helma-opentox-ruby-api-wrapper 0.1.5 → 0.2.0

data/Rakefile

@@ -11,7 +11,6 @@ begin
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
 		gem.add_dependency "rest-client"
-    gem.add_development_dependency "thoughtbot-shoulda"
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end
 rescue LoadError

data/VERSION

@@ -1 +1 @@
-0.1.5
+0.2.0

data/lib/opentox-ruby-api-wrapper.rb

@@ -1,4 +1,3 @@
-
 #['rubygems', 'rest_client', 'spork', 'helper' ].each do |lib|
 ['rubygems', 'rest_client', 'spork' ].each do |lib|
 	require lib
@@ -8,7 +7,7 @@ ENV['OPENTOX_COMPOUND'] = 'http://webservices.in-silico.ch/compound/v0/' unless
 ENV['OPENTOX_FEATURE']  = 'http://webservices.in-silico.ch/feature/v0/'  unless ENV['OPENTOX_FEATURE']
 ENV['OPENTOX_DATASET']  = 'http://webservices.in-silico.ch/dataset/v0/'  unless ENV['OPENTOX_DATASET']
 ENV['OPENTOX_FMINER']   = 'http://webservices.in-silico.ch/fminer/v0/'   unless ENV['OPENTOX_FMINER']
-ENV['OPENTOX_LAZAR']   = 'http://webservices.in-silico.ch/lazar/v0/'     unless ENV['OPENTOX_LAZAR']
+ENV['OPENTOX_LAZAR']    = 'http://webservices.in-silico.ch/lazar/v0/'     unless ENV['OPENTOX_LAZAR']
 
 module OpenTox
 
@@ -19,6 +18,22 @@ module OpenTox
 		def uri_escape(string)
 			URI.escape(string, /[^\w]/)
 		end
+
+		# Returns true if object creation has finished (for asynchronous processes)
+		def finished?
+			YAML.load(RestClient.get(@uri))[:finished]
+		end
+
+		# Get the object name
+		def name
+			RestClient.get @uri + '/name'
+		end
+
+		# Deletes an object
+		def destroy
+			RestClient.delete @uri
+		end
+
 	end
 
 	class Compound < OpenTox
@@ -74,11 +89,6 @@ module OpenTox
 			RestClient.get @uri + '/' + property
 		end
 
-		# Get the name of the feature
-		def name
-			RestClient.get @uri + '/name'
-		end
-
 	end
 
 	class Dataset < OpenTox
@@ -87,23 +97,20 @@ module OpenTox
 		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]}" #{ENV['OPENTOX_DATASET']}`
 			elsif params[:name] 
-				@uri = RestClient.post ENV['OPENTOX_DATASET'], :name => params[:name]
+				@uri = RestClient.post ENV['OPENTOX_DATASET'], :name => params[:name], :data => params[:data].to_yaml
 			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
+		# 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'))
 		end
 
@@ -119,7 +126,13 @@ module OpenTox
 
 		# Add a compound and a feature to a dataset
 		def add(compound,feature)
-			RestClient.post @uri, :compound_uri => compound.uri, :feature_uri => feature.uri
+			RestClient.put @uri, :compound_uri => compound.uri, :feature_uri => feature.uri
+		end
+
+		# Tell the dataset that it is complete
+		def close
+			puts @uri + '/finished'
+			RestClient.put @uri + '/finished', nil
 		end
 
 	end
@@ -143,14 +156,40 @@ module OpenTox
 		def initialize(params)
 			if params[:uri]
 				@uri = params[:uri]
-			elsif params[:dataset_ur]
-				@uri = RestClient.post ENV['OPENTOX_LAZAR'] + 'models/' , :dataset_uri => training_dataset.uri
+			elsif params[:dataset_uri]
+				@uri = RestClient.post ENV['OPENTOX_LAZAR'] + 'models' , :dataset_uri => params[:dataset_uri]
 			end
 		end
 
 		# Predict a compound
 		def predict(compound)
-			RestClient.post @uri, :compound_uri => compound.uri
+			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

data/opentox-ruby-api-wrapper.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "0.1.5"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
-  s.date = %q{2009-08-15}
+  s.date = %q{2009-08-17}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
   s.extra_rdoc_files = [
@@ -27,7 +27,9 @@ Gem::Specification.new do |s|
      "lib/opentox-ruby-api-wrapper.rb",
      "lib/spork.rb",
      "opentox-ruby-api-wrapper.gemspec",
+     "test/hamster_carcinogenicity.csv",
      "test/opentox-ruby-api-wrapper_test.rb",
+     "test/start-local-webservices.rb",
      "test/test_helper.rb"
   ]
   s.homepage = %q{http://github.com/helma/opentox-ruby-api-wrapper}
@@ -37,7 +39,8 @@ Gem::Specification.new do |s|
   s.summary = %q{Ruby wrapper for the OpenTox REST API}
   s.test_files = [
     "test/test_helper.rb",
-     "test/opentox-ruby-api-wrapper_test.rb"
+     "test/opentox-ruby-api-wrapper_test.rb",
+     "test/start-local-webservices.rb"
   ]
 
