not using rapper directly, use rest client and tmp-file

3 files changed, 13 insertions, 5 deletions

diff --git a/lib/model.rb b/lib/model.rb
index ae793e8..64d178f 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -31,7 +31,7 @@ module OpenTox
         return nil unless uri
         model = Generic.new(uri)
         model.load_metadata(subjectid)
-        raise "could not load model metadata" if model.metadata==nil or model.metadata.size==0
+        raise "could not load model metadata '"+uri.to_s+"'" if model.metadata==nil or model.metadata.size==0
         model
       end
     
@@ -134,7 +134,7 @@ 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)
         count = 0
         d.compounds.each do |compound_uri|
           begin
diff --git a/lib/parser.rb b/lib/parser.rb
index e055eec..27dfeee 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -35,10 +35,18 @@ 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 
diff --git a/lib/task.rb b/lib/task.rb
index 73d880e..ca18d7b 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -303,7 +303,7 @@ 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