New upstream version 2.4.14+dfsg (e78c2fae) · Commits · Debian Med / igv

.gitignore

+2 −1

Original line number	Diff line number	Diff line
		@@ -10,3 +10,4 @@ igv.log
		.classpath
		/.idea/
		/.settings
		/proguard_log
		No newline at end of file

ant/bcel-6.0.jar

deleted100644 → 0

−655 KiB

File deleted.

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build-shrink.xml

deleted100644 → 0

+0 −165

Original line number	Diff line number	Diff line
		<?xml version="1.0" encoding="UTF-8"?>
		<!--
		~ The MIT License (MIT)
		~
		~ Copyright (c) 2007-2018 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.
		-->

		<!-- Ant build script to create a unified IGV JAR, shrunk with BCEL.
		This is difficult to do in Gradle so it's handled here.

		We may eventually switch to a different method (e.g. ProGuard) that makes
		this unnecessary.
		-->
		<project name="igv-release" default="allBuild" basedir=".">
		<!-- build specific properties. Generally set through Jenkins, command line, or properties file-->
		<property name="build-number" value="0"/>
		<property name="version" value="user"/>
		<property name="vendor" value="user"/>

		<property name="include.libs" value="true" />
		<property name="main-class" value="org.broad.igv.ui.Main"/>

		<property name="lib.dir" value="${basedir}/lib/"/>
		<property name="tmp.dir" value="${basedir}/build/tmp/IGV-dist"/>
		<property name="jar.name" value="igv.jar"/>
		<property name="dist.dir" value="build/IGV-dist/"/>
		<property name="jar.path" value="${dist.dir}${jar.name}"/>

		<property name="batik-codec-finame" value="batik-codec-1.10.jar" />
		<property name="goby-io-finame" value="goby-io-igv-1.1.jar" />
		<property name="log4j-core-finame" value="log4j-core-2.11.0.jar" />

		<!-- These paths are dictated by Gradle. -->
		<property name="class.dir" value="build/classes/java/main" />
		<property name="resource.dir" value="build/resources/main" />

		<condition property="act.include.libs">
		<and>
		<available classname="org.apache.tools.ant.util.depend.bcel.FullAnalyzer" />
		<istrue value="${include.libs}" />
		</and>
		</condition>

		<!-- Unzip jars to the tmp directory and copy IGV classes & resources. Could do
		this step in Gradle, but may not be required in the future (ProGuard can work
		on jars directly, for example).
		-->
		<target name="prepare" if="act.include.libs">
		<mkdir dir="${dist.dir}" />
		<unzip dest="${tmp.dir}">
		<!-- Copy almost everything to tmp directory
		Certain jars we include whole, because we need their manifests
		Goby get copied later.
		Certain jars we just want to ignore (junit, appbundler).
		-->
		<patternset>
		<include name="*/"/>
		<exclude name="META-INF/**"/>
		<exclude name="${lib.dir}/*"/>
		</patternset>
		<fileset dir="${lib.dir}">
		<include name="*/.jar"/>
		<exclude name="appbundler*.jar"/>
		<exclude name="*/junit*.jar"/>
		<exclude name="**/${batik-codec-finame}"/>
		<exclude name="**/${goby-io-finame}"/>
		<exclude name="**/${log4j-core-finame}"/>
		<exclude name="*/AppleJavaExtensions.jar"/>
		</fileset>
		</unzip>

		<copy todir="${tmp.dir}">
		<fileset dir="${class.dir}" includes="*/" />
		</copy>
		<copy todir="${tmp.dir}">
		<fileset dir="${resource.dir}" includes="*/" />
		</copy>
		</target>

		<target name="shrinkJar" depends="prepare" if="act.include.libs"
		description="Build the unified IGV JAR, including libraries, using BCEL to take only required classes">

		<classfileset dir="${tmp.dir}" id="rootFiles">
		<rootfileset dir="${tmp.dir}" includes="org/broad/*/.class" />
		</classfileset>

		<property name="class-path" value="${batik-codec-finame} ${goby-io-finame} ${log4j-core-finame}" />

		<jar destfile="${jar.path}" basedir="${tmp.dir}" compress="true" duplicate="preserve">
		<fileset refid="rootFiles"/>
		<manifest>

		<attribute name="Permissions" value="all-permissions"/>
		<attribute name="Application-Name" value="IGV"/>
		<!-- Here just to be a good citizen. Apparently reading from the correct manifest
		is tricky. We rely on a separate properties file-->
		<attribute name="Class-Path" value="${class-path}"/>
		<attribute name="Built-By" value="${user.name}"/>
		<attribute name="Main-Class" value="${main-class}"/>

