Fixed feature metadata

2 files changed, 68 insertions, 55 deletions

diff --git a/lib/compound/pc_descriptors.rb b/lib/compound/pc_descriptors.rb
index 7ac75df..4bf1171 100644
--- a/lib/compound/pc_descriptors.rb
+++ b/lib/compound/pc_descriptors.rb
@@ -20,10 +20,9 @@ module OpenTox
         if (!@lib || @lib.include?("cdk"))
           cdk = CDKDescriptors.new(@params)
           cdk_master, cdk_ids = cdk.calculate
-          cdk_single_ids = cdk_master[0].collect { |id| id.to_s.sub(/[^-]*-/,"").gsub(/[\/.\\\(\)\{\}\[\]]/,"_") } # get column headers w/ nice '_'
-          cdk_master[0] = cdk_single_ids.collect{|x| x} # Single IDs as features in result ds
-          cdk_ids.shift # remove SMILES
-          cdk_single_ids.shift # remove SMILES
+          cdk_single_ids = cdk_master[0].to_a.collect { |id| id.to_s.sub(/[^-]*-/,"").gsub(/[\/.\\\(\)\{\}\[\]]/,"_") } # get column headers w/ nice '_'
+          cdk_master[0].each_index{ |idx| cdk_master[0][idx] = cdk_single_ids[idx] } # Single IDs as features in result ds
+          cdk_single_ids.shift # remove SMILES for IDs
         end
         if (!@lib || @lib.include?("openbabel"))
           openbabel = OpenBabelDescriptors.new(@params)
@@ -45,7 +44,7 @@ module OpenTox
       def master_join (m1, m2)
         if m2 && m1
           nr_cols = (m2[0].size)-1
-          $logger.debug "Merging #{nr_cols} new columns on #{m1[0].size}"
+          $logger.debug "Merging #{nr_cols} new columns on #{m1[0].size} (including ID), yields #{nr_cols + m1[0].size}"
           m1.each {|row| nr_cols.times { row.push(nil) }  }
           m2.each do |row|
             temp = m1.assoc(row[0]) # Finds the appropriate line in master
@@ -99,6 +98,7 @@ module OpenTox
       def calculate
         master = nil
         cdk_class = nil
+        ids_multiplied = nil
         begin
           cdk_class = Rjb::import('ApplyCDKDescriptors')
           pc_descriptors = YAML::load_file($keysfile)
@@ -133,6 +133,8 @@ module OpenTox
             master[0][0] = "InChI"
             master[1][0] = @inchi
             master[1].collect! { |x| x.to_s == "null" ? nil : x }
+            ids_multiplied = master[0].to_a.collect { |x| x.gsub(/-.*/,"") }
+            ids_multiplied.shift # remove ID
           end
         rescue Exception => e
           $logger.debug "#{e.class}: #{e.message}"
@@ -140,7 +142,7 @@ module OpenTox
         ensure
           [ csvfile ].each { |f| File.delete(f) } if csvfile
         end
-        [ master, ids ]
+        [ master, ids_multiplied ]
       end
     end
 
diff --git a/webapp/compound.rb b/webapp/compound.rb
index ba70198..da2384d 100644
--- a/webapp/compound.rb
+++ b/webapp/compound.rb
@@ -31,6 +31,9 @@ module OpenTox
       pc_type = params[:pc_type].nil? ? "" : params[:pc_type]
       pcdf = OpenTox::Compound::PcDescriptorFactory.new(params)
       master, cdk_ids, ob_ids, jl_ids, cdk_single_ids = pcdf.calculate
+      #$logger.debug cdk_ids.to_yaml
+      #cdk_single_ids.collect { |x| $logger.debug x }
+      #$logger.debug cdk_single_ids.to_yaml
       begin 
         if master
           feature_dataset = OpenTox::Dataset.new(nil, @subjectid)
@@ -45,13 +48,69 @@ module OpenTox
               { RDF::DC.title => "lib", RDF::OT.paramValue => lib },
               { RDF::DC.title => "pc_type", RDF::OT.paramValue => pc_type},
           ]
+
+          #cdk_single_ids && cdk_single_ids.each_with_index { |id,idx|
+          #  raise "Feature not found" if ! ds.features[File.join(ds.uri, "feature", id.to_s)]
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{DC.description => "#{pc_descriptors[cdk_ids[idx]][:name]} [#{pc_descriptors[cdk_ids[idx]][:pc_type]}, #{pc_descriptors[cdk_ids[idx]][:lib]}]"})
+          #  creator_uri = ds.uri.gsub(/\/dataset\/.*/, "/algorithm/pc")
+          #  creator_uri += "/#{cdk_ids[idx]}" if params[:add_uri]
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{DC.creator => creator_uri})
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{OT.hasSource => params[:dataset_uri]})
+          #}
+
+          #ob_ids && ob_ids.each { |id|
+          #  raise "Feature not found" if ! ds.features[File.join(ds.uri, "feature", id.to_s)]
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{DC.description => "#{pc_descriptors[id][:name]} [#{pc_descriptors[id][:pc_type]}, #{pc_descriptors[id][:lib]}]"})
+          #  creator_uri = ds.uri.gsub(/\/dataset\/.*/, "/algorithm/pc")
+          #  creator_uri += "/#{id}" if params[:add_uri]
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{DC.creator => creator_uri})
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{OT.hasSource => params[:dataset_uri]})
+          #}
+          #jl_ids && jl_ids.each { |id|
+          #  raise "Feature not found" if ! ds.features[File.join(ds.uri, "feature", id.to_s)]
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{DC.description => "#{pc_descriptors[id][:name]} [#{pc_descriptors[id][:pc_type]}, #{pc_descriptors[id][:lib]}]"})
+          #  creator_uri = ds.uri.gsub(/\/dataset\/.*/, "/algorithm/pc")
+          #  creator_uri += "/#{id}" if params[:add_uri]
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{DC.creator => creator_uri})
+          #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{OT.hasSource => params[:dataset_uri]})
+          #}
+
+
           features = []
+          pc_descriptors = YAML::load_file($keysfile)
           master[0].each_with_index { |f,idx|
             if (idx != 0)
+
+              # Description
+              description = ""
+              descriptor_name = ""
+              if cdk_single_ids # we have used CDK
+                idx = cdk_single_ids.index(f)
+                cdk_id = cdk_ids[idx] if idx
+              end
+              if cdk_id
+                #$logger.debug "#{f} in CDK: #{pc_descriptors[cdk_id][:name]}"
+                descriptor_name = pc_descriptors[cdk_id][:name]
+                description = "#{descriptor_name} [#{pc_descriptors[cdk_id][:pc_type]}, #{pc_descriptors[cdk_id][:lib]}]" 
+              else
+                #$logger.debug "#{f} not in CDK"
+                if pc_descriptors[f]
+                  descriptor_name = pc_descriptors[f][:name]
+                  description = "#{descriptor_name} [#{pc_descriptors[f][:pc_type]}, #{pc_descriptors[f][:lib]}]"
+                else
+                  internal_server_error "PC feature '#{f}' not found"
+                end
+              end
+
+              # Creator URI
+              creator_uri = File.join url_for("/compound/#{inchi}/pc",:full), f
+        
               feature = OpenTox::Feature.new nil, @subjectid
               feature.title = f.to_s
               feature.metadata = {
                 RDF.type => [RDF::OT.Feature],
+                RDF::DC.creator => creator_uri,
+                RDF::DC.description => description
               }
               features << feature
             end
@@ -60,61 +119,13 @@ module OpenTox
           master[1][0] = OpenTox::Compound.new(params[:compound], @subjectid) 
           feature_dataset << master[1].to_a
           format_output(feature_dataset)
+          
         end
       rescue => e
         $logger.debug "#{e.class}: #{e.message}"
         $logger.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
       end
 
