Merge remote branch 'helma/master' into test

12 files changed, 141 insertions, 235 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 30a41e0..9d87c7a 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -41,9 +41,7 @@ module OpenTox
 				LOGGER.debug params
 				LOGGER.debug File.basename(__FILE__) + ": creating model"
 				LOGGER.debug File.join(@@config[:services]["opentox-algorithm"], "lazar")
-        #resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml")
         resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml")
-        #@uri = resource.post(:dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).chomp
         @uri = resource.post(:dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).body.chomp
 			end
 
@@ -56,12 +54,12 @@ module OpenTox
     class Similarity
       def self.weighted_tanimoto(fp_a,fp_b,p)
         common_features = fp_a & fp_b
-        all_features = fp_a + fp_b
+        all_features = (fp_a + fp_b).uniq
         common_p_sum = 0.0
         if common_features.size > 0
-          common_features.each{|f| common_p_sum += p[f]}
+          common_features.each{|f| common_p_sum += OpenTox::Utils.gauss(p[f])}
           all_p_sum = 0.0
-          all_features.each{|f| all_p_sum += p[f]}
+          all_features.each{|f| all_p_sum += OpenTox::Utils.gauss(p[f])}
           common_p_sum/all_p_sum
         else
           0.0
diff --git a/lib/compound.rb b/lib/compound.rb
index 7c7c3d8..49c166f 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -1,3 +1,6 @@
+@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/"
+@@ambit_uri="http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search="
+
 module OpenTox
 
 	class Compound #< OpenTox
@@ -6,7 +9,6 @@ module 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)
-			@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/"
 			if params[:smiles]
 				@inchi = smiles2inchi(params[:smiles])
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
@@ -45,12 +47,35 @@ module OpenTox
 			obconversion(@inchi,'inchi','sdf')
 		end
 
-		def image
+		def gif
 			RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/image")
 		end
 
+		def png
+      RestClientWrapper.get(File.join @uri, "image")
+		end
+
+		def names
+      begin
+        RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/names")
+      rescue
+        "not available"
+      end
+		end
+
+    def display_smarts_uri(activating, deactivating, highlight = nil)
+      LOGGER.debug activating.to_yaml unless activating.nil?
+      activating_smarts = URI.encode "\"#{activating.join("\"/\"")}\""
+      deactivating_smarts = URI.encode "\"#{deactivating.join("\"/\"")}\""
+      if highlight.nil?
+        File.join @@config[:services]["opentox-compound"], "smiles", URI.encode(smiles), "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts)
+      else
+        File.join @@config[:services]["opentox-compound"], "smiles", URI.encode(smiles), "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts), "highlight", URI.encode(highlight)
+      end
+    end
+
 		def image_uri
-			"#{@@cactus_uri}#{@inchi}/image"
+      File.join @uri, "image"
 		end
 
 		# Matchs a smarts string
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 84b1ec0..654a275 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -31,8 +31,7 @@ module OpenTox
     def self.find(uri, accept_header=nil) 
     
       unless accept_header
-        #if uri.match(@@config[:services]["opentox-dataset"]) || uri=~ /188.40.32.88/ || uri =~ /informatik/
-        if (uri.match(@@config[:services]["opentox-dataset"]) || uri =~ /in-silico.ch/) && !@@config[:accept_headers]["opentox-dataset"].grep(/yaml/).empty?
+        if (@@config[:yaml_hosts].include?(URI.parse(uri).host))
           accept_header = 'application/x-yaml'
         else
           accept_header = "application/rdf+xml"
diff --git a/lib/environment.rb b/lib/environment.rb
index 312eec4..80899c5 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -1,6 +1,6 @@
-require 'logger'
+require "ot-logger"
 # set default environment
-ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
+ENV['RACK_ENV'] = 'production' unless ENV['RACK_ENV']
 
 # load/setup configuration
 basedir = File.join(ENV['HOME'], ".opentox")
@@ -44,69 +44,9 @@ end
 # load mail settings for error messages
 load File.join config_dir,"mail.rb" if File.exists?(File.join config_dir,"mail.rb")
 
