opentox-ruby 2.1.0 → 3.0.0

data/VERSION

@@ -1 +1 @@
-2.1.0
+3.0.0

data/lib/algorithm.rb

@@ -927,7 +927,7 @@ module OpenTox
     # @param [Array] Array to test, must indicate non-occurrence with 0.
     # @return [Boolean] Whether the feature has variance zero.
     def self.zero_variance?(array)
-      return (array.to_scale.variance_sample == 0.0)
+      return (array.to_scale.variance_population == 0.0)
     end
     
     # Sum of an array for Arrays.

data/lib/authorization.rb

@@ -216,7 +216,7 @@ module OpenTox
         LOGGER.debug "OpenTox::Authorization.delete_policy policy: #{policy} with token: #{subjectid}"
         return true if resource.delete(:subjectid => subjectid, :id => policy)        
       rescue
-        return nil
+        return false
       end
     end
 

data/lib/dataset.rb

@@ -46,6 +46,12 @@ module OpenTox
       dataset.save(subjectid)
       dataset
     end
+
+    def self.from_json(json, subjectid=nil) 
+      dataset = Dataset.new(nil,subjectid)
+      dataset.copy_hash Yajl::Parser.parse(json)
+      dataset
+    end
     
     # Find a dataset and load all data. This can be time consuming, use Dataset.new together with one of the load_* methods for a fine grained control over data loading.
     # @param [String] uri Dataset URI
@@ -84,12 +90,16 @@ module OpenTox
       copy YAML.load(yaml)
     end
 
-    def load_rdfxml(rdfxml)
+    def load_json(json)
+      copy_hash Yajl::Parser.parse(json)
+    end
+
+    def load_rdfxml(rdfxml, subjectid=nil)
       raise "rdfxml data is empty" if rdfxml.to_s.size==0
       file = Tempfile.new("ot-rdfxml")
       file.puts rdfxml
       file.close
-      load_rdfxml_file file
+      load_rdfxml_file file, subjectid
       file.delete
     end
 
@@ -145,8 +155,8 @@ module OpenTox
 
     # Load all data (metadata, data_entries, compounds and features) from URI
     def load_all(subjectid=nil)
-      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-        copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid}))
+      if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
+        copy_hash Yajl::Parser.parse(RestClientWrapper.get(@uri, {:accept => "application/json", :subjectid => subjectid}))
       else
         parser = Parser::Owl::Dataset.new(@uri, subjectid)
         copy parser.load_uri(subjectid)
@@ -169,8 +179,8 @@ module OpenTox
     # Load and return only features from the dataset service
     # @return [Hash]  Features of the dataset
     def load_features(subjectid=nil)
-      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-        @features = YAML.load(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/x-yaml", :subjectid => subjectid}))
+      if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
+        @features = Yajl::Parser.parse(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/json", :subjectid => subjectid}))
       else
         parser = Parser::Owl::Dataset.new(@uri, subjectid)
         @features = parser.load_features(subjectid)
@@ -203,6 +213,10 @@ module OpenTox
 =begin
 =end
 
+    def to_json
+      Yajl::Encoder.encode({:uri => @uri, :metadata => @metadata, :data_entries => @data_entries, :compounds => @compounds, :features => @features})
+    end
+
     # Get Spreadsheet representation
     # @return [Spreadsheet::Workbook] Workbook which can be written with the spreadsheet gem (data_entries only, metadata will will be discarded))
     def to_spreadsheet
@@ -358,12 +372,12 @@ module OpenTox
       # TODO: rewrite feature URI's ??
       @compounds.uniq!
       if @uri
-        if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-          RestClientWrapper.post(@uri,self.to_yaml,{:content_type =>  "application/x-yaml", :subjectid => subjectid})
+        if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
+          #LOGGER.debug self.to_json
+          RestClientWrapper.post(@uri,self.to_json,{:content_type =>  "application/json", :subjectid => subjectid})
         else
           File.open("ot-post-file.rdf","w+") { |f| f.write(self.to_rdfxml); @path = f.path }
           task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :subjectid => subjectid}).to_s.chomp
-          #task_uri = `curl -X POST -H "Accept:text/uri-list" -F "file=@#{@path};type=application/rdf+xml" http://apps.ideaconsult.net:8080/ambit2/dataset`
           Task.find(task_uri).wait_for_completion
           self.uri = RestClientWrapper.get(task_uri,{:accept => 'text/uri-list', :subjectid => subjectid})
         end
@@ -379,6 +393,19 @@ module OpenTox
       RestClientWrapper.delete(@uri, :subjectid => subjectid)
     end
 
+    # Copy a hash (eg. from JSON) into a dataset (rewrites URI)
+    def copy_hash(hash)
+      @metadata = hash["metadata"]
+      @data_entries = hash["data_entries"]
+      @compounds = hash["compounds"]
+      @features = hash["features"]
+      if @uri
+        self.uri = @uri 
+      else
+        @uri = hash["metadata"][XSD.anyURI]
+      end
+    end
+
     private
     # Copy a dataset (rewrites URI)
     def copy(dataset)

data/lib/environment.rb

@@ -40,8 +40,8 @@ else
 end
 
 # Regular expressions for parsing classification data
-TRUE_REGEXP = /^(true|active|1|1.0|tox|activating)$/i
-FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating)$/i
+TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
+FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
 
 # Task durations
 DEFAULT_TASK_MAX_DURATION = 36000
@@ -74,6 +74,13 @@ 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]
 
+ONTOLOGY_SERVER = CONFIG[:services]["opentox-ontology"] ? CONFIG[:services]["opentox-ontology"] : "http://apps.ideaconsult.net:8080/ontology"
+
+cookie_secret =  CONFIG[:authorization] ? CONFIG[:authorization][:cookie_secret] : nil 
+cookie_secret = cookie_secret ? cookie_secret : "ui6vaiNi-change_me"
+use Rack::Session::Cookie, :expire_after => 28800, 
+                           :secret => cookie_secret
+
 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/'