		<section name="org/broad/igv/">
		<attribute name="Specification-Title" value="IGV"/>
		<attribute name="Specification-Version" value="${version}"/>
		<attribute name="Specification-Vendor" value="${vendor}"/>
		<attribute name="Implementation-Version" value="${version} ${build-number}"/>
		<attribute name="Implementation-Vendor" value="${vendor}"/>
		</section>

		</manifest>
		</jar>
		<delete dir="${tmp.dir}" />
		<copy file="${lib.dir}${batik-codec-finame}" tofile="${dist.dir}${batik-codec-finame}" overwrite="true"/>
		<copy file="${lib.dir}${goby-io-finame}" tofile="${dist.dir}${goby-io-finame}" overwrite="true"/>
		<copy file="${lib.dir}${log4j-core-finame}" tofile="${dist.dir}${log4j-core-finame}" overwrite="true"/>
		</target>

		<!--Add permissions attribute to manifest of jars -->
		<!-- We use exec because it's easier, this will only run on *nix-->
		<macrodef name="addPermsMacro">
		<attribute name="jarfile"/>
		<sequential>
		<!--Newline is important!-->
		<echo file="tmp.txt">Permissions: all-permissions${line.separator}</echo>
		<exec executable="jar">
		<arg value="ufm"/>
		<arg value="@{jarfile}"/>
		<arg value="tmp.txt"/>
		</exec>
		<delete file="tmp.txt"/>
		</sequential>
		</macrodef>

		<target name="addPerms">
		<addPermsMacro jarfile="${dist.dir}${batik-codec-finame}"/>
		<addPermsMacro jarfile="${dist.dir}${goby-io-finame}"/>
		<addPermsMacro jarfile="${dist.dir}${log4j-core-finame}"/>
		</target>

		<target name="allBuild" depends="shrinkJar,addPerms">
		<copy file="scripts/igv.sh" todir="${dist.dir}" />
		<copy file="scripts/igv.bat" todir="${dist.dir}" />
		<copy file="scripts/igv.command" todir="${dist.dir}" />
		<chmod perm="775" file="${dist.dir}igv.sh" />
		<chmod perm="775" file="${dist.dir}igv.command" />
		</target>
		</project>
		No newline at end of file

build.gradle

+214 −12

Original line number	Diff line number	Diff line
		@@ -26,6 +26,16 @@ import org.apache.tools.ant.filters.ReplaceTokens
		// Define the main class for the application
		ext.mainClassName = 'org.broad.igv.ui.Main'

		// Set up the ProGuard optimizing task
		buildscript {
		repositories {
		flatDir dirs: 'lib_build'
		}
		dependencies {
		classpath ':proguard:'
		}
		}

		sourceSets {
		main {
		java {
		@@ -38,7 +48,14 @@ sourceSets {
		}
		}

		configurations {
		jarsToShipUntouched
		compile.extendsFrom jarsToShipUntouched
		}

		dependencies {
		jarsToShipUntouched fileTree(dir: 'lib',
		include: ['batik-codec-1.10.jar', 'goby-io-igv-1.1.jar', 'log4j-core-2.11.0.jar'])
		compile fileTree(dir: 'lib', include: '*.jar')
		testCompile fileTree(dir: 'test/lib', include: '*.jar')
		}
		@@ -52,7 +69,12 @@ targetCompatibility = 1.8

		processResources {
		// Set the current timestamp for release builds; pass in a blank property to enable (i.e. -Ptimestamp="" at CLI)
		if (timestamp.equals("")) { timestamp = new Date().format("MM/dd/yyyy hh:mm aa") }
		if (timestamp.equals("")) {
		ext.date = new Date()
		timestamp = date.format("MM/dd/yyyy hh:mm aa")
		// This is a more filesystem-friendly date format.
		timestamp_fs = date.format("yyyy-MM-dd_HHmmss")
		}

		filesMatching('resources/about.properties') {
		filter (ReplaceTokens,
		@@ -62,7 +84,7 @@ processResources {
		}

		jar {
		archiveName = 'igv.jar'
		archiveName = 'igv-minimal.jar'
		manifest {
		attributes(
		"Permissions": "all-permissions",
		@@ -74,6 +96,82 @@ jar {
		}
		}

		task fullJar(type: Jar, dependsOn: jar) {
		// Based on https://discuss.gradle.org/t/removing-dependencies-from-a-jar-file-during-jar-task/5521/3
		archiveName = 'igv.jar'
		from {
		((configurations.compile - configurations.jarsToShipUntouched) + "${buildDir}/libs/igv-minimal.jar").collect {
		zipTree(it)
		}
		} {
		exclude "META-INF/**"
		}

