Java

7 files changed, 15 insertions, 9 deletions

diff --git a/application.rb b/application.rb
index 4908917..a4dcfab 100644
--- a/application.rb
+++ b/application.rb
@@ -1,11 +1,11 @@
 # Java Klimbim
 ENV["JAVA_HOME"] = "/usr/lib/jvm/java-6-sun" unless ENV["JAVA_HOME"]
-ENV["JOELIB2"] = File.join File.expand_path(File.dirname(__FILE__)),"java"
+ENV["JAVA_CP"] = File.join File.expand_path(File.dirname(__FILE__)),"java"
 deps = []
 deps << "#{ENV["JAVA_HOME"]}/lib/tools.jar"
 deps << "#{ENV["JAVA_HOME"]}/lib/classes.jar"
-deps << "#{ENV["JOELIB2"]}"
-jars = Dir[ENV["JOELIB2"]+"/*.jar"].collect {|f| File.expand_path(f) }
+deps << "#{ENV["JAVA_CP"]}"
+jars = Dir[ENV["JAVA_CP"]+"/*.jar"].collect {|f| File.expand_path(f) }
 deps = deps + jars
 ENV["CLASSPATH"] = deps.join(":")
 
diff --git a/bbrc-sample b/bbrc-sample
-Subproject 0d1d349ac33ae2fcc1bbdf31617ed9132c7527c
+Subproject 1552da28ebbcbfb2128e5561cd8aff2ef534219
diff --git a/java/ApplyCDKDescriptors.class b/java/ApplyCDKDescriptors.class
index 363db88..dd00864 100644
--- a/java/ApplyCDKDescriptors.class
+++ b/java/ApplyCDKDescriptors.class
diff --git a/java/ApplyCDKDescriptors.java b/java/ApplyCDKDescriptors.java
index 4a4bd8f..f872026 100644
--- a/java/ApplyCDKDescriptors.java
+++ b/java/ApplyCDKDescriptors.java
@@ -58,14 +58,14 @@ public class ApplyCDKDescriptors
 	//{
 	//	String inpath = "hamster_3d.sdf";
   //  String outpath = "hamster_desc.csv";
-  //  getDescriptorCSV(inpath,outpath,"KappaShapeIndicesDescriptor");
+  //  getDescriptorCSV(inpath,outpath,"");
 	//}
 
  public static void getDescriptorCSV(String sdfInputPath, String csvOutputPath, String descNamesStr) throws java.io.IOException  {
     List<IMolecule> mols = readMolecules(sdfInputPath);
-		System.out.println("read " + mols.size() + " compounds");
+		System.err.println("read " + mols.size() + " compounds");
 		List<IDescriptor> descriptors = ENGINE.getDescriptorInstances();
-		System.out.println("found " + descriptors.size() + " descriptors");
+		System.err.println("found " + descriptors.size() + " descriptors");
 
     List<String> descNames = Arrays.asList(descNamesStr.split(","));
     ArrayList<String> colNames = new ArrayList<String>();
@@ -75,9 +75,13 @@ public class ApplyCDKDescriptors
         continue;
       String tname = desc.getClass().getName();
       String[] tnamebits = tname.split("\\.");
-      if (!descNames.contains(tnamebits[tnamebits.length-1]))
+      tname = tnamebits[tnamebits.length-1];
+      if ((descNamesStr.length()>0) && (!descNames.contains(tname)))
         continue;
       String[] colNamesArr = desc.getDescriptorNames();
+      for (int idx=0; idx<colNamesArr.length; idx++) {
+        colNamesArr[idx] = tname + "-" + colNamesArr[idx];
+      }
       colNames.addAll(Arrays.asList(colNamesArr));
       List<Double[]> valuesList = computeLists(mols, (IMolecularDescriptor) desc);
       values.addAll(valuesList);
diff --git a/last-utils b/last-utils
-Subproject efcc3f41dd9e2f590a1520dfee3bf709120b2e4
+Subproject 6562a3d581a6141f946098e68fc2a3f80f0446b
diff --git a/libfminer b/libfminer
-Subproject 4577dcacb352af3fdca925714dc570de9e02582
+Subproject a86af9e55225c5c04403efd0209f7aca800a982
diff --git a/pc.rb b/pc.rb
index 3718eeb..2ef95bb 100644
--- a/pc.rb
+++ b/pc.rb
@@ -82,9 +82,10 @@ post '/pc/AllDescriptors' do
     byteArray = Rjb::import('java.io.ByteArrayOutputStream'); printStream = Rjb::import('java.io.PrintStream'); 
     out = byteArray.new() ; Rjb::import('java.lang.System').out = printStream.new(out) # joelib is too verbose
     s = Rjb::import('JoelibFc') # import main class
+    t = Rjb::import('ApplyCDKDescriptors')
 
     LOGGER.debug "Running PC with pc_type '#{params[:pc_type]}' and lib '#{params[:lib]}'"
-    OpenTox::Algorithm.pc_descriptors( { :dataset_uri => params[:dataset_uri], :pc_type => params[:pc_type], :rjb => s, :add_uri => true, :task => task, :lib => params[:lib], :subjectid => @subjectid} )
+    OpenTox::Algorithm.pc_descriptors( { :dataset_uri => params[:dataset_uri], :pc_type => params[:pc_type], :rjb => {:jl=>s, :cdk => t}, :add_uri => true, :task => task, :lib => params[:lib], :subjectid => @subjectid} )
   end
   raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
   halt 202,task.uri.to_s+"\n"
@@ -106,7 +107,8 @@ post '/pc/:descriptor' do
     byteArray = Rjb::import('java.io.ByteArrayOutputStream'); printStream = Rjb::import('java.io.PrintStream'); 
     out = byteArray.new() ; Rjb::import('java.lang.System').out = printStream.new(out) # joelib is too verbose
     s = Rjb::import('JoelibFc') # import main class
-    OpenTox::Algorithm.pc_descriptors( { :dataset_uri => params[:dataset_uri], :pc_type => params[:pc_type], :descriptor => params[:descriptor], :rjb => s, :add_uri => false, :task => task, :subjectid => @subjectid} )
+    t = Rjb::import('ApplyCDKDescriptors')
+    OpenTox::Algorithm.pc_descriptors( { :dataset_uri => params[:dataset_uri], :pc_type => params[:pc_type], :descriptor => params[:descriptor], :rjb => {:jl=>s, :cdk => t}, :add_uri => false, :task => task, :subjectid => @subjectid} )
   end
   raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
   halt 202,task.uri.to_s+"\n"