opentox-ruby 1.0.2 → 2.0.0

data/Rakefile

@@ -28,8 +28,17 @@ begin
       "tmail",
       "rinruby",
       "ohm",
+      "ohm-contrib",
       "SystemTimer",
-      "rjb"
+      "rjb",
+      #valiation-gems
+      "dm-core", 
+      "dm-serializer", 
+      "dm-timestamps",
+      "dm-types", 
+      "dm-migrations", 
+      "dm-validations", 
+      "dm-sqlite-adapter"
     ].each { |dep| gem.add_dependency dep }
 =begin
     [ "dm-core",
@@ -41,11 +50,12 @@ begin
       "dm-validations",
     ].each {|dep| gem.add_dependency dep, ">= 1" }
 =end
+    #valiation-gem
     gem.add_dependency "haml", ">=3"
+    # validation-gems
+    gem.add_dependency "ruby-plot", "~>0.4.0"
     ['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

data/VERSION

@@ -1 +1 @@
-1.0.2
+2.0.0

data/lib/algorithm.rb

@@ -52,9 +52,9 @@ module OpenTox
       class BBRC
         include Fminer
         # Initialize bbrc algorithm
-        def initialize
+        def initialize(subjectid=nil)
           super File.join(CONFIG[:services]["opentox-algorithm"], "fminer/bbrc")
-          load_metadata
+          load_metadata(subjectid)
         end
       end
 
@@ -62,9 +62,9 @@ module OpenTox
       class LAST
         include Fminer
         # Initialize last algorithm
-        def initialize
+        def initialize(subjectid=nil)
           super File.join(CONFIG[:services]["opentox-algorithm"], "fminer/last")
-          load_metadata
+          load_metadata(subjectid)
         end
       end
 
@@ -74,9 +74,9 @@ module OpenTox
     class Lazar
       include Algorithm
       # Initialize lazar algorithm
-      def initialize
+      def initialize(subjectid=nil)
         super File.join(CONFIG[:services]["opentox-algorithm"], "lazar")
-        load_metadata
+        load_metadata(subjectid)
       end
     end
 
@@ -165,11 +165,19 @@ module OpenTox
       # @param [Hash] params Keys `:similarity_algorithm,:p_values` are required
       # @return [Hash] Hash with keys `:prediction, :confidence`
       def self.local_svm_regression(neighbors,params )
-        sims = neighbors.collect{ |n| n[:similarity] } # similarity values between query and neighbors
+        sims = neighbors.collect{ |n| Algorithm.gauss(n[:similarity]) } # similarity values between query and neighbors
         conf = sims.inject{|sum,x| sum + x }
+
+        # AM: Control log taking
+        take_logs=true
+        neighbors.each do |n| 
+          if (! n[:activity].nil?) && (n[:activity].to_f < 0.0)
+            take_logs = false
+          end
+        end
         acts = neighbors.collect do |n|
           act = n[:activity] 
-          Math.log10(act.to_f)
+          take_logs ? Math.log10(act.to_f) : act.to_f
         end # activities of neighbors for supervised learning
 
         neighbor_matches = neighbors.collect{ |n| n[:features] } # as in classification: URIs of matches
@@ -214,8 +222,8 @@ module OpenTox
           @r.eval "sims<-as.kernelMatrix(matrix(sims,1))"
           LOGGER.debug "Predicting ..."
           @r.eval "p<-predict(model,sims)[1,1]"
-          prediction = 10**(@r.p.to_f)
-          LOGGER.debug "Prediction is: '" + @prediction.to_s + "'."
+          prediction = 10**(@r.p.to_f) if take_logs
+          LOGGER.debug "Prediction is: '" + prediction.to_s + "'."
           @r.quit # free R
         end
         confidence = conf/neighbors.size if neighbors.size > 0

data/lib/authorization.rb

@@ -137,16 +137,23 @@ module OpenTox
     # Lists policies alongside with affected uris
     # @param [String] subjectid
     # @return [Hash] keys: all policies of the subjectid owner, values: uris affected by those policies
-    def self.list_policy_uris( subjectid )
+    def self.list_policies_uris( subjectid )
       names = list_policies(subjectid)
       policies = {}
       names.each do |n|
-        p = OpenTox::Policies.new
-        p.load_xml( list_policy(n, subjectid) )
-        policies[n] = p.uris
+        policies[n] = list_policy_uris( n, subjectid )
       end
       policies
     end
+
+    # Lists policies alongside with affected uris
+    # @param [String] subjectid
+    # @return [Hash] keys: all policies of the subjectid owner, values: uris affected by those policies
+    def self.list_policy_uris( policy, subjectid )
+      p = OpenTox::Policies.new
+      p.load_xml( list_policy(policy, subjectid) )
+      p.uris
+    end
     
