opentox-ruby-api-wrapper 1.5.6 → 1.5.7

data/VERSION

@@ -1 +1 @@
-1.5.6
+1.5.7

data/lib/dataset.rb

@@ -22,7 +22,6 @@ module OpenTox
           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 
@@ -52,6 +51,7 @@ module OpenTox
     # returns uri of new dataset
     def create_new_dataset( new_compounds, new_features, new_title, new_creator )
       
+      LOGGER.debug "create new dataset with "+new_compounds.size.to_s+"/"+compounds.size.to_s+" compounds"
       raise "no new compounds selected" unless new_compounds and new_compounds.size>0
       
       # load require features 
@@ -69,6 +69,7 @@ module OpenTox
       # PENDING: why storing feature values in an array? 
       new_compounds.each do |c|
         data_c = []
+        raise "no data for compound '"+c.to_s+"'" if @data[c]==nil
         @data[c].each do |d|
           m = {}
           new_features.each do |f|
@@ -76,7 +77,6 @@ module OpenTox
           end
           data_c << m 
         end
-        
         dataset.data[c] = data_c
       end
       return dataset.save
@@ -91,15 +91,16 @@ module OpenTox
         else
           return "no classification key"
         end
-      else
-        raise "predicted class value is not a hash\n"+
+      elsif v.is_a?(Array)
+        raise "predicted class 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
@@ -113,12 +114,14 @@ module OpenTox
           raise "no confidence key"
         end
       else
-        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"
+        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
     
@@ -173,7 +176,7 @@ module OpenTox
     
 			@features.uniq!
 			@compounds.uniq!
-      OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip 	
+        OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip 	
 		end
 
     def init_dirty_features(owl)

data/lib/environment.rb

@@ -13,6 +13,7 @@ LOG_DIR = File.join(basedir, "log")
 
 if File.exist?(config_file)
 	@@config = YAML.load_file(config_file)
+  raise "could not load config, config file: "+config_file.to_s unless @@config
 else
 	FileUtils.mkdir_p TMP_DIR
 	FileUtils.mkdir_p LOG_DIR
@@ -44,7 +45,7 @@ end
 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}
+before{ $sinatra = self unless $sinatra }
 
 class Sinatra::Base
   # overwriting halt to log halts (!= 202)
@@ -82,7 +83,7 @@ class MyLogger < Logger
   end
   
   def format(msg)
-    pwd.ljust(18)+" :: "+msg.to_s+"           :: "+trace+" :: "+ENV['REMOTE_ADDR'].to_s
+    pwd.ljust(18)+" :: "+msg.to_s+"           :: "+trace+" :: "+($sinatra ? $sinatra.request.env['REMOTE_ADDR'] : nil).to_s
   end
   
   def debug(msg)
@@ -132,6 +133,7 @@ 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

data/lib/model.rb

@@ -44,12 +44,6 @@ module OpenTox
      
      def self.build( algorithm_uri, algorithm_params )
         
-       if algorithm_uri =~ /ambit2/
-         LOGGER.warn "Ambit hack, replacing 'prediction_feature' with 'target'"
-         algorithm_params[:target] = algorithm_params[:prediction_feature]
-         algorithm_params.delete(:prediction_feature)
-       end
-       
        LOGGER.debug "Build model, algorithm_uri:"+algorithm_uri.to_s+", algorithm_parms: "+algorithm_params.inspect.to_s
        uri = OpenTox::RestClientWrapper.post(algorithm_uri,algorithm_params).to_s
        LOGGER.debug "Build model done: "+uri.to_s
@@ -60,7 +54,7 @@ module OpenTox
      def predict_dataset( dataset_uri )
 
