resclient wrapper: headers <-> payload, error report from rdf

11 files changed, 101 insertions, 49 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index ee3109c..ae05e16 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
diff --git a/lib/authorization.rb b/lib/authorization.rb
index b4c1ee5..dd7dc12 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -195,7 +195,7 @@ module OpenTox
 #        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 RestClientWrapper.post("#{AA_SERVER}/pol", policy, {:subjectid => subjectid, :content_type =>  "application/xml"})        
       rescue
         return false
       end
@@ -381,4 +381,9 @@ module OpenTox
   end
 end
 
+# PENDING delete as soon as new free uri handling is merged
+# this allows GET access to all URIS that do NOT end with /<number> or /<number>/
+OpenTox::Authorization.whitelist( /\/[0-9]+(\/?)$/, "GET", true )
+OpenTox::Authorization.whitelist( /\/[0-9]+(\/?)$/, "POST", true )
+
 
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 9c20968..a4716dc 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -285,7 +285,7 @@ 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..49756d5 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
@@ -61,10 +78,6 @@ module OpenTox
       c[OT.errorCause] = @errorCause.rdf_content if @errorCause
       c
     end
-
-    def self.from_rdf(rdf)
-      raise "not yet implemented"
-    end
     
     def to_rdfxml
       s = Serializer::Owl.new
diff --git a/lib/model.rb b/lib/model.rb
index 80d7ec4..7cf52ad 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -17,7 +17,7 @@ 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
@@ -303,7 +303,7 @@ 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/overwrite.rb b/lib/overwrite.rb
index e52618c..1e1cc43 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/
diff --git a/lib/parser.rb b/lib/parser.rb
index a913cf2..e055eec 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -30,7 +30,6 @@ module OpenTox
       # Read metadata from opentox service
       # @return [Hash] Object metadata
       def load_metadata(subjectid=nil)
-
         if @dataset
           uri = File.join(@uri,"metadata")
         else
@@ -55,6 +54,38 @@ 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..f59dce7 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 +47,41 @@ 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
       headers.each{ |k,v| headers.delete(k) if v==nil } if headers #remove keys with empty values, as this can cause problems
+      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]
+      
+      # 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 +92,10 @@ 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..f635b43 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, {}, 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
@@ -188,7 +187,7 @@ 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
     
diff --git a/lib/validation.rb b/lib/validation.rb
index 76c4529..83be91a 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -9,7 +9,7 @@ module OpenTox
       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)
+      uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/crossvalidation"),params,{},false)
 			OpenTox::Validation.new(uri)
 		end