     #Returns the owner (who created the first policy) of an URI
     # @param [String, String]uri,subjectid
@@ -220,7 +227,9 @@ module OpenTox
       begin
         resource = RestClient::Resource.new("#{AA_SERVER}/opensso/identity/search")
         grps = resource.post(:admin => subjectid, :attributes_names => "objecttype", :attributes_values_objecttype => "group")
-        grps.split("\n").collect{|x|  x.sub("string=","")}
+        grps = grps.split("\n").collect{|x|  x.sub("string=","")}
+        grps.delete_if{|g|g=="MemberManagement"||g=="Webmasters"}
+        grps
       rescue
         []
       end
@@ -279,10 +288,12 @@ module OpenTox
     # @return [Boolean]
     def self.delete_policies_from_uri(uri, subjectid)
       policies = list_uri_policies(uri, subjectid)
-      policies.each do |policy|
-        ret = delete_policy(policy, subjectid)
-        LOGGER.debug "OpenTox::Authorization delete policy: #{policy} - with result: #{ret}"
-      end    
+      if policies
+        policies.each do |policy|
+          ret = delete_policy(policy, subjectid)
+          LOGGER.debug "OpenTox::Authorization delete policy: #{policy} - with result: #{ret}"
+        end
+      end
       return true
     end
 

data/lib/dataset.rb

@@ -74,7 +74,7 @@ module OpenTox
     # @param [optional,String] uri URI of the dataset service, defaults to service specified in configuration
     # @return [Array] Array of dataset object without data (use one of the load_* methods to pull data from the server)
     def self.all(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil)
-      RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u, subjectid)}
+      RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u.chomp, subjectid)}
     end
 
     # Load YAML representation into the dataset
@@ -158,29 +158,42 @@ module OpenTox
     # Load and return only features from the dataset service
     # @return [Hash]  Features of the dataset
     def load_features(subjectid=nil)
-      parser = Parser::Owl::Dataset.new(@uri, subjectid)
-      @features = parser.load_features(subjectid)
+      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+        @features = YAML.load(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/x-yaml", :subjectid => subjectid}))
+      else
+        parser = Parser::Owl::Dataset.new(@uri, subjectid)
+        @features = parser.load_features(subjectid)
+      end
       @features
     end
 
+    def feature_classes(feature, subjectid=nil)
+      if Feature.find(feature, subjectid).feature_type == "classification"
+        classes = []
+        @data_entries.each do |c,e|
+          e[feature].each { |v| classes << v.to_s }
+        end
+        classes.uniq.sort
+      else
+        nil
+      end
+    end
+
+=begin
     # Detect feature type(s) in the dataset
     # @return [String] `classification", "regression", "mixed" or unknown`
     def feature_type(subjectid=nil)
       load_features(subjectid)
-      feature_types = @features.collect{|f,metadata| metadata[OT.isA]}.uniq
-      if feature_types.size > 1
-        "mixed"
+      feature_types = @features.collect{|f,metadata| metadata[RDF.type]}.flatten.uniq
+      if feature_types.include?(OT.NominalFeature)
+        "classification"
+      elsif feature_types.include?(OT.NumericFeature)
+        "regression"
       else
-        case feature_types.first
-        when /NominalFeature/
-          "classification"
-        when /NumericFeature/
-          "regression"
-        else
-          "unknown"
-        end
+        "unknown"
       end
     end
+=end
 
     # Get Spreadsheet representation
     # @return [Spreadsheet::Workbook] Workbook which can be written with the spreadsheet gem (data_entries only, metadata will will be discarded))
@@ -284,7 +297,7 @@ module OpenTox
       else
         compounds.each do |c|
           features.each do |f|
-            unless @data_entries[c][f]
+            if @data_entries[c]==nil or @data_entries[c][f]==nil
               dataset.add(c,f,nil)
             else
               @data_entries[c][f].each do |v|

data/lib/environment.rb

@@ -23,7 +23,7 @@ else
 end
 
 # database
-`redis-server /opt/redis/redis.conf` unless File.exists? "/var/run/redis.pid"
+#`redis-server /opt/redis/redis.conf` unless File.exists? "/var/run/redis.pid" # removed by AM
 Ohm.connect :thread_safe => true
 
