manually insert code from mguetlein repository | restclientwrapper.post event with changed method call

13 files changed, 357 insertions, 130 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index ee3109c..af8dfaf 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -16,7 +16,7 @@ module OpenTox
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [String] URI of new resource (dataset, model, ...)
     def run(params=nil, waiting_task=nil)
-      RestClientWrapper.post(@uri, {:accept => 'text/uri-list'}, params, waiting_task).to_s
+      RestClientWrapper.post(@uri, params, {:accept => 'text/uri-list'}, waiting_task).to_s
     end
     
     # Get OWL-DL representation in RDF/XML format
@@ -31,18 +31,15 @@ module OpenTox
     class Generic 
       include Algorithm
       
-      # Find Generic Opentox Algorithm via URI, and loads metadata
+      # Find Generic Opentox Algorithm via URI, and loads metadata, could raise NotFound/NotAuthorized error
       # @param [String] uri Algorithm URI
-      # @return [OpenTox::Algorithm::Generic] Algorithm instance, nil if alogrithm was not found
-      def self.find(uri, subjectid)
+      # @return [OpenTox::Algorithm::Generic] Algorithm instance
+      def self.find(uri, subjectid=nil)
         return nil unless uri
         alg = Generic.new(uri)
         alg.load_metadata( subjectid )
-        if alg.metadata==nil or alg.metadata.size==0
-          nil
-        else
-          alg
-        end
+        raise "cannot load algorithm metadata" if alg.metadata==nil or alg.metadata.size==0
+        alg
       end
       
     end
diff --git a/lib/authorization.rb b/lib/authorization.rb
index 12be037..16f1ee4 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -192,10 +192,10 @@ module OpenTox
     # return [Boolean] returns true if policy is created   
     def self.create_policy(policy, subjectid)
       begin
-#        resource = RestClient::Resource.new("#{AA_SERVER}/Pol/opensso-pol")
+        resource = RestClient::Resource.new("#{AA_SERVER}/Pol/opensso-pol")
         LOGGER.debug "OpenTox::Authorization.create_policy policy: #{policy[168,43]} with token:" + subjectid.to_s + " length: " + subjectid.length.to_s 
-#        return true if resource.post(policy, :subjectid => subjectid, :content_type =>  "application/xml")
-        return true if RestClientWrapper.post("#{AA_SERVER}/pol", {:subjectid => subjectid, :content_type =>  "application/xml"}, policy)        
+        return true if resource.post(policy, :subjectid => subjectid, :content_type =>  "application/xml")
+        #return true if RestClientWrapper.post("#{AA_SERVER}/pol", {:subjectid => subjectid, :content_type =>  "application/xml"}, policy)        
       rescue
         return false
       end
@@ -306,7 +306,6 @@ module OpenTox
         # if no policy exists, create a policy, return result of send policy
         send_policy(uri, subjectid)
       else
-        LOGGER.debug "OpenTox::Authorization.check_policy URI: #{uri} has already a Policy."
         # if policy exists check for POST rights 
         if authorize(uri, "POST", subjectid)
           true
@@ -356,7 +355,6 @@ module OpenTox
     def self.free_uri?(uri, request_method)
       if CONFIG[:authorization][:free_uris]
         CONFIG[:authorization][:free_uris].each do |request_methods,uris|
-          LOGGER.info "free uris "+request_methods.inspect+" -> "+uris.inspect
           if request_methods and uris and request_methods.include?(request_method.to_sym) 
             uris.each do |u|
               return true if u.match uri
@@ -380,9 +378,6 @@ module OpenTox
       return false
     end    
     
-    
-
-    
   end
 end
 
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 9c20968..02b89cb 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -56,6 +56,19 @@ module OpenTox
       dataset.load_all(subjectid)
       dataset
     end
+    
+    # replaces find as exist check, takes not as long, does NOT raise an un-authorized exception
+    # @param [String] uri Dataset URI
+    # @return [Boolean] true if dataset exists and user has get rights, false else 
+    def self.exist?(uri, subjectid=nil)
+      return false unless uri
+      dataset = Dataset.new(uri, subjectid)
+      begin
+        dataset.load_metadata( subjectid ).size > 0
+      rescue
+        false
+      end
+    end
 
