From f577119d827729fb540654c1391d35804a262649 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Wed, 19 Sep 2012 15:55:37 +0200 Subject: Java --- application.rb | 6 +++--- bbrc-sample | 2 +- java/ApplyCDKDescriptors.class | Bin 8549 -> 8632 bytes java/ApplyCDKDescriptors.java | 12 ++++++++---- last-utils | 2 +- libfminer | 2 +- pc.rb | 6 ++++-- 7 files changed, 18 insertions(+), 12 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 index 0d1d349..1552da2 160000 --- a/bbrc-sample +++ b/bbrc-sample @@ -1 +1 @@ -Subproject commit 0d1d349ac33ae2fcc1bbdf31617ed9132c7527ca +Subproject commit 1552da28ebbcbfb2128e5561cd8aff2ef534219e diff --git a/java/ApplyCDKDescriptors.class b/java/ApplyCDKDescriptors.class index 363db88..dd00864 100644 Binary files a/java/ApplyCDKDescriptors.class and b/java/ApplyCDKDescriptors.class differ 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 mols = readMolecules(sdfInputPath); - System.out.println("read " + mols.size() + " compounds"); + System.err.println("read " + mols.size() + " compounds"); List descriptors = ENGINE.getDescriptorInstances(); - System.out.println("found " + descriptors.size() + " descriptors"); + System.err.println("found " + descriptors.size() + " descriptors"); List descNames = Arrays.asList(descNamesStr.split(",")); ArrayList colNames = new ArrayList(); @@ -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 valuesList = computeLists(mols, (IMolecularDescriptor) desc); values.addAll(valuesList); diff --git a/last-utils b/last-utils index efcc3f4..6562a3d 160000 --- a/last-utils +++ b/last-utils @@ -1 +1 @@ -Subproject commit efcc3f41dd9e2f590a1520dfee3bf709120b2e41 +Subproject commit 6562a3d581a6141f946098e68fc2a3f80f0446b1 diff --git a/libfminer b/libfminer index 4577dca..a86af9e 160000 --- a/libfminer +++ b/libfminer @@ -1 +1 @@ -Subproject commit 4577dcacb352af3fdca925714dc570de9e02582c +Subproject commit a86af9e55225c5c04403efd0209f7aca800a9827 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" -- cgit v1.2.3