadata.json"
 
+        create_file "#{file_name}/sparql/.keep"
         create_file "#{file_name}/assets/#{stanza_id}/.keep"
       end
 

data/lib/togostanza/stanza/querying.rb

@@ -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

data/lib/togostanza/version.rb

@@ -1,3 +1,3 @@
 module TogoStanza
-  VERSION = '2.0.0'
+  VERSION = '2.1.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: togostanza
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.1.0
 platform: ruby
 authors:
 - Keita Urashima
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-11-10 00:00:00.000000000 Z
+date: 2015-11-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport