opentox-ruby 3.0.0 → 3.0.1

data/ChangeLog

@@ -0,0 +1,5 @@
+v3.0.1 2011-10-19
+    * feature: model registration to ontology service
+    * ontology lib gets endpoints from ontology service
+v3.0.0 2011-09-23
+    * datasets stored as json (with Yajl) to improve performance

data/VERSION

@@ -1 +1 @@
-3.0.0
+3.0.1

data/lib/authorization.rb

@@ -319,7 +319,7 @@ module OpenTox
         # if policy exists check for POST rights 
         if authorize(uri, "POST", subjectid)
           true
-       else
+        else
           LOGGER.error "OpenTox::Authorization.check_policy, already exists, but no POST-authorization with subjectid: #{subjectid}" 
           false
         end

data/lib/ontology.rb

@@ -4,13 +4,9 @@ module OpenTox
 
       def self.querystring(classname="Endpoints")
         return CGI.escape("PREFIX ot:<http://www.opentox.org/api/1.1#>
-        PREFIX ota:<http://www.opentox.org/algorithms.owl#>
-        PREFIX owl:<http://www.w3.org/2002/07/owl#>
         PREFIX dc:<http://purl.org/dc/elements/1.1/>
         PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-        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 *
           where {
             ?endpoint  rdfs:subClassOf  otee:#{classname}.
@@ -18,25 +14,22 @@ module OpenTox
           }")
       end
 
-      def self.make_option_list(endpoint="Endpoints", level=1)
-      out = ""
-        results = echa_endpoints(endpoint) rescue results = []
-        results.each do |result|
-          r = result.split(',')
-          endpointname = r.first.split("#").last
-          title = r[1..r.size-1]
-          out += "<option value='#{r.first}' id='#{endpointname}' class='level_#{level}'>#{title}</option>\n"
-          out += make_option_list(endpointname, level + 1)
+      # Gets Endpoint name of a specific endpoint URI
+      # @param [String] endpointuri e.G. "http://www.opentox.org/echaEndpoints.owl#EcotoxicEffects"
+      # @return [String] endpointname: e.G.: "Ecotoxic effects"
+      def self.get_endpoint_name(endpointuri)
+        qstring = CGI.escape("PREFIX dc:<http://purl.org/dc/elements/1.1/>
+        select distinct ?title
+          where {
+            ?endpoint dc:title ?title.
+            FILTER (?endpoint = <#{endpointuri}>)
+          }")
+        begin
+          RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{qstring}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.to_s != "title\r\n"}.uniq.compact.sort.first.to_s
+        rescue
+          LOGGER.warn "OpenTox::Ontology::Echa.get_endpoint_name(#{endpointuri}) ontology service is not reachable."
+          []
         end
-        return out
-      end
-
-      def self.endpoint_option_list(include_blank=true)
-        out = "<select id='endpoint' name='endpoint'>\n"
-        out += "<option value='' id='please_select'>Please select</option>\n" if include_blank 
-        out += make_option_list
-        out += "</select>\n"
-        return out
       end
 
       # Gets Endpoints of specific level from ontology service
@@ -115,11 +108,8 @@ module OpenTox
       # Query string to find a registered model
       # @param [String] uri, model URI
       def self.querystring(uri)
-        return CGI.escape("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-        PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-        PREFIX owl:<http://www.w3.org/2002/07/owl#>
+        return CGI.escape("PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
         PREFIX dc:<http://purl.org/dc/elements/1.1/>
-        PREFIX dcterms:<http://purl.org/dc/terms/>
         PREFIX ot:<http://www.opentox.org/api/1.1#>
         select distinct ?model ?title ?creator ?trainingDataset ?algorithm
           where {
@@ -132,6 +122,5 @@ module OpenTox
           }")
       end
     end
-
   end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby
 version: !ruby/object:Gem::Version 
-  hash: 7
+  hash: 5
   prerelease: 
   segments: 
   - 3
   - 0
-  - 0
-  version: 3.0.0
+  - 1
+  version: 3.0.1
 platform: ruby
 authors: 
 - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-26 00:00:00 +02:00
+date: 2011-10-24 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -536,9 +536,11 @@ executables: []
 extensions: []
 
 extra_rdoc_files: 
+- ChangeLog
 - LICENSE
 - README.markdown
 files: 
+- ChangeLog
 - LICENSE
 - README.markdown
 - Rakefile