clean uri now works for https, rdf parsing issues: /features and ?feature_uris, missing subjectid

4 files changed, 36 insertions, 17 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index efab0a3..3f530e6 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -141,8 +141,10 @@ module OpenTox
       if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
         copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid}))
       else
+        puts "loading all.."
         parser = Parser::Owl::Dataset.new(@uri, subjectid)
         copy parser.load_uri(subjectid)
+        puts "..done"
       end
     end
 
diff --git a/lib/helper.rb b/lib/helper.rb
index a1590d7..b30908c 100644
--- a/lib/helper.rb
+++ b/lib/helper.rb
@@ -32,8 +32,9 @@ helpers do
     uri = uri[0,uri.index("InChI=")] if uri.index("InChI=") 
     
     out = URI.parse(uri)
-    out.path = out.path[0, out.path.length - (out.path.reverse.rindex(/\/{1}\d+\/{1}/))] if out.path.index(/\/{1}\d+\/{1}/)  #cuts after /id/ for a&a 
-    "#{out.scheme}:" + (out.port != 80 ? out.port : "") + "//#{out.host}#{out.path.chomp('/')}"
+    out.path = out.path[0, out.path.length - (out.path.reverse.rindex(/\/{1}\d+\/{1}/))] if out.path.index(/\/{1}\d+\/{1}/)  #cuts after /id/ for a&a
+    port = (out.scheme=="http" && out.port==80)||(out.scheme=="https" && out.port==443) ? "" : ":#{out.port.to_s}" 
+    "#{out.scheme}://#{out.host}#{port}#{out.path.chomp("/")}" #"
   end
 
   #unprotected uri for login
diff --git a/lib/parser.rb b/lib/parser.rb
index d2beeac..f1249ad 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -39,7 +39,14 @@ module OpenTox
           file = File.new(@uri)
         else
           file = Tempfile.new("ot-rdfxml")
-          uri = @dataset ? File.join(@uri,"metadata") : @uri
+          if @dataset
+            # do not concat /metadata to uri string, this would not work for dataset/R401577?max=3 
+            uri = URI::parse(@uri)
+            uri.path = File.join(uri.path,"metadata")
+            uri = uri.to_s
+          else
+            uri = @uri
+          end
           file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false
           file.close
           to_delete = file.path
@@ -163,26 +170,31 @@ module OpenTox
               data[triple[0]] = {:compound => "", :values => []} unless data[triple[0]]
               data[triple[0]][:compound] = triple[2]  
             when /#{OT.feature}/i
-              feature[triple[0]] = triple[2] 
+              feature[triple[0]] = triple[2]
             else 
             end
           end
           File.delete(to_delete) if to_delete
           data.each do |id,entry|
-            entry[:values].each do |value_id|
-              split = feature_values[value_id].split(/\^\^/)
-              case split[-1]
-              when XSD.double, XSD.float 
-                value = split.first.to_f
-              when XSD.boolean
-                value = split.first=~/(?i)true/ ? true : false                
-              else
-                value = split.first
+            if entry[:values].size==0
+              # no feature values add plain compounds
+              @dataset.add_compound(entry[:compound])
+            else
+              entry[:values].each do |value_id|
+                split = feature_values[value_id].split(/\^\^/)
+                case split[-1]
+                when XSD.double, XSD.float 
+                  value = split.first.to_f
+                when XSD.boolean
+                  value = split.first=~/(?i)true/ ? true : false                
+                else
+                  value = split.first
+                end
+                @dataset.add entry[:compound],feature[value_id],value
               end
-              @dataset.add entry[:compound],feature[value_id],value
             end
           end
-          load_features
+          load_features subjectid
           @dataset.metadata = load_metadata(subjectid)
           @dataset
         end
@@ -194,7 +206,10 @@ module OpenTox
             file = File.new(@uri)
           else
             file = Tempfile.new("ot-rdfxml")
-            uri = File.join(@uri,"features")
+            # do not concat /features to uri string, this would not work for dataset/R401577?max=3 
+            uri = URI::parse(@uri)
+            uri.path = File.join(uri.path,"features")
+            uri = uri.to_s
             file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false
             file.close
             to_delete = file.path
diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb
index d3136c7..dac24dc 100644
--- a/lib/rest_client_wrapper.rb
+++ b/lib/rest_client_wrapper.rb
@@ -76,7 +76,8 @@ module OpenTox
         else
           result = resource.send(rest_call, headers)
         end
-        
+        #LOGGER.debug "result body size: #{result.body.size}"
+
         # PENDING NTUA does return errors with 200
         raise RestClient::ExceptionWithResponse.new(result) if uri=~/ntua/ and result.body =~ /about.*http:\/\/anonymous.org\/error/