   if s.respond_to? :specification_version then
@@ -46,13 +49,10 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<rest-client>, [">= 0"])
-      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     else
       s.add_dependency(%q<rest-client>, [">= 0"])
-      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     end
   else
     s.add_dependency(%q<rest-client>, [">= 0"])
-    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
   end
 end

data/test/hamster_carcinogenicity.csv

@@ -0,0 +1,85 @@
+CC=O,true
+C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,true
+O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,true
+C1(N=CNN=1)N,false
+Br(=O)(=O)[O-].[K+],true
+[Cl-].[Cd+2].[Cl-],false
+O=S(=O)([O-])[O-].[Cd+2],false
+ClC1=CC(=NC(=N1)SCC(=O)O)NC2=CC=CC(=C2C)C,false
+ClCOC,true
+C=C(Cl)C=C,false
+Clc1ccc(cc1)c2ccc(COC(C)(C)C(O)=O)cc2,false
+O=C1OC2=C(C=CC=C2)C=C1,false
+ClC(=C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)Cl,true
+ClC(C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)(Cl)Cl,false
+C=CCN(CC=C)N=O,true
+Cl\C2=C(/Cl)C3(Cl)C1C4CC(C1C2(Cl)C3(Cl)Cl)C5OC45,false
+O=C(N(C)C)Cl,true
+CN(C)N,true
+N(NC)C.[H]Cl.[H]Cl,true
+CCO,false
+O=C(N(CC)N=O)NCCO,true
+O=C(N(CC)N=O)NCC(=O)C,true
+C=O,false
+[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NNC=O,true
+O=CC1=CC=CO1,false
+OCC1CO1,true
+O=C2C1=C(OC)C=C(OC)C(Cl)=C1O[C@]32C(OC)=CC(C[C@@](C)3[H])=O,false
+ClC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,true
+NN,true
+OS(=O)(=O)O.NN,true
+CC(=O)N(O)C1=CC2=C(C=C1)C3=CC=CC=C3C2,true
+OCCNN,false
+O=C(C1=CC=NC=C1)NN,false
+OC(=O)C1=CC=NC=C1,false
+O=C(NC1=CC=CC(=C1)Cl)OC(C)C,false
+O=C(NC1=CC=CC=C1)OC(C)C,false
+[O-]C(C)=O.[O-]C(C)=O.[Pb+2].[OH-].[OH-].[Pb+2].[OH-].[OH-].[Pb+2],false
+CN(C)CCN(CC2=CC=CS2)C1=NC=CC=C1.Cl,false
+NC1=C2C(=NC(=N1)N)N=CC(=N2)CN(C3=CC=C(C=C3)C(=O)N[C@@H](CCC(=O)O)C(=O)O)C,false
+CN(N)C=O,true
+O=C(C(=C)C)OC,false
+CNN,true
+O=C(C1=CC=CN=C1)CCCN(N=O)C,false
+CC1=CC(=O)NC(=S)N1,true
+CC(C(O)=O)(OC1=CC=C(C=C1)C2CCCC3=C2C=CC=C3)C,false
+O=N[O-].[Na+],false
+[O-][N+](C1=CC=C(C2=CSC(NC(C)=O)=N2)O1)=O,true
+[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NC=O,true
+O=[N+](C1=CC=C2C3=C1C=CC=C3CC2)[O-],false
+N(CC(CO)O)(CC(O)C)N=O,true
+N(CC(CO)O)(CC(C)=O)N=O,true
+N(CC(CO)O)(CCO)N=O,false
+O=C(C)CN(N=O)CCO,true
+C1C(N(C(CN1N=O)C)C)C,true
+N(CC(C)=O)(CC=C)N=O,true
+N(CC(CO)O)(C)N=O,true
+O=NN1CCOCC1,true
+N1C=CC=C(C=1)C2N(N=O)CCC2,true
+C1=CC=C(C=[N+]1[O-])C2CCCN2N=O,false
+O=NN1CCCCC1,true
+O=NN1CCCC1,true
+O=C(N(CC(C)=O)N=O)NCCCl,true
+N(C(=O)N)(N=O)CC(C)=O,true
+C1(CCN=C=S)=CC=CC=C1,false
+O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,false
+C1=C2C(=CC=C1NC3=CC=CC=C3)C=CC=C2,false
+O=C1N2C(C3=C(C=CC=C3)CC2)CN(C1)C(=O)C4CCCCC4,false
+C1(=CC(=C(O)C=C1)O)C(O)=O,false
+O=C1C2=C(C=C(C=C2O)O)O/C(=C\1O)C3=CC(=C(C=C3)O)O.O.O,false
+C1=C(C=CC(=C1)C(C2=CC=C(N)C(=C2)C)=C3C=CC(=N)C=C3)N.[H]Cl,false
+C(C1=CC=C(C=C1)N)(C2=CC=C(C=C2)N)=C3C=CC(C=C3)=N.[H]Cl,false
+OC2=CC1=C(C(O)=C2)C(C(O[C@@H]4O[C@@H]([C@H]([C@H](O)[C@H]4O)O)CO[C@H]3[C@H](O)[C@H](O)[C@H]([C@H](C)O3)O)=C(C5=CC(O)=C(C=C5)O)O1)=O,false
+ClC(=CCl)Cl,false
+NC(=O)OCC,true
+C=CCl,true
+N#[N+]C1=CC=CC=C1.F[B-](F)(F)F,false
+C1(CN(CC(N1N=O)C)N=O)C,true
+N(CCN(C)C)(C)N=O,true
+C1(CN(N=O)CC(O1)C)C,true
+O1C(N(CC1C)N=O)=O,true
+CCOC(=O)N(C)N=O,true
+C1N(COC1)N=O,true
+O=C(N(CCC1=CC=CC=C1)N=O)N,true
+O=NN1CCC1,true
+F[B-](F)(F)F.[Na+],false

