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Merge pull request #771 from broadinstitute/ks_faster_builds 

Faster builds of GATK executables
This commit is contained in:
kshakir 2014-11-05 01:54:59 +08:00
parent f6af776590 0092a0b9eb
commit c14fccb571
24 changed files with 478 additions and 293 deletions
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28
ant-bridge.sh
View File

@ -1,6 +1,7 @@
#!/bin/sh
mvn_args="verify"
default_args="verify '-Ddisable.shadepackage'"
mvn_args="${default_args}"
mvn_properties=
mvn_clean=
unknown_args=
@ -44,22 +45,23 @@ for arg in "${@}" ; do
fi
else
if [[ "${arg}" != "dist" && "${mvn_args}" != "" && "${mvn_args}" != "verify" ]] ; then
if [[ "${arg}" != "dist" && "${mvn_args}" != "" && "${mvn_args}" != "${default_args}" ]] ; then
echo "Sorry, this script does not currently support mixing targets." >&2
exit 1
elif [[ "${arg}" == "dist" ]] ; then
mvn_args="verify"
mvn_args="${default_args}"
elif [[ "${arg}" == "gatk" ]] ; then
mvn_args="verify '-P!queue'"
mvn_args="${default_args} '-P!queue'"
elif [[ "${arg}" == "test.compile" ]] ; then
mvn_args="test-compile"
elif [[ "${arg}" == "gatkdocs" ]] ; then
local_repo="sitetemprepo"
mvn_args="install -Dmaven.repo.local=${local_repo} -Ddisable.queue && mvn site -Dmaven.repo.local=${local_repo} -Ddisable.queue"
mvn_args="install -Dmaven.repo.local=${local_repo} '-P!queue' && mvn site -Dmaven.repo.local=${local_repo} '-P!queue'"
mvn_pkg_args=
elif [[ "${arg}" == "package.gatk.full" ]] ; then
mvn_args="package '-P!private,!queue'"
@ -75,11 +77,11 @@ for arg in "${@}" ; do
# elif [[ "${arg}" == "release.gatk.full" ]] ; then
# mvn_args="package '-P!private,!queue'"
# post_script=" && private/src/main/scripts/shell/copy_release.sh public/gatk-package/target/GenomeAnalysisTK-*.tar.bz2"
# post_script=" && private/src/main/scripts/shell/copy_release.sh protected/gatk-package-distribution/target/GenomeAnalysisTK-*.tar.bz2"
# elif [[ "${arg}" == "release.queue.full" ]] ; then
# mvn_args="package '-P!private'"
# post_script=" && private/src/main/scripts/shell/copy_release.sh public/queue-package/target/Queue-*.tar.bz2"
# post_script=" && private/src/main/scripts/shell/copy_release.sh protected/gatk-queue-package-distribution/target/Queue-*.tar.bz2"
elif [[ "${arg}" == "build-picard-private" ]] ; then
mvn_args="mvn install -f private/picard-maven/pom.xml"
@ -113,7 +115,7 @@ for arg in "${@}" ; do
mvn_args="${mvn_args} -Dgatk.queuetests.run=true"
elif [[ "${arg}" == "committests" ]] ; then
mvn_args="verify -Dgatk.committests.skipped=false"
mvn_args="${default_args} -Dgatk.committests.skipped=false"
elif [[ "${arg}" == "test" ]] ; then
mvn_args="test -Dgatk.unittests.skipped=false"
@ -122,19 +124,19 @@ for arg in "${@}" ; do
mvn_args="test -Dgatk.unittests.skipped=false"
elif [[ "${arg}" == "integrationtest" ]] ; then
mvn_args="verify -Dgatk.integrationtests.skipped=false"
mvn_args="${default_args} -Dgatk.integrationtests.skipped=false"
elif [[ "${arg}" == "largescaletest" ]] ; then
mvn_args="verify -Dgatk.largescaletests.skipped=false"
mvn_args="${default_args} -Dgatk.largescaletests.skipped=false"
elif [[ "${arg}" == "knowledgebasetest" ]] ; then
mvn_args="verify -Dgatk.knowledgebasetests.skipped=false"
mvn_args="${default_args} -Dgatk.knowledgebasetests.skipped=false"
elif [[ "${arg}" == "queuetest" ]] ; then
mvn_args="verify -Dgatk.queuetests.skipped=false"
mvn_args="${default_args} -Dgatk.queuetests.skipped=false"
elif [[ "${arg}" == "queuetestrun" ]] ; then
mvn_args="verify -Dgatk.queuetests.skipped=false -Dgatk.queuetests.run=true"
mvn_args="${default_args} -Dgatk.queuetests.skipped=false -Dgatk.queuetests.run=true"
elif [[ "${arg}" == "fasttest" ]] ; then
mvn_args="verify -Dgatk.committests.skipped=false -pl private/gatk-tools-private -am -Dresource.bundle.skip=true"