-        #begin 
-        #  tf = Tempfile.open(['compound-','.csv'])
-        #  tf.puts master.collect { |row| row.join(",") }.join("\n")
-        #  tf.flush
-        #  ds = OpenTox::Dataset.new nil, nil
-        #  # Does not work here:
-        #  #ds.upload tf.path 
-        #  uri = RestClientWrapper.put(ds.uri, {:file => File.new(tf.path)}, {:subjectid => @subjectid})
-        #  $logger.debug "Waiting for upload (single CSV row): #{uri}"
-        #  OpenTox::Task.new(uri).wait if URI.task?(uri)
-        #  $logger.debug "Waiting finished"
-        #  ds.get
-        #  $logger.debug "AM: #{ds.uri}"
-        #rescue => e
-        #  $logger.debug "#{e.class}: #{e.message}"
-        #  $logger.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
-        #end
-
-
-
-        ## # # add feature metadata
-        #pc_descriptors = YAML::load_file($keysfile)
-        #cdk_single_ids && cdk_single_ids.each_with_index { |id,idx|
-        #  raise "Feature not found" if ! ds.features[File.join(ds.uri, "feature", id.to_s)]
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::DC.description => "#{pc_descriptors[cdk_ids[idx]][:name]} [#{pc_descriptors[cdk_ids[idx]][:pc_type]}, #{pc_descriptors[cdk_ids[idx]][:lib]}]"})
-        #  creator_uri = ds.uri.gsub(/\/dataset\/.*/, "/algorithm/pc")
-        #  creator_uri += "/#{cdk_ids[idx]}" if params[:add_uri]
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::DC.creator => creator_uri})
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::OT.hasSource => params[:dataset_uri]})
-        #}
-        #ob_ids && ob_ids.each { |id|
-        #  raise "Feature not found" if ! ds.features[File.join(ds.uri, "feature", id.to_s)]
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::DC.description => "#{pc_descriptors[id][:name]} [#{pc_descriptors[id][:pc_type]}, #{pc_descriptors[id][:lib]}]"})
-        #  creator_uri = ds.uri.gsub(/\/dataset\/.*/, "/algorithm/pc")
-        #  creator_uri += "/#{id}" if params[:add_uri]
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::DC.creator => creator_uri})
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::OT.hasSource => params[:dataset_uri]})
-        #}
-        #jl_ids && jl_ids.each { |id|
-        #  raise "Feature not found" if ! ds.features[File.join(ds.uri, "feature", id.to_s)]
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::DC.description => "#{pc_descriptors[id][:name]} [#{pc_descriptors[id][:pc_type]}, #{pc_descriptors[id][:lib]}]"})
-        #  creator_uri = ds.uri.gsub(/\/dataset\/.*/, "/algorithm/pc")
-        #  creator_uri += "/#{id}" if params[:add_uri]
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::DC.creator => creator_uri})
-        #  ds.add_feature_metadata(File.join(ds.uri, "feature", id.to_s),{RDF::OT.hasSource => params[:dataset_uri]})
-        #}
-      #$logger.debug master.size
-      #$logger.debug master.collect { |r| r.join(',') }.join("\n")
-      #$logger.debug ""
     end
 
   end