        LOGGER.debug "Predict dataset: "+dataset_uri.to_s+" with model "+@uri.to_s
-       uri = RestClientWrapper.post(@uri, {:dataset_uri=>dataset_uri})
+       uri = RestClientWrapper.post(@uri, {:accept => "text/uri-list", :dataset_uri=>dataset_uri})
        RestClientWrapper.raise_uri_error("Prediciton result no dataset uri: "+uri.to_s, @uri, {:dataset_uri=>dataset_uri} ) unless Utils.dataset_uri?(uri)
        uri
      end
@@ -73,7 +67,7 @@ module OpenTox
          return false
        elsif @uri =~/tu-muenchen/ and @title =~ /regression|M5P|GaussP/
          return false
-       elsif @uri =~/ambit2/ and @title =~ /pKa/
+       elsif @uri =~/ambit2/ and @title =~ /pKa/ || @title =~ /Regression|Caco/
          return false
        elsif @uri =~/majority/
          return (@uri =~ /class/) != nil

data/lib/owl.rb

@@ -32,6 +32,7 @@ class Redland::Literal
   @@type_date = XML["date"].uri
   @@type_boolean = XML["boolean"].uri
   @@type_datetime = XML["dateTime"].uri
+  @@type_integer = XML["integer"].uri
   
   # parses value according to datatype uri
   def self.parse_value(string_value, datatype_uri)
@@ -54,6 +55,8 @@ class Redland::Literal
       return string_value #PENDING date as string?
     when @@type_datetime.to_s
       return string_value #PENDING date as string?
+    when @@type_integer.to_s
+      return string_value.to_i
     else
       raise "unknown literal datatype: '"+datatype_uri.to_s+"', value is "+string_value
     end
@@ -74,6 +77,12 @@ class Redland::Literal
       return @@type_float
     elsif value.is_a?(TrueClass) or value.is_a?(FalseClass)
       return @@type_boolean
+    elsif value.is_a?(Integer)
+      return @@type_integer
+    elsif value.is_a?(DateTime)
+      return @@type_datetime
+    elsif value.is_a?(Time)
+      return @@type_datetime
     else
       raise "illegal datatype: "+value.class.to_s+" "+value.to_s
     end
@@ -98,7 +107,7 @@ module OpenTox
 			owl = OpenTox::Owl.new
       owl.ot_class = ot_class
       owl.root_node = Redland::Resource.new(uri.to_s.strip)
-			owl.set("type",owl.node(owl.ot_class))
+			owl.set("type",owl.node(owl.ot_class)) #,true))
 			owl
 	  end
   
@@ -169,8 +178,9 @@ module OpenTox
     
     public
     def set(name, value, datatype=nil)
+      
       raise "uri is no prop, cannot set uri" if name=="uri"
-      property_node = node(name.to_s)
+      property_node = node(name.to_s) #, true)
       begin # delete existing entry
         t = @model.object(@root_node, property_node)
         @model.delete @root_node, property_node, t
@@ -355,16 +365,30 @@ module OpenTox
     "date" => DC["date"],
     "format" => DC["format"]}
   
-  # this method has to purposes:
+#  @object_prop = OWL["ObjectProperty"]
+#  @@type = { "Validation" => OWL["Class"],
+#             "Model" => OWL["Class"],
+#             "title" => OWL["AnnotationProperty"],
+#             "creator" => OWL["AnnotationProperty"],
+#             "date" => OWL["AnnotationProperty"],
+#             "format" => OWL["AnnotationProperty"],
+#             "predictedVariables" => @object_prop}
+  
+  # this method has two purposes:
   # * distinguishing ot-properties from dc- and rdf- properties
   # * caching nodes, as creating nodes is costly
-  def node(name)
+  def node(name) #, write_type_to_model=false)
     raise "dc[identifier] deprecated, use owl.uri" if name=="identifier"
     n = @@property_nodes[name]
     unless n
       n = OT[name]
       @@property_nodes[name] = n
     end
+    
+#    if write_type_to_model and name!="type"
+#      raise "no type defined for '"+name+"'" unless @@type[name] 
+#      @model.add n,RDF['type'],@@type[name]
+#    end
     return n
   end
 

data/lib/rest_client_wrapper.rb

@@ -9,7 +9,7 @@ module OpenTox
     
     def initialize(code, body, uri, payload, headers)
       self.code = code
-      self.body = body
+      self.body = body.to_s[0..1000]
       self.uri = uri
       self.payload = payload
       self.headers = headers
@@ -90,8 +90,6 @@ module OpenTox
         raise "illegal status code: '"+res.code.to_s+"'" unless res.code==200
         return res
         
