Fixed classpath conflicts by compiling against specific CDK versions,…

… and only including Japex on the default classpath
egonw · Jul 13, 2011 · 83983db · 83983db
1 parent 40ff1f7
commit 83983db
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Showing 4 changed files with 125 additions and 4 deletions.
diff --git a/build.xml b/build.xml
@@ -22,7 +22,15 @@
   <property name="config" value="mx-cdk-sdf.xml"/>
   <!-- filesets -->
   <fileset dir="${lib.dir}" id="libs">
-    <include name="**/*.jar" />
+    <include name="slf4j*.jar" />
+    <include name="mail-1.4.jar" />
+    <include name="jsr173_api-1.0.jar" />
+    <include name="jfreechart-1.0.12.jar" />
+    <include name="jcommon-1.0.12.jar" />
+    <include name="jaxb-api-2.0.jar" />
+    <include name="japex-1.2.2.jar" />
+    <include name="activiation-1.1.jar" />
+    <include name="ant-*.jar" />
   </fileset>
   <!-- targets -->
   <target name="init" description="Create build directories." >
@@ -38,9 +46,26 @@
     <delete dir="${doc.dir}" />
   </target>
   <target name="compile" depends="init" description="Compile sources.">
-    <javac srcdir="${source.dir}" destdir="${class.dir}" includes="net/openmolecules/benchmark/**/*.java" debug="on" source="1.5" target="1.5">
+    <javac srcdir="${source.dir}" destdir="${class.dir}"
+        includes="net/openmolecules/benchmark/**/*.java"
+        excludes="net/openmolecules/benchmark/**/*14.java"
+        debug="on" source="1.5" target="1.5">
       <classpath>
         <fileset refid="libs" />
+        <fileset dir="lib">
+          <include name="cdk-1.3.*.jar"/>
+          <include name="mx*.jar"/>
+        </fileset>
+      </classpath>
+    </javac>
+    <javac srcdir="${source.dir}" destdir="${class.dir}"
+        includes="net/openmolecules/benchmark/**/*14.java"
+        debug="on" source="1.5" target="1.5">
+      <classpath> 
+        <fileset refid="libs" />
+        <fileset dir="lib">
+          <include name="cdk-1.4.0.jar"/>
+        </fileset>
       </classpath>
     </javac>
   </target>

diff --git a/lib/cdk-1.4.0.jar b/lib/cdk-1.4.0.jar
diff --git a/mx-cdk-sdf.xml b/mx-cdk-sdf.xml
@@ -3,8 +3,8 @@
   <param name="basedir" value="."/>
   <param name="japex.classPath" value="build/classes"/>
   <param name="japex.resultUnit" value="ms"/>
-  <param name="japex.warmupIterations" value="10"/>
-  <param name="japex.runIterations" value="50"/>
+  <param name="japex.warmupIterations" value="50"/>
+  <param name="japex.runIterations" value="500"/>
   <param name="japex.reportsDirectory" value="build/reports"/>
   <driverGroup name="MX-CDK-SDF" xmlns="http://www.sun.com/japex/testSuite">
     <driver name="CDK-1.2.x">
@@ -17,6 +17,11 @@
       <param name="japex.classPath" value="${basedir}/lib/cdk-1.3.x-20091008.jar"/>
       <param name="description" value="Reads SD file, prints sum of calculated molecular masses."/>
     </driver>
+    <driver name="CDK-1.4.x">
+      <param name="japex.driverClass" value="net.openmolecules.benchmark.driver.CDKSDFBench14"/>
+      <param name="japex.classPath" value="${basedir}/lib/cdk-1.4.0.jar"/>
+      <param name="description" value="Reads SD file, prints sum of calculated molecular masses."/>
+    </driver>
     <driver name="mx-0.108.1">
       <param name="japex.driverClass" value="net.openmolecules.benchmark.driver.MXSDFBench"/>
       <param name="japex.classPath" value="${basedir}/lib/mx-0.108.1.jar"/>

diff --git a/src/net/openmolecules/benchmark/driver/CDKSDFBench14.java b/src/net/openmolecules/benchmark/driver/CDKSDFBench14.java
@@ -0,0 +1,91 @@
+/*
+ * ChemBench - The Benchmark Suite for Cheminformatics
+ * 
+ * Copyright (c) 2009 Metamolecular, LLC (http://metamolecular.com)
+ *               2011 Egon Willighagen <egonw@users.sf.net>
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package net.openmolecules.benchmark.driver;
+
+import com.sun.japex.JapexDriverBase;
+import com.sun.japex.TestCase;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.io.iterator.IteratingMDLReader;
+import org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor;
+import org.openscience.cdk.qsar.result.DoubleResult;
+
+/**
+ * @author Richard L. Apodaca
+ */
+public class CDKSDFBench14 extends JapexDriverBase
+{
+
+  @Override
+  public void prepare()
+  {
+  }
+
+  @Override
+  public void run(TestCase testCase)
+  {
+    IteratingMDLReader reader = getReader(testCase.getParam("japex.inputFile"));
+    WeightDescriptor calculator = new WeightDescriptor();
+    double sum = 0;
+
+    while (reader.hasNext())
+    {
+      IMolecule molecule = (IMolecule) reader.next();
+      sum += (((DoubleResult)calculator.calculate(molecule).getValue()).doubleValue());
+    }
+
+    try
+    {
+      reader.close();
+    }
+
+    catch (IOException e)
+    {
+      throw new RuntimeException(e);
+    }
+  }
+
+  private IteratingMDLReader getReader(String filename)
+  {
+    IteratingMDLReader result = null;
+
+    try
+    {
+      Reader raw = new FileReader(filename);
+      //BufferedReader reader = new BufferedReader(raw);
+
+      result = new IteratingMDLReader(raw, DefaultChemObjectBuilder.getInstance());
+    } catch (Exception e)
+    {
+      throw new RuntimeException(e.getMessage(), e);
+    }
+
+    return result;
+  }
+}