data/test/opentox-ruby-api-wrapper_test.rb

@@ -1,7 +1,46 @@
 require 'test_helper'
 
 class OpentoxRubyApiWrapperTest < Test::Unit::TestCase
-  should "probably rename this file and start testing for real" do
-    flunk "hey buddy, you should probably rename this file and start testing for real"
-  end
+
+	def setup
+		if ENV['LOCAL']
+			port = 5000
+			[ "opentox-compound", "opentox-feature" , "opentox-dataset" , "opentox-fminer" , "opentox-lazar" ].each do |component|
+				ENV[component.upcase.gsub(/-/,'_')] = "http://localhost:#{port}/"
+				port += 1
+			end
+		end
+	end
+
+	def test_create_dataset_and_model_and_make_a_prediction
+		dataset = OpenTox::Dataset.new :name => "Hamster Carcinogenicity", :filename => "test/hamster_carcinogenicity.csv"
+		puts dataset.uri
+		wait_for_completion dataset
+		assert_match(/#{ENV['OPENTOX_DATASET']}\d+$/,dataset.uri)
+		assert_equal("Hamster Carcinogenicity",dataset.name)
+		assert_equal(true,dataset.finished?)
+		lazar = OpenTox::Lazar.new :dataset_uri => dataset.uri
+		puts lazar.uri
+		wait_for_completion lazar
+		assert_equal(true,lazar.finished?)
+		assert_match(/#{ENV['OPENTOX_LAZAR']}model\/\d+$/,lazar.uri)
+		query_structure = OpenTox::Compound.new :smiles => 'c1ccccc1NN'
+		puts query_structure.uri
+		prediction = lazar.predict query_structure
+		puts prediction.uri
+		wait_for_completion prediction
+		puts prediction.classification
+		puts prediction.confidence
+		puts prediction.neighbors
+		puts prediction.features
+		assert_equal(true, prediction.classification)
+		assert_match(/0\.\d+/, prediction.confidence.to_s)
+	end
+
+end
+
+def wait_for_completion(object)
+	while (!object.finished?)
+		sleep 1
+	end
 end

data/test/start-local-webservices.rb

@@ -0,0 +1,13 @@
+#!/usr/bin/env ruby
+require 'fileutils'
+
+port = 5000
+[ "opentox-compound", "opentox-feature" , "opentox-dataset" , "opentox-fminer" , "opentox-lazar" ].each do |component|
+	ENV[component.upcase.gsub(/-/,'_')] = "http://localhost:#{port}/"
+	Dir.chdir ENV['HOME'] + '/webservices/' + component
+	Dir["test.sqlite3"].each { |f| FileUtils.rm_rf(f) }
+	file = 'application.rb'
+	pid = fork {`urxvt -title #{component} -e thin --debug --rackup config.ru start -p #{port} -e test`}
+	Process.detach(pid)
+	port += 1
+end

data/test/test_helper.rb

@@ -1,9 +1,9 @@
 require 'rubygems'
 require 'test/unit'
-require 'shoulda'
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
+
 require 'opentox-ruby-api-wrapper'
 
 class Test::Unit::TestCase

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: helma-opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  version: 0.1.5
+  version: 0.2.0
 platform: ruby
 authors: 
 - Christoph Helma
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-08-15 00:00:00 -07:00
+date: 2009-08-17 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -22,16 +22,6 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
-- !ruby/object:Gem::Dependency 
-  name: thoughtbot-shoulda
-  type: :development
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
-    version: 
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email: helma@in-silico.ch
 executables: []
@@ -52,7 +42,9 @@ files:
 - lib/opentox-ruby-api-wrapper.rb
 - lib/spork.rb
 - opentox-ruby-api-wrapper.gemspec
+- test/hamster_carcinogenicity.csv
 - test/opentox-ruby-api-wrapper_test.rb
+- test/start-local-webservices.rb
 - test/test_helper.rb
 has_rdoc: false
 homepage: http://github.com/helma/opentox-ruby-api-wrapper
@@ -84,3 +76,4 @@ summary: Ruby wrapper for the OpenTox REST API
 test_files: 
 - test/test_helper.rb
 - test/opentox-ruby-api-wrapper_test.rb
+- test/start-local-webservices.rb