1 files changed, 137 insertions, 0 deletions
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index e69de29..647b357 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -0,0 +1,137 @@
+require 'rest_client'
+require 'crack/xml'
+
+module OpenTox
+
+	class OpenTox
+		attr_reader :uri
+
+		# Escape all nonword characters
+		def uri_escape(string)
+			URI.escape(string, /[^\w]/)
+		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 ENV['OPENTOX_COMPOUNDS'] ,:smiles => uri_escape(params[:smiles])
+			elsif params[:name]
+				@uri = RestClient.post ENV['OPENTOX_COMPOUNDS'] ,:name => uri_escape(params[:name])
+			end
+		end
+
+		# Get the (canonical) smiles
+		def smiles
+			RestClient.get @uri
+		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 = ENV['OPENTOX_FEATURES'] + 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
+		end
+
+		# Get the name of the feature
+		def name
+			RestClient.get @uri + '/name'
+		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] 
+				@uri = RestClient.post ENV['OPENTOX_DATASETS'], :name => params[:name]
+				RestClient.delete @uri + '/associations'
+			end
+		end
+
+		# Get the dataset name
+		def name
+			RestClient.get @uri + '/name'
+		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 features as values
+		def all_compounds_and_features
+			compounds = {}
+			Crack::XML.parse(RestClient.get @uri + '/compounds/features')['dataset']['compound'].each do |c|
+				features = c['feature_uri'].collect{ |f| Feature.new :uri => f }
+				compounds[c['uri']] = features
+			end
+			compounds
+		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
+
+	end
+
+	class Fminer < OpenTox
+
+		# Create a new dataset with BBRC features
+		def initialize(training_dataset)
+			@dataset_uri = RestClient.post ENV['OPENTOX_FMINER'], :dataset_uri => training_dataset.uri
+		end
+
+		def dataset
+			Dataset.new(:uri => @dataset_uri)
+		end
+
+	end
+
+end