 # load mail settings for error messages

data/lib/error.rb

@@ -69,7 +69,7 @@ module OpenTox
     
     def rdf_content()
       c = {
-        RDF.type => OT.ErrorReport,
+        RDF.type => [OT.ErrorReport],
         OT.statusCode => @http_code,
         OT.message => @message,
         OT.actor => @actor,
@@ -96,4 +96,4 @@ class Array
     end
     short.join("\n")
   end
-end
+end

data/lib/feature.rb

@@ -16,23 +16,19 @@ module OpenTox
       feature
     end
     
-    # provides domain (possible target values) of classification feature 
-    # @return [Array] list with possible target values
-    def domain
-      if metadata[OT.acceptValue]
-        raise "accept value found, remove hack and implement correctly"
-      else
-      if @uri=~/feature\/26221/ || @uri=~/feature\/221726/ 
-        return ["mutagen" , "nonmutagen"]
-      end
-        return [true, false]
-      end
-    end
-    
     # provides feature type, possible types are "regression" or "classification"
     # @return [String] feature type, unknown if OT.isA property is unknown/ not set
     def feature_type
-      case metadata[OT.isA]
+      if metadata[RDF.type].flatten.include?(OT.NominalFeature)
+        "classification"
+      elsif metadata[RDF.type].flatten.include?(OT.NumericFeature)
+        "regression"
+      else
+        #"unknown"
+        metadata[RDF.type].inspect
+      end
+=begin
+      case metadata[RDF.type]
       when /NominalFeature/
         "classification"
       when /NumericFeature/
@@ -40,6 +36,7 @@ module OpenTox
       else
         "unknown"
       end
+=end
     end    
     
   end

data/lib/helper.rb

@@ -44,21 +44,12 @@ helpers do
 
   def uri_available?(urlStr)
     url = URI.parse(urlStr)
-    unless @subjectid
-      Net::HTTP.start(url.host, url.port) do |http|
-        return http.head(url.request_uri).code == "200"
-      end
-    else
-      Net::HTTP.start(url.host, url.port) do |http|
-        return http.post(url.request_uri, "subjectid=#{@subjectid}").code == "202"
-      end
+    Net::HTTP.start(url.host, url.port) do |http|
+      return http.head("#{url.request_uri}?subjectid=#{CGI.escape @subjectid}").code == "200"
     end
   end
 
-end
-
-before do
-  unless !AA_SERVER or login_requests or CONFIG[:authorization][:free_request].include?(env['REQUEST_METHOD']) 
+  def get_subjectid
     begin
       subjectid = nil
       subjectid = session[:subjectid] if session[:subjectid]
@@ -69,31 +60,37 @@ before do
       subjectid = CGI.unescape(subjectid) if subjectid.include?("%23")
       @subjectid = subjectid
     rescue
-      #LOGGER.debug "OpenTox ruby api wrapper: helper before filter: NO subjectid for URI: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}"
-      subjectid = ""
+      subjectid = nil
     end
-    @subjectid = subjectid
-    protected!(subjectid)
-
-    extension = File.extname(request.path_info) # params[:id] is not yet available
+  end
+  def get_extension
+    extension = File.extname(request.path_info)
     unless extension.empty?
-     #request.path_info.sub!(/\.#{extension}$/,'')
-     case extension
-     when "html"
-       @accept = 'text/html'
-     when "yaml"
-       @accept = 'application/x-yaml'
-     when "csv"
-       @accept = 'text/csv'
-     when "rdfxml"
-       @accept = 'application/rdf+xml'
-     when "xls"
-       @accept = 'application/ms-excel'
-     else
-       halt 404, "File format #{extension} not supported."
-     end
-   end
-  
+      case extension.gsub(".","")
+      when "html"
+        @accept = 'text/html'
+      when "yaml"
+        @accept = 'application/x-yaml'
+      when "csv"
+         @accept = 'text/csv'
+      when "rdfxml"
+        @accept = 'application/rdf+xml'
+      when "xls"
+        @accept = 'application/ms-excel'
+      when "css"
+        @accept = 'text/css'
+      else
+        # halt 404, "File format #{extension} not supported."
+      end
+    end
+  end
+end
+
+before do 
+  @subjectid = get_subjectid()
+  @accept = get_extension()
+  unless !AA_SERVER or login_requests or CONFIG[:authorization][:free_request].include?(env['REQUEST_METHOD'])
+    protected!(@subjectid)
   end
 end
 