     # Get all datasets from a service
     # @param [optional,String] uri URI of the dataset service, defaults to service specified in configuration
@@ -285,7 +298,7 @@ module OpenTox
       @compounds.uniq!
       if @uri
         if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-          RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :subjectid => subjectid},self.to_yaml)
+          RestClientWrapper.post(@uri,self.to_yaml,{:content_type =>  "application/x-yaml", :subjectid => subjectid})
         else
           File.open("ot-post-file.rdf","w+") { |f| f.write(self.to_rdfxml); @path = f.path }
           task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :subjectid => subjectid}).to_s.chomp
diff --git a/lib/environment.rb b/lib/environment.rb
index 203ebc6..b30b3f3 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -54,8 +54,8 @@ else
 end
 
 # Regular expressions for parsing classification data
-TRUE_REGEXP = /^(true|active|1|1.0)$/i
-FALSE_REGEXP = /^(false|inactive|0|0.0)$/i
+TRUE_REGEXP = /^(true|active|1|1.0|tox)$/i
+FALSE_REGEXP = /^(false|inactive|0|0.0|low tox)$/i
 
 # Task durations
 DEFAULT_TASK_MAX_DURATION = 36000
diff --git a/lib/error.rb b/lib/error.rb
index 8c666f3..d086928 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -18,6 +18,10 @@ module OpenTox
   class NotFoundError < RuntimeError
     def http_code; 404; end
   end
+
+  class ServiceUnavailableError < RuntimeError
+    def http_code; 503; end
+  end
   
   class RestCallError < RuntimeError
     attr_accessor :rest_params
@@ -28,18 +32,31 @@ module OpenTox
     
     # TODO replace params with URIs (errorCause -> OT.errorCause)
     attr_reader :message, :actor, :errorCause, :http_code, :errorDetails, :errorType
+
+    private
+    def initialize( http_code, erroType, message, actor, errorCause, rest_params=nil, backtrace=nil )
+      @http_code = http_code
+      @errorType = erroType
+      @message = message
+      @actor = actor
+      @errorCause = errorCause
+      @rest_params = rest_params
+      @backtrace = backtrace
+    end
     
+    public
     # creates a error report object, from an ruby-exception object
-	# @param [Exception] error
-	# @param [String] actor, URI of the call that cause the error
-    def initialize( error, actor )
-      @http_code = error.http_code
-      @errorType = error.class.to_s
-      @message = error.message
-      @actor = actor
-      @errorCause = error.errorCause if error.errorCause
-      @rest_params = error.rest_params if error.is_a?(OpenTox::RestCallError) and error.rest_params
-      @backtrace = error.backtrace.short_backtrace if CONFIG[:backtrace]
+    # @param [Exception] error
+    # @param [String] actor, URI of the call that cause the error
+    def self.create( error, actor )
+      rest_params = error.rest_params if error.is_a?(OpenTox::RestCallError) and error.rest_params
+      backtrace = error.backtrace.short_backtrace if CONFIG[:backtrace]
+      ErrorReport.new( error.http_code, error.class.to_s, error.message, actor, error.errorCause, rest_params, backtrace )
+    end
+    
+    def self.from_rdf(rdf)
+      metadata = OpenTox::Parser::Owl.metadata_from_rdf( rdf, OT.ErrorReport )
+      ErrorReport.new(metadata[OT.statusCode], metadata[OT.errorCode], metadata[OT.message], metadata[OT.actor], metadata[OT.errorCause])
     end
     
     # overwrite sorting to make easier readable
diff --git a/lib/helper.rb b/lib/helper.rb
index 0bb489c..6ca3901 100644
--- a/lib/helper.rb
+++ b/lib/helper.rb
@@ -28,8 +28,9 @@ helpers do
   #cleans URI from querystring and file-extension. Sets port 80 to emptystring
   # @param [String] uri 
   def clean_uri(uri)
+    uri = uri.sub(" ", "%20")
     out = URI.parse(uri)
-    out.path = out.path[0, out.path.rindex(/[0-9]/) + 1] if out.path.rindex(/[0-9]/) #cuts after id for a&a
+    out.path = out.path[0, out.path.index(/[0-9]/)] if out.path.index(/[0-9]/) #cuts after id for a&a
     "#{out.scheme}:" + (out.port != 80 ? out.port : "") + "//#{out.host}#{out.path.chomp('/')}"
   end
 
