opentox-ruby-api-wrapper 1.6.0 → 1.6.1

data/Rakefile

@@ -26,7 +26,8 @@ begin
 			"spreadsheet",
 			"google-spreadsheet-ruby",
 			"tmail",
-			"rinruby"
+			"rinruby",
+			"rjb"
 		].each { |dep| gem.add_dependency dep }
 		[ "dm-core",
 			'dm-serializer',

data/VERSION

@@ -1 +1 @@
-1.6.0
+1.6.1

data/lib/algorithm.rb

@@ -22,9 +22,7 @@ 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
 
@@ -37,12 +35,12 @@ 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

data/lib/compound.rb

@@ -52,12 +52,30 @@ module OpenTox
 		end
 
 		def png
-			RestClientWrapper.get("#{@@ambit_uri}#{smiles}")
+      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
-			"#{@@ambit_uri}#{smiles}"
-			#"#{@@cactus_uri}#{@inchi}/image"
+      File.join @uri, "image"
 		end
 
 		# Matchs a smarts string

data/lib/dataset.rb

@@ -2,50 +2,64 @@ LOGGER.progname = File.expand_path(__FILE__)
 
 module OpenTox
   
-	class Dataset 
+  class Dataset 
 
-		attr_accessor :uri, :title, :creator, :data, :features, :compounds
+    attr_accessor :uri, :title, :creator, :data, :features, :compounds
 
-		def initialize 
-			@data = {}
-			@features = []
-			@compounds = []
-		end
-
-		def self.find(uri, accept_header=nil) 
+    def initialize( owl=nil )
+      @data = {}
+      @features = []
+      @compounds = []
+      
+      # creates dataset object from Opentox::Owl object
+      # use Dataset.find( <uri> ) to load dataset from rdf-supporting datasetservice
+      # note: does not load all feature values, as this is time consuming
+      if owl
+        raise "invalid param" unless owl.is_a?(OpenTox::Owl)
+        @title = owl.get("title")
+        @creator = owl.get("creator")
+        @uri = owl.uri
+        # when loading a dataset from owl, only compound- and feature-uris are loaded 
+        owl.load_dataset(@compounds, @features)
+        # all features are marked as dirty
+        # as soon as a feature-value is requested all values for this feature are loaded from the rdf
+        @dirty_features = @features.dclone
+        @owl = owl
+      end
+    end
+  
+    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 !@@config[:accept_headers]["opentox-dataset"].grep(/yaml/).empty?
+        if (uri.match(@@config[:services]["opentox-dataset"]) || uri =~ /in-silico.ch/) && !@@config[:accept_headers]["opentox-dataset"].grep(/yaml/).empty?
           accept_header = 'application/x-yaml'
         else
           accept_header = "application/rdf+xml"
         end
       end
+      
       case accept_header
       when "application/x-yaml"
-				d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s 
+        d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s 
         d.uri = uri unless d.uri
-			when "application/rdf+xml"
-				owl = OpenTox::Owl.from_uri(uri.to_s.strip, "Dataset")
-        
-        d = Dataset.new
-				d.title = owl.get("title")
-				d.creator = owl.get("creator")
-				d.uri = owl.uri
-        
-        # when loading a dataset from owl, only compound- and feature-uris are loaded 
-        owl.load_dataset(d.compounds, d.features)
-				# all features are marked as dirty, loaded dynamically later
-        d.init_dirty_features(owl)
-        
-        d.compounds.uniq!
-        d.features.uniq!
+      when "application/rdf+xml"
+        owl = OpenTox::Owl.from_uri(uri.to_s.strip, "Dataset")
+        d = Dataset.new(owl)
       else
         raise "cannot get datset with accept header: "+accept_header.to_s
-		  end
-      return d
-		end
+      end
+      d
+    end
+    
+    # converts a dataset represented in owl to yaml
+    # (uses a temporary dataset)
+    # note: to_yaml is overwritten, loads complete owl dataset values 
+    def self.owl_to_yaml( owl_data, uri)
+      owl = OpenTox::Owl.from_data(owl_data, uri, "Dataset")
+      d = Dataset.new(owl)
+      d.to_yaml
+    end
     
