initial minimal version

13 files changed, 161 insertions, 169 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 2652695..4c50d32 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,8 +1,8 @@
 # R integration
 # workaround to initialize R non-interactively (former rinruby versions did this by default)
 # avoids compiling R with X
-R = nil
-require "rinruby" 
+#R = nil
+#require "rinruby" 
 
 module OpenTox
 
@@ -16,6 +16,7 @@ module OpenTox
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [String] URI of new resource (dataset, model, ...)
     def run(params=nil, waiting_task=nil)
+      #puts @uri
       RestClientWrapper.post(@uri, params, {:accept => 'text/uri-list'}, waiting_task).to_s
     end
     
@@ -37,7 +38,7 @@ module OpenTox
       def self.find(uri, subjectid=nil)
         return nil unless uri
         alg = Generic.new(uri)
-        alg.load_metadata( subjectid )
+        alg.load_metadata
         raise "cannot load algorithm metadata" if alg.metadata==nil or alg.metadata.size==0
         alg
       end
@@ -54,7 +55,7 @@ module OpenTox
         # Initialize bbrc algorithm
         def initialize(subjectid=nil)
           super File.join(CONFIG[:services]["opentox-algorithm"], "fminer/bbrc")
-          load_metadata(subjectid)
+          load_metadata
         end
       end
 
@@ -64,7 +65,7 @@ module OpenTox
         # Initialize last algorithm
         def initialize(subjectid=nil)
           super File.join(CONFIG[:services]["opentox-algorithm"], "fminer/last")
-          load_metadata(subjectid)
+          load_metadata
         end
       end
 
@@ -76,10 +77,11 @@ module OpenTox
       # Initialize lazar algorithm
       def initialize(subjectid=nil)
         super File.join(CONFIG[:services]["opentox-algorithm"], "lazar")
-        load_metadata(subjectid)
+        load_metadata
       end
     end
 
+=begin
     # Utility methods without dedicated webservices
 
     # Similarity calculations
@@ -399,6 +401,7 @@ module OpenTox
       m_pos = array.size / 2
       return array.size % 2 == 1 ? array[m_pos] : (array[m_pos-1] + array[m_pos])/2
     end
+=end
 
   end
 end
diff --git a/lib/authorization.rb b/lib/authorization.rb
index 288733a..27ae734 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -2,7 +2,7 @@ module OpenTox
 
   #Module for Authorization and Authentication
   #@example Authentication
-  #  require "opentox-ruby-api-wrapper" 
+  #  require "opentox-ruby" 
   #  OpenTox::Authorization::AA_SERVER = "https://opensso.in-silico.ch" #if not set in .opentox/conf/[environment].yaml 
   #  token = OpenTox::Authorization.authenticate("benutzer", "passwort") 
   #@see http://www.opentox.org/dev/apis/api-1.2/AA OpenTox A&A API 1.2 specification
@@ -389,4 +389,4 @@ module OpenTox
     end    
     
   end
-end
\ No newline at end of file
+end
diff --git a/lib/compound.rb b/lib/compound.rb
index a85507b..189db7b 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -29,30 +29,21 @@ module OpenTox
     # @param [String] smiles Smiles string
     # @return [OpenTox::Compound] Compound
     def self.from_smiles(smiles)
-      c = Compound.new
-      c.inchi = Compound.smiles2inchi(smiles)
-      c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi))
-      c
+      Compound.new  RestClientWrapper.post(CONFIG[:services]["opentox-compound"], smiles, :content_type => 'chemical/x-daylight-smiles').to_s.chomp 
     end
 
     # Create a compound from inchi string
     # @param [String] smiles InChI string
     # @return [OpenTox::Compound] Compound
     def self.from_inchi(inchi)
-      c = Compound.new
-      c.inchi = inchi
-      c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi))
-      c
+      Compound.new  RestClientWrapper.post(CONFIG[:services]["opentox-compound"], inchi, :content_type => 'chemical/x-inchi').to_s.chomp 
     end
 
     # Create a compound from sdf string
     # @param [String] smiles SDF string
     # @return [OpenTox::Compound] Compound
     def self.from_sdf(sdf)
-      c = Compound.new
-      c.inchi = Compound.sdf2inchi(sdf)
-      c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi))
-      c
+      Compound.new  RestClientWrapper.post(CONFIG[:services]["opentox-compound"], sdf, :content_type => 'chemical/x-mdl-sdfile').to_s.chomp 
     end
 