126
pom.xml
View File

@ -33,11 +33,14 @@
<!-- TODO: Need a better a way to say "don't include hidden" by default -->
<gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
<gatk.shell.directory>${gatk.basedir}/public/src/main/scripts/shell</gatk.shell.directory>
<gatk.assembly.directory>${gatk.basedir}/public/src/main/assembly</gatk.assembly.directory>
<!--
Phases of the build that may be disabled to speed up compilation.
-->
<gatk.jar.phase>package</gatk.jar.phase>
<gatk.unpack.phase>prepare-package</gatk.unpack.phase>
<gatk.shade.phase>package</gatk.shade.phase>
<gatk.generate-resources.phase>generate-resources</gatk.generate-resources.phase>
<gatk.process-resources.phase>process-resources</gatk.process-resources.phase>
<gatk.process-test-resources.phase>process-test-resources</gatk.process-test-resources.phase>
@ -66,6 +69,16 @@
<gatk.serialqueuetests.skipped>${gatk.serialcommittests.skipped}</gatk.serialqueuetests.skipped>
<gatk.seriallargescaletests.skipped>true</gatk.seriallargescaletests.skipped>
<gatk.serialknowledgebasetests.skipped>true</gatk.serialknowledgebasetests.skipped>
<!-- Full path to write the executable MANIFEST.MF only jars, 10 seconds to create at 4KB each, and the accompanying lib directory -->
<gatk.executable.directory>${gatk.basedir}/target/executable</gatk.executable.directory>
<!-- Full path to write (symlinks to) the full shaded package jars, 1+ minute to create at 12MB+ each -->
<gatk.package.directory>${gatk.basedir}/target/package</gatk.package.directory>
<!--
Full path to write symlink to either an executable MANIFEST.MF only jar - OR - a fully shaded package jar.
NOTE: MANIFEST.MF only jars MUST be accompanied by the lib folder, or they will not run.
-->
<gatk.shortcut.directory>${gatk.basedir}/target</gatk.shortcut.directory>
</properties>
<dependencies>
@ -139,9 +152,19 @@
<excludes>${resource.bundle.path}</excludes>
</configuration>
</execution>
<execution>
<id>executable-jar-lib</id>
<goals>
<goal>copy-dependencies</goal>
</goals>
<phase>none</phase>
<configuration>
<outputDirectory>${gatk.executable.directory}/lib</outputDirectory>
<includeScope>runtime</includeScope>
</configuration>
</execution>
</executions>
</plugin>
<!-- TODO: Change the ResourceBundleExtractorDoclet to not require log4j.properties file -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
@ -160,25 +183,6 @@
</goals>
<phase>${gatk.process-test-resources.phase}</phase>
</execution>
<execution>
<id>copy-resource-bundle-log4j</id>
<goals>
<goal>copy-resources</goal>
</goals>
<phase>none</phase>
<configuration>
<!--
Just before running the resource bundle generation, copy a simple log4j
config file to the apidocs execution directory, so that logging prints out.
-->
<outputDirectory>${project.reporting.outputDirectory}/apidocs</outputDirectory>
<resources>
<resource>
<directory>${gatk.basedir}/public/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help</directory>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
@ -199,7 +203,7 @@
<docletPath>${project.build.outputDirectory}</docletPath>
<docletArtifact>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-utils</artifactId>
<artifactId>${project.artifactId}</artifactId>
<version>${project.version}</version>
</docletArtifact>
<maxmemory>2g</maxmemory>
@ -319,10 +323,40 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<executions>
<execution>
<id>executable-jar</id>
<goals>
<goal>jar</goal>
</goals>
<phase>none</phase>
<configuration>
<classesDirectory>${project.build.outputDirectory}/ignored_by_executable_jar</classesDirectory>
<outputDirectory>${gatk.executable.directory}</outputDirectory>
<finalName>${gatk.binary-dist.name}</finalName>
<archive>
<manifest>
<mainClass>${app.main.class}</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
</manifest>
</archive>
</configuration>
</execution>
<execution>
<id>default-jar</id>
<phase>${gatk.jar.phase}</phase>
</execution>
<!--
Maven keeps executing default-jar first, even if it's listed AFTER the executable-jar.
So while packaging: run executable-jar, disable default-jar, then run unshaded-default-jar.
-->
<execution>
<id>unshaded-default-jar</id>
<goals>
<goal>jar</goal>
</goals>
<phase>none</phase>
</execution>
<execution>
<id>test-jar</id>
<goals>
@ -341,13 +375,14 @@
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>gatk-executable</id>
<id>package-jar</id>
<goals>
<goal>shade</goal>
</goals>
<phase>none</phase>
<configuration>
<minimizeJar>true</minimizeJar>
<createDependencyReducedPom>false</createDependencyReducedPom>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:gsalib:tar.gz:*</exclude>
@ -405,7 +440,7 @@
<phase>none</phase>
<configuration>
<descriptors>
<descriptor>src/main/assembly/binary-dist.xml</descriptor>
<descriptor>${gatk.assembly.directory}/binary-dist.xml</descriptor>
</descriptors>
</configuration>
</execution>
@ -437,7 +472,7 @@
</configuration>
</execution>
<execution>
<id>link-binary-jar</id>
<id>link-executable-jar</id>
<goals>
<goal>link</goal>
</goals>
@ -445,7 +480,26 @@
<configuration>
<links>
<link>
<dst>${gatk.basedir}/target/${gatk.binary-dist.name}.${project.packaging}</dst>
<dst>${gatk.shortcut.directory}/${gatk.binary-dist.name}.${project.packaging}</dst>
<src>${gatk.executable.directory}/${gatk.binary-dist.name}.${project.packaging}</src>
</link>
</links>
</configuration>
</execution>
<execution>
<id>link-package-jar</id>
<goals>
<goal>link</goal>
</goals>
<phase>none</phase>
<configuration>
<links>
<link>
<dst>${gatk.package.directory}/${gatk.binary-dist.name}.${project.packaging}</dst>
<src>${project.build.directory}/${project.build.finalName}.${project.packaging}</src>
</link>
<link>
<dst>${gatk.shortcut.directory}/${gatk.binary-dist.name}.${project.packaging}</dst>
<src>${project.build.directory}/${project.build.finalName}.${project.packaging}</src>
</link>
</links>
@ -748,6 +802,26 @@
</modules>
</profile>
<!-- Optionally do not shade/package jars -->
<!--
NOTE: Profile id "fast" comes from comments in PR #771.
The name is meant to be memorable, but is highly non-specific. Users are forewarned that
behavior of this profile, or the identifier itself, may be heavily modified in the future.
Hardcode usage in non-VCS controlled scripts at your own risk.
-->
<profile>
<id>fast</id>
<activation>
<property>
<name>disable.shadepackage</name>
</property>
</activation>
<properties>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
</properties>
</profile>
<!-- Collection of properties for use during package testing -->
<profile>
<id>packagetests-enabled</id>
@ -761,6 +835,8 @@
<maven.javadoc.skip>true</maven.javadoc.skip>
<gatk.generate-gatk-extensions.skipped>true</gatk.generate-gatk-extensions.skipped>
<gatk.jar.phase>none</gatk.jar.phase>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
<gatk.generate-resources.phase>none</gatk.generate-resources.phase>
<gatk.process-resources.phase>none</gatk.process-resources.phase>
<gatk.process-test-resources.phase>none</gatk.process-test-resources.phase>