data/lib/model.rb

@@ -44,11 +44,10 @@ module OpenTox
         load_metadata(subjectid) if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
         algorithm = OpenTox::Algorithm::Generic.find(@metadata[OT.algorithm], subjectid)
         algorithm_title = algorithm ? algorithm.metadata[DC.title] : nil
-        algorithm_type = algorithm ? algorithm.metadata[OT.isA] : nil
+        algorithm_type = algorithm ? algorithm.metadata[RDF.type] : nil
         dependent_variable = OpenTox::Feature.find( @metadata[OT.dependentVariables],subjectid )
         dependent_variable_type = dependent_variable ? dependent_variable.feature_type : nil
-        type_indicators = [dependent_variable_type, @metadata[OT.isA], @metadata[DC.title], 
-          @uri, algorithm_type, algorithm_title] 
+        type_indicators = [dependent_variable_type, @metadata[RDF.type], @metadata[DC.title], @uri, algorithm_type, algorithm_title].flatten
         type_indicators.each do |type|
           case type
           when /(?i)classification/
@@ -113,9 +112,10 @@ module OpenTox
       # @param [optional,Hash] params Parameters for the lazar algorithm (OpenTox::Algorithm::Lazar)
       # @return [OpenTox::Model::Lazar] lazar model
       def self.create(params)
+        subjectid = params[:subjectid]
         lazar_algorithm = OpenTox::Algorithm::Generic.new File.join( CONFIG[:services]["opentox-algorithm"],"lazar")
         model_uri = lazar_algorithm.run(params)
-        OpenTox::Model::Lazar.find(model_uri, params[:subjectid])
+        OpenTox::Model::Lazar.find(model_uri, subjectid)      
       end
 
       # Get a parameter value
@@ -187,7 +187,7 @@ module OpenTox
 
         if @neighbors.size == 0
           @prediction_dataset.add_feature(prediction_feature_uri, {
-            OT.isA => OT.MeasuredFeature,
+            RDF.type => [OT.MeasuredFeature],
             OT.hasSource => @uri,
             DC.creator => @uri,
             DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )),
@@ -198,7 +198,7 @@ module OpenTox
 
         else
           @prediction_dataset.add_feature(prediction_feature_uri, {
-            OT.isA => OT.ModelPrediction,
+            RDF.type => [OT.ModelPrediction],
             OT.hasSource => @uri,
             DC.creator => @uri,
             DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )),
@@ -215,7 +215,7 @@ module OpenTox
                 feature_uri = File.join( @prediction_dataset.uri, "feature", "descriptor", f.to_s)
                 features[feature] = feature_uri
                 @prediction_dataset.add_feature(feature_uri, {
-                  OT.isA => OT.Substructure,
+                  RDF.type => [OT.Substructure],
                   OT.smarts => feature,
                   OT.pValue => @p_values[feature],
                   OT.effect => @effects[feature]
@@ -236,7 +236,7 @@ module OpenTox
                 OT.compound => neighbor[:compound],
                 OT.similarity => neighbor[:similarity],
                 OT.measuredActivity => neighbor[:activity],
-                OT.isA => OT.Neighbor
+                RDF.type => [OT.Neighbor]
               })
               @prediction_dataset.add @compound.uri, neighbor_uri, true
               f = 0 unless f
@@ -250,7 +250,7 @@ module OpenTox
                 unless features.has_key? feature
                   features[feature] = feature_uri
                   @prediction_dataset.add_feature(feature_uri, {
-                    OT.isA => OT.Substructure,
+                    RDF.type => [OT.Substructure],
                     OT.smarts => feature,
                     OT.pValue => @p_values[feature],
                     OT.effect => @effects[feature]

data/lib/{ontology_service.rb → ontology.rb}

@@ -1,6 +1,7 @@
 module OpenTox
-  module OntologyService
-    module Endpoints
+  module Ontology
+    module Echa
+=begin
       require 'sparql/client'
       @sparql = SPARQL::Client.new("http://apps.ideaconsult.net:8080/ontology")
       def self.qs(classname="Endpoints")
@@ -12,11 +13,11 @@ 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 +39,17 @@ module OpenTox
         out += "</select>\n"
         return out
       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
+      end
+
+      def self.datasets(endpoint)
+        RestClientWrapper.get("http://apps.ideaconsult.net:8080/ambit2/dataset?feature_sameas=#{URI.encode endpoint}", :accept => "text/uri-list").split("\n")
+      end
+
     end
+
   end
-end
+end

data/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

data/lib/opentox.rb

@@ -31,7 +31,14 @@ module OpenTox
   end
 
   def add_metadata(metadata)
-    metadata.each { |k,v| @metadata[k] = v }
+    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
 
   # Get OWL-DL representation in RDF/XML format

data/lib/overwrite.rb

@@ -8,6 +8,7 @@ before {
   $url_provider = self
   # stupid internet explorer does not ask for text/html, add this manually 
   request.env['HTTP_ACCEPT'] += ";text/html" if request.env["HTTP_USER_AGENT"]=~/MSIE/
+  request.env['HTTP_ACCEPT']=request.params["media"] if request.params["media"]
 }
 
