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Abandoning classfileset/rootfileset approach due to difficulting managing 

classloading of bcel*.jar/ant-apache-bcel*.jar.  Switching instead to manually
specifying a minimal set of packages/classes to include in the vcf.jar via
build.xml, and adding a unit test which creates a limited classloader
only aware of vcf.jar and tribble.jar and tries to use it to load the core
classes in the vcf jar.

Hopefully third time's the charm.
This commit is contained in:
Matt Hanna 2011-10-06 12:49:51 -04:00
parent efca1fdfd8
commit 4fa5045e84
2 changed files with 55 additions and 3 deletions
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7
build.xml
View File

@ -546,8 +546,9 @@
<target name="vcf.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/vcf.jar">
<fileset dir="${java.classes}">
<include name="**/utils/codecs/**/*.class"/>
<include name="**/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
<include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
</fileset>
@ -914,7 +915,7 @@
</target>
<!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest -->
<target name="test" depends="init.buildall,test.compile" description="Run unit tests">
<target name="test" depends="init.buildall,test.compile,vcf.jar" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}">
<not><isset property="single"/></not>
</condition>

51
public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java 100644
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@ -0,0 +1,51 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* 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 org.broadinstitute.sting.utils.variantcontext;
import org.testng.annotations.Test;
import java.io.File;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.net.URLClassLoader;
/**
* Test to ensure that, given only the VCF jar and its expected dependencies, core VCF classes will load.
*/
public class VCFJarClassLoadingUnitTest {
@Test
public void testVCFJarClassLoading() throws ClassNotFoundException, MalformedURLException {
URI vcfURI = new File("dist/vcf.jar").toURI();
URI tribbleURI = new File("lib/tribble-24.jar").toURI();
ClassLoader classLoader = new URLClassLoader(new URL[] {vcfURI.toURL(),tribbleURI.toURL()}, null);
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFWriter");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter");
}
}