     # Create a compound from name. Relies on an external service for name lookups.
@@ -77,13 +68,13 @@ module OpenTox
 		# Get (canonical) smiles
     # @return [String] Smiles string
 		def to_smiles
-			Compound.obconversion(@inchi,'inchi','can')
+      RestClientWrapper.get(@uri, :accept => 'chemical/x-daylight-smiles').chomp
 		end
 
     # Get sdf
     # @return [String] SDF string
 		def to_sdf
-			Compound.obconversion(@inchi,'inchi','sdf')
+      RestClientWrapper.get(@uri, :accept => 'chemical/x-mdl-sdfile').chomp
 		end
 
     # Get gif image
@@ -118,6 +109,7 @@ module OpenTox
       end
 		end
 
+=begin
 		# Match a smarts string
     # @example
     #   compound = OpenTox::Compound.from_name("Benzene")
@@ -195,5 +187,6 @@ module OpenTox
 				obconversion.write_string(obmol)
 			end
 		end
+=end
 	end
 end
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 5e6a29b..84dce65 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -1,6 +1,7 @@
 module OpenTox
   
   # Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset).
+  # TODO: fix API Doc
   class Dataset 
 
     include OpenTox
@@ -15,7 +16,7 @@ module OpenTox
     # @param [optional, String] uri Dataset URI
     # @return [OpenTox::Dataset] Dataset object
     def initialize(uri=nil,subjectid=nil)
-      super uri
+      super uri, subjectid
       @features = {}
       @compounds = []
       @data_entries = {}
@@ -28,7 +29,17 @@ module OpenTox
     # @return [OpenTox::Dataset] Dataset object
     def self.create(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil)
       dataset = Dataset.new(nil,subjectid)
-      dataset.save(subjectid)
+      dataset.save
+      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
+    # @return [OpenTox::Dataset] Dataset object with all data
+    def self.find(uri, subjectid=nil)
+      return nil unless uri
+      dataset = Dataset.new(uri, subjectid)
+      dataset.load_metadata
       dataset
     end
 
@@ -40,20 +51,9 @@ module OpenTox
     # @return [OpenTox::Dataset] Dataset object with CSV data
     def self.create_from_csv_file(file, subjectid=nil) 
       dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
-      parser = Parser::Spreadsheets.new
-      parser.dataset = dataset
-      parser.load_csv(File.open(file).read)
-      dataset.save(subjectid)
-      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
-    # @return [OpenTox::Dataset] Dataset object with all data
-    def self.find(uri, subjectid=nil)
-      return nil unless uri
-      dataset = Dataset.new(uri, subjectid)
-      dataset.load_all(subjectid)
+      #RestClientWrapper.post(dataset.uri,File.read(file), {:content_type => "text/csv", :subjectid => @subjectid}) 
+      RestClientWrapper.post(dataset.uri,{:file => File.new(file)},{:accept => "text/uri-list", :subjectid => subjectid})#, {:content_type => "text/csv", :subjectid => @subjectid}) 
+      dataset.load_metadata
       dataset
     end
     
@@ -64,7 +64,7 @@ module OpenTox
       return false unless uri
       dataset = Dataset.new(uri, subjectid)
       begin
-        dataset.load_metadata( subjectid ).size > 0
+        dataset.load_metadata.size > 0
       rescue
         false
       end
@@ -80,26 +80,20 @@ module OpenTox
     # Load YAML representation into the dataset
     # @param [String] yaml YAML representation of the dataset
     # @return [OpenTox::Dataset] Dataset object with YAML data
-    def load_yaml(yaml)
-      copy YAML.load(yaml)
+    def store_yaml(yaml)
+      RestClientWrapper.post(@uri,yaml, {:content_type => "application/x-yaml", :subjectid => @subjectid}) 
     end
 
-    def load_rdfxml(rdfxml)
-      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
-      file.delete
+    def store_rdfxml(rdfxml)
+      RestClientWrapper.post(@uri, rdfxml, {:content_type => "application/rdf+xml", :subjectid => @subjectid}) 
     end
 