		manifest {
		attributes(
		"Permissions": "all-permissions",
		"Application-Name": "IGV",
		"Built-By": System.getProperty('user.name'),
		"Main-Class": mainClassName,
		"Class-Path": configurations.jarsToShipUntouched.collect { it.getName() }.join(' ')
		)
		}
		}

		task toolJar(type: Jar, dependsOn: jar) {
		from {
		((configurations.compile - configurations.jarsToShipUntouched) + "${buildDir}/libs/igv-minimal.jar").collect {
		zipTree(it)
		}
		} {
		exclude "META-INF/**"
		}
		archiveName = 'igvtools.jar'
		manifest {
		attributes(
		"Implementation-Title": "IGVTools",
		"Built-By": System.getProperty('user.name'),
		"Main-Class": "org.broad.igv.tools.IgvTools",
		"Class-Path": configurations.jarsToShipUntouched.collect { it.getName() }.join(' ')
		)
		}
		}

		task optimizeFullJar(type: proguard.gradle.ProGuardTask, dependsOn: fullJar) {
		// EXPERIMENTAL: Optimize the fullJar to remove unused classes.
		// This still needs tuning for correctness, and as a result we are not distributing the
		// jar it creates. It is still useful because of the reports it generates, however.
		doFirst { mkdir "proguard_log" }

		verbose
		injars "${buildDir}/libs/igv.jar"
		outjars "${buildDir}/libs/igv-OPT.jar"
		// Note that this points to the JRE jars.
		libraryjars "${System.getProperty('java.home')}/lib",
		jarfilter: 'rt.jar,charsets.jar,jce.jar,jfr.jar,jsse.jar,resources.jar,ext/jfxrt.jar'
		libraryjars "lib", jarfilter: 'batik-codec-1.10.jar,goby-io-igv-1.1.jar,log4j-core-2.11.0.jar'
		configuration "lib_build/proguard_full_client.cfg"
		printusage "proguard_log/proguard_full_client_log_${timestamp_fs}.txt"
		printseeds "proguard_log/proguard_full_client_seeds_${timestamp_fs}.txt"
		}

		task optimizeMinJar(type: proguard.gradle.ProGuardTask, dependsOn: jar) {
		// EXPERIMENTAL: Optimize the minimal jar to remove unused classes (that is, our code base only).
		// As above, needs tuning for correctness. The IGV-focused report it produces is more useful.
		doFirst { mkdir "proguard_log" }

		verbose
		injars "${buildDir}/libs/igv-minimal.jar"
		outjars "${buildDir}/libs/igv-minimal-OPT.jar"
		libraryjars "${System.getProperty('java.home')}/lib",
		jarfilter: 'rt.jar,charsets.jar,jce.jar,jfr.jar,jsse.jar,resources.jar,ext/jfxrt.jar'
		// This is the difference from the above: consider all dependencies as libraryjars
		libraryjars "lib", filter: '!META-INF/**/module-info.class'
		configuration "lib_build/proguard_min_client.cfg"
		printusage "proguard_log/proguard_min_client_log_${timestamp_fs}.txt"
		printseeds "proguard_log/proguard_min_client_seeds_${timestamp_fs}.txt"
		}

		tasks.withType(Test) {
		systemProperties = System.getProperties()
		systemProperties['java.awt.headless'] = 'true'
		@@ -84,26 +182,50 @@ tasks.withType(Test) {
		forkEvery = 1
		}

		task createDist(type: Copy, dependsOn: jar) {
		task createDist(type: Copy, dependsOn: fullJar) {
		from ("scripts") {
		include 'igv.bat'
		include 'igv.command'
		include 'igv.sh'
		include 'readme.txt'
		}
		with copySpec {
		from ("${buildDir}/libs") {
		include 'igv*.jar'
		include 'igv.jar'
		}
		from ("lib") {
		include '*.jar'
		from (configurations.jarsToShipUntouched) { }
		into "lib"
		}