47
protected/gatk-package-distribution/pom.xml
View File

@ -15,8 +15,6 @@
<properties>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.unpack.phase>prepare-package</gatk.unpack.phase>
<gatk.shade.phase>package</gatk.shade.phase>
<app.main.class>org.broadinstitute.gatk.engine.CommandLineGATK</app.main.class>
<gatk.binary-dist.name>GenomeAnalysisTK</gatk.binary-dist.name>
</properties>
@ -169,6 +167,25 @@
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<executions>
<execution>
<id>executable-jar</id>
<phase>${gatk.jar.phase}</phase>
</execution>
<execution>
<id>default-jar</id>
<phase>none</phase>
</execution>
<execution>
<id>unshaded-default-jar</id>
<phase>${gatk.jar.phase}</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
@ -177,6 +194,10 @@
<id>unpack-direct-dependencies</id>
<phase>${gatk.unpack.phase}</phase>
</execution>
<execution>
<id>executable-jar-lib</id>
<phase>${gatk.jar.phase}</phase>
</execution>
</executions>
</plugin>
@ -185,7 +206,7 @@
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>gatk-executable</id>
<id>package-jar</id>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
@ -207,7 +228,11 @@
<artifactId>maven-junction-plugin</artifactId>
<executions>
<execution>
<id>link-binary-jar</id>
<id>link-executable-jar</id>
<phase>${gatk.jar.phase}</phase>
</execution>
<execution>
<id>link-package-jar</id>
<phase>${gatk.shade.phase}</phase>
</execution>
<execution>
@ -236,20 +261,6 @@
</build>
<profiles>
<profile>
<id>packagetests-enabled</id>
<activation>
<property>
<name>gatk.packagetests.enabled</name>
<value>true</value>
</property>
</activation>
<properties>
<gatk.jar.phase>none</gatk.jar.phase>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
</properties>
</profile>
<profile>
<id>gsadev</id>
<activation>

47
protected/gatk-queue-package-distribution/pom.xml
View File

@ -15,8 +15,6 @@
<properties>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.unpack.phase>prepare-package</gatk.unpack.phase>
<gatk.shade.phase>package</gatk.shade.phase>
<gatk.binary-dist.name>Queue</gatk.binary-dist.name>
<app.main.class>org.broadinstitute.gatk.queue.QCommandLine</app.main.class>
</properties>
@ -171,6 +169,25 @@
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<executions>
<execution>
<id>executable-jar</id>
<phase>${gatk.jar.phase}</phase>
</execution>
<execution>
<id>default-jar</id>
<phase>none</phase>
</execution>
<execution>
<id>unshaded-default-jar</id>
<phase>${gatk.jar.phase}</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
@ -179,6 +196,10 @@
<id>unpack-direct-dependencies</id>
<phase>${gatk.unpack.phase}</phase>
</execution>
<execution>
<id>executable-jar-lib</id>
<phase>${gatk.jar.phase}</phase>
</execution>
</executions>
</plugin>
@ -187,7 +208,7 @@
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>gatk-executable</id>
<id>package-jar</id>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
@ -209,7 +230,11 @@
<artifactId>maven-junction-plugin</artifactId>
<executions>
<execution>
<id>link-binary-jar</id>
<id>link-executable-jar</id>
<phase>${gatk.jar.phase}</phase>
</execution>
<execution>
<id>link-package-jar</id>
<phase>${gatk.shade.phase}</phase>
</execution>
<execution>
@ -238,20 +263,6 @@
</build>
<profiles>
<profile>
<id>packagetests-enabled</id>
<activation>
<property>
<name>gatk.packagetests.enabled</name>
<value>true</value>
</property>
</activation>
<properties>
<gatk.jar.phase>none</gatk.jar.phase>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
</properties>
</profile>
<profile>
<id>gsadev</id>
<activation>

23
protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml
View File

@ -1,23 +0,0 @@
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<id>binary-dist</id>
<formats>
<format>tar.bz2</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>
<dependencySet>
<includes>
<include>org.broadinstitute.gatk:gatk-queue-package-distribution</include>
</includes>
<outputFileNameMapping>${gatk.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
</dependencySet>
<dependencySet>
<outputDirectory>resources</outputDirectory>
<unpack>true</unpack>
<includes>
<include>org.broadinstitute.gatk:gatk-engine:tar.bz2:example-resources</include>
<include>org.broadinstitute.gatk:gatk-queue-extensions-public:tar.bz2:example-resources</include>
</includes>
</dependencySet>
</dependencySets>
</assembly>