@@ -51,7 +52,7 @@ before do
       subjectid = CGI.unescape(subjectid) if subjectid.include?("%23")
       @subjectid = subjectid
     rescue
-      LOGGER.debug "OpenTox ruby api wrapper: helper before filter: NO subjectid for URI: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}"
+      #LOGGER.debug "OpenTox ruby api wrapper: helper before filter: NO subjectid for URI: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}"
       subjectid = ""
     end
     @subjectid = subjectid
diff --git a/lib/model.rb b/lib/model.rb
index 0073ea4..64d178f 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -17,25 +17,22 @@ module OpenTox
         end
       end
       LOGGER.info "running model "+@uri.to_s+", params: "+params.inspect+", accept: "+accept_header.to_s
-      RestClientWrapper.post(@uri,{:accept => accept_header},params,waiting_task).to_s
+      RestClientWrapper.post(@uri,params,{:accept => accept_header},waiting_task).to_s
     end
 
     # Generic OpenTox model class for all API compliant services
     class Generic
       include Model
       
-      # Find Generic Opentox Model via URI, and loads metadata
+      # Find Generic Opentox Model via URI, and loads metadata, could raise NotFound/NotAuthorized error 
       # @param [String] uri Model URI
-      # @return [OpenTox::Model::Generic] Model instance, nil if model was not found
+      # @return [OpenTox::Model::Generic] Model instance
       def self.find(uri,subjectid=nil)
         return nil unless uri
         model = Generic.new(uri)
         model.load_metadata(subjectid)
-        if model.metadata==nil or model.metadata.size==0
-          nil
-        else
-          model
-        end
+        raise "could not load model metadata '"+uri.to_s+"'" if model.metadata==nil or model.metadata.size==0
+        model
       end
     
        # provides feature type, possible types are "regression" or "classification"
@@ -46,7 +43,7 @@ module OpenTox
         
         @algorithm = OpenTox::Algorithm::Generic.find(@metadata[OT.algorithm], subjectid) unless @algorithm
         algorithm_title = @algorithm ? @algorithm.metadata[DC.title] : nil
-        @dependentVariable = OpenTox::Feature.find( @metadata[OT.dependentVariables], subjectid) unless @dependentVariable
+        @dependentVariable = OpenTox::Feature.find( @metadata[OT.dependentVariables],subjectid ) unless @dependentVariable
         
         [@dependentVariable.feature_type, @metadata[OT.isA], @metadata[DC.title], @uri, algorithm_title].each do |type|
           case type
@@ -303,7 +300,7 @@ module OpenTox
 
       # Save model at model service
       def save(subjectid)
-        self.uri = RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :subjectid => subjectid},self.to_yaml)
+        self.uri = RestClientWrapper.post(@uri,self.to_yaml,{:content_type =>  "application/x-yaml", :subjectid => subjectid})
       end
 
       # Delete model at model service
diff --git a/lib/opentox.rb b/lib/opentox.rb
index f1af5c3..1992896 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -43,5 +43,10 @@ module OpenTox
     s.to_rdfxml
   end
 
+  # deletes the resource, deletion should have worked when no RestCallError raised
+  def delete(subjectid=nil)
+    RestClientWrapper.delete(uri,:subjectid => subjectid)
+  end
+
 end
 
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index e52618c..7b53122 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -16,13 +16,12 @@ before {
 # IMPT: set sinatra settings :show_exceptions + :raise_errors to false in config.ru, otherwise Rack::Showexceptions takes over
 error Exception do
   error = request.env['sinatra.error']
-  # log error to logfile
+  # log error message and backtrace to logfile
   LOGGER.error error.class.to_s+": "+error.message
-  # log backtrace only if code is 500 -> unwanted (Runtime)Exceptions and internal errors (see error.rb)
-  LOGGER.error ":\n"+error.backtrace.join("\n") if error.http_code==500
+  LOGGER.error ":\n"+error.backtrace.join("\n")
   
   actor = "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}"
-  rep = OpenTox::ErrorReport.new(error, actor)
+  rep = OpenTox::ErrorReport.create(error, actor)
 
   case request.env['HTTP_ACCEPT']
   when /rdf/
@@ -37,6 +36,27 @@ error Exception do
   end
 end
 
