descriptor calculation with descriptor_uris parameter working.

1 files changed, 32 insertions, 40 deletions

diff --git a/descriptor.rb b/descriptor.rb
index 18a44d6..96599d6 100644
--- a/descriptor.rb
+++ b/descriptor.rb
@@ -27,6 +27,7 @@ module OpenTox
       OpenBabel::OBDescriptor.list_as_string("descriptors").split("\n").each do |d|
         title,description = d.split(/\s+/,2)
         unless title =~ /cansmi|formula|InChI|smarts|title/ or title == "s"
+          uri = File.join $algorithm[:uri], "descriptor/openbabel" ,title
           title = "OpenBabel "+title
           feature = OpenTox::Feature.find_or_create({
               RDF::DC.title => title,
@@ -35,6 +36,7 @@ module OpenTox
             }, @subjectid)
           descriptors[:openbabel] << {
             :title => title,
+            :uri => uri,
             :description => description,
             :calculator => OpenBabel::OBDescriptor.find_type(title.split(" ").last),
             :feature => feature
@@ -45,7 +47,9 @@ module OpenTox
       # CDK
       cdk_descriptors = YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptorInfo`)
       cdk_descriptors.each do |descriptor|
-        descriptor[:title] = "Cdk " + descriptor[:java_class].split('.').last.sub(/Descriptor/,'')
+        title = descriptor[:java_class].split('.').last.sub(/Descriptor/,'')
+        descriptor[:title] = "Cdk " + title
+        descriptor[:uri] = File.join $algorithm[:uri], "descriptor/cdk" ,title
         descriptor[:features] = []
         descriptor[:names].each do |name|
           descriptor[:features] << OpenTox::Feature.find_or_create({
@@ -62,7 +66,9 @@ module OpenTox
       joelib_descriptors.each do |descriptor|
         # exclude Hashcode (not a physchem property) and GlobalTopologicalChargeIndex (Joelib bug)
         next if descriptor[:java_class] == "joelib2.feature.types.MoleculeHashcode" or descriptor[:java_class] == "joelib2.feature.types.GlobalTopologicalChargeIndex"
-        descriptor[:title] = "Joelib " + descriptor[:java_class].split('.').last
+        title = descriptor[:java_class].split('.').last
+        descriptor[:uri] = File.join $algorithm[:uri], "descriptor/joelib",title
+        descriptor[:title] = "Joelib " + title
         descriptor[:feature] = OpenTox::Feature.find_or_create({
             RDF::DC.title => descriptor[:title],
             RDF.type => [RDF::OT.Feature, RDF::OT.NumericFeature],
@@ -88,12 +94,9 @@ module OpenTox
 
       def cdk compounds, descriptors
         sdf_3d compounds
-        # rjb blocks within tasks
-        # Avoid "Argument list too long" error by sending only short descriptor names
-        #yaml = `export CDKDescriptors= ;echo "#{@sdf}" |java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptors #{descriptors.collect{|d| d[:title].split("\s").last}.join(" ")}`
-        #yaml = `export CDKDescriptors='#{descriptors.collect{|d| d[:title].split("\s").last}.join(" ")}';echo "#{@sdf}" |java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptors `
+        # use java system call (rjb blocks within tasks)
+        # use Tempfiles to avoid "Argument list too long" error 
         puts `java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptors #{@sdf_file.path} #{descriptors.collect{|d| d[:title].split("\s").last}.join(" ")}`
-        #puts yaml
         YAML.load_file(@sdf_file.path+"cdk.yaml").each_with_index do |calculation,i|
           $logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
           calculation.each do |name,value|
@@ -104,12 +107,10 @@ module OpenTox
       end
 
       def joelib compounds, descriptors
+        # use java system call (rjb blocks within tasks)
+        # use Tempfiles to avoid "Argument list too long" error 
         sdf_3d compounds
-        # rjb blocks within tasks
-        #yaml = `echo "#{@sdf}" |java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR}  JoelibDescriptors #{descriptors.collect{|d| d[:java_class]}.join(" ")}|grep "^[- ]"`
-        #puts "java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR}  JoelibDescriptors  #{@sdf_file.path} #{descriptors.collect{|d| d[:java_class]}.join(" ")}"
         puts `java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR}  JoelibDescriptors  #{@sdf_file.path} #{descriptors.collect{|d| d[:java_class]}.join(" ")}`
-        #YAML.load(yaml).each_with_index do |calculation,i|
         YAML.load_file(@sdf_file.path+"joelib.yaml").each_with_index do |calculation,i|
           $logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
           calculation.each do |java_class,value|
@@ -120,9 +121,8 @@ module OpenTox
       end
 