 # Error handling
@@ -39,20 +40,24 @@ end
 class Sinatra::Base
 
   def return_task( task )
-    code = task.running? ? 202 : 200
+    raise "http_code == nil" unless task.http_code!=nil
     case request.env['HTTP_ACCEPT']
     when /rdf/
       response['Content-Type'] = "application/rdf+xml"
-      halt code,task.to_rdfxml
+      halt task.http_code,task.to_rdfxml
     when /yaml/
       response['Content-Type'] = "application/x-yaml"
-      halt code,task.to_yaml # PENDING differs from task-webservice
+      halt task.http_code,task.to_yaml # PENDING differs from task-webservice
     when /html/
       response['Content-Type'] = "text/html"
-      halt code,OpenTox.text_to_html(task.to_yaml, @subjectid)
+      halt task.http_code,OpenTox.text_to_html(task.to_yaml, @subjectid)
     else # default /uri-list/
       response['Content-Type'] = "text/uri-list"
-      halt code,task.uri+"\n"
+      if task.completed?
+        halt task.http_code,task.resultURI+"\n"
+      else
+        halt task.http_code,task.uri+"\n"
+      end
     end
   end
 end

data/lib/parser.rb

@@ -55,7 +55,14 @@ module OpenTox
         parameter_ids = []
         `rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`.each_line do |line|
           triple = line.to_triple
-          @metadata[triple[1]] = triple[2].split('^^').first if triple[0] == @uri and triple[1] != RDF['type']
+          if triple[0] == @uri
+            if triple[1] == RDF.type # allow multiple types
+              @metadata[triple[1]] = [] unless @metadata[triple[1]]
+              @metadata[triple[1]] << triple[2].split('^^').first
+            else
+              @metadata[triple[1]] = triple[2].split('^^').first
+            end
+          end
           statements << triple 
           parameter_ids << triple[2] if triple[1] == OT.parameters
         end
@@ -156,6 +163,7 @@ module OpenTox
           data = {}
           feature_values = {}
           feature = {}
+          feature_accept_values = {}
           other_statements = {}
           `rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`.each_line do |line|
             triple = line.chomp.split(' ',3)
@@ -175,6 +183,9 @@ module OpenTox
               if triple[2]=~/#{OT.Compound}/i and !data[triple[0]]
                 data[triple[0]] = {:compound => triple[0], :values => []} 
               end
+            when /#{OT.acceptValue}/i # acceptValue in ambit datasets is only provided in dataset/<id> no in dataset/<id>/features  
+              feature_accept_values[triple[0]] = [] unless feature_accept_values[triple[0]]
+              feature_accept_values[triple[0]] << triple[2]
             else 
             end
           end
@@ -185,20 +196,25 @@ module OpenTox
               @dataset.add_compound(entry[:compound])
             else
               entry[:values].each do |value_id|
-                split = feature_values[value_id].split(/\^\^/)
-                case split[-1]
-                when XSD.double, XSD.float 
-                  value = split.first.to_f
-                when XSD.boolean
-                  value = split.first=~/(?i)true/ ? true : false                
-                else
-                  value = split.first
+                if feature_values[value_id]
+                  split = feature_values[value_id].split(/\^\^/)
+                  case split[-1]
+                  when XSD.double, XSD.float 
+                    value = split.first.to_f
+                  when XSD.boolean
+                    value = split.first=~/(?i)true/ ? true : false                
+                  else
+                    value = split.first
+                  end
                 end
                 @dataset.add entry[:compound],feature[value_id],value
               end
             end
           end
           load_features subjectid
+          feature_accept_values.each do |feature, values|
+            @dataset.features[feature][OT.acceptValue] = values
+          end
           @dataset.metadata = load_metadata(subjectid)
           @dataset
         end
@@ -223,7 +239,7 @@ module OpenTox
           `rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`.each_line do |line|
             triple = line.chomp.split('> ').collect{|i| i.sub(/\s+.$/,'').gsub(/[<>"]/,'')}[0..2]
             statements << triple
-            features << triple[0] if triple[1] == RDF['type'] and (triple[2] == OT.Feature || triple[2] == OT.NumericFeature) 
+            features << triple[0] if triple[1] == RDF.type and (triple[2] =~ /Feature|Substructure/) 
           end
           File.delete(to_delete) if to_delete
           statements.each do |triple|
@@ -289,7 +305,7 @@ module OpenTox
           else
             type = types.first
           end
-          @dataset.add_feature_metadata(feature,{OT.isA => type})
+          @dataset.add_feature_metadata(feature,{RDF.type => [type]})
           info += "\"#{@dataset.feature_name(feature)}\" detected as #{type.split('#').last}."
 