10
protected/gatk-tools-protected/pom.xml
View File

@ -71,16 +71,6 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<executions>
<execution>
<id>copy-resource-bundle-log4j</id>
<phase>prepare-package</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>

5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java
View File

@ -81,7 +81,6 @@ import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.engine.io.NWaySAMFileWriter;
import org.broadinstitute.gatk.utils.sam.ReadUtils;
import org.broadinstitute.gatk.utils.text.TextFormattingUtils;
import org.broadinstitute.gatk.utils.text.XReadLines;
import htsjdk.variant.variantcontext.VariantContext;
@ -476,10 +475,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( NO_PG_TAG ) return null;
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
try {
final String version = headerInfo.getString("org.broadinstitute.sting.gatk.version");
programRecord.setProgramVersion(version);
programRecord.setProgramVersion(CommandLineProgram.getVersionNumber());
} catch (MissingResourceException e) {
// this is left empty on purpose (perhaps Andrey knows why?)
}

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java
View File

@ -72,7 +72,6 @@ import org.broadinstitute.gatk.utils.*;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import htsjdk.variant.variantcontext.*;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.text.TextFormattingUtils;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import htsjdk.variant.vcf.VCFConstants;
@ -222,8 +221,7 @@ public class SimulateReadsForVariants extends RodWalker<Integer, Integer> {
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
if ( !NO_PG_TAG ) {
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText");
programRecord.setProgramVersion(headerInfo.getString("org.broadinstitute.gatk.tools.version"));
programRecord.setProgramVersion(CommandLineProgram.getVersionNumber());
programRecord.setCommandLine(getToolkit().createApproximateCommandLineArgumentString(getToolkit(), this));
}
header.setProgramRecords(Arrays.asList(programRecord));

34
public/external-example/pom.xml
View File

@ -28,7 +28,7 @@
<gatk.integrationtests.skipped>${gatk.committests.skipped}</gatk.integrationtests.skipped>
<!-- This flag is used by the package tests to disable re-shading -->
<gatk.unpack.phase>process-resources</gatk.unpack.phase>
<gatk.unpack.phase>prepare-package</gatk.unpack.phase>
<gatk.shade.phase>package</gatk.shade.phase>
</properties>
@ -119,9 +119,9 @@
<!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
<docletPath>${project.build.outputDirectory}</docletPath>
<docletArtifact>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-utils</artifactId>
<version>${gatk.version}</version>
<groupId>${project.groupId}</groupId>
<artifactId>${project.artifactId}</artifactId>
<version>${project.version}</version>
</docletArtifact>
<maxmemory>2g</maxmemory>
<useStandardDocletOptions>false</useStandardDocletOptions>
@ -145,6 +145,7 @@
</goals>
<configuration>
<minimizeJar>true</minimizeJar>
<createDependencyReducedPom>false</createDependencyReducedPom>
<!-- Explicitly include classes loaded via reflection from artifacts below -->
<filters>
<filter>
@ -259,7 +260,32 @@
</plugins>
</build>
<reporting>
<excludeDefaults>true</excludeDefaults>
</reporting>
<!-- These profiles are used by the GATK build in a multi-module setting. You do NOT need these profiles. -->
<profiles>
<!-- Optionally do not shade/package jars -->
<!--
NOTE: Profile id "fast" comes from comments in PR #771.
The name is meant to be memorable, but is highly non-specific. Users are forewarned that
behavior of this profile, or the identifier itself, may be heavily modified in the future.
Hardcode usage in non-VCS controlled scripts at your own risk.
-->
<profile>
<id>fast</id>
<activation>
<property>
<name>disable.shadepackage</name>
</property>
</activation>
<properties>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
</properties>
</profile>
<!-- Collection of properties for use during package testing -->
<profile>
<id>packagetests-enabled</id>
<activation>

10
public/gatk-engine/pom.xml
View File

@ -50,16 +50,6 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<executions>
<execution>
<id>copy-resource-bundle-log4j</id>
<phase>prepare-package</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>

2
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java
View File

@ -54,7 +54,7 @@ public class WalkerManager extends PluginManager<Walker> {
public WalkerManager() {
super(Walker.class,"walker","");
helpText = TextFormattingUtils.loadResourceBundle("GATKText");
helpText = TextFormattingUtils.GATK_RESOURCE_BUNDLE;
}
/**

6
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java
View File

@ -28,11 +28,11 @@ package org.broadinstitute.gatk.engine.io;
import htsjdk.samtools.*;
import htsjdk.samtools.util.ProgressLoggerInterface;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
import org.broadinstitute.gatk.utils.sam.SAMReaderID;
import org.broadinstitute.gatk.utils.exceptions.GATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter;
import org.broadinstitute.gatk.utils.text.TextFormattingUtils;
import java.io.File;
import java.util.*;
@ -141,10 +141,8 @@ public class NWaySAMFileWriter implements SAMFileWriter {
*/
public static SAMProgramRecord createProgramRecord(GenomeAnalysisEngine toolkit, Object walker, String PROGRAM_RECORD_NAME) {
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText");
try {
final String version = headerInfo.getString("org.broadinstitute.gatk.engine.version");
programRecord.setProgramVersion(version);
programRecord.setProgramVersion(CommandLineProgram.getVersionNumber());
} catch (MissingResourceException e) {
// couldn't care less if the resource is missing...
}