+class Sinatra::Base
+
+  def return_task( task )
+    code = task.running? ? 202 : 200
+    case request.env['HTTP_ACCEPT']
+    when /rdf/
+      response['Content-Type'] = "application/rdf+xml"
+      halt code,task.to_rdfxml
+    when /yaml/
+      response['Content-Type'] = "application/rdf+xml"
+      halt code,task.to_yaml # PENDING differs from task-webservice
+    when /html/
+      response['Content-Type'] = "text/html"
+      halt code,OpenTox.text_to_html(task.to_yaml)
+    else # default /uri-list/
+      response['Content-Type'] = "text/uri-list"
+      halt code,task.uri+"\n"
+    end
+  end
+end
+
 class String
   def task_uri?
     self.uri? && !self.match(/task/).nil?
diff --git a/lib/parser.rb b/lib/parser.rb
index a913cf2..1a872a0 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -36,10 +36,18 @@ module OpenTox
         else
           uri = @uri
         end
-        uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid 
+        # avoid using rapper directly because of 2 reasons:
+        # * http errors wont be noticed
+        # * subjectid cannot be sent as header
+        ##uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid 
+        ## `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line|
+        file = Tempfile.new("ot-rdfxml")
+        file.puts OpenTox::RestClientWrapper.get @uri,{:subjectid => subjectid,:accept => "application/rdf+xml"}
+        file.close
+        file = "file://"+file.path
         statements = []
         parameter_ids = []
-        `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line|
+        `rapper -i rdfxml -o ntriples #{file} 2>/dev/null`.each_line do |line|
           triple = line.to_triple
           @metadata[triple[1]] = triple[2].split('^^').first if triple[0] == @uri and triple[1] != RDF['type']
           statements << triple 
@@ -55,6 +63,38 @@ module OpenTox
         end
         @metadata
       end
+      
+      # loads metadata from rdf-data
+      # @param [String] rdf
+      # @param [String] type of the info (e.g. OT.Task, OT.ErrorReport) needed to get the subject-uri
+      # @return [Hash] metadata 
+      def self.metadata_from_rdf( rdf, type )
+        # write to file and read convert with rapper into tripples
+        file = Tempfile.new("ot-rdfxml")
+        file.puts rdf
+        file.close
+        file = "file://"+file.path
+        #puts "cmd: rapper -i rdfxml -o ntriples #{file} 2>/dev/null"
+        triples = `rapper -i rdfxml -o ntriples #{file} 2>/dev/null`
+        
+        # load uri via type
+        uri = nil
+        triples.each_line do |line|
+          triple = line.to_triple
+          if triple[1] == RDF['type'] and triple[2]==type
+             raise "uri already set, two uris found with type: "+type.to_s if uri
+             uri = triple[0]
+          end
+        end
+        
+        # load metadata
+        metadata = {}
+        triples.each_line do |line|
+          triple = line.to_triple
+          metadata[triple[1]] = triple[2].split('^^').first if triple[0] == uri and triple[1] != RDF['type']
+        end
+        metadata
+      end
 
       # Generic parser for all OpenTox classes
       class Generic
diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb
index 7c2d719..658f111 100644
--- a/lib/rest_client_wrapper.rb
+++ b/lib/rest_client_wrapper.rb
@@ -14,21 +14,21 @@ module OpenTox
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @param [wait,Boolean] wait set to false to NOT wait for task if result is task
     # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
-    def self.get(uri, headers=nil, waiting_task=nil, wait=true )
-      execute( "get", uri, headers, nil, waiting_task, wait)
+    def self.get(uri, headers={}, waiting_task=nil, wait=true )
+      execute( "get", uri, nil, headers, waiting_task, wait)
     end
     
