initial wrapper for new webservices

7 files changed, 52 insertions, 67 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 912e14d..33731af 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -3,23 +3,19 @@ module OpenTox
 
 		class Fminer < OpenTox
 			# Create a new dataset with BBRC features
-			def initialize(training_dataset)
-				@uri = RestClient.post @@config[:services]["opentox-fminer"], :dataset_uri => training_dataset.uri
+			def self.create(training_dataset_uri)
+				RestClient.post @@config[:services]["opentox-fminer"], :dataset_uri => training_dataset_uri
 			end
 		end
 
 		class Similarity < OpenTox
 
-			def initialize
-				@uri = @@config[:services]["opentox-similarity"]
+			def self.tanimoto(dataset1,compound1,dataset2,compound2)
+				RestClient.get File.join(@@config[:services]["opentox-dataset"], 'algorithm/tanimoto/dataset',dataset1.name,compound1.inchi,'dataset',dataset2.name,compound2.inchi)
 			end
 
-			def self.tanimoto(dataset,compounds)
-				RestClient.post @uri + 'tanimoto', :dataset_uri => dataset.uri, :compound_uris => compounds.collect{ |c| c.uri }
-			end
-
-			def self.weighted_tanimoto(dataset,compounds)
-				RestClient.post @uri + 'weighted_tanimoto', :dataset_uri => dataset.uri, :compound_uris => compounds.collect{ |c| c.uri }
+			def self.weighted_tanimoto(dataset1,compound1,dataset2,compound2)
+				RestClient.get URI.encode(File.join(@@config[:services]["opentox-dataset"], 'algorithm/weighted_tanimoto/dataset',dataset1.name,'compound',compound1.inchi,'dataset',dataset2.name,'compound',compound2.inchi))
 			end
 
 		end
diff --git a/lib/compound.rb b/lib/compound.rb
index 4652770..67c8004 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -44,8 +44,8 @@ module OpenTox
 		end
 
 		# Match an array of smarts features, returns matching features
-		def match(smarts_features)
-			smarts_features.all_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact
+		def match(smarts_dataset)
+			smarts_dataset.all_features.collect{ |uri| uri if self.match?(Feature.new(:uri => uri).name) }.compact
 		end
 
 		def smiles2inchi(smiles)
diff --git a/lib/dataset.rb b/lib/dataset.rb
index ca82f11..f6d0dd7 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -4,7 +4,7 @@ module OpenTox
 	# set: dataset uris
 	# key: /dataset/:dataset/compounds
 	# set: compound uris
-	# key: /dataset/:dataset/compound/:inchi/:feature_type
+	# key: /dataset/:dataset/compound/:inchi
 	# set: feature uris
 	class Dataset < OpenTox
 
@@ -19,31 +19,32 @@ module OpenTox
 		end
 
 		def self.find(params)
-			if params[:name]
-				uri = RestClient.get File.join(@@config[:services]["opentox-dataset"], params[:name])
-			elsif params[:uri]
-				uri = params[:uri]
-			end
-			if RestClient.get uri
-				Dataset.new(uri)
-			else
+			begin
+				if params[:name]
+					uri = File.join(@@config[:services]["opentox-dataset"], URI.encode(params[:name]))
+				elsif params[:uri]
+					uri = params[:uri]
+				end
+				RestClient.get uri # check if the resource is available
+				Dataset.new(uri) if uri
+			rescue
 				nil
 			end
 		end
 
+		def self.find_or_create(params)
+			self.create(params) unless self.find(params)
+		end
+
 		def import(params)
 			if params[:csv]
 				# RestClient seems not to work for file uploads
-				`curl -X POST -F "file=@#{params[:csv]};type=text/csv" -F compound_format=#{params[:compound_format]} -F feature_type=#{params[:feature_type]} #{@uri + '/import'}`
+				`curl -X POST -F "file=@#{params[:csv]};type=text/csv" -F compound_format=#{params[:compound_format]} #{@uri + '/import'}`
 			end
 		end
 
