A&A for GET requests

4 files changed, 26 insertions, 23 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 52b41a7..a85c2b5 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -60,7 +60,7 @@ module OpenTox
     # @param [optional,String] uri URI of the dataset service, defaults to service specified in configuration
     # @return [Array] Array of dataset object without data (use one of the load_* methods to pull data from the server)
     def self.all(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil)
-      RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u)}
+      RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u, subjectid)}
     end
 
     # Load YAML representation into the dataset
@@ -77,10 +77,10 @@ module OpenTox
     # Load RDF/XML representation from a file
     # @param [String] file File with RDF/XML representation of the dataset
     # @return [OpenTox::Dataset] Dataset object with RDF/XML data
-    def load_rdfxml_file(file)
-      parser = Parser::Owl::Dataset.new @uri
+    def load_rdfxml_file(file, subjectid=nil)
+      parser = Parser::Owl::Dataset.new @uri, subjectid
       parser.uri = file.path
-      copy parser.load_uri
+      copy parser.load_uri(subjectid)
     end
 
     # Load CSV string (format specification: http://toxcreate.org/help)
@@ -111,8 +111,8 @@ module OpenTox
     
     # Load and return only metadata of a Dataset object
     # @return [Hash] Metadata of the dataset
-    def load_metadata
-      add_metadata Parser::Owl::Dataset.new(@uri).load_metadata
+    def load_metadata(subjectid=nil)
+      add_metadata Parser::Owl::Dataset.new(@uri, subjectid).load_metadata(subjectid)
       self.uri = @uri if @uri # keep uri
       @metadata
     end
@@ -122,8 +122,8 @@ module OpenTox
       if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
         copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid}))
       else
-        parser = Parser::Owl::Dataset.new(@uri)
-        copy parser.load_uri
+        parser = Parser::Owl::Dataset.new(@uri, subjectid)
+        copy parser.load_uri(subjectid)
       end
     end
 
@@ -138,9 +138,9 @@ module OpenTox
 
     # Load and return only features from the dataset service
     # @return [Hash]  Features of the dataset
-    def load_features
-      parser = Parser::Owl::Dataset.new(@uri)
-      @features = parser.load_features
+    def load_features(subjectid=nil)
+      parser = Parser::Owl::Dataset.new(@uri, subjectid)
+      @features = parser.load_features(subjectid)
       @features
     end
 
diff --git a/lib/model.rb b/lib/model.rb
index 7aa3f5c..6ef4af2 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -99,7 +99,7 @@ module OpenTox
           OT.parameters => [{DC.title => "dataset_uri", OT.paramValue => dataset_uri}]
         })
         d = Dataset.new(dataset_uri,subjectid)
-        d.load_compounds
+        d.load_compounds(subjectid)
         d.compounds.each do |compound_uri|
           predict(compound_uri,false,subjectid)
         end
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 90683e5..f1af5c3 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -19,14 +19,14 @@ module OpenTox
 
   # Get all objects from a service
   # @return [Array] List of available URIs
-  def self.all(uri)
-    RestClientWrapper.get(uri,:accept => "text/uri-list").to_s.split(/\n/)
+  def self.all(uri, subjectid=nil)
+    RestClientWrapper.get(uri,:accept => "text/uri-list", :subjectid => subjectid).to_s.split(/\n/)
   end
 
   # Load (and return) metadata from object URI
   # @return [Hash] Metadata
-  def load_metadata
-    @metadata = Parser::Owl::Generic.new(@uri).load_metadata
+  def load_metadata(subjectid=nil)
+    @metadata = Parser::Owl::Generic.new(@uri).load_metadata(subjectid)
     @metadata
   end
 
diff --git a/lib/parser.rb b/lib/parser.rb
index b727412..a913cf2 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -29,14 +29,14 @@ module OpenTox
 
       # Read metadata from opentox service
       # @return [Hash] Object metadata
-      def load_metadata
+      def load_metadata(subjectid=nil)
 
         if @dataset
           uri = File.join(@uri,"metadata")
         else
           uri = @uri
         end
-
+        uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid 
         statements = []
         parameter_ids = []
         `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line|
@@ -71,9 +71,9 @@ module OpenTox
         # Create a new OWL-DL dataset parser
         # @param uri Dataset URI 
         # @return [OpenTox::Parser::Owl::Dataset] OWL-DL parser
-        def initialize(uri)
+        def initialize(uri, subjectid=nil)
           super uri
-          @dataset = ::OpenTox::Dataset.new(@uri)
+          @dataset = ::OpenTox::Dataset.new(@uri, subjectid)
         end
 
         # Read data from dataset service. Files can be parsed by setting #uri to a filename (after initialization with a real URI)
@@ -87,12 +87,14 @@ module OpenTox
         #   dataset = parser.load_uri
         #   dataset.save
         # @return [Hash] Internal dataset representation
-        def load_uri
+        def load_uri(subjectid=nil)
+          uri = @uri
+          uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid
           data = {}
           feature_values = {}
           feature = {}
           other_statements = {}
-          `rapper -i rdfxml -o ntriples #{@uri} 2>/dev/null`.each_line do |line|
+          `rapper -i rdfxml -o ntriples #{uri} 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] 
@@ -122,8 +124,9 @@ module OpenTox
 
         # Read only features from a dataset service. 
         # @return [Hash] Internal features representation
-        def load_features
+        def load_features(subjectid=nil)
           uri = File.join(@uri,"features")
+          uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid 
           statements = []
           features = Set.new
           `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line|