     # performs a POST REST call
     # raises OpenTox::Error if call fails (rescued in overwrite.rb -> halt 502)
     # per default: waits for Task to finish and returns result URI of Task
     # @param [String] uri destination URI
-    # @param [optional,Hash] headers contains params like accept-header
     # @param [optional,String] payload data posted to the service
+    # @param [optional,Hash] headers contains params like accept-header
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @param [wait,Boolean] wait set to false to NOT wait for task if result is task
     # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
-    def self.post(uri, headers, payload=nil, waiting_task=nil, wait=true )
-      execute( "post", uri, headers, payload, waiting_task, wait )
+    def self.post(uri, payload=nil, headers={}, waiting_task=nil, wait=true )
+      execute( "post", uri, payload, headers, waiting_task, wait )
     end
     
     # performs a PUT REST call
@@ -37,8 +37,8 @@ module OpenTox
     # @param [optional,Hash] headers contains params like accept-header
     # @param [optional,String] payload data put to the service
     # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
-    def self.put(uri, headers, payload=nil )
-      execute( "put", uri, headers, payload )
+    def self.put(uri, payload=nil, headers={} )
+      execute( "put", uri, payload, headers )
     end
 
     # performs a DELETE REST call
@@ -47,36 +47,42 @@ module OpenTox
     # @param [optional,Hash] headers contains params like accept-header
     # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
     def self.delete(uri, headers=nil )
-      execute( "delete", uri, headers, nil)
+      execute( "delete", uri, nil, headers)
     end
 
     private
-    def self.execute( rest_call, uri, headers, payload=nil, waiting_task=nil, wait=true )
+    def self.execute( rest_call, uri, payload=nil, headers={}, waiting_task=nil, wait=true )
       
       raise OpenTox::BadRequestError.new "uri is null" unless uri
       raise OpenTox::BadRequestError.new "not a uri: "+uri.to_s unless uri.to_s.uri?
-      raise OpenTox::BadRequestError.new "headers are no hash: "+headers.inspect unless headers==nil or headers.is_a?(Hash)
-      raise OpenTox::BadRequestError.new "nil headers for post not allowed, use {}" if rest_call=="post" and headers==nil
+      raise "headers are no hash: "+headers.inspect unless headers==nil or headers.is_a?(Hash)
+      raise OpenTox::BadRequestError.new "accept should go into the headers" if payload and payload.is_a?(Hash) and payload[:accept] 
+      raise OpenTox::BadRequestError.new "content_type should go into the headers" if payload and payload.is_a?(Hash) and payload[:content_type]
+      raise "__waiting_task__ must be 'nil' or '(sub)task', is "+waiting_task.class.to_s if
+        waiting_task!=nil and !(waiting_task.is_a?(Task) || waiting_task.is_a?(SubTask))
       headers.each{ |k,v| headers.delete(k) if v==nil } if headers #remove keys with empty values, as this can cause problems
       
+      # PENDING needed for NUTA, until we finally agree on how to send subjectid
+      headers[:subjectid] = payload.delete(:subjectid) if uri=~/ntua/ and payload and payload.is_a?(Hash) and payload.has_key?(:subjectid) 
+      
       begin
         #LOGGER.debug "RestCall: "+rest_call.to_s+" "+uri.to_s+" "+headers.inspect+" "+payload.inspect
-        resource = RestClient::Resource.new(uri,{:timeout => 60}) 
-        if payload
+        resource = RestClient::Resource.new(uri,{:timeout => 60})
+        if rest_call=="post" || rest_call=="put"
           result = resource.send(rest_call, payload, headers)
-        elsif headers
-          result = resource.send(rest_call, headers)
         else
-          result = resource.send(rest_call)
+          result = resource.send(rest_call, headers)
         end
         
+        # PENDING NTUA does return errors with 200
+        raise RestClient::ExceptionWithResponse.new(result) if uri=~/ntua/ and result.body =~ /about.*http:\/\/anonymous.org\/error/
+        
         # result is a string, with the additional fields content_type and code
         res = WrapperResult.new(result.body)
         res.content_type = result.headers[:content_type]
         raise "content-type not set" unless res.content_type
         res.code = result.code
         
