extend whitelisting, get feature_type from algorithm

6 files changed, 52 insertions, 19 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 58a2640..ee3109c 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -34,9 +34,10 @@ module OpenTox
       # Find Generic Opentox Algorithm via URI, and loads metadata
       # @param [String] uri Algorithm URI
       # @return [OpenTox::Algorithm::Generic] Algorithm instance, nil if alogrithm was not found
-      def self.find(uri)
+      def self.find(uri, subjectid)
+        return nil unless uri
         alg = Generic.new(uri)
-        alg.load_metadata
+        alg.load_metadata( subjectid )
         if alg.metadata==nil or alg.metadata.size==0
           nil
         else
diff --git a/lib/authorization.rb b/lib/authorization.rb
index a6253b7..1573da3 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -328,7 +328,10 @@ module OpenTox
     # @param [String] subjectid
     # @return [Boolean] true if access granted, else otherwise
     def self.authorized?(uri, request_method, subjectid)
-      return true if OpenTox::Authorization.whitelisted?(uri, request_method)
+      if OpenTox::Authorization.whitelisted?(uri, request_method)
+        LOGGER.debug "whitelisted! "+uri.to_s
+        return true 
+      end
       if CONFIG[:authorization][:authorize_request].include?(request_method)
         ret = OpenTox::Authorization.authorize(uri, request_method, subjectid)
         LOGGER.debug "OpenTox helpers OpenTox::Authorization authorized? method: #{request_method} , URI: #{uri}, subjectid: #{subjectid} with return >>#{ret}<<"
@@ -346,8 +349,12 @@ module OpenTox
     private
     def self.whitelisted?(uri, request_method)
       return false unless @@whitelist[request_method]
-      @@whitelist[request_method].each do |r|
-        return true if r.match(uri)
+      @@whitelist[request_method].each do |regexp,invert|
+        if invert
+          return true if !regexp.match(uri) 
+        else
+          return true if regexp.match(uri)
+        end
       end
       return false
     end
@@ -356,7 +363,8 @@ module OpenTox
     # adds uri/regexp-for-matching-uri to the whitelist for a request-method (i.e. access will be granted without cheking the A&A service)
     # @param [String or Regexp] uri_match if string match must be ecaxt
     # @param [String] request_method, must be GET, POST, PUT, DELETE
-    def self.whitelist(uri_match, request_method)
+    # @param [Boolean,optional] invert, set to true if you want to whitelist everything that does not match (careful!)
+    def self.whitelist(uri_match, request_method, invert=false)
       if uri_match.is_a?(Regexp)
         uri_regex = uri_match
       elsif uri_match.is_a?(String)
@@ -366,7 +374,7 @@ module OpenTox
       end
       LOGGER.info("whitelisted "+request_method.to_s+" "+uri_regex.to_s)
       @@whitelist[request_method] = [] unless @@whitelist[request_method]
-      @@whitelist[request_method] << uri_regex
+      @@whitelist[request_method] << [ uri_regex, invert ]
     end
     
   end
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 640e3da..9c20968 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -51,6 +51,7 @@ module OpenTox
     # @param [String] uri Dataset URI
     # @return [OpenTox::Dataset] Dataset object with all data
     def self.find(uri, subjectid=nil)
+      return nil unless uri
       dataset = Dataset.new(uri, subjectid)
       dataset.load_all(subjectid)
       dataset
diff --git a/lib/feature.rb b/lib/feature.rb
index 28ac0c5..be063dd 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -3,7 +3,8 @@ module OpenTox
     include OpenTox
 
     def self.find(uri, subjectid=nil)
-        feature = Feature.new uri
+      return nil unless uri   
+      feature = Feature.new uri
       if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host))
         feature.add_metadata YAML.load(RestClientWrapper.get(uri,{:accept => "application/x-yaml", :subjectid => subjectid}))
       else
diff --git a/lib/model.rb b/lib/model.rb
index 741eea6..80d7ec4 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -8,13 +8,16 @@ module OpenTox
     # @param [Hash] params Parameters for OpenTox model
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [text/uri-list] Task or resource URI
-    def run( params, waiting_task=nil )
-      if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
-        accept = 'application/x-yaml' 
-      else
-        accept = 'application/rdf+xml'
+    def run( params, accept_header=nil, waiting_task=nil )
+      unless accept_header
+        if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
+          accept_header = 'application/x-yaml' 
+        else
+          accept_header = 'application/rdf+xml'
+        end
       end
-      RestClientWrapper.post(@uri,{:accept => accept},params,waiting_task).to_s
+      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
     end
 
     # Generic OpenTox model class for all API compliant services
@@ -25,6 +28,7 @@ module OpenTox
       # @param [String] uri Model URI
       # @return [OpenTox::Model::Generic] Model instance, nil if model was not found
       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
@@ -39,9 +43,12 @@ module OpenTox
       def feature_type(subjectid=nil)
         # dynamically perform restcalls if necessary
         load_metadata(subjectid) if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
+        
+        @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.feature_type, @metadata[OT.isA], @metadata[DC.title], @uri].each do |type|
+        [@dependentVariable.feature_type, @metadata[OT.isA], @metadata[DC.title], @uri, algorithm_title].each do |type|
           case type
           when /(?i)classification/
             return "classification"
@@ -49,7 +56,8 @@ module OpenTox
             return "regression"
           end
         end
-        raise "unknown model "+[@dependentVariable.feature_type, @metadata[OT.isA], @metadata[DC.title], @uri].inspect
+        raise "unknown model "+[@dependentVariable.feature_type, @metadata[OT.isA],
+          @metadata[DC.title], @uri, algorithm_title].inspect
       end
       
     end
diff --git a/lib/task.rb b/lib/task.rb
index 3c6aba5..74940de 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -78,6 +78,7 @@ module OpenTox
     # @param [String] uri Task URI
     # @return [OpenTox::Task] Task object
     def self.find(uri)
+      return nil unless uri
       task = Task.new(uri)
       task.load_metadata
       task
@@ -94,10 +95,23 @@ module OpenTox
       @metadata = YAML.load(yaml)
     end
 
+    
     def self.from_rdfxml(rdfxml)
-      file = Tempfile.open("ot-rdfxml"){|f| f.write(rdfxml)}.path
+      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
+      metadata = parser.load_metadata
+      puts metadata.inspect
+      
+      task = Task.new(uri)
+      task.add_metadata(metadata)
+      task
     end
 
     def to_rdfxml
@@ -232,7 +246,7 @@ module OpenTox
         sleep dur
         load_metadata 
         # if another (sub)task is waiting for self, set progress accordingly 
-        waiting_task.progress(@metadata[OT.percentageCompleted]) if waiting_task
+        waiting_task.progress(@metadata[OT.percentageCompleted].to_f) if waiting_task
         check_state
         if (Time.new > due_to_time)
           raise "max wait time exceeded ("+DEFAULT_TASK_MAX_DURATION.to_s+"sec), task: '"+@uri.to_s+"'"