Passes tests in opentox-test

11 files changed, 150 insertions, 4658 deletions

diff --git a/Rakefile b/Rakefile
index 868e04a..2b5727a 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,6 +1,5 @@
 require 'rubygems'
 require 'rake'
-require 'tasks/redis'
 require 'tasks/opentox'
 
 @gems = "sinatra emk-sinatra-url-for builder opentox-ruby-api-wrapper"
diff --git a/application.rb b/application.rb
index ad60764..f94ebbe 100644
--- a/application.rb
+++ b/application.rb
@@ -1,112 +1,102 @@
-# SETUP
-[ 'rubygems', 'redis', 'opentox-ruby-api-wrapper' ].each do |lib|
-  require lib
-end
-
-case ENV['RACK_ENV']
-when 'production'
-  @@redis = Redis.new :db => 0
-when 'development'
-  @@redis = Redis.new :db => 1
-when 'test'
-  @@redis = Redis.new :db => 2
-  @@redis.flush_db
-end
-
-load File.join(File.dirname(__FILE__), 'dataset.rb')
+require 'rubygems'
+require 'opentox-ruby-api-wrapper'
+require File.join File.dirname(__FILE__), 'redis', 'dataset.rb'
 
 set :default_content, :yaml
 
 helpers do
 
 	def find
-		# + charges are dropped
-		uri = uri(params[:splat].first.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
-		#puts uri
+		uri = uri(params[:splat].first)
 		halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
 	end
 
 	def uri(name)
-=begin
-		if name =~ /InChI/
-			name = URI.encode(name,/[^#{URI::PATTERN::UNRESERVED}]/)
-		else
-			name = URI.encode(name)
-		end
-=end
 		name = URI.encode(name)
-		uri = url_for("/dataset/", :full) + name
+		uri = url_for("/", :full) + name
 	end
 
 end
 
 ## REST API
 
-load 'compound.rb'
-load 'feature.rb'
-
-get '/datasets/?' do
+get '/?' do
 	Dataset.find_all.join("\n")
 end
 
-get '/algorithm/tanimoto/dataset/*/dataset/*/?' do
+get '/*/name/?' do
 	find
-	@set.tanimoto(uri(params[:splat][1]))
+	URI.decode(URI.split(@set.uri)[5].split(/\//)[1])
 end
 
-
-get '/algorithm/weighted_tanimoto/dataset/*/dataset/*/?' do
+get '/*/features/?' do
 	find
-	@set.weighted_tanimoto(uri(params[:splat][1]))
+	@set.features.join("\n")
 end
 
-get '/dataset/*/name/?' do
+get '/*/compounds/?' do
 	find
-	URI.decode @set.name
+	@set.compounds.join("\n")
 end
 
-get '/dataset/*/features/?' do
+get '/*/compound/*/?' do
 	find
-	@set.features.join("\n")
+	inchi = params[:splat][1]#.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
+	@set.compound_features(inchi).join("\n")
 end
 
 # catch the rest
-get '/dataset/*/?' do
+get '/*/?' do
 	find
-	@set.members.join("\n")
+	dataset = {}
+	@set.compounds.each do |c|
+		dataset[c] = @set.compound_features(c)
+	end
+	dataset.to_yaml
 end
 
 # create a dataset
-post '/datasets/?' do
+post '/?' do
 	dataset_uri = uri(params[:name])
 	halt 403, "Dataset \"#{dataset_uri}\" exists." if Dataset.find(dataset_uri)
-	@set = Dataset.create(dataset_uri)
-	@set.add Dataset.create(File.join(dataset_uri, "compounds")).uri
-	@set.add Dataset.create(File.join(dataset_uri, "features")).uri
-	@set.uri
+	Dataset.create(dataset_uri).uri
 end
 
-load 'import.rb'
-
-# import yaml
-post '/dataset/*/?' do
+put '/*/import/?' do
 	find
-	@compounds_set = Dataset.find File.join(@set.uri, "compounds")
-	@features_set = Dataset.find File.join(@set.uri, "features")
-	YAML.load(params[:features]).each do |compound_uri,feature_uris|
-		# key: /dataset/:dataset/compound/:inchi
-		@compound_features = Dataset.find_or_create File.join(@set.uri,'compound',OpenTox::Compound.new(:uri => compound_uri).inchi)
-		feature_uris.each do |feature_uri|
-			@compounds_set.add compound_uri
-			@features_set.add feature_uri
-			@compound_features.add feature_uri
+	halt 404, "Compound format #{params[:compound_format]} not (yet) supported" unless params[:compound_format] =~ /smiles|inchi|name/
+	#task = OpenTox::Task.create(@set.uri)
+	data = {}
+	case	params[:file][:type]
+	when "text/csv"
+		File.open(params[:file][:tempfile].path).each_line do |line|
+			record = line.chomp.split(/,\s*/)
+			compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
+#			begin
+			feature_uri = OpenTox::Feature.new(:name => @set.name, :classification => record[1]).uri
+#			rescue
+#				puts "Error: " + line
+#				puts record.join("\t")
+#				puts @set.name.to_s
+#				#puts [record[0] , @set.name , record[1]].to_yaml
+#			end
+			data[compound_uri] = [] unless data[compound_uri]
+			data[compound_uri] << feature_uri
 		end
-  end
+	else
+		halt 404, "File format #{request.content_type} not (yet) supported"
+	end
+	@set.add(data.to_yaml)
 	@set.uri
 end
 
