OT.isA substituted by RDF.type, identification of feature_types by RDF.type

10 files changed, 68 insertions, 122 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index c61d86f..93fce18 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -163,24 +163,33 @@ module OpenTox
       @features
     end
 
+    def feature_classes(feature)
+      if Feature.find(feature).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))
diff --git a/lib/environment.rb b/lib/environment.rb
index 57ae014..59578c1 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -74,7 +74,7 @@ CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorizatio
 CONFIG[:authorization][:authorize_request] =  [""] unless CONFIG[:authorization][:authorize_request]
 CONFIG[:authorization][:free_request] =  [""] unless CONFIG[:authorization][:free_request]
 
-#RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
+RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
 OWL = OwlNamespace.new 'http://www.w3.org/2002/07/owl#'
 DC =  OwlNamespace.new 'http://purl.org/dc/elements/1.1/'
 OT =  OwlNamespace.new 'http://www.opentox.org/api/1.1#'
diff --git a/lib/error.rb b/lib/error.rb
index 7ca9767..b92f2a4 100644
--- a/lib/error.rb
+++ b/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
\ No newline at end of file
+end
diff --git a/lib/feature.rb b/lib/feature.rb
index e768f7b..f6e2dfd 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -32,7 +32,16 @@ module OpenTox
     # 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 +49,7 @@ module OpenTox
       else
         "unknown"
       end
+=end
     end    
     
   end
diff --git a/lib/model.rb b/lib/model.rb
index 74408d8..422acd2 100644
--- a/lib/model.rb
+++ b/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/
@@ -187,7 +186,7 @@ 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 +197,7 @@ 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 +214,7 @@ 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 +235,7 @@ 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 +249,7 @@ 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]
diff --git a/lib/ontology.rb b/lib/ontology.rb
index c3952c3..fa4ea6f 100644
--- a/lib/ontology.rb
+++ b/lib/ontology.rb
@@ -1,6 +1,7 @@
 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")
@@ -38,17 +39,16 @@ module OpenTox
         out += "</select>\n"
         return out
       end
+=end
 
-      def self.endpoints#(endpoint="Endpoints")
-        endpoint_datasets = {}
-        RestClientWrapper.get("http://apps.ideaconsult.net:8080/ambit2/query/ndatasets_endpoint",:accept => "text/csv").each do |line|
-          if line.match(/^http/)
-            e = line.split(',')
-            endpoint_datasets["#{e.first} (#{e[1]})"] = RestClientWrapper.get(e.last, :accept => "text/uri-list").split("\n")#[0..e[1].to_i-1] # hack to get only the first count entries
-          end
-        end
-        endpoint_datasets
+      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
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 1992896..c76e21a 100644
--- a/lib/opentox.rb
+++ b/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
diff --git a/lib/parser.rb b/lib/parser.rb
index f33017d..cc5f1c8 100644
--- a/lib/parser.rb
+++ b/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
@@ -289,7 +296,7 @@ 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
diff --git a/lib/serializer.rb b/lib/serializer.rb
index 44b4414..644a09f 100644
--- a/lib/serializer.rb
+++ b/lib/serializer.rb
@@ -67,7 +67,7 @@ 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 }] } ,
diff --git a/lib/templates/config.yaml b/lib/templates/config.yaml
deleted file mode 100644
index 8a5e460..0000000
--- a/lib/templates/config.yaml
+++ /dev/null
@@ -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,\/,_\-]*$/
-
-  
-  
\ No newline at end of file