X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=2c7f1389e00baacb75cdba452b755d11a4854c82;hb=db9f5c50215282a01e60cc37e4010f2a0276d5fb;hp=9059447070edb531a7ca94ff17ebe11d12579e4d;hpb=47cf12a87f6e308b65236516faaa41d24662cfe9;p=jalview.git diff --git a/build.gradle b/build.gradle index 9059447..2c7f138 100644 --- a/build.gradle +++ b/build.gradle @@ -3,41 +3,41 @@ import org.gradle.internal.os.OperatingSystem import org.gradle.plugins.ide.eclipse.model.Output import org.gradle.plugins.ide.eclipse.model.Library import java.security.MessageDigest - import groovy.transform.ExternalizeMethods +import groovy.util.XmlParser +import groovy.xml.XmlUtil + buildscript { + repositories { + mavenCentral() + mavenLocal() + } dependencies { - classpath 'org.openclover:clover:4.3.1' + classpath 'org.openclover:clover:4.4.1' } } + plugins { id 'java' id 'application' id 'eclipse' id 'com.github.johnrengelman.shadow' version '4.0.3' - id 'com.install4j.gradle' version '7.0.9' - id 'com.dorongold.task-tree' version '1.4' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree + id 'com.install4j.gradle' version '8.0.4' + id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree } repositories { jcenter() mavenCentral() mavenLocal() - flatDir { - dirs gradlePluginsDir - } -} - -dependencies { - compile 'org.apache.commons:commons-compress:1.18' } // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use def string(Object o) { - return o.toString() + return o == null ? "" : o.toString() } @@ -46,19 +46,31 @@ ext { jalviewDirRelativePath = jalviewDir // local build environment properties - def localProps = "${jalviewDirAbsolutePath}/local.properties" + // can be "projectDir/local.properties" + def localProps = "${projectDir}/local.properties" + def propsFile = null; if (file(localProps).exists()) { + propsFile = localProps + } + // or "../projectDir_local.properties" + def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties" + if (file(dirLocalProps).exists()) { + propsFile = dirLocalProps + } + if (propsFile != null) { try { def p = new Properties() - def localPropsFIS = new FileInputStream(localProps) + def localPropsFIS = new FileInputStream(propsFile) p.load(localPropsFIS) localPropsFIS.close() p.each { key, val -> - def over = getProperty(key) != null + def oldval = findProperty(key) setProperty(key, val) - if (over) { - println("Overriding property '${key}' with local.properties value '${val}'") + if (oldval != null) { + println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") + } else { + println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'") } } } catch (Exception e) { @@ -66,6 +78,26 @@ ext { } } + //// + // Import releaseProps from the RELEASE file + // or a file specified via JALVIEW_RELEASE_FILE if defined + // Expect jalview.version and target release branch in jalview.release + def releaseProps = new Properties(); + def releasePropFile = findProperty("JALVIEW_RELEASE_FILE"); + def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE"; + try { + (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { + releaseProps.load(it) + } + } catch (Exception fileLoadError) { + throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError); + } + //// + // Set JALVIEW_VERSION if it is not already set + if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) { + JALVIEW_VERSION = releaseProps.get("jalview.version") + } + // this property set when running Eclipse headlessly j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild") // this property set by Eclipse @@ -102,6 +134,7 @@ ext { // clover cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") + cloverDb = string("${buildDir}/clover/clover.db") classesDir = string("${jalviewDir}/${classes_dir}") if (clover.equals("true")) { use_clover = true @@ -114,55 +147,68 @@ ext { classes = classesDir getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") - getdownDir = string("") - reportRsyncCmd = false buildDist = true - buildProperties = build_properties_file + + // the following values might be overridden by the CHANNEL switch + getdownChannelName = CHANNEL.toLowerCase() + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}") + getdownAppDistDir = getdown_app_dir_alt + buildProperties = string("${classesDir}/${build_properties_file}") + reportRsyncCommand = false + jvlChannelName = CHANNEL.toLowerCase() + install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build + install4jDSStore = "DS_Store-NON-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png" + install4jInstallerName = "${jalview_name} Non-Release Installer" + install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase() + install4jExtraScheme = "jalviewx" switch (CHANNEL) { case "BUILD": // TODO: get bamboo build artifact URL for getdown artifacts getdown_channel_base = bamboo_channelbase - getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}") - getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${classesDir}/${build_properties_file}") + getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}") + getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") + jvlChannelName += "_${getdownChannelName}" + // automatically add the test group Not-bamboo for exclusion + if ("".equals(testngExcludedGroups)) { + testngExcludedGroups = "Not-bamboo" + } + install4jExtraScheme = "jalviewb" break case "RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_release - buildProperties = string("${classesDir}/${build_properties_file}") + getdownAppDistDir = getdown_app_dir_release reportRsyncCommand = true + install4jSuffix = "" + install4jDSStore = "DS_Store" + install4jDMGBackgroundImage = "jalview_dmg_background.png" + install4jInstallerName = "${jalview_name} Installer" break case "ARCHIVE": - getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt + getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { - print "Must provide an ARCHIVEDIR value to produce an archive distribution" - exit + throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { packageDir = string("${ARCHIVEDIR}/${packageDir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true + install4jExtraScheme = "jalviewa" break case "ARCHIVELOCAL": - getdown_channel_name = string("archive/${JALVIEW_VERSION}") - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt + getdownChannelName = string("archive/${JALVIEW_VERSION}") + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = file(getdownWebsiteDir).toURI().toString() if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { - print "Must provide an ARCHIVEDIR value to produce an archive distribution" - exit + throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { packageDir = string("${ARCHIVEDIR}/${packageDir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") @@ -170,50 +216,109 @@ ext { } reportRsyncCommand = true getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jSuffix = "Archive" + install4jExtraScheme = "jalviewa" break case "DEVELOP": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${classesDir}/${build_properties_file}") reportRsyncCommand = true + + // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version + JALVIEW_VERSION=JALVIEW_VERSION+"-develop" + + install4jSuffix = "Develop" + install4jDSStore = "DS_Store-DEVELOP" + install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png" + install4jExtraScheme = "jalviewd" + install4jInstallerName = "${jalview_name} Develop Installer" break case "TEST-RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${classesDir}/${build_properties_file}") reportRsyncCommand = true + + // TEST-RELEASE is usually associated with a Jalview release series so set the version + JALVIEW_VERSION=JALVIEW_VERSION+"-test" + + install4jSuffix = "Test" + install4jDSStore = "DS_Store-TEST-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" break case ~/^SCRATCH(|-[-\w]*)$/: - getdown_channel_name = CHANNEL - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${classesDir}/${build_properties_file}") + getdownChannelName = CHANNEL + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") reportRsyncCommand = true + install4jSuffix = "Scratch" + break + + case "TEST-LOCAL": + if (!file("${LOCALDIR}").exists()) { + throw new GradleException("Must provide a LOCALDIR value to produce a local distribution") + } else { + getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString() + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + } + JALVIEW_VERSION = "TEST" + install4jSuffix = "Test-Local" + install4jDSStore = "DS_Store-TEST-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" break case "LOCAL": - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${classesDir}/${build_properties_file}") + getdownAppBase = file(getdownWebsiteDir).toURI().toString() getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jExtraScheme = "jalviewl" break default: // something wrong specified - print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") - exit + throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") break } - - getdownAppDir = string("${getdownWebsiteDir}/${getdown_app_dir}") + // override getdownAppBase if requested + if (findProperty("getdown_appbase_override") != null) { + getdownAppBase = string(getProperty("getdown_appbase_override")) + println("Overriding getdown appbase with '${getdownAppBase}'") + } + // sanitise file name for jalview launcher file for this channel + jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_") + // install4j application and folder names + if (install4jSuffix == "") { + install4jApplicationName = "${jalview_name}" + install4jBundleId = "${install4j_bundle_id}" + install4jWinApplicationId = install4j_release_win_application_id + } else { + install4jApplicationName = "${jalview_name} ${install4jSuffix}" + install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase() + // add int hash of install4jSuffix to the last part of the application_id + def id = install4j_release_win_application_id + def idsplitreverse = id.split("-").reverse() + idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode() + install4jWinApplicationId = idsplitreverse.reverse().join("-") + } + // sanitise folder and id names + // install4jApplicationFolder = e.g. "Jalview Build" + install4jApplicationFolder = install4jApplicationName + .