-delete '/dataset/*/?' do
+# import yaml
+put '/*/?' do
+	find
+	@set.add(params[:features])
+end
+
+delete '/*/?' do
 	find
-	@set.members.each{|m| Dataset.find(m).delete} if @set.members
 	@set.delete
 end
diff --git a/compound.rb b/compound.rb
deleted file mode 100644
index 9c1552e..0000000
--- a/compound.rb
+++ /dev/null
@@ -1,33 +0,0 @@
-mime :uid, "text/plain"
-mime :smiles, "chemical/x-daylight-smiles"
-mime :inchi, "chemical/x-inchi"
-mime :sdf, "chemical/x-mdl-sdfile"
-mime :image, "image/gif"
-mime :names, "text/plain"
-
-set :default_content, :smiles
-
-get '/compound/*/match/*' do
-	"#{OpenTox::Compound.new(:inchi => params[:splat][0]).match(params[:splat][1])}"
-end
-
-get %r{/compound/(.+)} do |inchi| # catches all remaining get requests
-	inchi.gsub!(/ /,'+') # fix CGI? escaping of + signs
-	respond_to do |format|
-		format.smiles { inchi2smiles inchi }
-		format.names  { RestClient.get "#{CACTUS_URI}#{inchi}/names" }
-		format.inchi  { inchi }
-		format.sdf    { RestClient.get "#{CACTUS_URI}#{inchi}/sdf" }
-		format.image  { "#{CACTUS_URI}#{inchi}/image" }
-	end
-end
-
-post '/compound/?' do 
-	if params[:smiles]
-		OpenTox::Compound.new(:smiles => params[:smiles]).uri
-	elsif params[:inchi]
-		OpenTox::Compound.new(:inchi => params[:inchi]).uri
-	elsif params[:name]
-		OpenTox::Compound.new(:name => params[:name]).uri
-	end
-end
diff --git a/dataset.rb b/dataset.rb
deleted file mode 100644
index 5b4f95c..0000000
--- a/dataset.rb
+++ /dev/null
@@ -1,88 +0,0 @@
-class Dataset
-
-	include OpenTox::Utils
-	attr_reader :uri, :name, :members
-
-	def initialize(uri)
-		@uri = uri
-		begin
-			@name = URI.split(uri)[5].sub(/\/dataset\//,'')
-		rescue
-			puts "Bad URI #{uri}"
-		end
-		@members = @@redis.set_members(uri)
-	end
-
-	def self.create(uri)
-		@@redis.set_add "datasets", uri
-		Dataset.new(uri)
-	end
-
-	def self.find(uri)
-		#puts uri
-		if @@redis.set_member? "datasets", uri
-			Dataset.new(uri)
-		else
-			nil
-		end
-	end
-
-	def self.find_or_create(uri)
-		dataset = Dataset.create(uri) unless dataset = Dataset.find(uri)
-		dataset
-	end
-
-	def self.find_all_keys
-		@@redis.keys "*"
-	end
-
-	def self.find_all
-		@@redis.set_members "datasets"
-	end
-
-	def member?(uri)
-		@@redis.set_member? @uri, uri
-	end
-
-	def add(member_uri)
-		@@redis.set_add @uri , member_uri
-		@members << member_uri
-	end
-
-	def union(set_uri)
-		@@redis.set_union(@uri,set_uri)
-	end
-
-	def intersection(set_uri)
-		@@redis.set_intersect(@uri,set_uri)
-	end
-
-	def features
-		@@redis.set_members(File.join(@uri,'features'))
-	end
-
-	def tanimoto(set_uri)
-		union_size = @@redis.set_union(@uri,set_uri).size
-		intersect_size = @@redis.set_intersect(@uri,set_uri).size
-		"#{intersect_size.to_f/union_size.to_f}"
-	end
-
-	def weighted_tanimoto(set_uri)
-		union = @@redis.set_union(@uri,set_uri)
-		intersect = @@redis.set_intersect(@uri,set_uri)
-
-		p_sum_union = 0.0
-		p_sum_intersect = 0.0
-
-		union.each{ |f| p_sum_union += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
-		intersect.each{ |f| p_sum_intersect += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
-		"#{p_sum_intersect/p_sum_union}"
-	end
-
-	def delete
-		@@redis.delete @uri 
-		@@redis.set_delete "datasets", @uri
-	end
-
-end
-
diff --git a/feature.rb b/feature.rb
deleted file mode 100644
index 1f138be..0000000
--- a/feature.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-set :default_content, :yaml
-
-## REST API
-get '/feature/*/?' do
-	@feature = OpenTox::Feature.new(request.url)
-	respond_to do |format|
-		format.yaml { @feature.to_yaml }
-		format.xml {  builder :feature }
-	end
-end
-
-post '/feature/?' do
-	OpenTox::Feature.new(:name => params[:name], :values => params[:values]).uri
-end
diff --git a/import.rb b/import.rb
index 86b5480..81b9dcb 100644
--- a/import.rb
+++ b/import.rb
@@ -1,24 +1,27 @@
-post '/dataset/*/import/?' do
+post '/*/import/?' do
 	find
 	halt 404, "Compound format #{params[:compound_format]} not (yet) supported" unless params[:compound_format] =~ /smiles|inchi|name/
-	@compounds_set = Dataset.find File.join(@set.uri, "compounds")
-	@features_set = Dataset.find File.join(@set.uri, "features")
-	case	params[:file][:type]
-	when "text/csv"
-		File.open(params[:file][:tempfile].path).each_line do |line|
-			record = line.chomp.split(/,\s*/)
-			compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
-			feature_uri = OpenTox::Feature.new(:name => @set.name.sub(/dataset\//,''), :values => {:classification => record[1]}).uri
-			@compounds_set.add compound_uri #unless @compounds_set.member? compound_uri
-			@features_set.add feature_uri #unless @features_set.member? feature_uri
-			# key: /dataset/:dataset/compound/:inchi
-			@compound_features = Dataset.find_or_create File.join(@set.uri,'compound',OpenTox::Compound.new(:uri => compound_uri).inchi)
-			@compound_features.add feature_uri
+	task = OpenTox::Task.create(@set.uri)
+	Spork.spork do
+		@compounds_set = Dataset.find File.join(@set.uri, "compounds")
+		@features_set = Dataset.find File.join(@set.uri, "features")
+		case	params[:file][:type]
+		when "text/csv"
+			task.start
+			File.open(params[:file][:tempfile].path).each_line do |line|
+				record = line.chomp.split(/,\s*/)
+				compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
+				feature_uri = OpenTox::Feature.new(:name => @set.name, :values => {:classification => record[1]}).uri
+				@compounds_set.add compound_uri #unless @compounds_set.member? compound_uri
+				@features_set.add feature_uri #unless @features_set.member? feature_uri
+				# key: /dataset/:dataset/compound/:inchi