		into "${buildDir}/dist"
		into "${buildDir}/IGV-dist"
		}

		task createDistZip(type: Zip, dependsOn: createDist) {
		task signJars(dependsOn: createDist) {
		doLast {
		// Only sign if the keystoreFile exists
		ext.keystoreFile = file("${keystore}")
		if (keystoreFile.exists()) {
		ant.jar( update: true, file: "build/IGV-dist/lib/batik-codec-1.10.jar") {
		delegate.manifest { attribute(name: 'Permissions', value: 'all-permissions') }
		}
		ant.jar( update: true, file: "build/IGV-dist/lib/goby-io-igv-1.1.jar") {
		delegate.manifest { attribute(name: 'Permissions', value: 'all-permissions') }
		}
		ant.jar( update: true, file: "build/IGV-dist/lib/log4j-core-2.11.0.jar") {
		delegate.manifest { attribute(name: 'Permissions', value: 'all-permissions') }
		}
		ant.signjar( jar: 'build/IGV-dist/lib/*.jar', keystore:"${keystoreFile.absolutePath}",
		alias: "${alias}", keypass: "${keyPassword}", storepass: "${storePassword}", tsaurl: "${tsaurl}"
		)
		}
		}
		}

		task createDistZip(type: Zip, dependsOn: [createDist, signJars]) {
		archiveName = "IGV_${version}.zip"
		destinationDir = file("${buildDir}/distZip")
		baseName = "IGV"
		from "${buildDir}/dist"
		from "${buildDir}/IGV-dist" exclude "igv.bat"
		into createDistZip.baseName + "_${version}"

		doLast {
		@@ -111,4 +233,84 @@ task createDistZip(type: Zip, dependsOn: createDist) {
		}
		}

		build.dependsOn createDistZip
		task createMacDist(type: Copy, dependsOn: [createDist, signJars]) {
		with copySpec {
		from ("scripts/mac.app") exclude "Contents/Info.plist.template"
		into "IGV_${version}.app"
		}
		with copySpec {
		from ("scripts/mac.app/Contents/Info.plist.template")
		filter (ReplaceTokens, tokens: [ VERSION: version ])
		rename "Info.plist.template", "Info.plist"
		into "IGV_${version}.app/Contents"
		}
		with copySpec {
		from ("${buildDir}/IGV-dist/lib") include '*.jar'
		into "IGV_${version}.app/Contents/Java"
		}

		into "${buildDir}/IGV-Mac-dist"

		doLast {
		project.exec { commandLine('chmod', '775', "${buildDir}/IGV-Mac-dist/IGV_${version}.app" ) }
		}
		}

		task createMacDistZip(type: Zip, dependsOn: createMacDist) {
		archiveName = "IGV_${version}.app.zip"
		destinationDir = file("${buildDir}/distZip")
		from "${buildDir}/IGV-Mac-dist"

		doLast {
		project.exec { commandLine('chmod', '775', createMacDistZip.archivePath ) }
		}
		}

		task createWinDistZip(type: Zip, dependsOn: [createDist, signJars]) {
		archiveName = "IGV_Win_${version}.zip"
		destinationDir = file("${buildDir}/distZip")
		baseName = "IGV_Win"
		from("${buildDir}/IGV-dist") {
		exclude "igv.sh"
		exclude "igv.command"
		}
		into createWinDistZip.baseName + "_${version}"

		doLast {
		project.exec { commandLine('chmod', '775', createWinDistZip.archivePath ) }
		}
		}

		task createToolsDist(type: Copy, dependsOn: toolJar) {
		from ("scripts") {
		include 'igvtools*'
		include 'igvtools*.bat'
		include 'igvtools*.command'
		}
		with copySpec {
		from ("${buildDir}/libs") {
		include 'igvtools.jar'
		}
		from (configurations.jarsToShipUntouched) { }
		into "lib"
		}

		with copySpec { from ("genomes") { } into "genomes" }

		into "${buildDir}/IGVTools-dist"
		}

		task createToolsDistZip(type: Zip, dependsOn: createToolsDist) {
		destinationDir = file("${buildDir}/distZip")
		archiveName = "igvtools_${version}.zip"
		baseName = "IGVTools"

		from "${buildDir}/IGVTools-dist"
		into createToolsDistZip.baseName

		doLast {
		project.exec { commandLine('chmod', '775', createToolsDistZip.archivePath ) }
		}
		}

		build.dependsOn createDistZip,createMacDistZip,createWinDistZip,createToolsDistZip

build_java9.gradle

+121 −18

Original line number	Diff line number	Diff line
		@@ -78,6 +78,20 @@ jar {
		}
		}

		task tooljar(type: Jar, dependsOn: jar) {
		// This jar is the same as the client jar above, just a different jar name and manifest
		archiveName = 'igvtools.jar'
		from(sourceSets.main.output) { }

		manifest {
		attributes(
		"Implementation-Title": "IGVTools",
		"Built-By": System.getProperty('user.name'),
		"Main-Class": "org.broad.igv.tools.IgvTools",
		)
		}
		}