-# hack: store sinatra in global var to make url_for and halt methods accessible
-before{ $sinatra = self unless $sinatra }
-
-class Sinatra::Base
-  # overwriting halt to log halts (!= 202)
-  def halt(*response)
-    LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response and response.first and response.first >= 300
-    # orig sinatra code:
-    response = response.first if response.length == 1
-    throw :halt, response
-  end
-end
-
-# logging
-class MyLogger < Logger
-  
-  def pwd
-    path = Dir.pwd.to_s
-    index = path.rindex(/\//)
-    return path if index==nil
-    path[(index+1)..-1]
-  end
-  
-  def trace()
-    lines = caller(0)
-    n = 2
-    line = lines[n]
-    
-    while (line =~ /spork.rb/ or line =~ /as_task/ or line =~ /environment.rb/)
-      n += 1
-      line = lines[n]
-    end
-  
-    index = line.rindex(/\/.*\.rb/)
-    return line if index==nil
-    line[index..-1]
-  end
-  
-  def format(msg)
-    pwd.ljust(18)+" :: "+msg.to_s+"           :: "+trace+" :: "+($sinatra ? $sinatra.request.env['REMOTE_ADDR'] : nil).to_s
-  end
-  
-  def debug(msg)
-    super format(msg)
-  end
-  
-  def info(msg)
-    super format(msg)
-  end
-  
-  def warn(msg)
-    super format(msg)
-  end
-
-  def error(msg)
-    super format(msg)
-  end
-
-end
-
-
 logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
-LOGGER = MyLogger.new(logfile,'daily') # daily rotation
+#LOGGER = MyLogger.new(logfile,'daily') # daily rotation
+LOGGER = MyLogger.new(logfile) # no rotation
 LOGGER.formatter = Logger::Formatter.new #this is neccessary to restore the formating in case active-record is loaded
 if @@config[:logger] and @@config[:logger] == "debug"
 	LOGGER.level = Logger::DEBUG
@@ -128,18 +68,10 @@ rescue
   raise "Please edit #{user_file} and restart your application. Create at least one user with password."
 end
 
-# RDF namespaces
-RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
-OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#'
-DC = Redland::Namespace.new 'http://purl.org/dc/elements/1.1/'
-OT = Redland::Namespace.new 'http://www.opentox.org/api/1.1#'
-#OT = Redland::Namespace.new 'http://ortona.informatik.uni-freiburg.de/opentox.owl#'
-XML = Redland::Namespace.new 'http://www.w3.org/2001/XMLSchema#'
-
 # Regular expressions for parsing classification data
 TRUE_REGEXP = /^(true|active|1|1.0)$/i
 FALSE_REGEXP = /^(false|inactive|0|0.0)$/i
 
 # Task durations
-DEFAULT_TASK_MAX_DURATION = @@config[:default_task_max_duration]
-EXTERNAL_TASK_MAX_DURATION = @@config[:external_task_max_duration]
+DEFAULT_TASK_MAX_DURATION = 3600
+EXTERNAL_TASK_MAX_DURATION = 3600
diff --git a/lib/model.rb b/lib/model.rb
index 25266e3..e8f6048 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -103,6 +103,11 @@ module OpenTox
 			def self.find_all
 				RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
 			end
+
+      def self.predict(compound_uri,model_uri)
+        #RestClientWrapper.post(model_uri,{:compound_uri => compound_uri, :accept => 'application/x-yaml'})
+		`curl -X POST -d 'compound_uri=#{compound_uri}' -H 'Accept:application/x-yaml' #{model_uri}`
+      end
 		end
 	end
 end
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index 16c23fe..45a3428 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -8,6 +8,6 @@ rescue LoadError
 	puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
 end
 