data/lib/feature.rb

@@ -10,7 +10,7 @@ module OpenTox
     def self.find(uri, subjectid=nil)
       return nil unless uri   
       feature = Feature.new uri
-      if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host))
+      if (CONFIG[:json_hosts].include?(URI.parse(uri).host))
         feature.add_metadata YAML.load(RestClientWrapper.get(uri,{:accept => "application/x-yaml", :subjectid => subjectid}))
       else
         feature.add_metadata  Parser::Owl::Dataset.new(uri).load_metadata
@@ -23,9 +23,9 @@ module OpenTox
     # @return [String] feature type, unknown if OT.isA property is unknown/ not set
     def feature_type
       raise OpenTox::BadRequestError.new("rdf type of feature '"+uri.to_s+"' not set") unless metadata[RDF.type]
-      if metadata[RDF.type].flatten.include?(OT.NominalFeature)
+      if metadata[RDF.type].to_a.flatten.include?(OT.NominalFeature)
         "classification"
-      elsif metadata[RDF.type].flatten.include?(OT.NumericFeature)
+      elsif metadata[RDF.type].to_a.flatten.include?(OT.NumericFeature)
         "regression"
       elsif metadata[OWL.sameAs]
         metadata[OWL.sameAs].each do |f|
@@ -42,4 +42,15 @@ module OpenTox
       end
     end    
   end
+
+  # Get OWL-DL representation in RDF/XML format
+  # @return [application/rdf+xml] RDF/XML representation
+  def to_rdfxml
+    s = Serializer::Owl.new
+    s.add_feature(@uri,@metadata)
+    @metadata.values.grep(/model\/\d+$/).each{ |m| s.add_uri(m,OT.Model)}
+    @metadata.values.grep(/feature/).each{ |f| s.add_uri(f,OT.Feature)}
+    #s.add_parameters(@uri,@parameters) if @parameters
+    s.to_rdfxml
+  end
 end

data/lib/helper.rb

@@ -1,4 +1,34 @@
 helpers do
+  
+  def login(username, password)
+    logout
+    session[:subjectid] = OpenTox::Authorization.authenticate(username, password)
+    #LOGGER.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s
+    if session[:subjectid] != nil
+      session[:username] = username
+      return session[:subjectid]
+    else
+      session[:username] = ""
+      return nil
+    end
+  end
+
+  def logout
+    if session[:subjectid] != nil
+      session[:subjectid] = nil
+      session[:username] = ""
+      return true
+    end
+    return false
+  end
+
+  def logged_in()
+    return true if !AA_SERVER
+    if session[:subjectid] != nil
+      return OpenTox::Authorization.is_token_valid(session[:subjectid])
+    end
+    return false
+  end
 
   # Authentification
   def protected!(subjectid)
@@ -30,9 +60,9 @@ helpers do
   def clean_uri(uri)
     uri = uri.sub(" ", "%20")          #dirty hacks => to fix
     uri = uri[0,uri.index("InChI=")] if uri.index("InChI=") 
-    
     out = URI.parse(uri)
     out.path = out.path[0, out.path.length - (out.path.reverse.rindex(/\/{1}\d+\/{1}/))] if out.path.index(/\/{1}\d+\/{1}/)  #cuts after /id/ for a&a
+    out.path = out.path.split('.').first #cut extension
     port = (out.scheme=="http" && out.port==80)||(out.scheme=="https" && out.port==443) ? "" : ":#{out.port.to_s}" 
     "#{out.scheme}://#{out.host}#{port}#{out.path.chomp("/")}" #"
   end
@@ -56,15 +86,16 @@ helpers do
       subjectid = session[:subjectid] if session[:subjectid]
       subjectid = params[:subjectid]  if params[:subjectid] and !subjectid
       subjectid = request.env['HTTP_SUBJECTID'] if request.env['HTTP_SUBJECTID'] and !subjectid
-      subjectid = request.cookies["subjectid"] unless subjectid
       # see http://rack.rubyforge.org/doc/SPEC.html
       subjectid = CGI.unescape(subjectid) if subjectid.include?("%23")
       @subjectid = subjectid
     rescue
-      subjectid = nil
+      @subjectid = nil
     end
   end
   def get_extension
+    @accept = request.env['HTTP_ACCEPT']
+    @accept = 'application/rdf+xml' if @accept == '*/*' or @accept == '' or @accept.nil?
     extension = File.extname(request.path_info)
     unless extension.empty?
       case extension.gsub(".","")
@@ -78,6 +109,8 @@ helpers do
         @accept = 'application/rdf+xml'
       when "xls"
         @accept = 'application/ms-excel'
+      when "sdf"
+        @accept = 'chemical/x-mdl-sdfile'
       when "css"
         @accept = 'text/css'
       else
@@ -88,8 +121,8 @@ helpers do
 end
 
 before do 
-  @subjectid = get_subjectid()
-  @accept = get_extension()
+  get_subjectid()
+  get_extension()
   unless !AA_SERVER or login_requests or CONFIG[:authorization][:free_request].include?(env['REQUEST_METHOD'])
     protected!(@subjectid)
   end

data/lib/model.rb

@@ -10,8 +10,8 @@ module OpenTox
     # @return [text/uri-list] Task or resource URI
     def run( params, accept_header=nil, waiting_task=nil )
       unless accept_header
-        if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
-          accept_header = 'application/x-yaml' 
+        if CONFIG[:json_hosts].include?(URI.parse(@uri).host)
+          accept_header = 'application/json' 
         else
           accept_header = 'application/rdf+xml'
         end
@@ -144,7 +144,7 @@ module OpenTox
       # @param [String] uri Model URI
       # @return [OpenTox::Model::Lazar] lazar model
       def self.find(uri, subjectid=nil)
-        YAML.load RestClientWrapper.get(uri,{:accept => 'application/x-yaml', :subjectid => subjectid})
+        OpenTox::Model::Lazar.from_json RestClientWrapper.get(uri,{:accept => 'application/json', :subjectid => subjectid})
       end
 
       # Create a new lazar model
@@ -157,10 +157,42 @@ module OpenTox
         OpenTox::Model::Lazar.find(model_uri, subjectid)      
       end
 
