1 files changed, 10 insertions, 164 deletions
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index d74b412..e504e65 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -1,4 +1,5 @@
-['rubygems', 'sinatra', 'sinatra/respond_to', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'spork', 'environment'].each do |lib|
+#['rubygems', 'sinatra', 'sinatra/respond_to', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'spork', 'environment', 'openbabel', 'httpclient'].each do |lib|
+['rubygems', 'sinatra', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'spork', 'environment', 'openbabel', 'httpclient'].each do |lib|
 	require lib
 end
 
@@ -7,10 +8,8 @@ module OpenTox
 	class OpenTox
 		attr_reader :uri
 
-		# Escape all nonword characters
-		def uri_escape(string)
-			#URI.escape(string, /[^\w]/)
-			URI.escape(string, /[^#{URI::PATTERN::UNRESERVED}]/)
+		def initialize(uri)
+			@uri = uri
 		end
 
 		# Get the object name
@@ -23,168 +22,15 @@ module OpenTox
 			RestClient.delete @uri
 		end
 
-	end
-
-	class Compound < OpenTox
-
-		# Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc)
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri].to_s
-			elsif params[:smiles]
-				@uri = RestClient.post @@config[:services]["opentox-compound"] ,:smiles => uri_escape(params[:smiles])
-			elsif params[:name]
-				@uri = RestClient.post @@config[:services]["opentox-compound"] ,:name => uri_escape(params[:name])
-			end
-		end
-
-		# Get the (canonical) smiles
-		def smiles
-			RestClient.get @uri
-		end
-
-		# Get the unique id (URI encoded canonical smiles)
-		def uid
-			RestClient.get @uri + '.uid'
-		end
-
-		# Matchs a smarts string
-		def match?(smarts)
-			if RestClient.get(@uri + '/match/' + uri_escape(smarts)) == 'true'
-				true
-			else
-				false
-			end
-		end
-
-		# Match an array of smarts features, returns matching features
-		def match(smarts_features)
-			smarts_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact
-		end
-
-	end
-
-	class Feature < OpenTox
-
-		# Initialize with <tt>:uri => uri</tt>, or <tt>:name => name, :values => hash_of_property_names_and_values</tt>
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri].to_s
-			else
-				@uri = @@config[:services]["opentox-feature"] + uri_escape(params[:name]) 
-				params[:values].each do |k,v|
-					@uri += '/' + k.to_s + '/' + v.to_s
-				end
-			end
-		end
-
-		# Get the value of a property
-		def value(property)
-			RestClient.get @uri + '/' + property
+		# Object path without hostname
+		def path
+			URI.split(@uri)[5]
 		end
 
 	end
 
-	class Dataset < OpenTox
-
-		# Initialize with <tt>:uri => uri</tt> or <tt>:name => name</tt> (creates a new dataset)
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri].to_s
-			elsif params[:name] and params[:filename]
-				@uri = `curl -X POST -F file=@#{params[:filename]} -F name="#{params[:name]}" #{@@config[:services]["opentox-dataset"]}`
-			elsif params[:name] 
-				@uri = RestClient.post @@config[:services]["opentox-dataset"], :name => params[:name]
-			end
-		end
-
-		# Get all compounds from a dataset
-		def compounds
-			RestClient.get(@uri + '/compounds').split("\n").collect{ |c| Compound.new(:uri => c) }
-		end
-
-		# Get all compounds and features from a dataset, returns a hash with compound_uris as keys and arrays of feature_uris as values
-		def all_compounds_and_features_uris
-			YAML.load(RestClient.get(@uri + '/compounds/features.yaml'))
-		end
-
-		# Get all features from a dataset
-		def all_features
-			RestClient.get(@uri + '/features').split("\n").collect{|f| Feature.new(:uri => f)}
-		end
-
-		# Get all features for a compound
-		def features(compound)
-			RestClient.get(@uri + '/compound/' + uri_escape(compound.uri) + '/features').split("\n").collect{|f| Feature.new(:uri => f) }
-		end
-
-		# Add a compound and a feature to a dataset
-		def add(compound,feature)
-			RestClient.put @uri, :compound_uri => compound.uri, :feature_uri => feature.uri
-		end
-
-		# Tell the dataset that it is complete
-		def close
-			RestClient.put @uri, :finished => 'true'
-		end
-
-	end
-
-	class Fminer < OpenTox
-
-		# Create a new dataset with BBRC features
-		def initialize(training_dataset)
-			@dataset_uri = RestClient.post @@config[:services]["opentox-fminer"], :dataset_uri => training_dataset.uri
-		end
-
-		def dataset
-			Dataset.new(:uri => @dataset_uri)
-		end
-
-	end
-
-	class Lazar < OpenTox
-
-		# Create a new prediction model from a dataset
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri]
-			elsif params[:dataset_uri]
-				@uri = RestClient.post @@config[:services]["opentox-lazar"] + 'models' , :dataset_uri => params[:dataset_uri]
-			end
-		end
-
-		# Predict a compound
-		def predict(compound)
-			LazarPrediction.new(:uri => RestClient.post(@uri, :compound_uri => compound.uri))
-		end
-
-	end
-
-	class LazarPrediction < OpenTox
-
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri]
-			end
-		end
-
-		def classification
-			YAML.load(RestClient.get @uri)[:classification]
-		end
-
-		def confidence
-			YAML.load(RestClient.get @uri)[:confidence]
-		end
-
-		def neighbors
-			RestClient.get @uri + '/neighbors' 
-		end
-
-		def features
-			RestClient.get @uri + '/features' 
-		end
-
-	end
+end
 
+['compound','feature','dataset','algorithm','model','utils'].each do |lib|
+	require lib
 end