+				@compound_features = Dataset.find_or_create File.join(@set.uri,'compound',OpenTox::Compound.new(:uri => compound_uri).inchi)
+				@compound_features.add feature_uri
+			end
+			task.completed
+		else
+			halt 404, "File format #{request.content_type} not (yet) supported"
 		end
-	else
-		halt 404, "File format #{request.content_type} not (yet) supported"
 	end
-	@set.uri
-
+	task.uri
 end
-
diff --git a/redis/dataset.rb b/redis/dataset.rb
new file mode 100644
index 0000000..f7fafa0
--- /dev/null
+++ b/redis/dataset.rb
@@ -0,0 +1,75 @@
+class Dataset
+
+	attr_reader :uri, :members
+
+	# key: /datasets
+	# set: dataset uris
+	# key: :dataset_uri/compounds
+	# set: compound uris
+	# key: :dataset_uri/features
+	# set: feature uris
+	# key: :dataset_uri/compound/:inchi
+	# set: feature uris
+	
+	def initialize(uri)
+		@uri = uri
+	end
+
+	def name
+		URI.unescape File.basename(uri)
+	end
+
+	def self.create(uri)
+		@@redis.set_add "datasets", uri
+		Dataset.new(uri)
+	end
+
+	def self.find(uri)
+		Dataset.new(uri) if @@redis.set_member? "datasets", uri
+	end
+
+	def self.find_or_create(uri)
+		Dataset.find(uri) or Dataset.create(uri) 
+	end
+
+	def self.find_all
+		@@redis.set_members "datasets"
+	end
+
+	def compounds
+		@@redis.set_members(File.join(@uri,'compounds'))
+	end
+
+	def features
+		@@redis.set_members(File.join(@uri,'features'))
+	end
+
+	def compound_features(compound_uri)
+		@@redis.set_members(File.join(@uri,'compound',inchi(compound_uri)))
+	end
+
+	def add(yaml)
+		YAML.load(yaml).each do |compound_uri,feature_uris|
+			@@redis.set_add File.join(@uri,'compounds'), compound_uri
+			feature_uris.each do |feature_uri|
+				@@redis.set_add File.join(@uri,'features'), feature_uri
+				@@redis.set_add File.join(@uri,'compound',inchi(compound_uri)), feature_uri
+			end
+		end
+	end
+
+	def delete
+		@@redis.set_members(File.join(@uri,'compounds')).each do |compound_uri|
+			@@redis.delete File.join(@uri,'compound',inchi(compound_uri))
+		end
+		@@redis.delete(File.join(@uri,'compounds'))
+		@@redis.delete(File.join(@uri,'features'))
+		@@redis.delete @uri 
+		@@redis.set_delete "datasets", @uri
+	end
+
+	def inchi(compound_uri)
+		inchi = compound_uri.sub(/^.*\/InChI/,'InChI')
+	end
+
+end
diff --git a/tasks/redis.rb b/tasks/redis.rb
deleted file mode 100644
index ed317d3..0000000
--- a/tasks/redis.rb
+++ /dev/null
@@ -1,125 +0,0 @@
-# Inspired by rabbitmq.rake the Redbox project at http://github.com/rick/redbox/tree/master
-require 'fileutils'
-require 'open-uri'
-
-class RedisRunner
-  
-  def self.redisdir
-    "/tmp/redis/"
-  end
-  
-  def self.redisconfdir
-    '/etc/redis.conf'
-  end
-
-  def self.dtach_socket
-    '/tmp/redis.dtach'
-  end
-
-  # Just check for existance of dtach socket
-  def self.running?
-    File.exists? dtach_socket
-  end
-  
-  def self.start
-    puts 'Detach with Ctrl+\  Re-attach with rake redis:attach'
-    sleep 3
-    exec "dtach -A #{dtach_socket} redis-server #{redisconfdir}"
-  end
-  
-  def self.attach
-    exec "dtach -a #{dtach_socket}"
-  end
-  
-  def self.stop
-    sh 'echo "SHUTDOWN" | nc localhost 6379'
-  end
-
-end
-
-namespace :redis do
-  
-  desc 'About redis'
-  task :about do
-    puts "\nSee http://code.google.com/p/redis/ for information about redis.\n\n"
-  end
-  
-  desc 'Start redis'
-  task :start do
-    RedisRunner.start
-  end
-  
-  desc 'Stop redis'
-  task :stop do
-    RedisRunner.stop
-  end
-  
-  desc 'Restart redis'
-  task :restart do
-    RedisRunner.stop
-    RedisRunner.start
-  end
-
-  desc 'Attach to redis dtach socket'
-  task :attach do
-    RedisRunner.attach
-  end
-  
-  desc 'Install the lastest verison of Redis from Github (requires git, duh)'
-  task :install => [:about, :download, :make] do
-    %w(redis-benchmark redis-cli redis-server).each do |bin|
-      sh "sudo cp /tmp/redis/#{bin} /usr/bin/"
-    end
-
-    puts "Installed redis-benchmark, redis-cli and redis-server to /usr/bin/"
-        
-    unless File.exists?('/etc/redis.conf')
-      sh 'sudo cp /tmp/redis/redis.conf /etc/'
-      puts "Installed redis.conf to /etc/ \n You should look at this file!"
-    end  
-  end
-  
-  task :make do
-    sh "cd #{RedisRunner.redisdir} && make clean"
-    sh "cd #{RedisRunner.redisdir} && make"
-  end
-  
-  desc "Download package"
-  task :download do
-    sh 'rm -rf /tmp/redis/' if File.exists?("#{RedisRunner.redisdir}/.svn")
-    sh 'git clone git://github.com/antirez/redis.git /tmp/redis' unless File.exists?(RedisRunner.redisdir)
-    sh "cd #{RedisRunner.redisdir} && git pull" if File.exists?("#{RedisRunner.redisdir}/.git")
-  end    
-
-end
-
-namespace :dtach do
-  
-  desc 'About dtach'
-  task :about do
-    puts "\nSee http://dtach.sourceforge.net/ for information about dtach.\n\n"
-  end
-  
-  desc 'Install dtach 0.8 from source'
-  task :install => [:about] do
-    
-    Dir.chdir('/tmp/')
-    unless File.exists?('/tmp/dtach-0.8.tar.gz')
-      require 'net/http'
-      
-      url = 'http://downloads.sourceforge.net/project/dtach/dtach/0.8/dtach-0.8.tar.gz'
-      open('/tmp/dtach-0.8.tar.gz', 'wb') do |file| file.write(open(url).read) end
-    end
-
-    unless File.directory?('/tmp/dtach-0.8')    
-      system('tar xzf dtach-0.8.tar.gz')
-    end
-    
-    Dir.chdir('/tmp/dtach-0.8/')
-    sh 'cd /tmp/dtach-0.8/ && ./configure && make'    
-    sh 'sudo cp /tmp/dtach-0.8/dtach /usr/bin/'
-    
-    puts 'Dtach successfully installed to /usr/bin.'
-  end
-end
-  
diff --git a/test/hamster_carcinogenicity.csv b/test/hamster_carcinogenicity.csv
deleted file mode 100644
index 009808f..0000000
--- a/test/hamster_carcinogenicity.csv
+++ /dev/null
@@ -1,85 +0,0 @@
-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