+      def self.from_json(json)
+        hash = Yajl::Parser.parse(json)
+        #LOGGER.debug hash.to_yaml
+        lazar = OpenTox::Model::Lazar.new
+        #hash.each { |k,v| eval("lazar.#{k} = #{v}") }
+        lazar.uri = hash["uri"] if hash["uri"]
+        lazar.metadata = hash["metadata"] if hash["metadata"]
+        lazar.compound = hash["compound"] if hash["compound"]
+        lazar.prediction_dataset = hash["prediction_dataset"] if hash["prediction_dataset"]
+        lazar.features = hash["features"] if hash["features"]
+        lazar.effects = hash["effects"] if hash["effects"]
+        lazar.activities = hash["activities"] if hash["activities"]
+        lazar.p_values = hash["p_values"] if hash["p_values"]
+        lazar.fingerprints = hash["fingerprints"] if hash["fingerprints"]
+        lazar.feature_calculation_algorithm = hash["feature_calculation_algorithm"] if hash["feature_calculation_algorithm"]
+        lazar.similarity_algorithm = hash["similarity_algorithm"] if hash["similarity_algorithm"]
+        lazar.prediction_algorithm = hash["prediction_algorithm"] if hash["prediction_algorithm"]
+        lazar.min_sim = hash["min_sim"] if hash["min_sim"]
+        lazar.subjectid = hash["subjectid"] if hash["subjectid"]
+        lazar.prop_kernel = hash["prop_kernel"] if hash["prop_kernel"]
+        lazar.value_map = hash["value_map"] if hash["value_map"]
+        lazar.nr_hits = hash["nr_hits"] if hash["nr_hits"]
+        lazar.transform = hash["transform"] if hash["transform"]
+        lazar.conf_stdev = hash["conf_stdev"] if hash["conf_stdev"]
+        lazar.prediction_min_max = hash["prediction_min_max"] if hash["prediction_min_max"]
+        lazar
+      end
+
+      def to_json
+        Yajl::Encoder.encode({:uri => @uri,:metadata => @metadata, :compound => @compound, :prediction_dataset => @prediction_dataset, :features => @features, :effects => @effects, :activities => @activities, :p_values => @p_values, :fingerprints => @fingerprints, :feature_calculation_algorithm => @feature_calculation_algorithm, :similarity_algorithm => @similarity_algorithm, :prediction_algorithm => @prediction_algorithm, :min_sim => @min_sim, :subjectid => @subjectid, :prop_kernel => @prop_kernel, :value_map => @value_map, :nr_hits => @nr_hits, :transform => @transform, :conf_stdev => @conf_stdev, :prediction_min_max => @prediction_min_max})
+      end
+
       def run( params, accept_header=nil, waiting_task=nil )
       unless accept_header
-        if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
-          accept_header = 'application/x-yaml' 
+        if CONFIG[:json_hosts].include?(URI.parse(@uri).host)
+          accept_header = 'application/json' 
         else
           accept_header = 'application/rdf+xml'
         end
@@ -199,7 +231,7 @@ module OpenTox
             count += 1
             waiting_task.progress( count/d.compounds.size.to_f*100.0 ) if waiting_task
           rescue => ex
-            LOGGER.warn "prediction for compound "+compound_uri.to_s+" failed: "+ex.message
+            LOGGER.warn "prediction for compound "+compound_uri.to_s+" failed: "+ex.message+" subjectid: #{subjectid}"
           end
         end
         #@prediction_dataset.save(subjectid)
@@ -215,6 +247,7 @@ module OpenTox
         @compound = Compound.new compound_uri
         features = {}
 
+        #LOGGER.debug self.to_yaml
         unless @prediction_dataset
           @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
           @prediction_dataset.add_metadata( {
@@ -225,7 +258,7 @@ module OpenTox
           } )
         end
 
-        if OpenTox::Feature.find(metadata[OT.dependentVariables]).feature_type == "regression"
+        if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "regression"
           all_activities = [] 
           all_activities = @activities.values.flatten.collect! { |i| i.to_f }
           @prediction_min_max[0] = (all_activities.to_scale.min/2)
@@ -255,7 +288,7 @@ module OpenTox
           @prediction_dataset.metadata[OT.predictedVariables] = [value_feature_uri, confidence_feature_uri] unless @prediction_dataset.metadata[OT.predictedVariables] 
 
           if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "classification"
-            @prediction_dataset.add @compound.uri, value_feature_uri, @value_map[prediction[:prediction]]
+            @prediction_dataset.add @compound.uri, value_feature_uri, @value_map[prediction[:prediction].to_s]
           else
             @prediction_dataset.add @compound.uri, value_feature_uri, prediction[:prediction]
           end
@@ -365,7 +398,7 @@ module OpenTox
       def database_activity(subjectid)
         if @activities[@compound.uri]
           if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "classification"
-            @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], @value_map[act] }
+            @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], @value_map[act.to_s] }
           else
             @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], act }
           end
@@ -385,7 +418,7 @@ module OpenTox
         dependent_uri = @metadata[OT.dependentVariables].first
         feature = OpenTox::Feature.new File.join( @uri, "predicted", "value")
         feature.add_metadata( {
-          RDF.type => [OT.ModelPrediction],
+          RDF.type => OT.ModelPrediction,
           OT.hasSource => @uri,
           DC.creator => @uri,
           DC.title => URI.decode(File.basename( dependent_uri )),
@@ -398,7 +431,7 @@ module OpenTox
         dependent_uri = @metadata[OT.dependentVariables].first
         feature = OpenTox::Feature.new File.join( @uri, "predicted", "confidence")
         feature.add_metadata( {
-          RDF.type => [OT.ModelPrediction],
+          RDF.type => OT.ModelPrediction,
           OT.hasSource => @uri,
           DC.creator => @uri,
           DC.title => "#{URI.decode(File.basename( dependent_uri ))} confidence"
@@ -408,7 +441,7 @@ module OpenTox
 
       # Save model at model service
       def save(subjectid)
-        self.uri = RestClientWrapper.post(@uri,self.to_yaml,{:content_type =>  "application/x-yaml", :subjectid => subjectid})
+        self.uri = RestClientWrapper.post(@uri,self.to_json,{:content_type =>  "application/json", :subjectid => subjectid})
       end
 
       # Delete model at model service

data/lib/ontology.rb

@@ -1,11 +1,9 @@
 module OpenTox
   module Ontology
     module Echa
-=begin
-      require 'sparql/client'
-      @sparql = SPARQL::Client.new("http://apps.ideaconsult.net:8080/ontology")
-      def self.qs(classname="Endpoints")
-        return "PREFIX ot:<http://www.opentox.org/api/1.1#>
+
+      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/>
@@ -17,29 +15,44 @@ module OpenTox
           where {
             ?endpoint  rdfs:subClassOf  otee:#{classname}.
             ?endpoint dc:title ?title.
-          }"
+          }")
       end
-      
+
       def self.make_option_list(endpoint="Endpoints", level=1)
-        out = ""
-        results = @sparql.query(qs(endpoint)) rescue results = []
+      out = ""
+        results = echa_endpoints(endpoint) rescue results = []
         results.each do |result|
-          endpointname = result.Endpoints.to_s.split('#').last
-          title = result.bound?(:title) ? result.title : endpointname     
-          out += "<option value='#{title}' id='#{endpointname}' class='level_#{level}'>#{title}</option>\n"
+          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)
         end
         return out
       end
-    
-      def self.get_endpoint_selectlist(include_blank=true)
+
+      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
-=end
+
+      # Gets Endpoints of specific level from ontology service
+      # Top level with endpoint="Endpoints"
+      # e.G. Ecotoxic effects endpoints with  endpoint="EcotoxicEffects"
+      # if ontology service is not reachable it returns an empty array
+      # @param [String] endpoint
+      # @return [Array] of endpoints: e.G. "http://www.opentox.org/echaEndpoints.owl#EcotoxicEffects,Ecotoxic effects"
+      def self.echa_endpoints(endpoint)
+        begin
+          RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{querystring(endpoint)}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.match(/^http/)}.uniq.compact.sort
+        rescue
+          LOGGER.warn "OpenTox::Ontology::Echa.echa_endpoints ontology service is not reachable."
+          []
+        end
+      end
 