-      rescue RestClient::RequestFailed => ex
-        do_halt ex.http_code,ex.http_body,uri,headers,payload
       rescue RestClient::RequestTimeout => ex
         do_halt 408,ex.message,uri,headers,payload
       rescue => ex
@@ -112,7 +110,7 @@ module OpenTox
                           
       task = nil
       case res.content_type
-      when /application\/rdf\+xml|text\/x-yaml/
+      when /application\/rdf\+xml|application\/x-yaml/
         task = OpenTox::Task.from_data(res, res.content_type, res.code, base_uri)
       when /text\//
         raise "uri list has more than one entry, should be a task" if res.content_type=~/text\/uri-list/ and
@@ -142,15 +140,15 @@ module OpenTox
         error = [Error.new(code, body, uri, payload, headers)]
       end
 
-#      #debug utility: write error to file       
-#      error_dir = "/tmp/ot_errors"
-#      FileUtils.mkdir(error_dir) unless File.exist?(error_dir)
-#      raise "could not create error dir" unless File.exist?(error_dir) and File.directory?(error_dir)
-#      file_name = "error"
-#      time=Time.now.strftime("%m.%d.%Y-%H:%M:%S")
-#      count = 1
-#      count+=1 while File.exist?(File.join(error_dir,file_name+"_"+time+"_"+count.to_s))
-#      File.new(File.join(error_dir,file_name+"_"+time+"_"+count.to_s),"w").puts(body)
+      #debug utility: write error to file       
+      error_dir = "/tmp/ot_errors"
+      FileUtils.mkdir(error_dir) unless File.exist?(error_dir)
+      raise "could not create error dir" unless File.exist?(error_dir) and File.directory?(error_dir)
+      file_name = "error"
+      time=Time.now.strftime("%m.%d.%Y-%H:%M:%S")
+      count = 1
+      count+=1 while File.exist?(File.join(error_dir,file_name+"_"+time+"_"+count.to_s))
+      File.new(File.join(error_dir,file_name+"_"+time+"_"+count.to_s),"w").puts(body)
       
       # handle error
       # we are either in a task, or in sinatra

data/lib/task.rb

@@ -71,7 +71,7 @@ module OpenTox
 		end
 
 		def error(description)
-			RestClientWrapper.put(File.join(@uri,'Error'),{:description => description})
+      RestClientWrapper.put(File.join(@uri,'Error'),{:description => description.to_s[0..2000]})
       reload
 		end
     
@@ -113,7 +113,7 @@ module OpenTox
         end
 			end
       
-      LOGGER.debug "task no longer running: "+@uri.to_s+", result: "+@resultURI.to_s
+      LOGGER.debug "Task '"+@hasStatus+"': "+@uri.to_s+", Result: "+@resultURI.to_s
 	  end
   
     def check_state

data/lib/templates/config.yaml

@@ -43,23 +43,18 @@
      - "text/plain"
    opentox-dataset:       
      - "application/x-yaml"
-     - "text/x-yaml"
      - "application/rdf+xml"
    opentox-algorithm:     
      - "application/x-yaml"
-     - "text/x-yaml"
      - "application/rdf+xml"
    opentox-model:         
      - "application/x-yaml"
-     - "text/x-yaml"
      - "application/rdf+xml"
    opentox-task:          
      - "application/x-yaml"
-     - "text/x-yaml"
      - "application/rdf+xml"
    opentox-validation:    
      - "application/x-yaml"
-     - "text/x-yaml"
      - "application/rdf+xml"
 
 # Timeouts:

data/lib/utils.rb

@@ -28,8 +28,9 @@ module OpenTox
         return false
       end
     end
-  end
   
+  end
+
 #  ['rubygems', 'rest_client'].each do |r|
 #    require r
 #  end
@@ -37,5 +38,6 @@ module OpenTox
 #    puts u+"? "+Utils.is_uri?(u).to_s
 #  end
 
+
 end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  hash: 15
+  hash: 13
   prerelease: false
   segments: 
   - 1
   - 5
-  - 6
-  version: 1.5.6
+  - 7
+  version: 1.5.7
 platform: ruby
 authors: 
 - Christoph Helma, Martin Guetlein
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-06-15 00:00:00 +02:00
+date: 2010-06-28 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -357,8 +357,8 @@ dependencies:
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email: helma@in-silico.ch
 executables: 
-- opentox-install-ubuntu.sh
 - yaml2owl.rb
+- opentox-install-ubuntu.sh
 - opentox-install-debian.sh
 extensions: []