     # Load RDF/XML representation from a file
     # @param [String] file File with RDF/XML representation of the dataset
     # @return [OpenTox::Dataset] Dataset object with RDF/XML data
-    def load_rdfxml_file(file, subjectid=nil)
-      parser = Parser::Owl::Dataset.new @uri, subjectid
-      parser.uri = file.path
-      copy parser.load_uri(subjectid)
+    def store_rdfxml_file(file)
+      #RestClientWrapper.post(@uri, :file => File.new(file))#, {:content_type => "application/rdf+xml", :subjectid => @subjectid}) 
+      RestClientWrapper.post(@uri, File.read(file), {:content_type => "application/rdf+xml", :subjectid => @subjectid}) 
     end
 
     # Load CSV string (format specification: http://toxcreate.org/help)
@@ -108,11 +102,8 @@ module OpenTox
     # - you will have to set remaining metadata manually
     # @param [String] csv CSV representation of the dataset
     # @return [OpenTox::Dataset] Dataset object with CSV data
-    def load_csv(csv, subjectid=nil) 
-      save(subjectid) unless @uri # get a uri for creating features
-      parser = Parser::Spreadsheets.new
-      parser.dataset = self
-      parser.load_csv(csv)
+    def store_csv(csv) 
+      RestClientWrapper.post(@uri, csv, {:content_type => "text/csv", :subjectid => @subjectid}) 
     end
 
     # Load Spreadsheet book (created with roo gem http://roo.rubyforge.org/, excel format specification: http://toxcreate.org/help)
@@ -121,35 +112,36 @@ module OpenTox
     # - you will have to set remaining metadata manually
     # @param [Excel] book Excel workbook object (created with roo gem)
     # @return [OpenTox::Dataset] Dataset object with Excel data
-    def load_spreadsheet(book, subjectid=nil)
-      save(subjectid) unless @uri # get a uri for creating features
-      parser = Parser::Spreadsheets.new
-      parser.dataset = self
-      parser.load_spreadsheet(book)
+    def store_spreadsheet_file(file)
+      RestClientWrapper.post(@uri, :file => File.new(file))#, {:content_type => "application/vnd.ms-excel", :subjectid => @subjectid}) 
     end
     
     # Load and return only metadata of a Dataset object
     # @return [Hash] Metadata of the dataset
-    def load_metadata(subjectid=nil)
-      add_metadata Parser::Owl::Dataset.new(@uri, subjectid).load_metadata(subjectid)
+    def load_metadata
+      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+        @metadata = YAML.load(RestClientWrapper.get(File.join(@uri,"metadata"), {:accept => "application/x-yaml", :subjectid => @subjectid}))
+      else
+        add_metadata Parser::Owl::Dataset.new(@uri, @subjectid).load_metadata
+      end
       self.uri = @uri if @uri # keep uri
       @metadata
     end
 
     # Load all data (metadata, data_entries, compounds and features) from URI
-    def load_all(subjectid=nil)
+    def load_all
       if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-        copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid}))
+        copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => @subjectid}))
       else
-        parser = Parser::Owl::Dataset.new(@uri, subjectid)
-        copy parser.load_uri(subjectid)
+        parser = Parser::Owl::Dataset.new(@uri, @subjectid)
+        copy parser.load_uri
       end
     end
 
     # Load and return only compound URIs from the dataset service
     # @return [Array]  Compound URIs in the dataset
-    def load_compounds(subjectid=nil)
-      RestClientWrapper.get(File.join(uri,"compounds"),{:accept=> "text/uri-list", :subjectid => subjectid}).to_s.each_line do |compound_uri|
+    def load_compounds
+      RestClientWrapper.get(File.join(uri,"compounds"),{:accept=> "text/uri-list", :subjectid => @subjectid}).to_s.each_line do |compound_uri|
         @compounds << compound_uri.chomp
       end
       @compounds.uniq!
@@ -157,12 +149,12 @@ module OpenTox
 
     # Load and return only features from the dataset service
     # @return [Hash]  Features of the dataset
-    def load_features(subjectid=nil)
+    def load_features
       if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-        @features = YAML.load(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/x-yaml", :subjectid => subjectid}))
+        @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)
+        parser = Parser::Owl::Dataset.new(@uri, @subjectid)
+        @features = parser.load_features
       end
       @features
     end
@@ -171,6 +163,7 @@ module OpenTox
     # @param [String] feature the URI of the feature
     # @return [Array] return array with strings, nil if value is not set (e.g. when feature is numeric)
     def accept_values(feature)
+      load_features
       accept_values = features[feature][OT.acceptValue]
       accept_values.sort if accept_values
       accept_values
@@ -178,8 +171,8 @@ module OpenTox
 