           # TODO: rewrite feature values
@@ -341,16 +357,23 @@ module OpenTox
           when OT.NominalFeature
             case value.to_s
             when TRUE_REGEXP
-              @dataset.add(compound.uri, feature, true )
+              val = true
             when FALSE_REGEXP
-              @dataset.add(compound.uri, feature, false )
+              val = false
             end
           when OT.NumericFeature
-            @dataset.add compound.uri, feature, value.to_f
+            val = value.to_f
           when OT.StringFeature
-            @dataset.add compound.uri, feature, value.to_s
+            val = value.to_s
             @activity_errors << smiles+", "+row.join(", ")
           end
+          if val!=nil
+            @dataset.add(compound.uri, feature, val)
+            if type!=OT.NumericFeature
+              @dataset.features[feature][OT.acceptValue] = [] unless @dataset.features[feature][OT.acceptValue]
+              @dataset.features[feature][OT.acceptValue] << val.to_s unless @dataset.features[feature][OT.acceptValue].include?(val.to_s)
+            end
+          end
         end
       end
 

data/lib/rest_client_wrapper.rb

@@ -98,6 +98,8 @@ module OpenTox
         
       rescue RestClient::RequestTimeout => ex
         received_error ex.message, 408, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
+      rescue Errno::ETIMEDOUT => ex
+        received_error ex.message, 408, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
       rescue Errno::ECONNREFUSED => ex
         received_error ex.message, 500, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
       rescue RestClient::ExceptionWithResponse => ex

data/lib/serializer.rb

@@ -26,6 +26,8 @@ module OpenTox
           OT.Algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.Parameter => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.Task => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
+          OTA.PatternMiningSupervised => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
+
           #classes for validation
           OT.Validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.ClassificationStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
@@ -40,10 +42,10 @@ module OpenTox
           OT.compound => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.feature => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.dataEntry => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
-          OT.acceptValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.values => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.parameters => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
+
           #object props for validation#           
           OT.model => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.trainingDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
@@ -67,12 +69,14 @@ module OpenTox
           DC.creator => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           DC.description => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           DC.date => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
-          OT.isA => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
+          #OT.isA => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           OT.Warnings => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           XSD.anyURI => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           OT.hasStatus => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           OT.resultURI => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           OT.percentageCompleted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
+          OT.acceptValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
+
           # annotation props for validation        
           OT.numUnpredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           OT.crossvalidationFold => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
@@ -256,7 +260,8 @@ module OpenTox
       def add_metadata(uri,metadata)
         id = 0
         metadata.each do |u,v|
-          if v.is_a? Array and u == OT.parameters
+          #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
@@ -267,7 +272,13 @@ module OpenTox
                 @object[genid][name] = [{"type" => type(entry), "value" => entry }]
               end
             end
-          else # v.is_a? String
+          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
@@ -309,6 +320,7 @@ module OpenTox
           OT.value => v
         }
         @object[feature][RDF["type"]] << { "type" => "uri", "value" => featuretype(value) }
+        #@object[feature][RDF["type"]] = { "type" => "uri", "value" => featuretype(value) }
       end
 
       # Serializers

data/lib/task.rb

@@ -8,6 +8,7 @@ module OpenTox
     
     def initialize(uri=nil)
       super uri
+      @http_code = 202
       @metadata = {
         DC.title => "",
         DC.date => "",
@@ -154,6 +155,7 @@ module OpenTox
     
     # not stored just for to_rdf
     def add_error_report( error_report )
+      raise "not an error report: "+error_report.class.to_s unless error_report.is_a?(ErrorReport)
       @error_report = error_report
     end
     

data/lib/validation.rb

@@ -12,6 +12,40 @@ module OpenTox
       val
     end
     
+    # returns a filtered list of validation uris
+    # @param [Hash,optional] params, validation-params to filter the uris (could be model, training_dataset, ..)  
+    # @return [Array]    
+    def self.list( params={} )
+      filter_string = ""
+      params.each do |k,v|
+        filter_string = "?" if filter_string.length==0 
+        filter_string += k.to_s+"="+v
+      end
+      (OpenTox::RestClientWrapper.get(CONFIG[:services]["opentox-validation"]+filter_string).split("\n"))
+    end
+    
+    # creates a training test split validation, waits until it finishes, may take some time
+    # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,split_ratio(0.67),random_seed(1))
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::Validation]
+    def self.create_training_test_split( params, subjectid=nil, waiting_task=nil )
+      params[:subjectid] = subjectid if subjectid
+      uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"training_test_split"),
+        params,{:content_type => "text/uri-list"},waiting_task )
+      Validation.new(uri)
+    end
+    
+    # looks for report for this validation, creates a report if no report is found
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [String] report uri
+    def find_or_create_report( subjectid=nil, waiting_task=nil )
+      @report = ValidationReport.find_for_validation(@uri, subjectid) unless @report
+      @report = ValidationReport.create(@uri, subjectid, waiting_task) unless @report
+      @report.uri
+    end
+    
     # creates a validation object from crossvaldiation statistics, raise error if not found
     # (as crossvaldiation statistics are returned as an average valdidation over all folds)
     # @param [String] crossvalidation uri
@@ -42,7 +76,7 @@ module OpenTox
             res[:true_negatives] = s[OT.numTrueNegatives]
             res[:false_negatives] = s[OT.numFalseNegatives]
             res[:sensitivity] = s[OT.truePositiveRate]
-            res[:specificity] = s[OT.falsePositiveRate]
+            res[:specificity] = s[OT.trueNegativeRate]
             break
           end
         end
@@ -72,6 +106,18 @@ module OpenTox
       cv.load_metadata( subjectid )
       cv
     end
+    
+    # returns a filtered list of crossvalidation uris
+    # @param [Hash,optional] params, crossvalidation-params to filter the uris (could be algorithm, dataset, ..)  
+    # @return [Array]    
+    def self.list( params={} )
+      filter_string = ""
+      params.each do |k,v|
+        filter_string = "?" if filter_string.length==0 
+        filter_string += k.to_s+"="+v
+      end
+      (OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation")+filter_string).split("\n"))
+    end
 		