       def self.endpoints
         RestClientWrapper.get("http://apps.ideaconsult.net:8080/ambit2/query/ndatasets_endpoint",:accept => "text/csv").collect { |line| line.split(',').first if line.match(/^http/) }.compact
@@ -51,5 +64,74 @@ module OpenTox
 
     end
 
+    #Model Class for OpenTox::Ontology to register/deregister and check models in the ontology service
+    #@example Register a model URI to the ontology service, check if model URI exists and delete it 
+    #  uri = "http://mymodelservice.net/model/1" # model uri will be checked by the ontology service itself
+    #  OpenTox::Ontology::Model.register(uri)
+    #  puts OpenTox::Ontology::Model.exists?(uri) # => should return true
+    #  OpenTox::Ontology::Model.delete(uri)
+    #  puts OpenTox::Ontology::Model.exists?(uri) # => should return false
+    module Model
+
+      # Register an OpenTox resource into ontology service
+      # @param [String] uri, URI of recource to register
+      # @param [String] subjectid
+      def self.register(uri, subjectid=nil)
+        begin
+          RestClientWrapper.post(ONTOLOGY_SERVER, {:uri => uri}, {:subjectid => CGI.escape(subjectid)})
+        rescue
+          LOGGER.warn "OpenTox::Ontology::Model.register ontology service is not reachable. Failed to register URI: #{uri} with subjectid: #{subjectid}"
+          false
+        end
+      end
+
+      # Deregister an OpenTox resource into ontology service
+      # @param [String] uri, URI of recource to deregister/delete
+      # @param [String] subjectid
+      def self.delete(uri, subjectid=nil)
+        begin
+          RestClientWrapper.delete("#{ONTOLOGY_SERVER}?uri=#{CGI.escape(uri)}", {:subjectid => CGI.escape(subjectid)})
+        rescue
+          LOGGER.warn "OpenTox::Ontology::Model.exists ontology service is not reachable. Failed to delete URI: #{uri} with subjectid: #{subjectid}"
+          false
+        end
+      end
+
+      # Find an OpenTox resource in the ontology service
+      # @param [String] uri, URI of recource to find
+      # @param [String] subjectid
+      def self.exists?(uri, subjectid=nil)
+        begin
+          out = RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{querystring(uri)}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.match(/^http/)}.uniq.compact
+          return true if out.size > 0
+          false
+        rescue
+          LOGGER.warn "OpenTox::Ontology::Model.exists ontology service is not reachable. Failed to check for URI: #{uri} with subjectid: #{subjectid}"
+          false
+        end
+      end
+
+      private
+      # 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#>
+        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 {
+          ?model rdf:type ot:Model;
+            OPTIONAL {?model dc:title ?title}.
+            OPTIONAL {?model dc:creator ?creator}.
+            OPTIONAL {?model ot:trainingDataset ?trainingDataset}.
+            OPTIONAL {?model ot:algorithm ?algorithm }.
+            FILTER (?model = <#{uri}>)
+          }")
+      end
+    end
+
   end
-end
+end

data/lib/opentox.rb

@@ -31,12 +31,14 @@ module OpenTox
   end
 
   def add_metadata(metadata)
-    metadata.each do |k,v|
-      if v.is_a? Array
-        @metadata[k] = [] unless @metadata[k]
-        @metadata[k] << v
-      else
-        @metadata[k] = v 
+    if !metadata.nil?
+      metadata.each do |k,v|
+        if v.is_a? Array
+          @metadata[k] = [] unless @metadata[k]
+          @metadata[k] << v
+        else
+          @metadata[k] = v 
+        end
       end
     end
   end
@@ -46,7 +48,6 @@ module OpenTox
   def to_rdfxml
     s = Serializer::Owl.new
     s.add_metadata(@uri,@metadata)
-    #s.add_parameters(@uri,@parameters) if @parameters
     s.to_rdfxml
   end
 

data/lib/serializer.rb

@@ -1,5 +1,6 @@
 require 'spreadsheet'
 require 'yajl'
+require 'yajl/json_gem'
 
 module OpenTox
 
@@ -21,6 +22,7 @@ module OpenTox
           OT.NominalFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.NumericFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.StringFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
+          OT.ModelPrediction => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.Dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.DataEntry => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.FeatureValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
@@ -69,6 +71,7 @@ module OpenTox
           OT.validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.crossvalidationInfo => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
+          OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
 
           DC.title => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           DC.identifier => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
@@ -131,7 +134,7 @@ module OpenTox
           OT.actor => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           OT.errorCode => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
 
-          OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
+          #OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
           OT.value => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
           OT.paramScope => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
           #OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
@@ -216,20 +219,24 @@ module OpenTox
         @@content_id = 1
         add_content uri, content
       end
+
+      def add_uri(uri,type)
+        @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => type }] }
+      end
       
