ohm-contrib added

4 files changed, 23 insertions, 12 deletions

diff --git a/Rakefile b/Rakefile
index b496cc2..215aeb2 100644
--- a/Rakefile
+++ b/Rakefile
@@ -28,6 +28,7 @@ begin
       "tmail",
       "rinruby",
       "ohm",
+      "ohm-contrib",
       "SystemTimer",
       "rjb"
     ].each { |dep| gem.add_dependency dep }
@@ -44,8 +45,6 @@ begin
     gem.add_dependency "haml", ">=3"
     ['jeweler'].each { |dep| gem.add_development_dependency dep }
     gem.files =  FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']
-    #gem.files.include %w(lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/model.rb, lib/validation.rb, lib/templates/*)
-    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end
   Jeweler::GemcutterTasks.new
 rescue LoadError
diff --git a/lib/environment.rb b/lib/environment.rb
index 59578c1..57ae014 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -74,7 +74,7 @@ CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorizatio
 CONFIG[:authorization][:authorize_request] =  [""] unless CONFIG[:authorization][:authorize_request]
 CONFIG[:authorization][:free_request] =  [""] unless CONFIG[:authorization][:free_request]
 
-RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
+#RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
 OWL = OwlNamespace.new 'http://www.w3.org/2002/07/owl#'
 DC =  OwlNamespace.new 'http://purl.org/dc/elements/1.1/'
 OT =  OwlNamespace.new 'http://www.opentox.org/api/1.1#'
diff --git a/lib/ontology_service.rb b/lib/ontology.rb
index 4ff688f..c3952c3 100644
--- a/lib/ontology_service.rb
+++ b/lib/ontology.rb
@@ -1,6 +1,6 @@
 module OpenTox
-  module OntologyService
-    module Endpoints
+  module Ontology
+    module Echa
       require 'sparql/client'
       @sparql = SPARQL::Client.new("http://apps.ideaconsult.net:8080/ontology")
       def self.qs(classname="Endpoints")
@@ -12,11 +12,11 @@ module OpenTox
         PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
         PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
         PREFIX toxcast:<http://www.opentox.org/toxcast.owl#>
-          select ?Endpoints ?title ?id
-          where {?Endpoints rdfs:subClassOf otee:#{classname}.
-          OPTIONAL {?Endpoints dc:title ?title}.
-          OPTIONAL {?Endpoints dc:identifier ?id}.}
-          ORDER BY ?title"
+        select *
+          where {
+            ?endpoint  rdfs:subClassOf  otee:#{classname}.
+            ?endpoint dc:title ?title.
+          }"
       end
       
       def self.make_option_list(endpoint="Endpoints", level=1)
@@ -38,6 +38,18 @@ module OpenTox
         out += "</select>\n"
         return out
       end
+
+      def self.endpoints#(endpoint="Endpoints")
+        endpoint_datasets = {}
+        RestClientWrapper.get("http://apps.ideaconsult.net:8080/ambit2/query/ndatasets_endpoint",:accept => "text/csv").each do |line|
+          if line.match(/^http/)
+            e = line.split(',')
+            endpoint_datasets["#{e.first} (#{e[1]})"] = RestClientWrapper.get(e.last, :accept => "text/uri-list").split("\n")#[0..e[1].to_i-1] # hack to get only the first count entries
+          end
+        end
+        endpoint_datasets
+      end
     end
+
   end
-end
\ No newline at end of file
+end
diff --git a/lib/opentox-ruby.rb b/lib/opentox-ruby.rb
index ab8d824..ae05cb2 100644
--- a/lib/opentox-ruby.rb
+++ b/lib/opentox-ruby.rb
@@ -9,6 +9,6 @@ rescue LoadError
 end
 
 ['opentox', 'compound','dataset', 'parser','serializer', 'algorithm','model','task','validation','feature', 
- 'rest_client_wrapper', 'authorization', 'policy', 'helper', 'to-html' ].each do |lib|
+ 'rest_client_wrapper', 'authorization', 'policy', 'helper', 'to-html', 'ontology' ].each do |lib|
 	require lib
 end