     # creates a crossvalidations, waits until it finishes, may take some time
     # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,num_folds(10),random_seed(1),stratified(false))
@@ -110,6 +156,17 @@ module OpenTox
   class ValidationReport
     include OpenTox
     
+    # finds ValidationReport via uri, raises error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::ValidationReport]
+    def self.find( uri, subjectid=nil )
+      OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
+      rep = ValidationReport.new(uri)
+      rep.load_metadata( subjectid )
+      rep
+    end
+    
     # finds ValidationReport for a particular validation
     # @param [String] crossvalidation uri 
     # @param [String,optional] subjectid
@@ -120,6 +177,17 @@ module OpenTox
       uris.size==0 ? nil : ValidationReport.new(uris[-1])
     end
     
+    # creates a validation report via validation
+    # @param [String] validation uri 
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::ValidationReport]
+    def self.create( validation_uri, subjectid=nil, waiting_task=nil )
+      uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/validation"),
+        { :validation_uris => validation_uri, :subjectid => subjectid }, {}, waiting_task )
+      ValidationReport.new(uri)
+    end
+    
   end
 
   class CrossvalidationReport
@@ -132,7 +200,9 @@ module OpenTox
     def self.find( uri, subjectid=nil )
       # PENDING load report data?
       OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
-      CrossvalidationReport.new(uri)
+      rep = CrossvalidationReport.new(uri)
+      rep.load_metadata( subjectid )
+      rep
     end
     
     # finds CrossvalidationReport for a particular crossvalidation

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby
 version: !ruby/object:Gem::Version 
-  hash: 19
+  hash: 15
   prerelease: 
   segments: 
-  - 1
-  - 0
   - 2
-  version: 1.0.2
+  - 0
+  - 0
+  version: 2.0.0
 platform: ruby
 authors: 
 - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-16 00:00:00 +01:00
+date: 2011-05-23 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -257,7 +257,7 @@ dependencies:
   type: :runtime
   version_requirements: *id017
 - !ruby/object:Gem::Dependency 
-  name: SystemTimer
+  name: ohm-contrib
   prerelease: false
   requirement: &id018 !ruby/object:Gem::Requirement 
     none: false
@@ -271,7 +271,7 @@ dependencies:
   type: :runtime
   version_requirements: *id018
 - !ruby/object:Gem::Dependency 
-  name: rjb
+  name: SystemTimer
   prerelease: false
   requirement: &id019 !ruby/object:Gem::Requirement 
     none: false
@@ -285,9 +285,121 @@ dependencies:
   type: :runtime
   version_requirements: *id019
 - !ruby/object:Gem::Dependency 
-  name: haml
+  name: rjb
   prerelease: false
   requirement: &id020 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id020
+- !ruby/object:Gem::Dependency 
+  name: dm-core
+  prerelease: false
+  requirement: &id021 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id021
+- !ruby/object:Gem::Dependency 
+  name: dm-serializer
+  prerelease: false
+  requirement: &id022 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id022
+- !ruby/object:Gem::Dependency 
+  name: dm-timestamps
+  prerelease: false
+  requirement: &id023 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id023
+- !ruby/object:Gem::Dependency 
+  name: dm-types
+  prerelease: false
+  requirement: &id024 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id024
+- !ruby/object:Gem::Dependency 
+  name: dm-migrations
+  prerelease: false
+  requirement: &id025 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id025
+- !ruby/object:Gem::Dependency 
+  name: dm-validations
+  prerelease: false
+  requirement: &id026 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id026
+- !ruby/object:Gem::Dependency 
+  name: dm-sqlite-adapter
+  prerelease: false
+  requirement: &id027 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id027
+- !ruby/object:Gem::Dependency 
+  name: haml
+  prerelease: false
+  requirement: &id028 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -297,11 +409,27 @@ dependencies:
         - 3
         version: "3"
   type: :runtime
-  version_requirements: *id020
+  version_requirements: *id028
+- !ruby/object:Gem::Dependency 
+  name: ruby-plot
+  prerelease: false
+  requirement: &id029 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 15
+        segments: 
+        - 0
+        - 4
+        - 0
+        version: 0.4.0
+  type: :runtime
+  version_requirements: *id029
 - !ruby/object:Gem::Dependency 
   name: jeweler
   prerelease: false
-  requirement: &id021 !ruby/object:Gem::Requirement 
+  requirement: &id030 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -311,7 +439,7 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id021
+  version_requirements: *id030
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email: helma@in-silico.ch
 executables: 
@@ -339,7 +467,7 @@ files:
 - lib/feature.rb
 - lib/helper.rb
 - lib/model.rb
-- lib/ontology_service.rb
+- lib/ontology.rb
 - lib/opentox-ruby.rb
 - lib/opentox.owl
 - lib/opentox.rb
@@ -350,7 +478,6 @@ files:
 - lib/serializer.rb
 - lib/spork.rb
 - lib/task.rb
-- lib/templates/config.yaml
 - lib/templates/default_guest_policy.xml
 - lib/templates/default_policy.xml
 - lib/to-html.rb
@@ -385,7 +512,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.4.2
+rubygems_version: 1.5.2
 signing_key: 
 specification_version: 3
 summary: Ruby wrapper for the OpenTox REST API