       private
       @@content_id = 1
       
-      # Recursiv function to add content
-      # @example
-      # { DC.description => "bla",
-      #   OT.similar_resources => [ "http://uri1", "http://uri2" ],
-      #   OT.matrixCells => 
-      #     [ { RDF.type => OT.MatrixCell, OT.cellIndex=1 OT.cellValue => "xy" },
-      #       { RDF.type => OT.MatrixCell, OT.cellIndex=2 OT.cellValue => "z" } ],
-      #   OT.info => { RDF.type => OT.ImportantInfo, 
-      #                DC.description => "blub" }
-      # } 
+      #Recursiv function to add content
+      #@example
+      #  { DC.description => "bla",
+      #    OT.similar_resources => [ "http://uri1", "http://uri2" ],
+      #    OT.matrixCells =>
+      #      [ { RDF.type => OT.MatrixCell, OT.cellIndex=1 OT.cellValue => "xy" },
+      #        { RDF.type => OT.MatrixCell, OT.cellIndex=2 OT.cellValue => "z" } ],
+      #    OT.info => { RDF.type => OT.ImportantInfo,
+      #                 DC.description => "blub" }
+      #  }
       # @param [String] uri
       # @param [Hash] content as hash, uri must already have been added to @object
       def add_content(uri, hash)
@@ -268,28 +275,30 @@ module OpenTox
       # @param [Hash] metadata
       def add_metadata(uri,metadata)
         id = 0
-        metadata.each do |u,v|
-          #if v.is_a? Array and (u == OT.parameters or u == RDF.type)
-          if v.is_a? Array and u == OT.parameters#or u == RDF.type)
-            @object[uri][u] = [] unless @object[uri][u]
-            v.each do |value|
-              id+=1
-              genid = "_:genid#{id}"
-              @object[uri][u] << {"type" => "bnode", "value" => genid}
-              @object[genid] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Parameter}] }
-              value.each do |name,entry|
-                @object[genid][name] = [{"type" => type(entry), "value" => entry }]
-              end
-            end
-          elsif v.is_a? Array #and u == RDF.type
-            @object[uri] = {} unless @object[uri]
-            v.each do |value|
+        if !metadata.nil?
+          metadata.each do |u,v|
+            #if v.is_a? Array and (u == OT.parameters or u == RDF.type)
+            if v.is_a? Array and u == OT.parameters#or u == RDF.type)
               @object[uri][u] = [] unless @object[uri][u]
-              @object[uri][u] << {"type" => type(value), "value" => value }
+              v.each do |value|
+                id+=1
+                genid = "_:genid#{id}"
+                @object[uri][u] << {"type" => "bnode", "value" => genid}
+                @object[genid] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Parameter}] }
+                value.each do |name,entry|
+                  @object[genid][name] = [{"type" => type(entry), "value" => entry }]
+                end
+              end
+            elsif v.is_a? Array #and u == RDF.type
+              @object[uri] = {} unless @object[uri]
+              v.each do |value|
+                @object[uri][u] = [] unless @object[uri][u]
+                @object[uri][u] << {"type" => type(value), "value" => value }
+              end
+            elsif v.is_a? String
+              @object[uri] = {} unless @object[uri]
+              @object[uri][u] = [{"type" => type(v), "value" => v }]
             end
-          elsif v.is_a? String
-            @object[uri] = {} unless @object[uri]
-            @object[uri][u] = [{"type" => type(v), "value" => v }]
           end
         end
       end

data/lib/task.rb

@@ -182,7 +182,7 @@ module OpenTox
     end
 
     def load_metadata
-      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+      if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
         result = RestClientWrapper.get(@uri, {:accept => 'application/x-yaml'}, nil, false)
         @metadata = YAML.load result.to_s
         @http_code = result.code
@@ -209,7 +209,7 @@ module OpenTox
 
     def reload( accept_header=nil )
       unless accept_header 
-        if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host))
+        if (CONFIG[:json_hosts].include?(URI.parse(uri).host))
           accept_header = "application/x-yaml"
         else
           accept_header = 'application/rdf+xml'

data/lib/to-html.rb

@@ -33,10 +33,10 @@ module OpenTox
       user = OpenTox::Authorization.get_user(subjectid) if subjectid
       html +=  "<pre><p align=\"right\">"
       unless user
-        html += "You are currently not signed in to "+$url_provider.url_for("",:full)+
+        html += "You are currently not signed in to "+$url_provider.request.host.to_s+
           ", <a href="+$url_provider.url_for("/sign_in",:full)+">sign in</a>"
       else
-        html += "You are signed in as '#{user}' to "+$url_provider.url_for("",:full)+
+        html += "You are signed in as '#{user}' to "+$url_provider.request.host.to_s+
           ", <a href="+$url_provider.url_for("/sign_out",:full)+">sign out</a>"
       end
       html += "  </p></pre>"
@@ -61,7 +61,7 @@ module OpenTox
     html += "<form method='POST' action='"+$url_provider.url_for("/sign_in",:full)+"'>"
     html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
     html += msg+"\n\n" if msg
-    html += "Please sign in to "+$url_provider.url_for("",:full)+"\n\n"
+    html += "Please sign in to "+$url_provider.request.host.to_s+"\n\n"
     html += "<table border=0>"
     html += "<tr><td>user:</td><td><input type='text' name='user' size='15' /></td></tr>"+
           "<tr><td>password:</td><td><input type='password' name='password' size='15' /></td></tr>"+
@@ -111,9 +111,10 @@ module OpenTox
 end
 
 get '/sign_out/?' do
-  response.set_cookie("subjectid",{:value=>nil})
+  logout
   content_type "text/html"
-  content = "Sucessfully signed out from "+$url_provider.url_for("",:full)
+  content = "Sucessfully signed out from "+$url_provider.request.host.to_s+" ( Back to "+
+      $url_provider.url_for("",:full)+" )"
   OpenTox.text_to_html(content)
 end
 
@@ -123,11 +124,11 @@ get '/sign_in/?' do
 end
 
 post '/sign_in/?' do
-  subjectid = OpenTox::Authorization.authenticate(params[:user], params[:password])
+  subjectid = login(params[:user], params[:password])
   if (subjectid)
-    response.set_cookie("subjectid",{:value=>subjectid})
     content_type "text/html"
-    content = "Sucessfully signed in as '"+params[:user]+"' to "+$url_provider.url_for("",:full)
+    content = "Sucessfully signed in as '"+params[:user]+"' to "+$url_provider.request.host.to_s+" ( Back to "+
+      $url_provider.url_for("",:full)+" )"
     OpenTox.text_to_html(content,subjectid)    
   else
     content_type "text/html"

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby
 version: !ruby/object:Gem::Version 
-  hash: 11
+  hash: 7
   prerelease: 
   segments: 
-  - 2
-  - 1
+  - 3
   - 0
-  version: 2.1.0
+  - 0
+  version: 3.0.0
 platform: ruby
 authors: 
 - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-08-08 00:00:00 +02:00
+date: 2011-09-26 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -531,9 +531,8 @@ dependencies:
   version_requirements: *id032
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email: helma@in-silico.ch
-executables: 
-- opentox-install-debian.sh
-- opentox-install-ubuntu.sh
+executables: []
+
 extensions: []
 
 extra_rdoc_files: 
@@ -544,8 +543,6 @@ files:
 - README.markdown
 - Rakefile
 - VERSION
-- bin/opentox-install-debian.sh
-- bin/opentox-install-ubuntu.sh
 - lib/algorithm.rb
 - lib/authorization.rb
 - lib/compound.rb