-        #LOGGER.debug "RestCall result: "+res.to_s+" "+res.code.to_s+" "+res.content_type.to_s
         # TODO: Ambit returns task representation with 200 instead of result URI
         return res if res.code==200 || !wait
         
@@ -87,10 +93,10 @@ module OpenTox
         return res
         
       rescue RestClient::RequestTimeout => ex
-        received_error ex.message, 408, nil, {:rest_uri => uri, :headers => headers}
+        received_error ex.message, 408, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
       rescue RestClient::ExceptionWithResponse => ex
         # error comming from a different webservice, 
-        received_error ex.http_body, ex.http_code, ex.response.net_http_res.content_type, {:rest_uri => uri, :headers => headers}
+        received_error ex.http_body, ex.http_code, ex.response.net_http_res.content_type, {:rest_uri => uri, :headers => headers, :payload => payload}
       rescue OpenTox::RestCallError => ex
         # already a rest-error, probably comes from wait_for_task, just pass through
         raise ex       
diff --git a/lib/task.rb b/lib/task.rb
index 74940de..1a684df 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -33,7 +33,7 @@ module OpenTox
     def self.create( title=nil, creator=nil, max_duration=DEFAULT_TASK_MAX_DURATION, description=nil )
       
       params = {:title=>title, :creator=>creator, :max_duration=>max_duration, :description=>description }
-      task_uri = RestClientWrapper.post(CONFIG[:services]["opentox-task"], params, nil, false).to_s
+      task_uri = RestClientWrapper.post(CONFIG[:services]["opentox-task"], params, {}, nil, false).to_s
       task = Task.new(task_uri.chomp)
 
       # measure current memory consumption
@@ -64,9 +64,8 @@ module OpenTox
           task.completed(result)
         rescue => error
           LOGGER.error "task failed: "+error.class.to_s+": "+error.message
-          # log backtrace only if code is 500 -> unwanted (Runtime)Exceptions and internal errors (see error.rb)
-          LOGGER.error ":\n"+error.backtrace.join("\n") if error.http_code==500
-          task.error(OpenTox::ErrorReport.new(error, creator))
+          LOGGER.error ":\n"+error.backtrace.join("\n")
+          task.error(OpenTox::ErrorReport.create(error, creator))
         end
       end  
       task.pid = task_pid
@@ -81,9 +80,20 @@ module OpenTox
       return nil unless uri
       task = Task.new(uri)
       task.load_metadata
+      raise "could not load task metadata" if task.metadata==nil or task.metadata.size==0
       task
     end
 
+    # Find a task for querying, status changes
+    # @param [String] uri Task URI
+    # @return [OpenTox::Task] Task object
+    def self.exist?(uri)
+      begin
+        return find(uri)
+      rescue
+      end 
+    end
+
     # Get a list of all tasks
     # @param [optional, String] uri URI of task service
     # @return [text/uri-list] Task URIs
@@ -188,7 +198,7 @@ module OpenTox
     
     # create is private now, use OpenTox::Task.as_task
     #def self.create( params )
-      #task_uri = RestClientWrapper.post(CONFIG[:services]["opentox-task"], params, nil, false).to_s
+      #task_uri = RestClientWrapper.post(CONFIG[:services]["opentox-task"], params, {}, false).to_s
       #Task.find(task_uri.chomp)
     #end
     