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-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

diff --git a/test/kazius.csv b/test/kazius.csv
deleted file mode 100644
index c1e8999..0000000
--- a/test/kazius.csv
+++ /dev/null
@@ -1,4069 +0,0 @@
-COC1=CC=C(C=C1)C2=NC(=C([NH]2)C3=CC=CC=C3)C4=CC=CC=C4,true
-CC1=C(C=CC=C1N=C=O)N=C=O,true
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-[O-][N+](=O)C1=CC(=CS1)C(=O)NC2=CC(=CC=C2)Br,true
-CN(N=O)C1=CC=CC=C1,true
-CN2C1=C(C=CC=C1)C(=O)C3=C2C4=C(C=C3O)OC(C4)C5(C)CO5,true
-CS(=O)(=O)NC1=CC=C(C=C1)NC3=C2C=CC=CC2=NC4=CC=CC=C34,true
-[O-][N+](=O)C1=CC=C(C=C1)OC2=C(C=C(C=C2)Cl)Cl,true
-OC1=C(C=CC(=C1)[N+]([O-])=O)[N+]([O-])=O,true
-C[N]2C(=NC3=C1N=CC=NC1=C(C)C(=C23)C)N,true
-CSC1=C(C(=C(C(=C1)SC)N)C)N,true
-OC1=CC4=C(C=C1)C3=CC2=CC=CC=C2C=C3C5=CC=CC=C45,true
-CC(=O)C(Br)=C,true
-NCCNCCNCCN,true
-CN(C)C1=CC=C(C=C1)CCO,true
-COC4=CC(=O)C3=C2[NH]C1=CC=NC=C1C2=CN=C3C4=O,true
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-CC1=C(C=C(C(=C1)N=NC2=CC=CC=C2)N)N,true
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-[O-][N+](=O)C3=C1CCC2=CC=CC(=C12)C=C3,true
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-[O-][N+](=O)C1=C(C=CC=C1)C(Cl)=O,true
-ClCCOP(OCCCl)OCCCl,true
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-CC(=O)OC1=CC=C(C=C1)CCl,true
-NC1=CC=C(C=C1)OC2=CC=C(C=C2)[N+]([O-])=O,true
-[O-][N+](=O)C1=CC=C(C=C1)C2=C(C=C(C=C2)[N+]([O-])=O)[N+]([O-])=O,true
-COC1=C(C=CC=C1)[N+]([O-])=O,true
-C1=CC2=C(C=C1)C4=C(C=C2)C3=NC=CC=C3C=C4,true
-OC2=C3C=CC4=CC=C(C5=C1C=CC=CC1=C(C=C2)C3=C45)[N+]([O-])=O,true
-[O-][N+](=O)C1=CC(=C(C(=C1)[N+]([O-])=O)Cl)[N+]([O-])=O,true
-[O-][N+](=O)C1=C3C(=CC=C1)C2=CC=CC=C2C(O3)=O,true
-CC3=C2C1=CC=CC=C1C=CC2=C(C4=CC=CC=C34)CO,true
-CC3=C2C=CC1=CC=CC=C1C2=CC4=CC=CC=C34,true
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-OC3C1OC1C2=C4C(=C(C=C2)O)C7=C5C(=C34)C(=CC=C5C6OC6C7=O)O,true
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-COC1=C(C=C(C=C1)N)N,true
-CC(=O)NC1=CC=C(C=C1)C(=O)C2OC2C3=CC=CC=C3,true
-C[N]1C(=NC2=C1C=C(C)C3=NC(=CN=C23)C4=CC=CC=C4)N,true
-[O-][N+]([O-])=C1CCCC1,true
-COC2=C1OC(=CC1=C(C=C2)N(CCCl)CCCl)[N+]([O-])=O,true
-COC3=C(C=C2N=C1C=C(C(=CC1=NC2=C3)N)OC)N,true
-C[N]2C(=NC3=NC1=CC=CC=C1C=C23)N,true
-OC5C(O)C4=C(C3=NC2=C1C=CC=CC1=CC=C2C=C3C=C4)C6OC56,true
-NC3=C2C=C1C=CC=CC1=NC2=CC=C3,true
-[O-][N+](=O)C1=CC4=C2C(=C1)CCC3=C2C(=CC(=C3)[N+]([O-])=O)CC4,true
-[O-][N+](=O)C3=CC2=NC1=CC=CC=C1N=C2C=C3,true
-CCOP(=O)(OC1=CC=C(C=C1)[N+]([O-])=O)C2=CC=CC=C2,true
-[O-][N+](=O)C3=C2C=CC1=CC=CC4=C1C2=C(C=C3)C(=O)C4=O,true
-CC(C)S(Cl)(=O)=O,true
-CC3=C2C1=CC=CC=C1[NH]C2=CC(=N3)N,true
-ClCC(Cl)CBr,true
-CC2=C(N=C1C(=C(C=CC1=N2)N)C)C,true
-CC1=CC4=C(C=C1)C5=C2C=CC=CC2=CC6=C3C=CC=CC3=CC4=C56,true
-NC1=CC(=CC=C1)[N+]([O-])=O,true
-[O-][N+](=O)C2=C1SN=C(C1=CC=C2)Cl,true
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-[O-][N+](=O)C1=C(C=CC=C1)SSC(Cl)=C(Cl)Cl,true
-CN(C)CCCNC2=C1C(=CC=C(C1=NC3=CC=CC=C23)Cl)[N+]([O-])=O,true
-COC4=CC(=O)C3=C2[NH]C1=C(CCCC1)C2=C(C)N=C3C4=O,true
-CC=CC=O,true
-C[N+]2=C1C=CC(=CC1=CC3=CC=CC=C23)N,true
-CC(=O)ON(C(C)=O)C1=CC=C(C=C1)SC2=CC=CC=C2,true
-CC1C=C(C=O)C(=CC2(O)CC(C)(C)CC12)C=O,true
-C1=CC2=C(C=C1)C3=CC=C4C=CC=C5C=CC(=C2)C3=C45,true
-ClC2=C1C=CC=CC1=CC=C2,true
-C2C1=C(C=CC=C1)C3=C2C4=C(C=C3)C=CC5=C4C=CC=C5,true
-CC1=C(C=CC(=C1)N)N,true
-COC1=CC(=C(C=C1)OC)N=NC3=C2C=CC=CC2=CC=C3O,true
-CN(C)C1=CC=C(C=C1)N=NC3=C2C=CC=CC2=CC=C3,true
-COP(=O)(OC)OC,true
-ClC(Cl)C#N,true
-[O-][N+](=O)C1=CC2=C(C=C1)NCC2,true
