opentox-ruby-api-wrapper 1.5.7 → 1.6.0

data/Rakefile

@@ -25,7 +25,8 @@ begin
 			"roo",
 			"spreadsheet",
 			"google-spreadsheet-ruby",
-			"tmail"
+			"tmail",
+			"rinruby"
 		].each { |dep| gem.add_dependency dep }
 		[ "dm-core",
 			'dm-serializer',

data/VERSION

@@ -1 +1 @@
-1.5.7
+1.6.0

data/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 +47,17 @@ module OpenTox
 			obconversion(@inchi,'inchi','sdf')
 		end
 
-		def image
+		def gif
 			RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/image")
 		end
 
+		def png
+			RestClientWrapper.get("#{@@ambit_uri}#{smiles}")
+		end
+
 		def image_uri
-			"#{@@cactus_uri}#{@inchi}/image"
+			"#{@@ambit_uri}#{smiles}"
+			#"#{@@cactus_uri}#{@inchi}/image"
 		end
 
 		# Matchs a smarts string
@@ -69,6 +76,12 @@ module OpenTox
 			smarts_array.collect{|s| s if match?(s)}.compact
 		end
 
+		# AM
+		# Match an array of smarts features, returns (0)1 for (non)matching features at each pos
+		def match_all(smarts_array)
+			smarts_array.collect{|s| match?(s) ? 1 : 0 }
+		end
+
 		def sdf2inchi(sdf)
 			obconversion(sdf,'sdf','inchi')
 		end

data/lib/dataset.rb

@@ -86,8 +86,10 @@ module OpenTox
     def get_predicted_class(compound, feature)
       v = get_value(compound, feature)
       if v.is_a?(Hash)
-        if v.has_key?(:classification)
-          return v[:classification]
+				k = v.keys.grep(/classification/).first
+				unless k.empty?
+        #if v.has_key?(:classification)
+          return v[k]
         else
           return "no classification key"
         end
@@ -103,12 +105,37 @@ module OpenTox
       end
     end
     
+    # returns regression value
+    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?
+          return v[k]
+        else
+          return "no regression key"
+        end
+      elsif v.is_a?(Array)
+        raise "predicted regression value is an array\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"
+      else
+        return v
+      end
+    end
+    
     # returns prediction confidence if available
     def get_prediction_confidence(compound, feature)
       v = get_value(compound, feature)
       if v.is_a?(Hash)
-        if v.has_key?(:confidence)
-          return v[:confidence].abs
+				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
         else
           # PENDING: return nil isntead of raising an exception
           raise "no confidence key"

data/lib/environment.rb

@@ -41,7 +41,7 @@ if @@config[:database]
 	end
 end
 
-# mail for error messages
+# 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
@@ -107,12 +107,12 @@ end
 
 logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
 LOGGER = MyLogger.new(logfile,'daily') # daily rotation
-LOGGER.level = Logger::WARN if ENV["RACK_ENV"] == 'production'
-
-#LOGGER = MyLogger.new(STDOUT)
-#LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
-
-#LOGGER.level = Logger::DEBUG
+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
+else
+	LOGGER.level = Logger::WARN 
+end
 
 if File.exist?(user_file)
   @@users = YAML.load_file(user_file)
@@ -137,8 +137,8 @@ OT = Redland::Namespace.new 'http://www.opentox.org/api/1.1#'
 XML = Redland::Namespace.new 'http://www.w3.org/2001/XMLSchema#'
 
 # Regular expressions for parsing classification data
-TRUE_REGEXP = /^(true|active|$1^)/
-FALSE_REGEXP = /^(false|inactive|$0^)/
+TRUE_REGEXP = /^(true|active|1|1.0)$/i
+FALSE_REGEXP = /^(false|inactive|0|0.0)$/i
 