     # Detect feature type(s) in the dataset
     # @return [String] `classification", "regression", "mixed" or unknown`
-    def feature_type(subjectid=nil)
-      load_features(subjectid)
+    def feature_type
+      load_features
       feature_types = @features.collect{|f,metadata| metadata[RDF.type]}.flatten.uniq
       if feature_types.include?(OT.NominalFeature)
         "classification"
@@ -189,13 +182,11 @@ module OpenTox
         "unknown"
       end
     end
-=begin
-=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
-      Serializer::Spreadsheets.new(self).to_spreadsheet
+      Spreadsheet::Workbook.new(RestClientWrapper.get(@uri, {:accept => "application/vnd.ms-excel", :subjectid => @subjectid}))
     end
 
     # Get Excel representation (alias for to_spreadsheet)
@@ -207,33 +198,31 @@ module OpenTox
     # Get CSV string representation (data_entries only, metadata will be discarded)
     # @return [String] CSV representation
     def to_csv
-      Serializer::Spreadsheets.new(self).to_csv
+      RestClientWrapper.get(@uri, {:accept => "text/csv", :subjectid => @subjectid})
     end
 
     # Get OWL-DL in ntriples format
     # @return [String] N-Triples representation
     def to_ntriples
-      s = Serializer::Owl.new
-      s.add_dataset(self)
-      s.to_ntriples
+      RestClientWrapper.get(@uri, {:accept => "application/rdf+xml", :subjectid => @subjectid})
     end
 
     # Get OWL-DL in RDF/XML format
     # @return [String] RDF/XML representation
     def to_rdfxml
-      s = Serializer::Owl.new
-      s.add_dataset(self)
-      s.to_rdfxml
+      RestClientWrapper.get(@uri, {:accept => "application/rdf+xml", :subjectid => @subjectid})
     end
 
     # Get name (DC.title) of a feature
     # @param [String] feature Feature URI
     # @return [String] Feture title
     def feature_name(feature)
+      load_features
       @features[feature][DC.title]
     end
 
     def title
+      load_metadata
       @metadata[DC.title]
     end
 
@@ -251,14 +240,6 @@ module OpenTox
       @data_entries[compound][feature] << value if value!=nil
     end
 
-    # Add/modify metadata, existing entries will be overwritten
-    # @example
-    #   dataset.add_metadata({DC.title => "any_title", DC.creator => "my_email"})
-    # @param [Hash] metadata Hash mapping predicate_uris to values
-    def add_metadata(metadata)
-      metadata.each { |k,v| @metadata[k] = v }
-    end
-
     # Add a feature
     # @param [String] feature Feature URI
     # @param [Hash] metadata Hash with feature metadata
@@ -285,10 +266,10 @@ module OpenTox
     # @param [Hash] metadata Hash containing the metadata for the new dataset
     # @param [String] subjectid
     # @return [OpenTox::Dataset] newly created dataset, already saved
-    def split( compounds, features, metadata, subjectid=nil)
+    def split( compounds, features, metadata)
       LOGGER.debug "split dataset using "+compounds.size.to_s+"/"+@compounds.size.to_s+" compounds"
       raise "no new compounds selected" unless compounds and compounds.size>0
-      dataset = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"],subjectid)
+      dataset = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"],@subjectid)
       if features.size==0
         compounds.each{ |c| dataset.add_compound(c) }
       else
@@ -311,7 +292,7 @@ module OpenTox
         end
       end
       dataset.add_metadata(metadata)
-      dataset.save(subjectid)
+      dataset.save
       dataset
     end
 
@@ -319,29 +300,23 @@ module OpenTox
     # - creates a new dataset if uri is not set
     # - overwrites dataset if uri exists
     # @return [String] Dataset URI
-    def save(subjectid=nil)
-      # TODO: rewrite feature URI's ??
+    def save
       @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})
-        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
+      # create dataset if uri is empty
+      self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:subjectid => @subjectid}).to_s.chomp unless @uri
+      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+        RestClientWrapper.post(@uri,self.to_yaml,{:content_type =>  "application/x-yaml", :subjectid => @subjectid})
       else
-        # create dataset if uri is empty
-        self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:subjectid => subjectid}).to_s.chomp
+        s = Serializer::Owl.new
+        s.add_dataset(self)
+        RestClientWrapper.post(@uri, s.to_rdfxml,{:content_type => "application/rdf+xml" , :subjectid => @subjectid})
       end
       @uri
     end
 