-		def add_features(features,feature_type)
-			#puts @uri
-			#puts feature_type
-			#puts features.to_yaml
-			HTTPClient.post @uri, {:feature_type => feature_type, :features => features.to_yaml}
-			#`curl -X POST -F feature_type="#{feature_type}" -F features="#{features.to_yaml}" #{@uri}`
+		def add(features)
+			HTTPClient.post @uri, {:features => features.to_yaml}
 		end
 
 		# Get all compounds from a dataset
@@ -56,14 +57,17 @@ module OpenTox
 		end
 
 		# Get all features for a compound
-		def feature_uris(compound,feature_type)
-			#puts File.join(@uri, 'compound', compound.inchi, feature_type)
-			RestClient.get(File.join(@uri, 'compound', compound.inchi, feature_type)).split("\n")
+		def feature_uris(compound)
+			RestClient.get(File.join(@uri, 'compound', compound.inchi)).split("\n")
 		end
 
 		# Get all features for a compound
-		def features(compound,feature_type)
-			feature_uris(compound,feature_type).collect{|uri| Feature.new(:uri => uri)}
+		def features(compound)
+			feature_uris(compound).collect{|uri| Feature.new(:uri => uri)}
+		end
+
+		def all_features
+			RestClient.get(File.join(@uri, 'features')).split("\n")
 		end
 
 		# Delete a dataset
@@ -71,6 +75,14 @@ module OpenTox
 			RestClient.delete @uri
 		end
 
+		def tanimoto(dataset)
+			RestClient.get(File.join(@uri,'tanimoto',dataset.path))
+		end
+
+		def weighted_tanimoto(dataset)
+			RestClient.get(File.join(@uri,'weighted_tanimoto',dataset.path))
+		end
+
 	end
 
 end
diff --git a/lib/feature.rb b/lib/feature.rb
index 0cad7c0..8b0839f 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -9,15 +9,16 @@ module OpenTox
 			if params[:uri]
 				@uri = params[:uri]
 				items = URI.split(@uri)[5].split(/\//)
-				@name = items[1]
+				@name = items[2]
 				@values = {}
-				i = 3
+				i = 4
 				while i < items.size
 					@values[items[i]] = items[i+1]
 					i += 2
 				end
 			else 
-				@name = URI.encode(URI.decode(params[:name]))
+				@name = params[:name]
+				#@name = URI.encode(URI.decode(params[:name]))
 				@values = params[:values]
 				@uri = File.join(@@config[:services]["opentox-dataset"],"feature",path)
 			end
diff --git a/lib/model.rb b/lib/model.rb
index 7f43860..c50a458 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,4 +1,7 @@
 module OpenTox
+
+	# key: /models
+	# set: dataset uris
 	module Model 
 
 		class Lazar < OpenTox
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index e504e65..9d7e5e5 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -1,36 +1,8 @@
 #['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|
+['rubygems', 'sinatra', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'environment', 'openbabel', 'httpclient'].each do |lib|
 	require lib
 end
 
-module OpenTox
-
-	class OpenTox
-		attr_reader :uri
-
-		def initialize(uri)
-			@uri = uri
-		end
-
-		# Get the object name
-		def name
-			RestClient.get @uri + '/name'
-		end
-
-		# Deletes an object
-		def destroy
-			RestClient.delete @uri
-		end
-
-		# Object path without hostname
-		def path
-			URI.split(@uri)[5]
-		end
-
-	end
-
-end
-
-['compound','feature','dataset','algorithm','model','utils'].each do |lib|
+['opentox', 'compound','feature','dataset','algorithm','model','utils'].each do |lib|
 	require lib
 end
diff --git a/lib/tasks/opentox.rb b/lib/tasks/opentox.rb
index afb8cb6..0dace9a 100644
--- a/lib/tasks/opentox.rb
+++ b/lib/tasks/opentox.rb
@@ -19,7 +19,8 @@ namespace :opentox do
 			@@config[:services].each do |service,uri|
 				dir = File.join(@@config[:base_dir], service)
 				server = @@config[:webserver]
-				`redis-server &`
+				#puts "Starting Redis database"
+				#puts `redis-server /etc/redis.conf &`
 				case server
 				when /thin|mongrel|webrick/
 					port = uri.sub(/^.*:/,'').sub(/\/$/,'')