27
public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala
View File

@ -34,8 +34,7 @@ import org.broadinstitute.gatk.utils.classloader.PluginManager
import org.broadinstitute.gatk.utils.exceptions.UserException
import org.broadinstitute.gatk.utils.io.IOUtils
import org.broadinstitute.gatk.utils.help.ApplicationDetails
import java.util.{ResourceBundle, Arrays}
import org.broadinstitute.gatk.utils.text.TextFormattingUtils
import java.util.Arrays
import org.apache.commons.io.FilenameUtils
/**
@ -260,33 +259,11 @@ class QCommandLine extends CommandLineProgram with Logging {
}
private def createQueueHeader() : Seq[String] = {
Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp),
Seq(String.format("Queue v%s, Compiled %s", CommandLineProgram.getVersionNumber, CommandLineProgram.getBuildTime),
"Copyright (c) 2012 The Broad Institute",
"For support and documentation go to http://www.broadinstitute.org/gatk")
}
private def getQueueVersion : String = {
val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("GATKText")
if ( stingResources.containsKey("org.broadinstitute.gatk.queue.QueueVersion.version") ) {
stingResources.getString("org.broadinstitute.gatk.queue.QueueVersion.version")
}
else {
"<unknown>"
}
}
private def getBuildTimestamp : String = {
val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("GATKText")
if ( stingResources.containsKey("build.timestamp") ) {
stingResources.getString("build.timestamp")
}
else {
"<unknown>"
}
}
def shutdown() = {
shuttingDown = true
qGraph.shutdown()

10
public/gatk-tools-public/pom.xml
View File

@ -54,16 +54,6 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<executions>
<execution>
<id>copy-resource-bundle-log4j</id>
<phase>prepare-package</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>

10
public/gatk-utils/pom.xml
View File

@ -137,16 +137,6 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<executions>
<execution>
<id>copy-resource-bundle-log4j</id>
<phase>prepare-package</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>

7
public/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help/log4j.properties
View File

@ -1,7 +0,0 @@
# Root logger option
log4j.rootLogger=INFO, stdout
# Direct log messages to stdout
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
log4j.appender.stdout.Target=System.out
log4j.appender.stdout.layout=org.apache.log4j.SimpleLayout

74
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java
View File

@ -53,6 +53,14 @@ public class Utils {
public static void resetRandomGenerator() { randomGenerator.setSeed(GATK_RANDOM_SEED); }
public static void resetRandomGenerator(long seed) { randomGenerator.setSeed(seed); }
private static final int TEXT_WARNING_WIDTH = 68;
private static final String TEXT_WARNING_PREFIX = "* ";
private static final String TEXT_WARNING_BORDER = dupString('*', TEXT_WARNING_PREFIX.length() + TEXT_WARNING_WIDTH);
private static final char ESCAPE_CHAR = '\u001B';
// ASCII codes for making text blink
public static final String TEXT_BLINK = ESCAPE_CHAR + "[5m";
public static final String TEXT_RESET = ESCAPE_CHAR + "[m";
/** our log, which we want to capture anything from this class */
private static Logger logger = Logger.getLogger(Utils.class);
@ -106,28 +114,66 @@ public class Utils {
}
public static void warnUser(final Logger logger, final String msg) {
logger.warn(String.format("********************************************************************************"));
logger.warn(String.format("* WARNING:"));
logger.warn(String.format("*"));
prettyPrintWarningMessage(logger, msg);
logger.warn(String.format("********************************************************************************"));
for (final String line: warnUserLines(msg))
logger.warn(line);
}
public static List<String> warnUserLines(final String msg) {
List<String> results = new ArrayList<>();
results.add(String.format(TEXT_WARNING_BORDER));
results.add(String.format(TEXT_WARNING_PREFIX + "WARNING:"));
results.add(String.format(TEXT_WARNING_PREFIX));
prettyPrintWarningMessage(results, msg);
results.add(String.format(TEXT_WARNING_BORDER));
return results;
}
/**
* pretty print the warning message supplied
*
* @param logger logger for the message
* @param results the pretty printed message
* @param message the message
*/
private static void prettyPrintWarningMessage(Logger logger, String message) {
StringBuilder builder = new StringBuilder(message);
while (builder.length() > 70) {
int space = builder.lastIndexOf(" ", 70);
if (space <= 0) space = 70;
logger.warn(String.format("* %s", builder.substring(0, space)));
builder.delete(0, space + 1);
private static void prettyPrintWarningMessage(final List<String> results, final String message) {
for (final String line: message.split("\\r?\\n")) {
final StringBuilder builder = new StringBuilder(line);
while (builder.length() > TEXT_WARNING_WIDTH) {
int space = getLastSpace(builder, TEXT_WARNING_WIDTH);
if (space <= 0) space = TEXT_WARNING_WIDTH;
results.add(String.format("%s%s", TEXT_WARNING_PREFIX, builder.substring(0, space)));
builder.delete(0, space + 1);
}
results.add(String.format("%s%s", TEXT_WARNING_PREFIX, builder));
}
logger.warn(String.format("* %s", builder));
}
/**
* Returns the last whitespace location in string, before width characters.
* @param message The message to break.
* @param width The width of the line.
* @return The last whitespace location.
*/
private static int getLastSpace(final CharSequence message, int width) {
final int length = message.length();
int stopPos = width;
int currPos = 0;
int lastSpace = -1;
boolean inEscape = false;
while (currPos < stopPos && currPos < length) {
final char c = message.charAt(currPos);
if (c == ESCAPE_CHAR) {
stopPos++;
inEscape = true;
} else if (inEscape) {
stopPos++;
if (Character.isLetter(c))
inEscape = false;
} else if (Character.isWhitespace(c)) {
lastSpace = currPos;
}
currPos++;
}
return lastSpace;
}
/**