data/lib/templates/config.yaml

@@ -1,86 +0,0 @@
-# Example configuration for OpenTox, please adjust to your settings
-# 
-# Database setup:
-#
-# Example MySql:
-#
-:database: 
-  :adapter:  mysql
-  :database: production
-  :username: root
-  :password: opentox
-  :host:     localhost
-#
-# Example 1: Using external test services
-#
-# :services:
-#  opentox-compound:      "http://webservices.in-silico.ch/compound/"
-#  opentox-dataset:       "http://webservices.in-silico.ch/dataset/"
-#  opentox-algorithm:     "http://webservices.in-silico.ch/algorithm/"
-#  opentox-model:         "http://webservices.in-silico.ch/model/"
-#  opentox-task:          "http://webservices.in-silico.ch/task/"
-#  opentox-validation:    "http://opentox.informatik.uni-freiburg.de/validation/"
-#
-# Example 2: Using local services
-:base_dir: /home/ist/webservices
-:webserver: passenger
-:services:
-  opentox-compound:      "http://localhost/compound/"
-  opentox-dataset:       "http://localhost/dataset/"
-  opentox-algorithm:     "http://localhost/algorithm/"
-  opentox-model:         "http://localhost/model/"
-  opentox-task:          "http://localhost/task/"
-  opentox-validation:    "http://localhost/validation/"
-#
-# Yaml capable hosts (faster than OWL-DL)
-#
-:yaml_hosts:
-  - "localhost"
-
-# Uncomment for verbose logging
-# :logger: debug
-# :backtrace: 1
-  
-  
-# OpenSSO Authorization
-# set ":server: " to disable A&A
-:authorization:
-  :server: "https://opensso.in-silico.ch"
-  :free_request: #request-method not controlled by A&A
-    - "GET"
-  :authenticate_request: #only for authenticated user
-    - "POST"
-  :authorize_request:  #only for authenticated and authorizeduser
-    - "DELETE"
-    - "PUT"
-  # Exceptions:
-  :free_uris: #request-method for uri not controlled by A&A
-    ? - :GET
-    : - !ruby/regexp /localhost\/algorithm/
-      - "http://localhost/dataset"
-      - "http://localhost/model"
-      - "http://localhost/validation"
-      - "http://localhost/validation/crossvalidation"
-      - "http://localhost/validation/reach_report"      
-      - "http://localhost/validation/reach_report/crossvalidation"
-      - "http://localhost/validation/report"   
-      - "http://localhost/validation/report/crossvalidation"
-      - "http://localhost/validation/reach_report/qmrf"
-    ? - :GET
-      - :POST
-    : - !ruby/regexp /localhost\/toxcreate/
-      - !ruby/regexp /localhost\/task/
-      - !ruby/regexp /localhost\/compound/
-    ? - :PUT
-    : - !ruby/regexp /localhost\/task/
-
-  :authorize_exceptions: #request-method for uri only authenticated, no authorization
-    ? - :POST
-    : - !ruby/regexp /localhost\/algorithm/
-      - "http://localhost/dataset"
-      - "http://localhost/model"
-      - "http://localhost/validation"
-      - !ruby/regexp /localhost\/validation\/[a-z,A-Z,\/,_\-]*$/
-
-  
-