fix rdf parsing to work with ambit dataset service with a&a, minor changes

5 files changed, 50 insertions, 41 deletions

diff --git a/lib/error.rb b/lib/error.rb
index 49756d5..7ca9767 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -55,7 +55,7 @@ module OpenTox
     end
     
     def self.from_rdf(rdf)
-      metadata = OpenTox::Parser::Owl.metadata_from_rdf( rdf, OT.ErrorReport )
+      metadata = OpenTox::Parser::Owl.from_rdf( rdf, OT.ErrorReport ).metadata
       ErrorReport.new(metadata[OT.statusCode], metadata[OT.errorCode], metadata[OT.message], metadata[OT.actor], metadata[OT.errorCause])
     end
     
diff --git a/lib/model.rb b/lib/model.rb
index 64d178f..9622d65 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -43,9 +43,11 @@ module OpenTox
         
         @algorithm = OpenTox::Algorithm::Generic.find(@metadata[OT.algorithm], subjectid) unless @algorithm
         algorithm_title = @algorithm ? @algorithm.metadata[DC.title] : nil
+        algorithm_type = @algorithm ? @algorithm.metadata[OT.isA] : nil
         @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|
+        type_indicators = [@dependentVariable.feature_type, @metadata[OT.isA], @metadata[DC.title], 
+          @uri, algorithm_type, algorithm_title] 
+        type_indicators.each do |type|
           case type
           when /(?i)classification/
             return "classification"
@@ -53,8 +55,7 @@ module OpenTox
             return "regression"
           end
         end
-        raise "unknown model "+[@dependentVariable.feature_type, @metadata[OT.isA],
-          @metadata[DC.title], @uri, algorithm_title].inspect
+        raise "unknown model "+type_indicators.inspect
       end
       
     end
diff --git a/lib/parser.rb b/lib/parser.rb
index 27dfeee..2f59d15 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -41,17 +41,17 @@ module OpenTox
         ##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.puts OpenTox::RestClientWrapper.get @uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false
         file.close
-        file = "file://"+file.path
         statements = []
         parameter_ids = []
-        `rapper -i rdfxml -o ntriples #{file} 2>/dev/null`.each_line do |line|
+        `rapper -i rdfxml -o ntriples file://#{file.path} 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 
           parameter_ids << triple[2] if triple[1] == OT.parameters
         end
+        File.delete(file.path)
         unless parameter_ids.empty?
           @metadata[OT.parameters] = []
           parameter_ids.each do |p|
@@ -63,18 +63,17 @@ module OpenTox
         @metadata
       end
       
-      # loads metadata from rdf-data
+      # creates owl object 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 )
+      # @return [Owl] with uri and metadata set 
+      def self.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`
+        triples = `rapper -i rdfxml -o ntriples file://#{file.path} 2>/dev/null`
         
         # load uri via type
         uri = nil
@@ -85,19 +84,23 @@ module OpenTox
              uri = triple[0]
           end
         end
-        
+        File.delete(file)
         # 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
+        owl = Owl::Generic.new(uri)
+        owl.metadata = metadata
+        owl
       end
-
+      
       # Generic parser for all OpenTox classes
       class Generic
         include Owl
+        
+        attr_accessor :uri, :metadata
       end
 
       # OWL-DL parser for datasets
@@ -128,12 +131,21 @@ module OpenTox
         # @return [Hash] Internal dataset representation
         def load_uri(subjectid=nil)
           uri = @uri
-          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 #{file} 2>/dev/null`.each_line do |line| 
+          file = Tempfile.new("ot-rdfxml")
+          file.puts OpenTox::RestClientWrapper.get @uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false
+          file.close
+          
           data = {}
           feature_values = {}
           feature = {}
           other_statements = {}
-          `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line|
+          `rapper -i rdfxml -o ntriples file://#{file.path} 2>/dev/null`.each_line do |line|
             triple = line.chomp.split(' ',3)
             triple = triple[0..2].collect{|i| i.sub(/\s+.$/,'').gsub(/[<>"]/,'')}
             case triple[1] 
@@ -150,6 +162,7 @@ module OpenTox
             else 
             end
           end
+          File.delete(file.path)
           data.each do |id,entry|
             entry[:values].each do |value_id|
               value = feature_values[value_id].split(/\^\^/).first # remove XSD.type
@@ -157,7 +170,7 @@ module OpenTox
             end
           end
           load_features
-          @dataset.metadata = load_metadata
+          @dataset.metadata = load_metadata(subjectid)
           @dataset
         end
 
diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb
index 658f111..fcc0d08 100644
--- a/lib/rest_client_wrapper.rb
+++ b/lib/rest_client_wrapper.rb
@@ -61,9 +61,8 @@ module OpenTox
       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) 
+      ## PENDING partner services accept subjectid only in header
+      headers[:subjectid] = payload.delete(:subjectid) if 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
@@ -94,6 +93,8 @@ module OpenTox
         
       rescue RestClient::RequestTimeout => ex
         received_error ex.message, 408, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
+      rescue Errno::ECONNREFUSED => ex
+        received_error ex.message, 500, 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, :payload => payload}
@@ -107,7 +108,9 @@ module OpenTox
     end
     
     def self.wait_for_task( res, base_uri, waiting_task=nil )
-                          
+      #TODO remove TUM hack
+      content_type = "text/uri-list" if base_uri =~/tu-muenchen/ and res.content_type == "application/x-www-form-urlencoded;charset=UTF-8"
+s
       task = nil
       case res.content_type
       when /application\/rdf\+xml/
@@ -118,7 +121,7 @@ module OpenTox
         raise "uri list has more than one entry, should be a task" if res.content_type=~/text\/uri-list/ and res.split("\n").size > 1 #if uri list contains more then one uri, its not a task
         task = OpenTox::Task.find(res.to_s.chomp) if res.to_s.uri?
       else
-        raise "unknown content-type for task: '"+res.content_type.to_s+"'" #+"' content: "+res[0..200].to_s
+        raise "unknown content-type for task : '"+res.content_type.to_s+"'"+" content: "+res[0..200].to_s
       end
       
       LOGGER.debug "result is a task '"+task.uri.to_s+"', wait for completion"
diff --git a/lib/task.rb b/lib/task.rb
index 742afb4..27dc1c2 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -94,23 +94,11 @@ module OpenTox
     def self.from_yaml(yaml)
       @metadata = YAML.load(yaml)
     end
-
     
     def self.from_rdfxml(rdfxml)
-      file = Tempfile.new("ot-rdfxml")
-      file.puts rdfxml
-      file.close
-      file = "file://"+file.path
-       
-      # PENDING
-      raise "Parse from file not working: what is the base-object-uri??? (omitted in triples)"    
-          
-      parser = Parser::Owl::Generic.new file
-      metadata = parser.load_metadata
-      puts metadata.inspect
-      
-      task = Task.new(uri)
-      task.add_metadata(metadata)
+      owl = OpenTox::Parser::Owl.from_rdf(rdfxml, OT.Task)
+      task = Task.new(owl.uri)
+      task.add_metadata(owl.metadata)
       task
     end
 
@@ -176,7 +164,7 @@ module OpenTox
     end
 
     def load_metadata
-      if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host))
+      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
         result = RestClientWrapper.get(@uri, {:accept => 'application/x-yaml'}, nil, false)
         @metadata = YAML.load result.to_s
         @http_code = result.code
@@ -184,6 +172,7 @@ module OpenTox
         @metadata = Parser::Owl::Generic.new(@uri).load_metadata
         @http_code = RestClientWrapper.get(uri, {:accept => 'application/rdf+xml'}, nil, false).code
       end
+      raise "could not load task metadata for task "+@uri.to_s if @metadata==nil || @metadata.size==0
     end
     
     # create is private now, use OpenTox::Task.as_task
@@ -274,11 +263,14 @@ module OpenTox
     end
     
     private
+    VALID_TASK_STATES = ["Cancelled", "Completed", "Running", "Error"]
+    
     def check_state
       begin
+        raise "illegal task state, invalid status: '"+@metadata[OT.hasStatus].to_s+"'" unless 
+          @metadata[OT.hasStatus] unless VALID_TASK_STATES.include?(@metadata[OT.hasStatus])
         raise "illegal task state, task is completed, resultURI is no URI: '"+@metadata[OT.resultURI].to_s+
             "'" unless @metadata[OT.resultURI] and @metadata[OT.resultURI].to_s.uri? if completed?
-        
         if @http_code == 202
           raise "#{@uri}: illegal task state, code is 202, but hasStatus is not Running: '"+@metadata[OT.hasStatus]+"'" unless running?
         elsif @http_code == 201