5
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
View File

@ -296,13 +296,12 @@ public abstract class CommandLineProgram {
}
public static String getVersionNumber() {
// TODO: Confirm that version is available elsewhere not on tools.
ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText");
ResourceBundle headerInfo = TextFormattingUtils.GATK_RESOURCE_BUNDLE;
return headerInfo.containsKey("org.broadinstitute.gatk.utils.version") ? headerInfo.getString("org.broadinstitute.gatk.utils.version") : "<unknown>";
}
public static String getBuildTime() {
ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText");
ResourceBundle headerInfo = TextFormattingUtils.GATK_RESOURCE_BUNDLE;
return headerInfo.containsKey("build.timestamp") ? headerInfo.getString("build.timestamp") : "<unknown>";
}

12
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java
View File

@ -49,7 +49,7 @@ public class DocletUtils {
}
protected static Class getClassForDoc(ProgramElementDoc doc) throws ClassNotFoundException {
return Class.forName(getClassName(doc));
return Class.forName(getClassName(doc, true));
}
protected static Field getFieldForFieldDoc(FieldDoc fieldDoc) {
@ -67,10 +67,14 @@ public class DocletUtils {
* @param doc the Javadoc model for the given class.
* @return The (string) class name of the given class.
*/
protected static String getClassName(ProgramElementDoc doc) {
protected static String getClassName(ProgramElementDoc doc, boolean binaryName) {
PackageDoc containingPackage = doc.containingPackage();
String className = doc.name();
if (binaryName) {
className = className.replaceAll("\\.", "\\$");
}
return containingPackage.name().length() > 0 ?
String.format("%s.%s", containingPackage.name(), doc.name()) :
String.format("%s", doc.name());
String.format("%s.%s", containingPackage.name(), className) :
String.format("%s", className);
}
}