@@ -304,7 +314,7 @@ module OpenTox
   class SubTask
     
     def initialize(task, min, max)
-      raise "not a task or subtask" unless task.is_a?(Task) or task.is_a?(SubTask) 
+      raise "not a task or subtask" if task!=nil and !(task.is_a?(Task) or task.is_a?(SubTask)) 
       raise "invalid max ("+max.to_s+"), min ("+min.to_s+") params" unless 
         min.is_a?(Numeric) and max.is_a?(Numeric) and min >= 0 and max <= 100 and max > min 
       @task = task
diff --git a/lib/validation.rb b/lib/validation.rb
index 23b246b..2ea19a9 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -1,70 +1,196 @@
 module OpenTox
-	class Validation
+  class Validation
     include OpenTox
-
-		attr_accessor :report_uri, :qmrf_report_uri
-		
-		def self.create_crossvalidation(params)
-			params[:uri] = File.join(CONFIG[:services]['opentox-validation'], "crossvalidation")
-      params[:num_folds] = 10 unless params[:num_folds]
-		 	params[:random_seed] = 2 unless params[:random_seed]
-		 	params[:stratified] = false unless params[:stratified]
-      uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/crossvalidation"),params,nil,false)
-			OpenTox::Validation.new(uri)
-		end
-
-    def create_report(subjectid=nil)
-			@report_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), {:validation_uris => @uri, :subjectid => subjectid}).to_s
-      @report_uri
+    
+    # find validation, raises error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::Validation]
+    def self.find( uri, subjectid=nil )
+      val = Validation.new(uri)
+      val.load_metadata( subjectid )
+      val
     end
-
-    def create_qmrf_report(subjectid=nil)
-      @qmrf_report_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), {:model_uri => @uri, :subjectid => subjectid}).to_s
-      @qmrf_report_uri
+    
+    # creates a validation object from crossvaldiation statistics, raise error if not found
+    # (as crossvaldiation statistics are returned as an average valdidation over all folds)
+    # @param [String] crossvalidation uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::Validation]
+    def self.from_cv_statistics( crossvalidation_uri, subjectid=nil )
+      find( File.join(crossvalidation_uri, 'statistics'),subjectid )
     end
-
-    def summary(type, subjectid=nil)
-      v = YAML.load OpenTox::RestClientWrapper.get(File.join(@uri, 'statistics'),{:accept => "application/x-yaml", :subjectid => subjectid}).to_s
-
-      case type
-      when "classification"
-        tp=0; tn=0; fp=0; fn=0; n=0
-        v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
-          if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
-            tp = cell[:confusion_matrix_value]
-            n += tp
-          elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
-            tn = cell[:confusion_matrix_value]
-            n += tn
-          elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
-            fn = cell[:confusion_matrix_value]
-            n += fn
-          elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
-            fp = cell[:confusion_matrix_value]
-            n += fp
+    
+    # loads metadata via yaml from validation object
+    # fields (like for example the validated model) can be acces via validation.metadata[OT.model]
+    def load_metadata( subjectid=nil )
+      @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"}))
+    end
+    
+    # PENDING: creates summary as used for ToxCreate
+    def summary
+      if @metadata[OT.classificationStatistics]
+        res = {
+          :nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
+          :correct_predictions => @metadata[OT.classificationStatistics][OT.percentCorrect],
+          :weighted_area_under_roc => @metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc],
+        }
+        @metadata[OT.classificationStatistics][OT.classValueStatistics].each do |s|
+          if s[OT.classValue].to_s=="true"
+            res[:true_positives] = s[OT.numTruePositives]
+            res[:false_positives] = s[OT.numFalsePositives]
+            res[:true_negatives] = s[OT.numTrueNegatives]
+            res[:false_negatives] = s[OT.numFalseNegatives]
+            res[:sensitivity] = s[OT.truePositiveRate]
+            res[:specificity] = s[OT.falsePositiveRate]
+            break
           end
         end
+        res
+      elsif @metadata[OT.regressionStatistics]
         {
-          :nr_predictions => n,
-          :true_positives => tp,
-          :false_positives => fp,
-          :true_negatives => tn,
-          :false_negatives => fn,
-          :correct_predictions => 100*(tp+tn).to_f/n,
-          :weighted_area_under_roc => v[:classification_statistics][:weighted_area_under_roc].to_f,
-          :sensitivity => tp.to_f/(tp+fn),
-          :specificity => tn.to_f/(tn+fp),
-        }
-      when "regression"
-        {
-          :nr_predictions => v[:num_instances] - v[:num_unpredicted],
-          :r_square => v[:regression_statistics][:r_square],
-          :root_mean_squared_error => v[:regression_statistics][:root_mean_squared_error],
-          :mean_absolute_error => v[:regression_statistics][:mean_absolute_error],
+          :nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
+          :r_square => @metadata[OT.regressionStatistics][OT.rSquare],
+          :root_mean_squared_error => @metadata[OT.regressionStatistics][OT.rootMeanSquaredError],
+          :mean_absolute_error => @metadata[OT.regressionStatistics][OT.meanAbsoluteError],
         }
       end
     end
+  end
+  
+  class Crossvalidation
+    include OpenTox
+
+    attr_reader :report
+    
+    # find crossvalidation, raises error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::Crossvalidation]
+    def self.find( uri, subjectid=nil )
+      cv = Crossvalidation.new(uri)
+      cv.load_metadata( subjectid )
+      cv
+    end
+		
+    # creates a crossvalidations, waits until it finishes, may take some time
+    # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,num_folds(10),random_seed(1),stratified(false))
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::Crossvalidation]
+    def self.create( params, subjectid=nil, waiting_task=nil )
+      params[:subjectid] = subjectid if subjectid
+      uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"crossvalidation"),
+        params,{:content_type => "text/uri-list"},waiting_task )
+      Crossvalidation.new(uri)
+    end
 