     # Delete dataset at the dataset service
-    def delete(subjectid=nil)
-      RestClientWrapper.delete(@uri, :subjectid => subjectid)
+    def delete
+      RestClientWrapper.delete(@uri, :subjectid => @subjectid)
     end
 
     private
@@ -367,7 +342,7 @@ module OpenTox
     # @return [OpenTox::Dataset] Prediction dataset object with all data
     def self.find(uri, subjectid=nil)
       prediction = LazarPrediction.new(uri, subjectid)
-      prediction.load_all(subjectid)
+      prediction.load_all
       prediction
     end
 
@@ -392,10 +367,5 @@ module OpenTox
       @data_entries[compound.uri].collect{|f,v| @features[f] if f.match(/neighbor/)}.compact
     end
 
-#    def errors(compound)
-#      features = @data_entries[compound.uri].keys
-#      features.collect{|f| @features[f][OT.error]}.join(" ") if features
-#    end
-
   end
 end
diff --git a/lib/environment.rb b/lib/environment.rb
index 28a9a66..cae743c 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -24,7 +24,7 @@ end
 
 # database
 #`redis-server /opt/redis/redis.conf` unless File.exists? "/var/run/redis.pid" # removed by AM
-Ohm.connect :thread_safe => true
+# Ohm.connect :thread_safe => true
 
 # load mail settings for error messages
 #load File.join config_dir,"mail.rb" if File.exists?(File.join config_dir,"mail.rb")
@@ -69,11 +69,6 @@ class OwlNamespace
 
 end
 
-AA_SERVER = CONFIG[:authorization] ? (CONFIG[:authorization][:server] ? CONFIG[:authorization][:server] : nil) : nil
-CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorization][:authenticate_request]
-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#'
 OWL = OwlNamespace.new 'http://www.w3.org/2002/07/owl#'
 DC =  OwlNamespace.new 'http://purl.org/dc/elements/1.1/'
@@ -81,3 +76,8 @@ OT =  OwlNamespace.new 'http://www.opentox.org/api/1.1#'
 OTA =  OwlNamespace.new 'http://www.opentox.org/algorithmTypes.owl#'
 XSD = OwlNamespace.new 'http://www.w3.org/2001/XMLSchema#'
 
+AA_SERVER = CONFIG[:authorization] ? (CONFIG[:authorization][:server] ? CONFIG[:authorization][:server] : nil) : nil
+CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorization][:authenticate_request]
+CONFIG[:authorization][:authorize_request] =  [""] unless CONFIG[:authorization][:authorize_request]
+CONFIG[:authorization][:free_request] =  [""] unless CONFIG[:authorization][:free_request]
+
diff --git a/lib/error.rb b/lib/error.rb
index b92f2a4..45b7545 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -1,4 +1,3 @@
-
 # adding additional fields to Exception class to format errors according to OT-API
 class Exception
   attr_accessor :errorCause
diff --git a/lib/feature.rb b/lib/feature.rb
index f3bec5c..84a85b9 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -6,12 +6,12 @@ module OpenTox
 
     # Find a feature
     # @param [String] uri Feature URI
-    # @return [OpenTox::Task] Feature object
+    # @return [OpenTox::Feature] Feature object
     def self.find(uri, subjectid=nil)
       return nil unless uri   
-      feature = Feature.new uri
+      feature = Feature.new uri, subjectid
       if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host))
-        feature.add_metadata YAML.load(RestClientWrapper.get(uri,{:accept => "application/x-yaml", :subjectid => subjectid}))
+        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
       end
diff --git a/lib/helper.rb b/lib/helper.rb
index 995f3e9..04300e0 100644
--- a/lib/helper.rb
+++ b/lib/helper.rb
@@ -1,3 +1,4 @@
+=begin
 helpers do
 