203
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java
View File

@ -39,6 +39,11 @@ import java.util.*;
* @version 0.1
*/
public class ResourceBundleExtractorDoclet {
// NOTE: Using log4j during javadoc generation requires
// a proper Log4J initialization (see CommandLineProgram),
// or a log4.properties file. This doclet has neither.
//private static Logger logger = Logger.getLogger(ResourceBundleExtractorDoclet.class);
/**
* Taglet for the particular version number.
*/
@ -46,16 +51,12 @@ public class ResourceBundleExtractorDoclet {
public static final String SUMMARY_TAGLET_NAME = "help.summary";
public static final String DESCRIPTION_TAGLET_NAME = "help.description";
/**
* Maintains a collection of resources in memory as they're accumulated.
*/
protected final Properties resourceText = new Properties();
/**
* Maintains a collection of classes that should really be documented.
*/
protected final Set<String> undocumentedClasses = new HashSet<String>();
private final RootDoc rootDoc;
private final Set<ClassDoc> classDocs;
private final Set<PackageDoc> packageDocs;
private final Set<Doc> allDocs;
protected File outFile = null;
protected String buildTimestamp = null, absoluteVersion = null;
/**
@ -65,75 +66,22 @@ public class ResourceBundleExtractorDoclet {
* @throws IOException if output can't be written.
*/
public static boolean start(RootDoc rootDoc) throws IOException {
ResourceBundleExtractorDoclet doclet = new ResourceBundleExtractorDoclet();
PrintStream out = doclet.loadData(rootDoc, true);
doclet.processDocs(rootDoc, out);
ResourceBundleExtractorDoclet doclet = new ResourceBundleExtractorDoclet(rootDoc);
doclet.checkUndocumentedClasses();
if (doclet.isUpToDate()) {
rootDoc.printNotice("Docs up to date. Not regenerating.");
return true;
}
doclet.processDocs();
return true;
}
protected PrintStream loadData(RootDoc rootDoc, boolean overwriteResourcesFile) {
PrintStream out = System.out;
for(String[] options: rootDoc.options()) {
if(options[0].equals("-out")) {
try {
loadExistingResourceFile(options[1], rootDoc);
if ( overwriteResourcesFile )
out = new PrintStream(options[1]);
} catch ( FileNotFoundException e ) {
throw new RuntimeException(e);
} catch ( IOException e ) {
throw new RuntimeException(e);
}
}
if(options[0].equals("-build-timestamp"))
buildTimestamp = options[1];
if (options[0].equals("-absolute-version"))
absoluteVersion = options[1];
}
resourceText.setProperty("build.timestamp",buildTimestamp);
return out;
}
protected void processDocs(RootDoc rootDoc, PrintStream out) {
// Cache packages as we see them, since there's no direct way to iterate over packages.
Set<PackageDoc> packages = new HashSet<PackageDoc>();
for(ClassDoc currentClass: rootDoc.classes()) {
PackageDoc containingPackage = currentClass.containingPackage();
packages.add(containingPackage);
if(isRequiredJavadocMissing(currentClass) && shouldDocument(currentClass))
undocumentedClasses.add(currentClass.name());
renderHelpText(DocletUtils.getClassName(currentClass),currentClass);
}
for(PackageDoc currentPackage: packages)
renderHelpText(currentPackage.name(),currentPackage);
try {
resourceText.store(out,"Strings displayed by the GATK help system");
} catch ( FileNotFoundException e ) {
throw new RuntimeException(e);
} catch ( IOException e ) {
throw new RuntimeException(e);
}
// ASCII codes for making text blink
final String blink = "\u001B\u005B\u0035\u006D";
final String reset = "\u001B\u005B\u006D";
if(undocumentedClasses.size() > 0)
Utils.warnUser(String.format("The following are currently undocumented: %s%s%s", blink, Utils.join(" ", undocumentedClasses), reset));
}
/**
* Validate the given options against options supported by this doclet.
* @param option Option to validate.
* @return Number of potential parameters; 0 if not supported.
*/
@SuppressWarnings("unused") // Used by javadoc system
public static int optionLength(String option) {
if(option.equals("-build-timestamp") || option.equals("-out") || option.equals("-absolute-version") ) {
return 2;
@ -141,25 +89,111 @@ public class ResourceBundleExtractorDoclet {
return 0;
}
/**
* Creates a new resource extractor doclet.
* @param rootDoc the documentation root.
*/
private ResourceBundleExtractorDoclet(RootDoc rootDoc) {
this.rootDoc = rootDoc;
this.classDocs = new TreeSet<>();
this.packageDocs = new TreeSet<>();
this.allDocs = new TreeSet<>();
for (final ClassDoc classDoc: rootDoc.classes()) {
this.classDocs.add(classDoc);
// Cache packages as we see them, since there's no direct way to iterate over packages.
this.packageDocs.add(classDoc.containingPackage());
}
this.allDocs.addAll(classDocs);
this.allDocs.addAll(packageDocs);
for(final String[] options: rootDoc.options()) {
if(options[0].equals("-out"))
this.outFile = new File(options[1]);
if(options[0].equals("-build-timestamp"))
this.buildTimestamp = options[1];
if (options[0].equals("-absolute-version"))
this.absoluteVersion = options[1];
}
}
private void checkUndocumentedClasses() {
final Set<String> undocumentedClasses = new TreeSet<>();
for (final ClassDoc classDoc: classDocs) {
if(isRequiredJavadocMissing(classDoc) && shouldDocument(classDoc))
undocumentedClasses.add(classDoc.name());
}
if(undocumentedClasses.size() > 0) {
final String message = String.format("The following are currently undocumented: %s%s%s",
Utils.TEXT_BLINK, Utils.join(" ", undocumentedClasses), Utils.TEXT_RESET);
for (final String line: Utils.warnUserLines(message)) {
rootDoc.printWarning(line);
}
}
}
private boolean isUpToDate() {
if (outFile == null)
return false;
final long outFileMillis = outFile.lastModified();
if (outFileMillis == 0L) {
return false;
}
for (final Doc doc: allDocs) {
final File docFile = doc.position() == null ? null : doc.position().file();
if (docFile != null && docFile.lastModified() > outFileMillis) {
rootDoc.printNotice("At least one item is out of date: " + docFile.getAbsolutePath());
return false;
}
}
return true;
}
protected void processDocs() throws IOException {
final PrintStream out;
if (outFile != null) {
out = new PrintStream(outFile);
} else {
out = System.out;
}
try {
// Maintains a collection of resources in memory as they're accumulated.
final Properties resourceText = new Properties();
loadExistingResourceFile(resourceText);
resourceText.setProperty("build.timestamp", buildTimestamp);
for (final ClassDoc currentClass : classDocs)
renderHelpText(resourceText, DocletUtils.getClassName(currentClass, false), currentClass);
for (final PackageDoc currentPackage : packageDocs)
renderHelpText(resourceText, currentPackage.name(), currentPackage);
resourceText.store(out, "Strings displayed by the GATK help system");
} finally {
if (outFile != null) {
out.close();
}
}
}
/**
* Attempts to load the contents of the resource file named by resourceFileName into
* our in-memory resource collection resourceText. If the resource file doesn't exist,
* prints a notice to the user but does not throw an exception back to the calling method,
* since we'll just create a new resource file from scratch in that case.
* @param resourceFileName name of the resource file to attempt to load.
* @param rootDoc the documentation root.
* @throws IOException if there is an I/O-related error other than FileNotFoundException
* while attempting to read the resource file.
*/
private void loadExistingResourceFile( String resourceFileName, RootDoc rootDoc ) throws IOException {
private void loadExistingResourceFile(final Properties resourceText) throws IOException {
try {
BufferedReader resourceFile = new BufferedReader(new FileReader(resourceFileName));
try {
try (final BufferedReader resourceFile = new BufferedReader(new FileReader(outFile))) {
resourceText.load(resourceFile);
}
finally {
resourceFile.close();
}
}
catch ( FileNotFoundException e ) {
rootDoc.printNotice("Resource file not found -- generating a new one from scratch.");
@ -172,11 +206,14 @@ public class ResourceBundleExtractorDoclet {
* @return True if the class should be documented. False otherwise.
*/
protected static boolean shouldDocument(ClassDoc classDoc) {
if (classDoc.isAbstract()) {
return false;
}
// TODO: Code duplication with GATKDoclet, including DocletUtils.getClassForDoc().
// TODO: Refactor common methods into DocletUtils, and possibly just use DocumentGATKFeatureObjects.
final Class<? extends Object> docClass;
final Class<?> docClass;
try {
docClass = (Class<? extends Object>) DocletUtils.getClassForDoc(classDoc);
docClass = (Class<?>) DocletUtils.getClassForDoc(classDoc);
} catch (ClassNotFoundException e) {
return false;
} catch (NoClassDefFoundError e) {
@ -184,6 +221,9 @@ public class ResourceBundleExtractorDoclet {
} catch (UnsatisfiedLinkError e) {
return false; // naughty BWA bindings
}
if (Throwable.class.isAssignableFrom(docClass)) {
return false; // UserExceptions
}
final DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class);
return f != null && f.enable();
}
@ -199,10 +239,11 @@ public class ResourceBundleExtractorDoclet {
/**
* Renders all the help text required for a given name.
* @param resourceText resource text properties
* @param elementName element name to use as the key
* @param element Doc element to process.
*/
private void renderHelpText(String elementName, Doc element) {
private void renderHelpText(final Properties resourceText, final String elementName, final Doc element) {
StringBuilder summaryBuilder = new StringBuilder();
for(Tag tag: element.firstSentenceTags())
summaryBuilder.append(tag.text());