     # creates a new dataset, using only those compounsd specified in new_compounds
     # returns uri of new dataset
@@ -86,8 +100,8 @@ module OpenTox
     def get_predicted_class(compound, feature)
       v = get_value(compound, feature)
       if v.is_a?(Hash)
-				k = v.keys.grep(/classification/).first
-				unless k.empty?
+        k = v.keys.grep(/classification/).first
+        unless k.empty?
         #if v.has_key?(:classification)
           return v[k]
         else
@@ -109,8 +123,8 @@ module OpenTox
     def get_predicted_regression(compound, feature)
       v = get_value(compound, feature)
       if v.is_a?(Hash)
-				k = v.keys.grep(/regression/).first
-				unless k.empty?
+        k = v.keys.grep(/regression/).first
+        unless k.empty?
           return v[k]
         else
           return "no regression key"
@@ -131,11 +145,11 @@ module OpenTox
     def get_prediction_confidence(compound, feature)
       v = get_value(compound, feature)
       if v.is_a?(Hash)
-				k = v.keys.grep(/confidence/).first
-				unless k.empty?
+        k = v.keys.grep(/confidence/).first
+        unless k.empty?
         #if v.has_key?(:confidence)
           return v[k].abs
-					#return v["http://ot-dev.in-silico.ch/model/lazar#confidence"].abs
+          #return v["http://ot-dev.in-silico.ch/model/lazar#confidence"].abs
         else
           # PENDING: return nil isntead of raising an exception
           raise "no confidence key"
@@ -143,12 +157,6 @@ module OpenTox
       else
         LOGGER.warn "no confidence for compound: "+compound.to_s+", feature: "+feature.to_s
         return 1
-#        raise "prediction confidence value is not a hash value\n"+
-#          "value "+v.to_s+"\n"+
-#          "value-class "+v.class.to_s+"\n"+
-#          "dataset "+@uri.to_s+"\n"+
-#          "compound "+compound.to_s+"\n"+
-#          "feature "+feature.to_s+"\n"
       end
     end
     
@@ -159,7 +167,7 @@ module OpenTox
       end
       
       v = @data[compound]
-      raise "no values for compound "+compound.to_s if v==nil
+      return nil if v == nil # missing values for all features
       if v.is_a?(Array)
         # PENDING: why using an array here?
         v.each do |e|
@@ -171,7 +179,7 @@ module OpenTox
             raise "invalid internal value type"
           end
         end
-        raise "feature value no found: "+feature.to_s
+        return nil #missing value
       else
         raise "value is not an array\n"+
               "value "+v.to_s+"\n"+
@@ -186,31 +194,33 @@ module OpenTox
     def load_feature_values(feature=nil)
       if feature
         raise "feature already loaded" unless @dirty_features.include?(feature)
-        @owl.load_dataset_feature_values(@compounds, @data, feature)
+        @owl.load_dataset_feature_values(@compounds, @data, [feature])
         @dirty_features.delete(feature)
       else
-        @data = {}
-        @owl.load_dataset_feature_values(@compounds, @data)
+        @data = {} unless @data
+        @owl.load_dataset_feature_values(@compounds, @data, @dirty_features)
         @dirty_features.clear
       end
     end
-
-		def save
-      # loads all features before loading  
+    
+    # overwrite to yaml:
+    # in case dataset is loaded from owl:
+    # * load all values
+    # * set @owl to nil (not necessary in yaml) 
+    def to_yaml
+      # loads all features  
       if ((defined? @dirty_features) && @dirty_features.size > 0)
-        load_feature_values()
+        load_feature_values
       end
-    
-			@features.uniq!
-			@compounds.uniq!
-        OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip 	
-		end
+      @owl = nil
+      super.to_yaml
+    end
 
-    def init_dirty_features(owl)
-      @dirty_features = @features
-      @owl = owl
+    # saves (changes) as new dataset in dataset service
+    # returns uri
+    # uses to yaml method (which is overwritten)
+    def save
+      OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip   
     end
   end
-
-
 end

data/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
@@ -128,14 +68,6 @@ 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

data/lib/model.rb

@@ -104,6 +104,11 @@ 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

data/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

data/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
+