   # Authentification
@@ -94,4 +95,4 @@ before do
     protected!(@subjectid)
   end
 end
-
+=end
diff --git a/lib/model.rb b/lib/model.rb
index 02fabfa..a806b74 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -4,6 +4,24 @@ module OpenTox
 
     include OpenTox
 
+    # Find a lazar model
+    # @param [String] uri Model URI
+    # @return [OpenTox::Model::Lazar] lazar model
+    def self.find(uri, subjectid=nil)
+      if CONFIG[:yaml_hosts].include?(URI.parse(uri).host)
+        YAML.load RestClientWrapper.get(uri,{:accept => 'application/x-yaml', :subjectid => subjectid})
+      else
+        parser = Parser::Owl::Feature.new(uri, @subjectid)
+        @metadata = parser.load_uri.metadata
+      end
+    end
+
+    # Get URIs of all models
+    # @return [Array] List of lazar model URIs
+    def self.all(subjectid=nil)
+      RestClientWrapper.get(CONFIG[:services]["opentox-model"], :subjectid => subjectid).to_s.split("\n")
+    end
+
     # Run a model with parameters
     # @param [Hash] params Parameters for OpenTox model
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
@@ -29,35 +47,35 @@ module OpenTox
       # @return [OpenTox::Model::Generic] Model instance
       def self.find(uri,subjectid=nil)
         return nil unless uri
-        model = Generic.new(uri)
-        model.load_metadata(subjectid)
+        model = Generic.new(uri,subjectid)
+        model.load_metadata
         raise "could not load model metadata '"+uri.to_s+"'" if model.metadata==nil or model.metadata.size==0
         model
       end
 
       # provides feature type, possible types are "regression" or "classification"
       # @return [String] feature type, "unknown" if type could not be estimated
-      def feature_type(subjectid=nil)
+      def feature_type
         unless @feature_type
-          load_predicted_variables( subjectid ) unless @predicted_variable
-          @feature_type = OpenTox::Feature.find( @predicted_variable, subjectid ).feature_type
+          load_predicted_variables unless @predicted_variable
+          @feature_type = OpenTox::Feature.find( @predicted_variable, @subjectid ).feature_type
         end
         @feature_type
       end
     
-      def predicted_variable( subjectid )
-        load_predicted_variables( subjectid ) unless @predicted_variable
+      def predicted_variable
+        load_predicted_variables unless @predicted_variable
         @predicted_variable
       end
 
-      def predicted_confidence( subjectid )
-        load_predicted_variables( subjectid ) unless @predicted_confidence
+      def predicted_confidence
+        load_predicted_variables unless @predicted_confidence
         @predicted_confidence
       end
   
       private
-      def load_predicted_variables( subjectid=nil )
-        load_metadata(subjectid) if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
+      def load_predicted_variables
+        load_metadata if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
         if @metadata[OT.predictedVariables]
           predictedVariables = @metadata[OT.predictedVariables]
           if predictedVariables.is_a?(Array)
@@ -86,14 +104,14 @@ module OpenTox
     end
 
     # Lazy Structure Activity Relationship class
-    class Lazar
+    class Lazar < Generic
 
-      include Model
+      #include Model
       include Algorithm
 
       attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid, :prop_kernel, :value_map
 
-      def initialize(uri=nil)
+      def initialize(uri=nil,subjectid=nil)
 
         if uri
           super uri
@@ -119,17 +137,15 @@ module OpenTox
 
       end
 
-      # Get URIs of all lazar models
-      # @return [Array] List of lazar model URIs
-      def self.all(subjectid=nil)
-        RestClientWrapper.get(CONFIG[:services]["opentox-model"], :subjectid => subjectid).to_s.split("\n")
-      end
-
-      # Find a lazar model
+      # Find a lazar model via URI, and loads metadata, could raise NotFound/NotAuthorized error 
       # @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})
+      # @return [OpenTox::Model::Generic] Model instance
+      def self.find(uri,subjectid=nil)
+        return nil unless uri
+        model = Lazar.new(uri,subjectid)
+        model.load_metadata
+        raise "could not load model metadata '"+uri.to_s+"'" if model.metadata==nil or model.metadata.size==0
+        model
       end
 
       # Create a new lazar model
@@ -142,6 +158,7 @@ module OpenTox
         OpenTox::Model::Lazar.find(model_uri, subjectid)      
       end
 