-['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization','features', 'rest_client_wrapper'].each do |lib|
+['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization','features', 'ot-logger', 'overwrite', 'rest_client_wrapper'].each do |lib|
 	require lib
 end
diff --git a/lib/ot-logger.rb b/lib/ot-logger.rb
new file mode 100644
index 0000000..6c35ed2
--- /dev/null
+++ b/lib/ot-logger.rb
@@ -0,0 +1,48 @@
+require 'logger'
+# logging
+class MyLogger < Logger
+  
+  def pwd
+    path = Dir.pwd.to_s
+    index = path.rindex(/\//)
+    return path if index==nil
+    path[(index+1)..-1]
+  end
+  
+  def trace()
+    lines = caller(0)
+    n = 2
+    line = lines[n]
+    
+    while (line =~ /spork.rb/ or line =~ /as_task/ or line =~ /environment.rb/)
+      n += 1
+      line = lines[n]
+    end
+  
+    index = line.rindex(/\/.*\.rb/)
+    return line if index==nil
+    line[index..-1]
+  end
+  
+  def format(msg)
+    pwd.ljust(18)+" :: "+msg.to_s+"           :: "+trace+" :: "+($sinatra ? $sinatra.request.env['REMOTE_ADDR'] : nil).to_s
+  end
+  
+  def debug(msg)
+    super format(msg)
+  end
+  
+  def info(msg)
+    super format(msg)
+  end
+  
+  def warn(msg)
+    super format(msg)
+  end
+
+  def error(msg)
+    super format(msg)
+  end
+
+end
+
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
new file mode 100644
index 0000000..1d0161b
--- /dev/null
+++ b/lib/overwrite.rb
@@ -0,0 +1,14 @@
+# class overwrites aka monkey patches
+# hack: store sinatra in global var to make url_for and halt methods accessible
+before{ $sinatra = self unless $sinatra }
+
+class Sinatra::Base
+  # overwriting halt to log halts (!= 202)
+  def halt(*response)
+    LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response and response.first and response.first >= 300
+    # orig sinatra code:
+    response = response.first if response.length == 1
+    throw :halt, response
+  end
+end
+
diff --git a/lib/owl.rb b/lib/owl.rb
index 245dcc7..a4c2e68 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -1,3 +1,10 @@
+# RDF namespaces
+RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
+OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#'
+DC = Redland::Namespace.new 'http://purl.org/dc/elements/1.1/'
+OT = Redland::Namespace.new 'http://www.opentox.org/api/1.1#'
+#OT = Redland::Namespace.new 'http://ortona.informatik.uni-freiburg.de/opentox.owl#'
+XML = Redland::Namespace.new 'http://www.w3.org/2001/XMLSchema#'
 