data/bin/opentox-install-debian.sh

@@ -1,105 +0,0 @@
-#!/bin/bash
-#Installation is tested on Debian Lenny Ubuntu 9.04
-#Update the system
-
-ERRLOG='install_err.log'
-INSTALLLOG='install_log.log'
-DATE=$(date +%Y/%m/%d\ %H:%M:%S)
-
-echo "================================================="
-echo "Please enshure that the sudo package is installed"
-echo "on your system. "
-echo "On Ubuntu Linux sudo is installed by default."
-echo "If you are unshure check with it 'sudo ls'"
-echo "and installed it with 'apt-get install sudo'"
-echo "and add your username with visudo."
-echo "================================================="
-echo -n "To continue installation press y: "
-read answer
-if [ "$answer" != "y" ]
-then
-  echo "exiting the script..."
-  exit 1
-fi
-
-echo "opentox webservice install log - " $DATE > $INSTALLLOG
-echo "Installing: build-essential"
-sudo apt-get install build-essential >> $INSTALLLOG 2>>$ERRLOG
-echo "Installing: ruby 1.8 with its dev files"
-sudo apt-get install ruby ruby1.8-dev >> $INSTALLLOG 2>>$ERRLOG
-echo "Installing: gems rdoc rubygems and rake"
-sudo apt-get install gems rdoc rubygems rake >> $INSTALLLOG 2>>$ERRLOG
-
-echo "Installing rubygems from source. This may take some time"
-wget http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz >> $INSTALLLOG 2>>$ERRLOG
-tar xzfv rubygems-1.3.5.tgz 2>>$ERRLOG
-cd rubygems-1.3.5 >> $INSTALLLOG 2>>$ERRLOG
-sudo ruby setup.rb 2>>$ERRLOG
-cd ..
-
-echo "Adding http://gems.github.com to ruby gem sources"
-sudo gem sources -a http://gems.github.com >> $INSTALLLOG 2>>$ERRLOG
-
-#for debian lenny:
-echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5"
-sudo apt-get install zlib1g-dev tcl curl perl ssh tcl tk8.5  >> $INSTALLLOG 2>>$ERRLOG
-echo "Installing git from source"
-wget http://www.kernel.org/pub/software/scm/git/git-1.6.5.2.tar.gz >> $INSTALLLOG 2>>$ERRLOG
-tar xzfv git-1.6.5.2.tar.gz  2>>$ERRLOG
-cd git-1.6.5.2 >> $INSTALLLOG 2>>$ERRLOG
-./configure 2>>$ERRLOG
-make 2>>$ERRLOG
-make install 2>>$ERRLOG
-
-echo "Installing the opentox webservices"
-mkdir webservices >> $INSTALLLOG 2>>$ERRLOG
-cd webservices >> $INSTALLLOG 2>>$ERRLOG
-
-git clone git://github.com/helma/opentox-compound.git >> $INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-feature.git >> $INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-dataset.git >> $INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-algorithm.git >> $INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-model.git >> $INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-test.git  >> $INSTALLLOG 2>>$ERRLOG
-
-cd opentox-compound >> $INSTALLLOG 2>>$ERRLOG
-git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
-cd ../opentox-feature >> $INSTALLLOG 2>>$ERRLOG
-git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
-cd ../opentox-dataset >> $INSTALLLOG 2>>$ERRLOG
-git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
-cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
-git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
-cd ../opentox-model >> $INSTALLLOG 2>>$ERRLOG
-git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
-cd .. >> $INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-ruby-api-wrapper.git >> $INSTALLLOG 2>>$ERRLOG
-cd opentox-ruby-api-wrapper >> $INSTALLLOG 2>>$ERRLOG
-git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
-rake install >> $INSTALLLOG 2>>$ERRLOG
-
-
-cd ../opentox-compound >> $INSTALLLOG 2>>$ERRLOG
-echo "Installing libopenssl-ruby"
-sudo apt-get install libopenssl-ruby >> $INSTALLLOG 2>>$ERRLOG
-echo "Installing dtach"
-rake dtach:install >> $INSTALLLOG 2>>$ERRLOG
-echo "Installing openbabel"
-rake openbabel:install >> $INSTALLLOG 2>>$ERRLOG
-
-#debian lenny missed liblink:
-ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERRLOG
-
-rake redis:download >> $INSTALLLOG 2>>$ERRLOG
-rake redis:install >> $INSTALLLOG 2>>$ERRLOG
-#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
-sudo apt-get install libgsl0-dev >> $INSTALLLOG 2>>$ERRLOG
-sudo apt-get install swig >> $INSTALLLOG 2>>$ERRLOG
-sudo apt-get install curl >> $INSTALLLOG 2>>$ERRLOG
-cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
-echo "Installing fminer"
-rake fminer:install >> $INSTALLLOG 2>>$ERRLOG
-sudo apt-get install libsqlite3-dev >> $INSTALLLOG 2>>$ERRLOG
-
-
-mkdir ../opentox-model/db >> $INSTALLLOG 2>>$ERRLOG