-[O-][N+](=O)C1=CC(=CS1)C(=O)NC2=C(C=CC=C2)F,true
-C[N]1C(=NC=C1[N+]([O-])=O)C2NC(CO)(CO)CO2,true
-COC1=C(C=CC(=C1)O)NC3=C2C=CC=CC2=NC4=CC=CC=C34,true
-COC(=O)C1=C(C=CC=C1)O,true
-O1C4C1C2=C(C=CC3=CC=CC=C23)C5=C4C=CC=C5,true
-CC1=CC(=C(C=C1)[N+]([O-])=O)[N+]([O-])=O,true
-O=C5C=C3C2=C(C=C1C=CC=CC1=C2)C4=C3C(=CC=C4)C5=O,true
-[O-][N+](=O)C1=CC=C(O1)C=CC=NN2CC(=O)NC2=O,true
-C[N]1C(=NC2=NC=C(C=C12)C3=CC=CC=C3)N,true
-BrC(=C)C=O,true
-CC(=O)NC(CSC(Cl)=C(Cl)C(Cl)=C(Cl)Cl)C(O)=O,true
-[O-][N+](=O)C2=C1C(=CC=CC1=CC=C2)[N+]([O-])=O,true
-COC4=C1C5=C(C(OC1=C3C2C=COC2OC3=C4)=O)C(CC5)O,true
-CC(=C)C2=CC=C(C)C1=CC=C(C=O)C1=C2,true
-CC1=CC=C[N]2C1=NC3=CC=C(N)N=C23,true
-C1=CC2=C(C=C1)C3=CN=C4C=CC=C5C=CC(=C2)C3=C45,true
-COC(=O)C(=CC1=CC=C(O1)[N+]([O-])=O)[N+]([O-])=O,true
-ClCC4=CC=C3C2=C1C(=CC=CC1=CC=C2)C3=C4,true
-[O-][N+](=O)C1=CC(=C(C=C1)Cl)[N+]([O-])=O,true
-COC(=O)C(=CC1=CC=C(O1)[N+]([O-])=O)C#N,true
-C(N1C3C1C2=C(C=CC=C2)C4=C3C=CC=C4)C5=CC=CC=C5,true
-OC1C(O)C5=C4C2=C1C=CC=C2C3=CC=CC=C3C4=C(C=C5)[N+]([O-])=O,true
-CN(C)C1=CC=C(C=C1)C=CC2=CC(C=C(C)O2)=C(C#N)C#N,true
-CCCCOCC1CO1,true
-OC(=O)C=CC1=CC(=CC=C1)[N+]([O-])=O,true
-NC(O)=NO,true
-FCC1CO1,true
-ClC(C(=O)NCC1=CC=CC=C1)C2=CC=CC=C2,true
-CC1(C)CC(O)CC(C)(C)N1O,true
-CC(=O)NC1=CC=C(C=C1)SC2=CC=CC=C2,true
-OC1=C(C=CC=C1)NC2=C(C=C(C=C2)[N+]([O-])=O)[N+]([O-])=O,true
-CCC(=O)N(O)C1=CC=C(C=C1)C2=CC=CC=C2,true
-O=CC1CC(=O)C(=O)CO1,true
-C(COCC1CO1)OCC2CO2,true
-C1CN1,true
-OCC(CBr)(CBr)CBr,true
-CCCCCCCCCCCCCCCCCC(=O)OCC1=CC=C2C(=CCC(C=C12)C(C)=C)C,true
-OC(=O)C1=CC=C(C=C1)C=NN4N=NC2=C([NH]C3=CC=CC=C23)C4=O,true
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-ClC1=NC=CC=C1,true
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-CN(C)CCNC(=O)C2=C1C(C3=C(C(C1=CC=C2)=O)C=CC=C3)=O,true
-NC1=CC=C(C=C1)N,true
-[O-][N+](=O)C3=CC2=C(C=C1C=CC=CC1=C2C=C3)[N+]([O-])=O,true
-[O-][N+](=O)C1=CC4=C3C(=C1[N+]([O-])=O)C2=CC=CC=C2C3=CC=C4,true
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-CC(C)C1CCC(C)CC1=O,true
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-OC2=C3C=CC4=C1C=CC=CC1=CC5=CC=C(C=C2)C3=C45,true
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-[O-][N+](=O)C1=C(C=CC(=C1)N=[N+]=[N-])F,true
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-CC(=O)OCC1=COC=C2C(=CC=[C]12)C=O,true
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-CCC[N]3C=C2CC1C(C=C(C)CN1C)C4=C2C3=CC=C4,true
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-[O-][N+](=O)C1=CC3=C(C=C1)C2=CC4=C(C=C2CC3)CCCC4,true
-[O-][N+](=O)C2=C1N=CC=CC1=CC=C2,true
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-CC(C)N(C(C)C)C(=O)SCC(Cl)=CCl,true
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-[O-][N+](=O)C3=CC2=C1C=CC(=CC1=CC=C2O3)N(CCCl)CCCl,true
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-NC2=NC1=N[NH]N=C1C(=N2)O,false
-CCCCCCCCCCCCCCCC(=O)OCC(O)C1=C(C(=C(O1)O)O)O,false
-CCCCCC(CC)OC(=O)C1=CC(=CC=C1)C(=O)OC(CC)CCCCC,false
-OC2=C1C=CC=CC1=C(N=N2)O,false
-SC2=NC1=CC=CC=C1S2,false
-OCC(O)C(O)CO,false
-CC2(C)C3CC1OC1(C)C2C3,false
-CC(=O)C1=C(O)[N]5C(=C1O)C2C(CC4=C3C2=C[NH]C3=CC=C4)C5(C)C,false
-CC(C)CC(=O)OC4CC1(OC(C)=O)C(OC2C(O)C(OC(C)=O)C1(C)C23CO3)C=C4C,false
-CC(=O)OCC12CCC(=CC1OC3C(O)C(OC(C)=O)C2(C)C34CO4)C,false
-CC4CC3OC1C(O)C(OC(C)=O)C(C)(C12CO2)C3(CO)C(=O)C4=O,false
-CC4CC3OC1C(O)C(O)C(C)(C12CO2)C3(CO)C(=O)C4=O,false
-NC1=NN=C(S1)S,false
-ClCC1C(CCl)C2(Cl)C(=C(Cl)C1(Cl)C2(Cl)Cl)Cl,false
-ClC1=CC3=C(C=C1)N2C=NNC2=CN=C3C4=CC=CC=C4,false
-C=CC1CC2CC1C=C2,false