51
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java
View File

@ -26,7 +26,14 @@
package org.broadinstitute.gatk.utils.io;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.SequenceInputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
/**
* Stores a resource by path and a relative class.
@ -34,6 +41,7 @@ import java.io.InputStream;
public class Resource {
private final String path;
private final Class<?> relativeClass;
private final ClassLoader relativeClassLoader;
/**
* Create a resource with a path and a relative class.
@ -45,12 +53,20 @@ public class Resource {
public Resource(String path, Class<?> relativeClass) {
this.path = path;
this.relativeClass = relativeClass;
ClassLoader classLoader = null;
if (relativeClass != null)
classLoader = relativeClass.getClassLoader();
this.relativeClassLoader = classLoader != null ? classLoader : ClassLoader.getSystemClassLoader();
}
public Class<?> getRelativeClass() {
return relativeClass;
}
public ClassLoader getRelativeClassLoader() {
return relativeClassLoader;
}
public String getPath() {
return path;
}
@ -88,4 +104,39 @@ public class Resource {
return inputStream;
}
/**
* Get the contents of this resource as an InputStream
* @throws IllegalArgumentException if resource cannot be read
* @return an input stream that will read the contents of these resources
*/
public List<InputStream> getAllResourcesContentsAsStreams() {
final List<InputStream> resourceStreams = new ArrayList<InputStream>();
try {
final Enumeration<URL> resources = getRelativeClassLoader().getResources(path);
while (resources.hasMoreElements()) {
try {
resourceStreams.add(resources.nextElement().openStream());
} catch (IOException ignored) {
/* skip exceptions, just like ClassLoader.getSystemResourceAsStream() */
}
}
} catch (IOException ignoredAlso) {
/* skip exceptions, just like ClassLoader.getSystemResourceAsStream() */
}
if (resourceStreams.isEmpty()) {
throw new IllegalArgumentException("Resource not found: " + path);
}
return resourceStreams;
}
/**
* Get the contents of this resource as an InputStream
* @throws IllegalArgumentException if resource cannot be read
* @return an input stream that will read the contents of these resources
*/
public InputStream getAllResourcesContentsAsStream() {
final List<InputStream> resourceStreams = getAllResourcesContentsAsStreams();
return new SequenceInputStream(Collections.enumeration(resourceStreams));
}
}

18
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.gatk.utils.text;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.io.Resource;
import java.io.IOException;
import java.io.StringReader;
@ -44,7 +45,12 @@ public class TextFormattingUtils {
/**
* our log, which we want to capture anything from this class
*/
private static Logger logger = Logger.getLogger(TextFormattingUtils.class);
private static Logger logger = Logger.getLogger(TextFormattingUtils.class);
/**
* The contents of the GATK bundle. If no such resource exists, warn the user and create an empty bundle.
*/
public static final ResourceBundle GATK_RESOURCE_BUNDLE = loadResourceBundle("GATKText", null);
/**
* The default line width, for GATK output written to the screen.
@ -96,14 +102,18 @@ public class TextFormattingUtils {
* Load the contents of a resource bundle with the given name. If no such resource exists, warn the user
* and create an empty bundle.
* @param bundleName The name of the bundle to load.
* @param relativeClass The relative class or null to load a bundle from the root.
* @return The best resource bundle that can be found matching the given name.
*/
public static ResourceBundle loadResourceBundle(String bundleName) {
public static ResourceBundle loadResourceBundle(String bundleName, Class<?> relativeClass) {
final ResourceBundle.Control c = ResourceBundle.Control.getControl(ResourceBundle.Control.FORMAT_DEFAULT);
final String resourceName = c.toResourceName(c.toBundleName(bundleName, Locale.ROOT), "properties");
final Resource resource = new Resource(resourceName, relativeClass);
ResourceBundle bundle;
try {
bundle = ResourceBundle.getBundle(bundleName);
bundle = new PropertyResourceBundle(resource.getAllResourcesContentsAsStream());
}
catch(MissingResourceException ex) {
catch(Exception ex) {
//logger.warn("Unable to load help text. Help output will be sparse.");
// Generate an empty resource bundle.
try {

8
public/gsalib/pom.xml
View File

@ -32,6 +32,14 @@
</goals>
<phase>${gatk.generate-resources.phase}</phase>
<configuration>
<!--
Looking at the assembly plugin 2.4(.1) source code, <updateOnly>true</updateOnly>
is equivalent to plexus_archiver.setForced(false). Unlike the docs say, this
does work even if the file does not exist.
Also, why..? "archiver.setUseJvmChmod( configSource.isUpdateOnly() );"
Appears to only affect the plexus dir/DirectoryArchiver.
-->
<updateOnly>true</updateOnly>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>src/assembly/gsalib.xml</descriptor>

4
protected/gatk-package-distribution/src/main/assembly/binary-dist.xml → public/src/main/assembly/binary-dist.xml
View File

@ -7,7 +7,7 @@
<dependencySets>
<dependencySet>
<includes>
<include>org.broadinstitute.gatk:gatk-package-distribution</include>
<include>${groupId}:${artifactId}</include>
</includes>
<outputFileNameMapping>${gatk.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
</dependencySet>
@ -15,7 +15,7 @@
<outputDirectory>resources</outputDirectory>
<unpack>true</unpack>
<includes>
<include>org.broadinstitute.gatk:gatk-engine:tar.bz2:example-resources</include>
<include>org.broadinstitute.gatk:*:tar.bz2:example-resources</include>
</includes>
</dependencySet>
</dependencySets>