first steps towards version 2.0, yard documentation started, passes compound, dataset, feature, algorithm, fminer tests

1 files changed, 38 insertions, 68 deletions

diff --git a/lib/opentox.rb b/lib/opentox.rb
index 453ca66..7e1deec 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,79 +1,49 @@
 module OpenTox
 
-  # Generic OpenTox class
-  module OtObject
-
-    attr_reader :uri
-    attr_accessor :metadata
-
-    # Initialize OpenTox object with optional uri
-    def initialize(uri=nil)
-      @metadata = {}
-      self.uri = uri if uri
-    end
-
-    # Set URI
-    def uri=(uri)
-      @uri = uri
-      @metadata[XSD.anyUri] = uri
-    end
-    
-    # Get title
-    def title
-      load_metadata unless @metadata[DC.title]
-      @metadata[DC.title]
-    end
-    
-    # Set title
-    def title=(title)
-      @metadata[DC.title] = title
-    end
-
-    # Get all objects from a service
-    def self.all(uri)
-    #def OtObject.all(uri)
-      RestClientWrapper.get(uri,:accept => "text/uri-list").to_s.split(/\n/)
-    end
-
-    # Load metadata from URI
-    def load_metadata
-      #if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-        # TODO: fix metadata retrie
-       #@metadata = YAML.load(RestClientWrapper.get(@uri, :accept => "application/x-yaml"))
-      #else
-        @metadata = Parser::Owl::Generic.new(@uri).metadata
-      #end
-      @metadata
-      #Parser::Owl::Generic.new(@uri).metadata
-    end
-
+  attr_reader :uri
+  attr_accessor :metadata, :parameters
+
+  # Initialize OpenTox object with optional uri
+  # @param [optional, String] URI
+  def initialize(uri=nil)
+    @metadata = {}
+    self.uri = uri if uri
   end
 
-  module Owl
-
-    class Namespace
-
-      def initialize(uri)
-        @uri = uri
-      end
+  # Set URI
+  # @param [String] URI
+  def uri=(uri)
+    @uri = uri
+    @metadata[XSD.anyURI] = uri
+  end
 
-      def [](property)
-        @uri+property.to_s
-      end
+  # Get all objects from a service
+  # @return [Array] List of available URIs
+  def self.all(uri)
+    RestClientWrapper.get(uri,:accept => "text/uri-list").to_s.split(/\n/)
+  end
 
-      def method_missing(property)
-        @uri+property.to_s
-      end
+  # Load (and return) metadata from object URI
+  # @return [Hash] Metadata
+  def load_metadata
+    @metadata = Parser::Owl::Generic.new(@uri).metadata
+    @metadata
+  end
 
-    end
+  # Load parameters from URI
+  #def load_parameters
+    #@parameters = Parser::Owl::Generic.new(@uri).parameters
+    #@parameters
+  #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_metadata(@uri,@metadata)
+    #s.add_parameters(@uri,@parameters) if @parameters
+    s.to_rdfxml
   end
 
 end
-#
-# OWL Namespaces
-RDF = OpenTox::Owl::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
-OWL = OpenTox::Owl::Namespace.new 'http://www.w3.org/2002/07/owl#'
-DC =  OpenTox::Owl::Namespace.new 'http://purl.org/dc/elements/1.1/'
-OT =  OpenTox::Owl::Namespace.new 'http://www.opentox.org/api/1.1#'
-XSD = OpenTox::Owl::Namespace.new 'http://www.w3.org/2001/XMLSchema#'