-ClC3=C(Cl)C4(Cl)C2C1CC(C=C1)C2C3(Cl)C4(Cl)Cl,false
-CC1C(=O)OC2CCN3CC=C(COC(=O)C(C)(O)C1(C)O)C23,false
-OC2CC(O)(CC(OC(=O)C=CC1=CC(=C(C=C1)O)O)C2O)C(O)=O,false
-CN(C=NC=NC1=C(C=C(C=C1)C)C)C2=C(C=C(C=C2)C)C,false
-NC3=NC(=C2N=C(O)[N](C1OC(CO)C(O)C1O)C2=N3)O,false
-CC1(CO)C(O)CCC2(C)C1CCC3CC4CC23CCC4(O)CO,false
-CNC(=N)N[N+]([O-])=O,false
-CC(=O)OC4(CCC5C3C=C(Cl)C2=CC(=O)C1CC1C2(C)C3CCC45C)C(C)=O,false
-CC12CCC(CC1)C(C)(C)O2,false
-CC12CCCC(C)(C1CCC34CC(=C)C(O)(CCC23)C4)C(O)=O,false
-CNC3=C1CC(=O)C(=CC=C1C2=C(C(=C(C=C2CC3)OC)OC)OC)OC,false
-CC34CC(O)C1C(CCC2=CC(=O)C=CC12C)C3CCC4(O)C(O)C=O,false
-CC34CCC1C(CCC2=C1C=CC(=C2)O)C3CC(O)C4O,false
-CC34CCC1C(CCC2=C1C=CC(=C2)O)C3CCC4O,false
-CC2=CN(C1CC(O)C(CO)O1)C(=O)NC2=O,false
-OC1=NC(=C(C=N1)F)O,false
-CC(=O)OC3(CCC4C2CCC1=C(CCC(=O)C1)C2CCC34C)C#C,false
-CC1CCC6(OC1)OC5CC4C3CC=C2CC(O)CCC2(C)C3CCC4(C)C5C6C,false
-CC4CC3OC1C(O)CC(C)(C12CO2)C3(CO)C(=O)C4=O,false
-OC3=C(C=C2C1C4=C(OCC1(CC2=C3)O)C(=C(O)C=C4)O)O,false
-COC1=C(C(=CC(=C1)C3C2C(COC2=O)C(O)C5=C3C=C4OCOC4=C5)OC)OC,false
-CC2OC=C1C(=O)C(C(O)=O)C(=O)C(=C1C2C)C,false
-NC2=C1C(=NN=C(C1=CC=C2)O)O,false
-CC34CCC1C(CC=C2CC(O)CCC12C)C3CCC4=O,false
-CN1CCCC1C2=CN=CC=C2,false
-OCC1OC(CC1O)N2C=C(I)C(=O)NC2=O,false
-CC(C)C12CC1C(C)C(=O)C2,false
-CC(N)(CC1=CC(=C(C=C1)O)O)C(O)=O,false
-CC1=NC(=NC(=C1)O)S,false
-CC34CCC1C(CCC2=C1C=CC(=C2)O)C3CCC4(O)C#C,false
-CC(=O)C3CCC4C2CC=C1CC(=O)CCC1(C)C2CCC34C,false
-NC2=C1N=C[N](C1=NC=N2)C3OC(CO)C(O)C3O,false
-OC(=O)CCCCC1SCC2NC(=O)NC12,false
-NS(=O)(=O)C1=C(C=C2C(=C1)S(NC=N2)(=O)=O)Cl,false
-SC2=NC1=CC=CC=C1[NH]2,false
-OCC1OC(CC1O)N2C=C(Br)C(=O)NC2=O,false
-NC2=NC1=NC=C(N=C1C(=N2)O)CNC3=CC=C(C=C3)C(=O)NC(CCC(O)=O)C(O)=O,false
-CC1=C(N=C(N=C1)S)O,false
-CC=CC(=O)OC2CC3OC1=CC(C)C(=O)CC1(C)C2(C)C34CO4,false
-CC(C)CCCC(C)C1CCC2C(CCCC12C)=CC=C3CC(O)CCC3=C,false
-NC(CC1=CC=CC=C1)C(O)=O,false
-CC34CCC1C(CC=C2CC(=O)CCC12)C3CCC4(O)C#C,false
-CC(=O)OC3(CCC4C2CC(=C1CC(=O)CCC1(C)C2CCC34C)C)C(C)=O,false
-CC14C(O)C=CC5(OC1=O)C2CCC3(O)CC2(CC3=C)C(C45)C(O)=O,false
-C2C=CC3C1CC(C=C1)C23,false
-CC1=CCC2CC1C2(C)C,false
-CC6CCC5C(C)C3C(CC4C2CC=C1CC(O)CCC1(C)C2CCC34C)N5C6,false
-CC(CCC(O)=O)C3CCC4C2C(O)CC1CC(O)CCC1(C)C2CC(O)C34C,false
-[O-][N+](=O)OC1COC2C(COC12)O[N+]([O-])=O,false
-CC2=CCCC(=C)C1CC(C)(C)C1CC2,false
-CC1=C(N=C(N=N1)O)O,false
-OCC1OC(CC1O)N2C=CC(=O)NC2=O,false
-NC2=C1N=C[N](C1=NC=N2)C3CC(O)C(CO)O3,false
-CCCC(=O)OCC,false
-CC(=O)C1=CC=NC=C1,false
-ClC1=NC(=CC=C1)Cl,false
-CC(O)CO,false
-CC(C)CO,false
-CC1CCC(=O)C1=O,false
-CC1=CC(=O)OC2=C1C=CC(=C2)O,false
-CCN(CC)C1=CC=CC=C1,false
-CCCCOC(=O)C(C)=C,false
-CN(C)C(=O)OC1=C[N+](=CC=C1)C,false
-CCC(CO)NCCNC(CC)CO,false
-CC12CCC(CC1O2)C=C,false
-NC2=C1C=CC=CC1=CC=C2O,false
-CN1CCC(C1)CN3C2=C(C=CC=C2)SC4=C3C=CC=C4,false
-CCCCCC(=O)OC3(CCC4C2CCC1=C(CCC(=O)C1)C2CCC34C)C(C)=O,false
-O=C1NS(=O)(=O)C2=C1C=CC=C2,false
-OC2=C(C=C1C=C(C=CC1=C2)S(O)(=O)=O)S(O)(=O)=O,false
-NC1=CC=CC=C1,false
-COC1=C(C4=C(C=C1Cl)C3(C(C25SSC(C(N2C3N4C)=O)(C)N(C5=O)C)O)O)OC,false
-CCCCCCCCCCCCOS(O)(=O)=O,false
-OC(=O)CC1=C(C=CC=C1)NC2=C(C=CC=C2Cl)Cl,false
-NC2=C1N=C[N](C1=NC(=N2)O)C3OC(CO)C(O)C3O,false
-COC1=C(C(=CC(=C1)CC2NCCC3=C2C=C(C(=C3)O)O)OC)OC,false
-OC(=O)C2=NN(C1=CC=C(C=C1)S(O)(=O)=O)C(=O)C2N=NC3=CC=C(C=C3)S(O)(=O)=O,false
-CN(C)C4C3C(O)C2C(C(=O)C1=C(C=CC=C1O)C2(C)O)C(=O)C3(O)C(=O)C(C(N)=O)C4=O,false
-CCNC1=NC(=NC(=N1)O)NC(C)C,false
-ON1CN(Cl)CN(Cl)C1,false
-C[N+]1(C)CCOCC1,false
-ClC1=CC=C(C=C1)COC(C[N]2C=CN=C2)C3=C(C=C(C=C3)Cl)Cl,false
-O[N]1N=NC2=CC=CC=C12,false
-CN2CCN=C(C1=CC=CC=C1)C3=C2C=CC(=C3)Cl,false