 # overriding literal to give nice access to datatype
 # and to access the stored value as correct ruby type
@@ -537,4 +544,4 @@ module OpenTox
       end
     end
   end
-end
\ No newline at end of file
+end
diff --git a/lib/tasks/opentox.rb b/lib/tasks/opentox.rb
deleted file mode 100644
index 7fce35b..0000000
--- a/lib/tasks/opentox.rb
+++ /dev/null
@@ -1,107 +0,0 @@
-require File.join(File.dirname(__FILE__), '..', 'opentox-ruby-api-wrapper.rb')
-
-namespace :opentox do
-
-	namespace :services do
-
-		desc "Run opentox services"
-		task :start do
-			@@config[:services].each do |service,uri|
-				dir = File.join(@@config[:base_dir], service)
-				server = @@config[:webserver]
-				case server
-				when /thin|mongrel|webrick/
-					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
-					Dir.chdir dir
-					pid_file = File.join(TMP_DIR,"#{service}.pid") 
-					begin
-						`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
-						puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
-					rescue
-						puts "Cannot start #{service} on port #{port}."
-					end
-				when 'passenger'
-					FileUtils.mkdir_p File.join(dir, 'tmp')
-					FileUtils.touch File.join(dir, 'tmp/restart.txt')
-					puts "#{service} restarted."
-				else
-					puts "not yet implemented"
-				end
-			end
-		end
-
-		desc "Stop opentox services"
-		task :stop do
-			server = @@config[:webserver]
-			if server =~ /thin|mongrel|webrick/
-				@@config[:services].each do |service,uri|
-					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
-					pid_file = File.join(TMP_DIR,"#{service}.pid") 
-					begin
-						puts `#{server} stop -P #{pid_file}` 
-						puts "#{service} stopped on localhost:#{port}"
-					rescue
-						puts "Cannot stop #{service} on port #{port}."
-					end
-				end
-			end
-		end
-
-		desc "Restart opentox services"
-		task :restart => [:stop, :start]
-
-	end
-
-	desc "Run all OpenTox tests"
-	task :test do
-		@@config[:services].each do |service,uri|
-			dir = File.join(@@config[:base_dir], service)
-			Dir.chdir dir
-			puts "Running tests in #{dir}"
-			`rake test -t 1>&2`
-		end
-	end
-
-end
-
-desc "Start service in current directory"
-task :start do
-	service = File.basename(Dir.pwd).intern
-	server = @@config[:webserver]
-	case server 
-		when /thin|mongrel|webrick/
-			port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
-			pid_file = File.join(TMP_DIR,"#{service}.pid") 
-			begin
-				`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
-				puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
-			rescue
-				puts "Cannot start #{service} on port #{port}."
-			end
-		when 'passenger'
-			FileUtils.mkdir_p File.join(dir, 'tmp')
-			FileUtils.touch File.join(dir, 'tmp/restart.txt')
-			puts "#{service} restarted."
-		else
-			puts "not yet implemented"
-		end
-end
-
-desc "Stop service in current directory"
-task :stop do
-	service = File.basename(Dir.pwd).intern
-	server = @@config[:webserver]
-	if server =~ /thin|mongrel|webrick/
-		port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
-		pid_file = File.join(TMP_DIR,"#{service}.pid") 
-		begin
-			puts `thin stop -P #{pid_file}` 
-			puts "#{service} stopped on localhost:#{port}"
-		rescue
-			puts "Cannot stop #{service} on port #{port}."
-		end
-	end
-end
-
-desc "Restart service in current directory"
-task :restart  => [:stop, :start]
diff --git a/lib/templates/config.yaml b/lib/templates/config.yaml
index dba0bf3..00c00cb 100644
--- a/lib/templates/config.yaml
+++ b/lib/templates/config.yaml
@@ -4,12 +4,12 @@
 #
 # Example MySql:
 #
- :database: 
-   :adapter:  mysql
-   :database: production
-   :username: root
-   :password: opentox
-   :host:     localhost
+:database: 
+  :adapter:  mysql
+  :database: production
+  :username: root
+  :password: opentox
+  :host:     localhost
 #
 # Example 1: Using external test services
 #
@@ -22,42 +22,20 @@
 #  opentox-validation:    "http://opentox.informatik.uni-freiburg.de/validation/"
 #
 # Example 2: Using local services
- :base_dir: /home/ist/webservices
- :webserver: passenger
- :services:
-   opentox-compound:      "http://localhost/compound/"
-   opentox-dataset:       "http://localhost/dataset/"
-   opentox-algorithm:     "http://localhost/algorithm/"
-   opentox-model:         "http://localhost/model/"
-   opentox-task:          "http://localhost/task/"
-   opentox-validation:    "http://opentox.informatik.uni-freiburg.de/validation/"
+:base_dir: /home/ist/webservices
+:webserver: passenger
+:services:
+  opentox-compound:      "http://localhost/compound/"
+  opentox-dataset:       "http://localhost/dataset/"
+  opentox-algorithm:     "http://localhost/algorithm/"
+  opentox-model:         "http://localhost/model/"
+  opentox-task:          "http://localhost/task/"
+  opentox-validation:    "http://localhost/validation/"
 #
-# Accept headers:
+# Yaml capable hosts (faster than OWL-DL)
 #
- :accept_headers:
-   opentox-compound:      
-     - "chemical/x-daylight-smiles"
-     - "chemical/x-inchi"
-     - "chemical/x-mdl-sdfile"
-     - "image/gif"
-     - "text/plain"
-   opentox-dataset:       
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-algorithm:     
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-model:         
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-task:          
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-validation:    
-     - "application/x-yaml"
-     - "application/rdf+xml"
+:yaml_hosts:
+  - "localhost"
 
-# Timeouts:
-# 
- :default_task_max_duration: 3600
- :external_task_max_duration: 3600
+# Uncomment for verbose logging
+# :logger: debug
diff --git a/lib/utils.rb b/lib/utils.rb
index 741fbd6..a0e0cbe 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -28,6 +28,13 @@ module OpenTox
         return false
       end
     end
+    
+    def self.median(array)
+      return nil if array.empty?
+      array.sort!
+      m_pos = array.size / 2
+      return array.size % 2 == 1 ? array[m_pos] : (array[m_pos-1] + array[m_pos])/2
+    end
   
   end