data/bin/opentox-install-ubuntu.sh

@@ -1,375 +0,0 @@
-#!/bin/bash
-#Installation is tested on Debian Ubuntu 9.10
-#Update the system
-
-FAILED=0
-STARTPATH=$PWD
-ERRLOG=$PWD/'install_err.log'
-INSTALLLOG=$PWD/'install_log.log'
-DATE=$(date +%Y/%m/%d\ %H:%M:%S)
-BRANCH=$1
-GEMVERSION="1.3.5"
-GITVERSION="1.6.5.2"
-RAPTORVERSION="1.4.20"
-RASQALVERSION="0.9.16"
-RASQALVERSION2="0.9.15"
-REDLANDVERSION="1.0.7"
-REDBINDVERSION="1.0.7.1"
-
-if [ "$BRANCH" = '' ]
-then
-  echo "Please enter: sudo ./[filename] [brunchtpy]"
-  exit 1
-fi
-echo "================================================="
-echo "Selected branch is: $BRANCH"
-echo "================================================="
-echo "Please enshure that the sudo package is installed"
-echo "on your system. "
-echo "On Ubuntu Linux sudo is installed by default."
-echo "If you are unsure check with it 'sudo ls'"
-echo "and installed it with 'apt-get install sudo'"
-echo "and add your username with visudo."
-echo "================================================="
-echo "Some programs and the OpenTox webservices will be installed in the current folder."
-echo "================================================="
-echo -n "To continue installation press y: "
-read answer
-if [ "$answer" != "y" ]
-then
-  echo "exiting the script..."
-  exit 1
-fi
-
-echo "opentox webservice install log - " $DATE > $INSTALLLOG
-echo "opentox webservice install err log - " $DATE > $ERRLOG
-echo "Installing: build-essential"
-sudo apt-get install build-essential  | tee -a $INSTALLLOG
-
-echo "Installing: ruby 1.8 with its dev files"
-sudo apt-get install ruby ruby1.8-dev  | tee -a $INSTALLLOG
-
-echo "Installing: gems rdoc rubygems libxml-parser-ruby1.8 libxml++2.6-dev libyaml-ruby libzlib-ruby sqlite3 libsqlite3-dev libsqlite3-ruby1.8 and rake"
-sudo apt-get install gems rdoc rubygems libxml-parser-ruby1.8 libxml++2.6-dev libyaml-ruby libzlib-ruby rake sqlite3 libsqlite3-dev libsqlite3-ruby1.8 | tee -a $INSTALLLOG  
-
-#RUBYGEMS
-echo "Installing rubygems from source. This may take some time"
-if [ ! -d $STARTPATH/rubygems-$GEMVERSION ]; 
-then
-	wget http://rubyforge.org/frs/download.php/60718/rubygems-$GEMVERSION.tgz >>$INSTALLLOG 2>>$ERRLOG 
-	tar xzfv rubygems-$GEMVERSION.tgz  >>$INSTALLLOG 2>>$ERRLOG
-	cd rubygems-$GEMVERSION  
-	sudo ruby setup.rb  >>$INSTALLLOG 2>>$ERRLOG
-	cd ..
-	sudo rm rubygems-$GEMVERSION.tgz  
-	CHECKGEM=`gem -v` 
-	if [ "$CHECKGEM"  == "$GEMVERSION" ]
-	then
-		echo "Adding http://gems.github.com to ruby gem sources"
-		sudo gem sources -a http://gems.github.com  >>$INSTALLLOG 2>>$ERRLOG
-
-		echo "================================================="
-		echo "Rubygems version $GEMVERSION successfully installed."
-		echo "================================================="
-	else
-	    echo "Rubygems version $GEMVERSION installation failed."
-	    FAILED=1
-        exit $FAILED
-	fi
-else
-	echo "rubygems-$GEMVERSION folder already exist. "
-fi
-
-echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5 libopenssl-ruby libgsl0-dev swig r-base rinruby"
-sudo apt-get install zlib1g-dev tcl curl perl libopenssl-ruby libgsl0-dev r-base | tee -a $INSTALLLOG
-sudo apt-get install ssh tcl tk8.5 | tee -a $INSTALLLOG
-sudo apt-get install swig | tee -a $INSTALLLOG
-sudo apt-get install postgresql-server-dev-8.4 | tee -a $INSTALLLOG
-
-
-#echo "Installing gems jeweler sinatra emk-sinatra-url-for dm-core cehoffman-sinatra-respond_to rest-client rack-contrib thin cucumber datamapper data_objects do_sqlite3 rinruby"
-sudo gem install jeweler  | tee -a $INSTALLLOG
-sudo gem install sinatra | tee -a $INSTALLLOG
-sudo gem install emk-sinatra-url-for  -s http://gems.github.com | tee -a $INSTALLLOG
-sudo gem install dm-core  | tee -a $INSTALLLOG
-sudo gem install sinatra-respond_to | tee -a $INSTALLLOG
-sudo gem install rest-client | tee -a $INSTALLLOG
-sudo gem install rack-contrib | tee -a $INSTALLLOG
-sudo gem install thin | tee -a $INSTALLLOG
-sudo gem install cucumber | tee -a $INSTALLLOG
-sudo gem install datamapper | tee -a $INSTALLLOG
-sudo gem install data_objects | tee -a $INSTALLLOG
-sudo gem install do_sqlite3 | tee -a $INSTALLLOG
-sudo gem install rinruby | tee -a $INSTALLLOG
-sudo gem cleanup | tee -a $INSTALLLOG
-
-echo "Installing LibRDF-ruby"
-sudo apt-get install librdf0 librdf-ruby | tee -a $INSTALLLOG
-
-#GIT
-echo "Installing git from source"
-echo "This could take a while..."
-if [ ! -d $STARTPATH/git-$GITVERSION ];  
-then
-	wget http://www.kernel.org/pub/software/scm/git/git-$GITVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	tar xzfv git-$GITVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	cd git-$GITVERSION
-	./configure   >>$INSTALLLOG 2>>$ERRLOG
-	make   >>$INSTALLLOG 2>>$ERRLOG
-	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
-	cd ..
-	sudo rm git-$GITVERSION.tar.gz
-	CHECKGIT=`git --version`
-	if [ "$CHECKGIT"  == "git version $GITVERSION" ]
-	then
-		echo "================================================="
-    		echo "Git version $GITVERSION successfully installed."
-		echo "================================================="
-	else
-	    echo "Git version $GITVERSION installation failed."
-	    FAILED=1
-        exit $FAILED
-	fi
-else
-	echo "git-$GITVERSION folder exists."
-fi
-
-#REDLAND
-if [ ! -d $STARTPATH/redland ];
-then
-	echo "Making Redland folder."
-	mkdir redland >>$INSTALLLOG 2>>$ERRLOG
-	cd redland
-	echo "Installing Redland raptor"
-	if [ ! -d $STARTPATH/redland/raptor-$RAPTORVERSION ];
-	then
-		wget wget http://download.librdf.org/source/raptor-$RAPTORVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-		tar xzfv raptor-$RAPTORVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-		cd raptor-$RAPTORVERSION
-		./configure  >>$INSTALLLOG 2>>$ERRLOG
-		sudo make   >>$INSTALLLOG 2>>$ERRLOG
-		sudo make install   >>$INSTALLLOG 2>>$ERRLOG
-		cd ..
-		sudo rm raptor-$RAPTORVERSION.tar.gz
-		CHECKRAPTOR=`raptor-config --version`
-		if [ "$CHECKRAPTOR"  == "$RAPTORVERSION" ]
-		then
-			echo "================================================="
-			echo "Raptor version $RAPTORVERSION successfully installed."
-			echo "================================================="
-		else
-		    echo "Raptor version $RAPTORVERSION installation failed."
-		    FAILED=1
-            exit $FAILED
-		fi
-	else
-		echo "raptor-$RAPTORVERSION folder exists."
-	fi
-
-	echo "Installing Redland rasqal"
-	wget wget http://download.librdf.org/source/rasqal-$RASQALVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	tar xzfv rasqal-$RASQALVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	cd rasqal-$RASQALVERSION
-	./configure  >>$INSTALLLOG 2>>$ERRLOG
-	sudo make   >>$INSTALLLOG 2>>$ERRLOG
-	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
-	cd ..
-	sudo rm rasqal-$RASQALVERSION.tar.gz
-	CHECKRASQAL=`rasqal-config --version`
-	if [ "$CHECKRASQAL"  == "$RASQALVERSION2" -o  "$CHECKRASQAL"  == "$RASQALVERSION" ]
-	then
-		echo "================================================="
-		echo "Raptor version $RASQALVERSION2 or higher successfully installed."
-		echo "================================================="