-CC(CCC(O)=O)C3CCC4C2CCC1CC(=O)CCC1(C)C2CC(=O)C34C,false
-NC(CSCC1=CC=CC=C1)C(O)=O,false
-CCNC(=O)CCC(N)C(O)=O,false
-CCC3CN2CCC1=C(C=C(C(=C1)OC)OC)C2CC3CC4NCCC5=C4C=C(C(=C5)OC)OC,false
-NC1=CC(=C(C=C1)Cl)C(F)(F)F,false
-CCN(CC)CCCN(C2CC1=C(C=CC=C1)C2)C3=CC=CC=C3,false
-OC1C(O)C(OC1COP(O)(O)=O)N2C=CC(=O)NC2=O,false
-NCCC1=C[NH]C2=CC=CC=C12,false
-CCCC(=O)NC1=CC(=C(C=C1)OCC(O)CNC(C)C)C(C)=O,false
-FC1=CC=C(C=C1)CCl,false
-CCCC(=O)NC2=C1N=C[N](C1=NC=N2)C4OC3COP(O)(=O)OC3C4OC(=O)CCC,false
-FC1=CN=CC=C1,false
-CCCCCCC(=O)OC3(CCC4C2CCC1=CC(=O)CCC1C2CCC34C)C#C,false
-OCC1OC(C(O)C1O)[N]3C=NC4=C(NCC2=CC=C(C=C2)[N+]([O-])=O)N=CN=C34,false
-OCC1OC(CC1O)N2C=C(C=O)C(=O)NC2=O,false
-OC1C(O)C(OC1COP(O)(O)=O)[N]2C=NC3=C(O)N=CN=C23,false
-OC2=C1C=CC=CC1=NC=N2,false
-CCC5=C(CC1NCCC2=C1C=C(C(=C2)OC)OC)CC3N(CCC4=C3C=C(C(=C4)OC)OC)C5,false
-CC(C)C3=CC2=CCC1C(C)(CCCC1(C)C(O)=O)C2CC3,false
-OC1=CC2=C(C=C1)C4(C3=C(O2)C=C(O)C=C3)OC(=O)C5=C4C=CC=C5,false
-OC2=CC(=C1C=C(O)C(=[O+]C1=C2)C3=CC(=C(C(=C3)O)O)O)O,false
-CCCCCCC(O)CC=CCCCCCCCC(O)=O,false
-C[N+]1=CC(=CC=C1)C(O)=O,false
-OC(=O)C1=C(C=CC=C1)O,false
-NC2=NC1=CC=C(C=C1[NH]2)Cl,false
-CCCOC(C(=O)OC1CCN(C)CC1)(C2=CC=CC=C2)C3=CC=CC=C3,false
-NC3=NC(=C2N=C[N](C1OC(COP(O)(O)=O)C(O)C1O)C2=N3)O,false
-CNC(=O)OC1=CC2=C(C=C1)N(C)C3N(C)CCC23C,false
-CC(C)CCCC(C)C3CCC4C2CC=C1CCCCC1(C)C2CCC34C,false
-CC4CC2(C)C(CCC3C1CCC(O)C1(C)CCC23)CC4=O,false
-CC1=C(C(=C(C=N1)CO)CO)O,false
-CC1=CC(=C(C=C1)N=NC3=C2C=CC=CC2=CC(=C3O)C(O)=O)S(O)(=O)=O,false
-CN,false
-CC1=C(C(=CC=C1)OCC(O)CNC(C)(C)C)C,false
-CN[N+]([O-])=O,false
-ClC4=C(Cl)C5(Cl)C3C1CC(C2OC12)C3C4(Cl)C5(Cl)Cl,false
-CC(C)CC(NC(=O)C(CC1=CC=CC=C1)NC(=O)CNC(=O)CN)C(O)=O,false
-CC1=NCCC2=C1[NH]C3=CC(=CC=C23)O,false
-CC(C)CCCC(C)C3CCC4C2CC=C1CC(CCC1(C)C2CCC34C)OC(C)=O,false
-CNCC(O)C1=CC(=CC=C1)O,false
-NC1=NC=N[NH]1,false
-NC1=NC(=O)N(C=C1I)C2CC(O)C(CO)O2,false
-NC(CC1=CC(=C(C=C1)O)[N+]([O-])=O)C(O)=O,false
-COC1=CC=C(C=C1)CN(CCN(C)C)C2=NC=CC=N2,false
-CN(C)C4C3CC2C(C(=O)C1=C(C=CC=C1O)C2(C)O)C(=O)C3(O)C(=O)C(C(N)=O)C4=O,false
-COC1=CC=C2C(=CC1=O)C(CCC3=C2C(=C(C(=C3)OC)OC)OC)NC(C)=O,false
-CN1C2CC(CC1C3OC23)OC(=O)C(CO)C4=CC=CC=C4,false
-CNC(C=[N+](O)[O-])=NCCSCC1=CC=C(O1)CN(C)C,false
-OCC1OC(C(O)C1O)N2C=CC(=N)NC2=O,false
-OC1=NC(=NC=N1)O,false
-CC2(C)C1CCC(C1)C2=C,false
-CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO,false
-OCC1=CC(C(O)C1O)N2C=CC(=N)NC2=O,false
-O=C1NC(=S)NC(=O)C1C(=O)NC2=CC=CC=C2,false
diff --git a/test/test.rb b/test/test.rb
deleted file mode 100644
index b6d9a99..0000000
--- a/test/test.rb
+++ /dev/null
@@ -1,161 +0,0 @@
-require 'application'
-require 'test/unit'
-require 'rack/test'
-require 'ruby-prof'
-
-set :environment, :test
-@@redis.flush_db
-
-class DatasetsTest < Test::Unit::TestCase
-  include Rack::Test::Methods
-	#include RubyProf::Test
-
-  def app
-    Sinatra::Application
-  end
-
-	def test_index
-		get '/datasets'
-		assert last_response.ok?
-	end
-
-	def test_create_dataset
-		post '/datasets', :name => "Test dataset"
-		assert last_response.ok?
-		uri = last_response.body
-		assert_equal "http://example.org/dataset/Test%20dataset", uri
-		get uri
-		assert last_response.ok?
-		get uri + '/name'
-		assert last_response.ok?
-		assert_equal "Test dataset", last_response.body
-		delete uri
-		assert last_response.ok?
-		get uri
-		assert !last_response.ok?
-	end
-
-	def test_create_dataset_from_csv
-		[
-			['F[B-](F)(F)F.[Na+]','false'],
-			['CC(=O)Nc1scc(n1)c1ccc(o1)[N+](=O)[O-]','true'],
-			['NN.OS(=O)(=O)O','true'],