		compileJava {
		inputs.property("moduleName", moduleName)
		doFirst {
		@@ -131,7 +145,17 @@ test {
		}
		}

		def modulepathContent = copySpec {
		task createDist(type: Copy, dependsOn: jar) {
		from ('scripts/java9') {
		include 'igv.bat'
		include 'igv.command'
		include 'igv.sh'
		include 'igv_hidpi.*'
		include 'igv.args'
		include 'readme.txt'
		}

		with copySpec {
		from ("lib") {
		include '*.jar'
		exclude 'jide-oss-3.5.5.jar'
		@@ -140,28 +164,19 @@ def modulepathContent = copySpec {
		include '*.jar'
		}
		from ("${buildDir}/libs") {
		include 'igv*.jar'
		include 'igv.jar'
		}
		into "lib"
		}

		task createDist(type: Copy, dependsOn: jar) {
		from ('scripts/java9') {
		include 'igv.bat'
		include 'igv.command'
		include 'igv.sh'
		include 'igv.args'
		}

		with modulepathContent

		into "${buildDir}/dist"
		into "${buildDir}/IGV-dist"
		}

		task createDistZip(type: Zip, dependsOn: createDist) {
		archiveName = "IGV_${version}.zip"
		destinationDir = file("${buildDir}/distZip")
		baseName = "IGV"
		from "${buildDir}/dist"
		from "${buildDir}/IGV-dist" exclude "*.bat"
		into createDistZip.baseName + "_${version}"

		doLast {
		@@ -169,4 +184,92 @@ task createDistZip(type: Zip, dependsOn: createDist) {
		}
		}

		build.dependsOn createDistZip
		task createMacDist(type: Copy, dependsOn: createDist) {
		with copySpec {
		from ("scripts/mac.app") exclude "Contents/Info.plist.template"
		into "IGV_${version}.app"
		}
		with copySpec {
		from ("scripts/java9/Info.plist.template")
		filter (ReplaceTokens, tokens: [ VERSION: version ])
		rename "Info.plist.template", "Info.plist"
		into "IGV_${version}.app/Contents"
		}
		with copySpec {
		from ("${buildDir}/IGV-dist/lib") include '*.jar'
		into "IGV_${version}.app/Contents/Java"
		}

		into "${buildDir}/IGV-Mac-dist"

		doLast {
		project.exec { commandLine('chmod', '775', "${buildDir}/IGV-Mac-dist/IGV_${version}.app" ) }
		}
		}

		task createMacDistZip(type: Zip, dependsOn: createMacDist) {
		archiveName = "IGV_${version}.app.zip"
		destinationDir = file("${buildDir}/distZip")
		from "${buildDir}/IGV-Mac-dist"

		doLast {
		project.exec { commandLine('chmod', '775', createMacDistZip.archivePath ) }
		}
		}

		task createWinDistZip(type: Zip, dependsOn: createDist) {
		archiveName = "IGV_Win_${version}.zip"
		destinationDir = file("${buildDir}/distZip")
		baseName = "IGV_Win"
		from("${buildDir}/IGV-dist") {
		exclude "*.sh"
		exclude "igv.command"
		}
		into createWinDistZip.baseName + "_${version}"

		doLast {
		project.exec { commandLine('chmod', '775', createWinDistZip.archivePath ) }
		}
		}

		task createToolsDist(type: Copy, dependsOn: tooljar) {
		from ("scripts/java9") {
		include 'igvtools*'
		include 'igvtools*.bat'
		include 'igvtools*.command'
		include 'igv.args'
		}

		with copySpec {
		from ("${buildDir}/libs") {
		include 'igvtools.jar'
		}
		from ("lib") {
		include '*.jar'
		exclude 'jide-oss-3.5.5.jar'
		}
		from ("lib_java9") {
		include '*.jar'
		}
		into "lib"
		}

		with copySpec { from ("genomes") { } into "genomes" }

		into "${buildDir}/IGVTools-dist"
		}

		task createToolsDistZip(type: Zip, dependsOn: createToolsDist) {
		archiveName = "igvtools_${version}.zip"
		destinationDir = file("${buildDir}/distZip")
		baseName = "IGVTools"

		from "${buildDir}/IGVTools-dist"
		into createToolsDistZip.baseName

		doLast {
		project.exec { commandLine('chmod', '775', createToolsDistZip.archivePath ) }
		}
		}

		build.dependsOn createDistZip,createMacDistZip,createWinDistZip,createToolsDistZip