 # Task durations
 DEFAULT_TASK_MAX_DURATION = @@config[:default_task_max_duration]

data/lib/features.rb

@@ -1,3 +1,7 @@
+# CH: should go into validation service
+# - not a complete OT object
+# - only used twice
+# - what about ./validation/validation/validation_service.rb:241:            value = OpenTox::Feature.new(:uri => a.uri).value(prediction_feature).to_s
 module OpenTox
   
   module Feature
@@ -12,4 +16,4 @@ module OpenTox
     end
 
   end
-end
+end

data/lib/model.rb

@@ -61,8 +61,10 @@ module OpenTox
     
      def classification?
        #HACK replace with request to ontology server
-       if @title =~ /lazar classification/
+       if @title =~ /(?i)classification/
          return true
+       elsif @title =~ /(?i)regression/
+         return false
        elsif @uri =~/ntua/ and @title =~ /mlr/
          return false
        elsif @uri =~/tu-muenchen/ and @title =~ /regression|M5P|GaussP/

data/lib/templates/config.yaml

@@ -30,7 +30,7 @@
    opentox-algorithm:     "http://localhost/algorithm/"
    opentox-model:         "http://localhost/model/"
    opentox-task:          "http://localhost/task/"
-   opentox-validation:    "http://opentox.informatik.uni-freiburg.de/validation/"
+   opentox-validation:    "http://localhost/validation/"
 #
 # Accept headers:
 #

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  hash: 13
+  hash: 15
   prerelease: false
   segments: 
   - 1
-  - 5
-  - 7
-  version: 1.5.7
+  - 6
+  - 0
+  version: 1.6.0
 platform: ruby
 authors: 
 - Christoph Helma, Martin Guetlein
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-06-28 00:00:00 +02:00
+date: 2010-07-19 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -229,21 +229,21 @@ dependencies:
   type: :runtime
   version_requirements: *id015
 - !ruby/object:Gem::Dependency 
-  name: dm-core
+  name: rinruby
   prerelease: false
   requirement: &id016 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 1
+        hash: 3
         segments: 
-        - 1
-        version: "1"
+        - 0
+        version: "0"
   type: :runtime
   version_requirements: *id016
 - !ruby/object:Gem::Dependency 
-  name: dm-serializer
+  name: dm-core
   prerelease: false
   requirement: &id017 !ruby/object:Gem::Requirement 
     none: false
@@ -257,7 +257,7 @@ dependencies:
   type: :runtime
   version_requirements: *id017
 - !ruby/object:Gem::Dependency 
-  name: dm-timestamps
+  name: dm-serializer
   prerelease: false
   requirement: &id018 !ruby/object:Gem::Requirement 
     none: false
@@ -271,7 +271,7 @@ dependencies:
   type: :runtime
   version_requirements: *id018
 - !ruby/object:Gem::Dependency 
-  name: dm-types
+  name: dm-timestamps
   prerelease: false
   requirement: &id019 !ruby/object:Gem::Requirement 
     none: false
@@ -285,7 +285,7 @@ dependencies:
   type: :runtime
   version_requirements: *id019
 - !ruby/object:Gem::Dependency 
-  name: dm-migrations
+  name: dm-types
   prerelease: false
   requirement: &id020 !ruby/object:Gem::Requirement 
     none: false
@@ -299,7 +299,7 @@ dependencies:
   type: :runtime
   version_requirements: *id020
 - !ruby/object:Gem::Dependency 
-  name: dm-mysql-adapter
+  name: dm-migrations
   prerelease: false
   requirement: &id021 !ruby/object:Gem::Requirement 
     none: false
@@ -313,9 +313,23 @@ dependencies:
   type: :runtime
   version_requirements: *id021
 - !ruby/object:Gem::Dependency 
-  name: haml
+  name: dm-mysql-adapter
   prerelease: false
   requirement: &id022 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 1
+        segments: 
+        - 1
+        version: "1"
+  type: :runtime
+  version_requirements: *id022
+- !ruby/object:Gem::Dependency 
+  name: haml
+  prerelease: false
+  requirement: &id023 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -325,11 +339,11 @@ dependencies:
         - 3
         version: "3"
   type: :runtime
-  version_requirements: *id022
+  version_requirements: *id023
 - !ruby/object:Gem::Dependency 
   name: cucumber
   prerelease: false
-  requirement: &id023 !ruby/object:Gem::Requirement 
+  requirement: &id024 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -339,11 +353,11 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id023
+  version_requirements: *id024
 - !ruby/object:Gem::Dependency 
   name: jeweler
   prerelease: false
-  requirement: &id024 !ruby/object:Gem::Requirement 
+  requirement: &id025 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -353,12 +367,12 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id024
+  version_requirements: *id025
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email: helma@in-silico.ch
 executables: 
-- yaml2owl.rb
 - opentox-install-ubuntu.sh
+- yaml2owl.rb
 - opentox-install-debian.sh
 extensions: []