       def sdf_3d compounds
-        #unless @sdf_file and File.exists? @sdf_file.path
-        unless @sdf
-          @sdf = ""
+        unless @sdf_file and File.exists? @sdf_file.path
+          @sdf_file = Tempfile.open("sdf")
           @@obconversion.set_out_format 'sdf'
           # create 3d sdf file (faster in Openbabel than in CDK)
           compounds.each do |compound|
@@ -134,13 +134,11 @@ module OpenTox
               warning = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure."
               $logger.warn warning
               @feature_dataset[RDF::OT.Warnings] ? @feature_dataset[RDF::OT.Warnings] << warning : @feature_dataset[RDF::OT.Warnings] = warning
-              @sdf << sdf_2d
+              @sdf_file.puts sdf_2d
             else
-              @sdf << sdf_3d
+              @sdf_file.puts sdf_3d
             end
           end
-          @sdf_file = Tempfile.open("sdf")
-          @sdf_file.puts @sdf
           @sdf_file.close
         end
       end
@@ -182,7 +180,7 @@ module OpenTox
         elsif params[:dataset_uri]
           @feature_dataset.parameters = [ { RDF::DC.title => "dataset_uri", RDF::OT.paramValue => params[:dataset_uri] }]
         else
-          bad_request_error "Please provide a dataset_uri or compound_uri paramaeter", @uri
+          bad_request_error "Please provide a dataset_uri or compound_uri parameter", @uri
         end
       end
     end
@@ -193,9 +191,11 @@ module OpenTox
       @descriptor = @descriptors.first
     end
 
-    after do
-      #@sdf_file.unlink if @sdf_file and File.exists @sdf_file.path
-      #TODO cleanup yamls
+    after do # Tempfile cleanup
+      if @sdf_file and File.exists? @sdf_file.path
+        FileUtils.rm Dir["#{@sdf_file.path}*.yaml"]
+        @sdf_file.unlink
+      end
       @sdf_file = nil
     end
 
@@ -219,12 +219,13 @@ module OpenTox
 
     post '/descriptor/?' do
       task = OpenTox::Task.run "Calculating PC descriptors", @uri, @subjectid do |task|
-        if params[:descriptors]
+        if params[:descriptor_uris]
           descriptors = {}
-          params[:descriptors].each do |descriptor|
+          params[:descriptor_uris].each do |descriptor_uri|
             #lib, title = descriptor.split('/')
+            lib = descriptor_uri.split('/')[-2]
             descriptors[lib.to_sym] ||= []
-            descriptors[lib.to_sym] << DESCRIPTORS[lib.to_sym].select{|d| d[:title] == descriptor}
+            descriptors[lib.to_sym] += DESCRIPTORS[lib.to_sym].select{|d| d[:uri] == descriptor_uri}
           end
         else
           descriptors = DESCRIPTORS
@@ -242,22 +243,13 @@ module OpenTox
       halt 202, task.uri
     end
 
+    # use /descriptor with dataset_uri and descriptor_uri parameters for efficient calculation of multiple compounds/descriptors
     post '/descriptor/:lib/:descriptor/?' do
-      if params[:compound_uri]
-        compounds = [ Compound.new(params[:compound_uri], @subjectid) ]
-        send params[:lib].to_sym, compounds, @descriptors
-        @feature_dataset.put
-        @feature_dataset.uri
-      elsif params[:dataset_uri]
-        task = OpenTox::Task.run "Calculating PC descriptors", @uri, @subjectid do |task|
-          compounds = Dataset.new(params[:dataset_uri]).compounds
-          send params[:lib].to_sym, compounds, @descriptors
-          @feature_dataset.put
-          @feature_dataset.uri
-        end
-        response['Content-Type'] = 'text/uri-list'
-        halt 202, task.uri
-      end
+      bad_request_error "Please provide a compound_uri parameter", @uri unless params[:compound_uri]
+      compounds = [ Compound.new(params[:compound_uri], @subjectid) ]
+      send params[:lib].to_sym, compounds, @descriptors
+      @feature_dataset.put
+      @feature_dataset.uri
     end
 
   end