-	end
+    # looks for report for this crossvalidation, creates a report if no report is found
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::CrossvalidationReport]
+    def find_or_create_report( subjectid=nil, waiting_task=nil )
+      @report = CrossvalidationReport.find_for_crossvalidation(@uri, subjectid) unless @report
+      @report = CrossvalidationReport.create(@uri, subjectid, waiting_task) unless @report
+      @report.uri
+    end
+    
+    # loads metadata via yaml from crossvalidation object
+    # fields (like for example the validations) can be acces via validation.metadata[OT.validation]
+    def load_metadata( subjectid=nil )
+      @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"}))
+    end
+    
+    # PENDING: creates summary as used for ToxCreate
+    def summary( subjectid=nil )
+      Validation.from_cv_statistics( @uri, subjectid ).summary
+    end
+  end
+  
+  class ValidationReport
+    include OpenTox
+    
+    # finds ValidationReport for a particular validation
+    # @param [String] crossvalidation uri 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::ValidationReport] nil if no report found
+    def self.find_for_validation( validation_uri, subjectid=nil )
+      uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
+        "/report/validation?validation="+validation_uri), {:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : ValidationReport.new(uris[-1])
+    end
+    
+  end
+
+  class CrossvalidationReport
+    include OpenTox
+    
+    # finds CrossvalidationReport via uri, raises error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::CrossvalidationReport]
+    def self.find( uri, subjectid=nil )
+      # PENDING load report data?
+      OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
+      CrossvalidationReport.new(uri)
+    end
+    
+    # finds CrossvalidationReport for a particular crossvalidation
+    # @param [String] crossvalidation uri 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::CrossvalidationReport] nil if no report found
+    def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil )
+      uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
+        "/report/crossvalidation?crossvalidation="+crossvalidation_uri), {:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : CrossvalidationReport.new(uris[-1])
+    end
+    
+    # creates a crossvalidation report via crossvalidation
+    # @param [String] crossvalidation uri 
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::CrossvalidationReport]
+    def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil )
+      uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"),
+        { :validation_uris => crossvalidation_uri, :subjectid => subjectid }, {}, waiting_task )
+      CrossvalidationReport.new(uri)
+    end
+  end
+  
+  class QMRFReport
+    include OpenTox
+    
+    # finds QMRFReport, raises Error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::QMRFReport]
+    def self.find( uri, subjectid=nil )
+      # PENDING load crossvalidation data?
+      OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
+      QMRFReport.new(uri)
+    end
+    
+    # finds QMRF report for a particular model
+    # @param [String] model_uri 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::QMRFReport] nil if no report found
+    def self.find_for_model( model_uri, subjectid=nil )
+      uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
+        "/reach_report/qmrf?model="+model_uri), {:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : QMRFReport.new(uris[-1])
+    end
+    
+    # creates a qmrf report via model
+    # @param [String] model_uri 
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::QMRFReport]
+    def self.create( model_uri, subjectid=nil, waiting_task=nil )
+      uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), 
+        { :model_uri => model_uri, :subjectid => subjectid }, {}, waiting_task )
+      QMRFReport.new(uri)
+    end
+  end
+  
 end