-			['[Cd+2].[O-]S(=O)(=O)[O-]','false']
-		].each do |items|
-			smiles = items[0]
-			activity = items[1]
-
-			compound = OpenTox::Compound.new(:smiles => smiles)
-			post '/datasets', :name => "Hamster Carcinogenicity"
-			uri = last_response.body
-			assert last_response.ok?
-			post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"), "text/csv"), :compound_format => "smiles"
-			get uri
-			assert last_response.ok?
-			get uri + '/compounds'
-			assert last_response.ok?
-			assert last_response.body.include?(compound.inchi)
-			get File.join(uri , 'compound', compound.inchi)
-			puts last_response.body
-			assert last_response.ok?
-			assert last_response.body.include?("Hamster%20Carcinogenicity/classification/#{activity}")
-			get File.join(uri , 'features')
-			puts last_response.body.to_yaml
-			delete uri
-			assert last_response.ok?
-			get uri
-			assert !last_response.ok?
-		end
-	end
-
-=begin
-	def test_create_large_dataset_from_csv
-		post '/datasets', :name => "Salmonella Mutagenicity"
-		uri = last_response.body
-		post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"), "text/csv"), :compound_format => "smiles"
-		uri = last_response.body
-		get uri
-		assert last_response.ok?
-	end
-=end
-
-	def test_tanimoto_similarity
-		#@feature_set = OpenTox::Algorithms::Fminer.new :dataset_uri => @dataset
-		name = "Similarity test dataset"
-		data = {
-			#'c1ccccc1' =>
-			'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' =>
-			{
-				'A' => 1.0,
-				'B' => 0.9,
-				'C' => 0.8,
-				'D' => 0.7,
-				'E' => 0.5
-			},
-				'CCCNN' =>
-			#'F[B-](F)(F)F.[Na+]' => 
-			{
-				'F' => 0.9,
-				'B' => 0.9,
-				'C' => 0.8,
-				'D' => 0.7,
-				'E' => 0.5
-			},
-				'C1CO1' =>
-			#'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' => 
-			{
-				'A' => 1.0,
-				'B' => 0.9,
-				'F' => 0.9,
-			}
-		}
-		post '/datasets', :name => name
-		assert last_response.ok?
-		uri = last_response.body
-		get uri
-		assert last_response.ok?
-		name = URI.encode(name)
-		feature_data = {}
-
-		data.each do |smiles,features|
-			compound = OpenTox::Compound.new(:smiles => smiles).uri
-			feature_data[compound] = []
-			features.each do |k,v|
-				feature= OpenTox::Feature.new(:name => k, :values => {:p_value => v}).uri
-				feature_data[compound] << feature
-			end
-		end
-
-		post uri , :features => feature_data.to_yaml
-		assert last_response.ok?
-
-		data.each do |smiles,features|
-			compound= OpenTox::Compound.new(:smiles => smiles).inchi
-			data.each do |s,f|
-				unless s == smiles
-					neighbor= OpenTox::Compound.new(:smiles => s).inchi
-					get "/dataset/#{name}/compounds"
-					assert last_response.ok?
-					get "/dataset/#{name}/compound/#{compound}"
-					assert last_response.ok?
-					get "/algorithm/tanimoto/dataset/#{name}/compound/#{compound}/dataset/#{name}/compound/#{neighbor}"
-					puts last_response.body
-					assert last_response.ok?
-					sim = last_response.body
-					features_a = data[smiles].keys
-					features_b = data[s].keys
-					union = features_a | features_b
-					intersect  = features_a & features_b
-					mysim = intersect.size.to_f/union.size.to_f
-					assert_equal sim, mysim.to_s
-					puts "tanimoto::#{smiles}::#{s}::#{last_response.body}"
-					get "/algorithm/weighted_tanimoto/dataset/#{name}/compound/#{compound}/dataset/#{name}/compound/#{neighbor}"
-					assert last_response.ok?
-					puts "weighted_tanimoto::#{smiles}::#{s}::#{last_response.body}"
-				end
-			end
-		end
-
-	end
-
-end