-	else
-	    echo "Raptor version $RASQALVERSION2 or higher installation failed."
-	    FAILED=1
-        exit $FAILED
-	fi
-
-	echo "Installing Redland redland"
-	wget wget http://download.librdf.org/source/redland-$REDLANDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	tar xzfv redland-$REDLANDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	cd redland-$REDLANDVERSION
-	./configure  >>$INSTALLLOG 2>>$ERRLOG
-	sudo make   >>$INSTALLLOG 2>>$ERRLOG
-	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
-	cd ..
-	sudo rm redland-$REDLANDVERSION.tar.gz
-	CHECKREDLAND=`redland-config --version`
-	if [ "$CHECKREDLAND"  == "$REDLANDVERSION" ]
-	then
-		echo "================================================="
-		echo "Redland version $REDLANDVERSION successfully installed."
-		echo "================================================="
-	else
-	    echo "Redland version $REDLANDVERSION installation failed."
-	    FAILED=1
-        exit $FAILED
-	fi
-
-
-	echo "Installing Redland Bindings with ruby"
-	wget http://download.librdf.org/source/redland-bindings-$REDBINDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	tar xzfv redland-bindings-$REDBINDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
-	cd redland-bindings-$REDBINDVERSION
-	./configure --with-ruby  >>$INSTALLLOG 2>>$ERRLOG
-	sudo make   >>$INSTALLLOG 2>>$ERRLOG
-	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
-	cd ..
-	sudo rm redland-bindings-$REDBINDVERSION.tar.gz
-	cd ..
-	#CHECKREDBIND=`??? --version`
-	#if [ "$CHECKREDBIND"  == "$REDBINDVERSION" ]
-	#then
-	#	echo "================================================="
-	#	echo "Redland Bindings version $REDBINDVERSION successfully installed."
-	#	echo "================================================="
-	#else
-	#    echo "Redland Bindings version $REDBINDVERSION installation failed."
-	#    FAILED=1
-    #    exit $FAILED
-	#fi
-else
-	echo "Redland folder exists."
-fi
-
-echo "Installing the opentox webservices"
-mkdir webservices  
-cd webservices  
-
-echo "Install the opentox-ruby-api-wrapper"
-echo "This could take a while..."
-git clone git://github.com/helma/opentox-ruby-api-wrapper.git >>$INSTALLLOG 2>>$ERRLOG
-cd opentox-ruby-api-wrapper
-git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
-OTAPIVERSION=`cat VERSION`
-sudo rake install  | tee -a $INSTALLLOG
-cd ..
-CHECKOTAPI=`gem list | grep "opentox-ruby-api-wrapper" | grep "$OTAPIVERSION"`
-if [ ! "$CHECKOTAPI" = '' ]
-then
-	echo "================================================="
-    	echo "opentox-ruby-api-wrapper ($OTAPIVERSION) successfully installed."
-	echo "================================================="
-else
-	echo "opentox-ruby-api-wrapper ($OTAPIVERSION) installation failed."
-	FAILED=1
-    exit $FAILED
-fi
-
-echo "Installing the webservices: compound, dataset, algorithm, model, task, feature"
-git clone git://github.com/helma/opentox-compound.git >>$INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-dataset.git >>$INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-algorithm.git >>$INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-model.git >>$INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-task.git >>$INSTALLLOG 2>>$ERRLOG
-git clone git://github.com/helma/opentox-feature.git >>$INSTALLLOG 2>>$ERRLOG
-
-cd opentox-compound  
-git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG 
-cd ../opentox-dataset  
-git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
-cd ../opentox-algorithm  
-git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
-cd ../opentox-model  
-git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
-cd ../opentox-task
-git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
-cd ../opentox-task
-git checkout -b development origin/development >>$INSTALLLOG 2>>$ERRLOG
-cd ..  
-
-#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
-
-echo "Installing the tests"                                                   
-git clone git://github.com/helma/opentox-test.git  >>$INSTALLLOG 2>>$ERRLOG   
-cd opentox-test                                                               
-git checkout -b $BRANCH origin/$BRANCH  >>$INSTALLLOG 2>>$ERRLOG       
-
-echo "Installing openbabel"
-cd ../opentox-compound
-sudo rake openbabel:install | tee -a $INSTALLLOG
-sudo ldconfig >>$INSTALLLOG 2>>$ERRLOG
-
-ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERR
-#VERSION=` --version`
-#if [ "$VERSION"  == "$RAPTORVERSION" ]
-#then
-#	echo "================================================="
-#    	echo "Raptor version $RAPTORVERSION successfully installed."
-#	echo "================================================="
-#else
-#    echo "Raptor version $RAPTORVERSION installation failed."
-#    FAILED=1
-#    exit $FAILED
-#fi
-
-
-#check /webservices/opentox-algorithm/fminer.rb for 1,0/ture,false bug
-BUGCHECK1=`grep "@@fminer.AddActivity(true, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
-BUGCHECK2=`grep "@@fminer.AddActivity(false, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
-if [ -z "$BUGCHECK1$BUGCHECK2" ]
-then
-        echo "fminer.rb is correct."
-else
-        sed -i 's/@@fminer.AddActivity(true, id)/@@fminer.AddActivity(1, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
-        sed -i 's/@@fminer.AddActivity(false, id)/@@fminer.AddActivity(0, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
-        echo "fminer.rb updated."
-fi
-
-#todo: configure libfminer Makefile (location of ruby.h)
-#-> fixed by using davor's repository
-
-
-cd ../opentox-algorithm
-echo "Installing fminer"
-echo "This could take a while..."
-sudo updatedb
-sudo rake fminer:install | tee -a $INSTALLLOG
-cd ..
-FMINERVERSION=`ls $STARTPATH/webservices/opentox-algorithm/libfminer | grep "fminer.so"`
-if [ "$FMINERVERSION"  == "fminer.so" ]
-then
-	echo "================================================="
-    	echo "Fminer successfully installed."
-	echo "================================================="
-else
-    echo "Fminer installation failed."
-    FAILED=1
-    exit $FAILED
-fi
-
-if [ $FAILED == 0 ]
-then
-	#get username
-	echo "Please enter username:"
-	read USERNAME
-
-	#change rights from root to user
-	sudo chown -R $USERNAME: $STARTPATH/webservices/
-	sudo chown -R $USERNAME: ~/.opentox/
-fi
-
-if [ "$FAILED" == "1" ]
-then
-	echo "================================================="
-    	echo "Installation script failed!"
-	echo "================================================="
-    	exit 1
-else
-echo "================================================="
-echo "opentox-install-script is completed."
-echo "================================================="
-echo "Configuration:"
-echo "Edit the settings in $HOME/.opentox/config/{development|production|test}.yaml for your environment."
-echo "================================================="
-echo "Start the webservices local:"
-echo "cd webservices/opentox-test/"
-echo "rake opentox:services:start"
-echo "================================================="
-echo "Test local webservices:"
-echo "rake features"
-echo "================================================="
-fi
-exit 0