+=begin
       # Get a parameter value
       # @param [String] param Parameter name
       # @return [String] Parameter value
@@ -465,6 +482,7 @@ module OpenTox
         RestClientWrapper.delete(@uri, :subjectid => subjectid) unless @uri == CONFIG[:services]["opentox-model"]
       end
 
+=end
     end
   end
 end
diff --git a/lib/opentox-ruby.rb b/lib/opentox-ruby.rb
index ae05cb2..16abee9 100644
--- a/lib/opentox-ruby.rb
+++ b/lib/opentox-ruby.rb
@@ -1,14 +1,15 @@
-['rubygems', 'sinatra', 'sinatra/url_for', 'ohm', 'rest_client', 'yaml', 'cgi', 'spork', 'error', 'overwrite', 'environment'].each do |lib|
+#['rubygems', 'sinatra', 'sinatra/url_for', 'ohm', 'rest_client', 'yaml', 'cgi', 'spork', 'error', 'overwrite', 'environment'].each do |lib|
+['rubygems', 'rest_client', 'yaml', 'cgi', 'spork', 'error', 'overwrite', 'environment'].each do |lib|
 	require lib
 end
 
-begin
-	require 'openbabel'
-rescue LoadError
-	puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
-end
+#begin
+	#require 'openbabel'
+#rescue LoadError
+	#puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
+#end
 
-['opentox', 'compound','dataset', 'parser','serializer', 'algorithm','model','task','validation','feature', 
- 'rest_client_wrapper', 'authorization', 'policy', 'helper', 'to-html', 'ontology' ].each do |lib|
+#['opentox', 'compound','dataset', 'parser','serializer', 'algorithm','model','task','validation','feature', 'rest_client_wrapper', 'authorization', 'policy', 'helper', 'to-html', 'ontology' ].each do |lib|
+['opentox', 'compound','dataset', 'parser','serializer', 'algorithm','model','task','validation','feature', 'rest_client_wrapper', 'authorization', 'policy', 'ontology' ].each do |lib|
 	require lib
 end
diff --git a/lib/opentox.rb b/lib/opentox.rb
index c76e21a..6250d86 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -5,8 +5,9 @@ module OpenTox
 
   # Initialize OpenTox object with optional uri
   # @param [optional, String] URI
-  def initialize(uri=nil)
+  def initialize(uri=nil,subjectid=nil)
     @metadata = {}
+    @subjectid = subjectid
     self.uri = uri if uri
   end
 
@@ -25,11 +26,15 @@ module OpenTox
 
   # Load (and return) metadata from object URI
   # @return [Hash] Metadata
-  def load_metadata(subjectid=nil)
-    @metadata = Parser::Owl::Generic.new(@uri).load_metadata(subjectid)
+  def load_metadata
+    @metadata = Parser::Owl::Generic.new(@uri).load_metadata
     @metadata
   end
 
+  # Add/modify metadata, existing entries will be overwritten
+  # @example
+  #   dataset.add_metadata({DC.title => "any_title", DC.creator => "my_email"})
+  # @param [Hash] metadata Hash mapping predicate_uris to values
   def add_metadata(metadata)
     metadata.each do |k,v|
       if v.is_a? Array
@@ -46,13 +51,12 @@ 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
 
   # deletes the resource, deletion should have worked when no RestCallError raised
-  def delete(subjectid=nil)
-    RestClientWrapper.delete(uri,:subjectid => subjectid)
+  def delete
+    RestClientWrapper.delete(uri,:subjectid => @subjectid)
   end
 
 end
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index df4e1b7..efc570d 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -1,3 +1,4 @@
+=begin
 # class overwrites aka monkey patches
 # hack: store sinatra instance in global var $url_provider to make url_for and halt methods accessible
 before {
@@ -61,6 +62,7 @@ class Sinatra::Base
     end
   end
 end
+=end
 
 class String
   def task_uri?
@@ -143,8 +145,10 @@ class OTLogger < Logger
 end
 
 # make migration from datamapper more straightforward
+=begin
 class Ohm::Model
   def self.get(id)
     self[id]
   end
 end
+=end
diff --git a/lib/to-html.rb b/lib/to-html.rb
index 2c29f7d..04fa158 100644
--- a/lib/to-html.rb
+++ b/lib/to-html.rb
@@ -1,4 +1,3 @@
-
 OT_LOGO = File.join(CONFIG[:services]["opentox-validation"],"resources/ot-logo.png")
 
 class String