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \ + .replaceAll("_+", "_") // collapse __ + install4jInternalId = install4jApplicationName + .replaceAll(" ","_") + .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] + .replaceAll("_+", "") // collapse __ + //.replaceAll("_*-_*", "-") // collapse _-_ + install4jUnixApplicationFolder = install4jApplicationName + .replaceAll(" ","_") + .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] + .replaceAll("_+", "_") // collapse __ + .replaceAll("_*-_*", "-") // collapse _-_ + .toLowerCase() + + getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}") //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}") getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}") @@ -238,22 +343,22 @@ ext { compile_source_compatibility = 1.8 compile_target_compatibility = 1.8 // these are getdown.txt properties defined dependent on the JAVA_VERSION - getdown_alt_java_min_version = getdown_alt_java8_min_version - getdown_alt_java_max_version = getdown_alt_java8_max_version + getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version")) + getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version")) // this property is assigned below and expanded to multiple lines in the getdown task - getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location + getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location")) // this property is for the Java library used in eclipse - eclipse_java_runtime_name = string("JavaSE-1.8") + eclipseJavaRuntimeName = string("JavaSE-1.8") } else if (JAVA_VERSION.equals("11")) { JAVA_INTEGER_VERSION = string("11") libDir = j11libDir libDistDir = j11libDir compile_source_compatibility = 11 compile_target_compatibility = 11 - getdown_alt_java_min_version = getdown_alt_java11_min_version - getdown_alt_java_max_version = getdown_alt_java11_max_version - getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = string("JavaSE-11") + getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) + getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version")) + getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location")) + eclipseJavaRuntimeName = string("JavaSE-11") /* compile without modules -- using classpath libraries additional_compiler_args += [ '--module-path', modules_compileClasspath.asPath, @@ -266,10 +371,10 @@ ext { libDistDir = j11libDir compile_source_compatibility = JAVA_VERSION compile_target_compatibility = JAVA_VERSION - getdown_alt_java_min_version = getdown_alt_java11_min_version - getdown_alt_java_max_version = getdown_alt_java11_max_version - getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = string("JavaSE-11") + getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) + getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version")) + getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location")) + eclipseJavaRuntimeName = string("JavaSE-11") /* compile without modules -- using classpath libraries additional_compiler_args += [ '--module-path', modules_compileClasspath.asPath, @@ -284,13 +389,19 @@ ext { // for install4j JAVA_MIN_VERSION = JAVA_VERSION JAVA_MAX_VERSION = JAVA_VERSION - macosJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre") - macosJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz") - windowsJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre") - windowsJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz") + def jreInstallsDir = string(jre_installs_dir) + if (jreInstallsDir.startsWith("~/")) { + jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1) + } + macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre") + macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz") + windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre") + windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz") + linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre") + linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz") install4jDir = string("${jalviewDir}/${install4j_utils_dir}") - install4jConfFileName = string("jalview-installers-java${JAVA_VERSION}.install4j") - install4jConfFile = string("${install4jDir}/${install4jConfFileName}") + install4jConfFileName = string("jalview-install4j-conf.install4j") + install4jConfFile = file("${install4jDir}/${install4jConfFileName}") install4jHomeDir = install4j_home_dir if (install4jHomeDir.startsWith("~/")) { install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1) @@ -301,8 +412,7 @@ ext { buildingHTML = string("${jalviewDir}/${docDir}/building.html") helpFile = string("${classesDir}/${help_dir}/help.jhm") helpParentDir = string("${jalviewDir}/${help_parent_dir}") - helpDir = string("${help_dir}") - helpSourceDir = string("${helpParentDir}/${helpDir}") + helpSourceDir = string("${helpParentDir}/${help_dir}") relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) @@ -340,11 +450,13 @@ sourceSets { resources { srcDirs resourceDir + srcDirs += helpParentDir } jar.destinationDir = file("${jalviewDir}/${packageDir}") compileClasspath = files(sourceSets.main.java.outputDir) + //compileClasspath += files(sourceSets.main.resources.srcDirs) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath @@ -381,7 +493,7 @@ sourceSets { compileClasspath = files( sourceSets.test.java.outputDir ) if (use_clover) { - compileClasspath += sourceSets.clover.compileClasspath + compileClasspath = sourceSets.clover.compileClasspath } else { compileClasspath += files(sourceSets.main.java.outputDir) } @@ -398,17 +510,18 @@ sourceSets { // clover bits dependencies { if (use_clover) { - cloverCompile 'org.openclover:clover:4.3.1' - testCompile 'org.openclover:clover:4.3.1' + cloverCompile 'org.openclover:clover:4.4.1' + testCompile 'org.openclover:clover:4.4.1' } } - configurations { cloverRuntime cloverRuntime.extendsFrom cloverCompile } + +// eclipse project and settings files creation, also used by buildship eclipse { project { name = eclipse_project_name @@ -453,8 +566,8 @@ eclipse { cp.entries.removeAll(removeTheseToo) //cp.entries += new Output("${eclipse_bin_dir}/main") - if (file(helpSourceDir).isDirectory()) { - cp.entries += new Library(fileReference(helpSourceDir)) + if (file(helpParentDir).isDirectory()) { + cp.entries += new Library(fileReference(helpParentDir)) } if (file(resourceDir).isDirectory()) { cp.entries += new Library(fileReference(resourceDir)) @@ -462,7 +575,7 @@ eclipse { HashMap alreadyAddedLibPath = new HashMap<>(); - sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each { + sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //don't want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath, especially if they don't exist @@ -482,7 +595,6 @@ eclipse { } } - //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each { sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //no longer want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { @@ -516,7 +628,7 @@ eclipse { // for the IDE, use java 11 compatibility sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility - javaRuntimeName = eclipse_java_runtime_name + javaRuntimeName = eclipseJavaRuntimeName // add in jalview project specific properties/preferences into eclipse core preferences file { @@ -544,18 +656,24 @@ eclipse { } -task cloverInstr() { +task cloverInstr { // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"])) + inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) outputs.dir cloverInstrDir doFirst { delete cloverInstrDir - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-d", "${buildDir}/${cloverSourcesInstrDir}"] - argsList.addAll(inputs.files.files.collect({ file -> - file.absolutePath - })) + def argsList = [ + "--initstring", + cloverDb, + "-d", + cloverInstrDir.getPath(), + ] + argsList.addAll( + inputs.files.files.collect( + { file -> file.absolutePath } + ) + ) String[] args = argsList.toArray() println("About to instrument "+args.length +" files") com.atlassian.clover.CloverInstr.mainImpl(args) @@ -563,26 +681,57 @@ task cloverInstr() { } +cloverClasses.dependsOn cloverInstr + + task cloverReport { group = "Verification" - description = "Createst the Clover report" - inputs.dir "${buildDir}/clover" - outputs.dir "${reportsDir}/clover" - onlyIf { - file("${buildDir}/clover/clover.db").exists() - } + description = "Creates the Clover report" + inputs.dir "${buildDir}/clover" + outputs.dir "${reportsDir}/clover" + onlyIf { + file(cloverDb).exists() + } doFirst { - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover"] + def argsList = [ + "--initstring", + cloverDb, + "-o", + "${reportsDir}/clover" + ] String[] args = argsList.toArray() com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) // and generate ${reportsDir}/clover/clover.xml - args = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover/clover.xml"].toArray() + args = [ + "--initstring", + cloverDb, + "-o", + "${reportsDir}/clover/clover.xml" + ].toArray() com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) } } + + +compileCloverJava { + + doFirst { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs += additional_compiler_args + print ("Setting target compatibility to "+targetCompatibility+"\n") + } + classpath += configurations.cloverRuntime +} + + +task cleanClover { + doFirst { + delete cloverInstrDir + delete cloverDb + } +} // end clover bits @@ -614,18 +763,6 @@ compileTestJava { } -compileCloverJava { - - doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs += additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") - } - classpath += configurations.cloverRuntime -} - - clean { doFirst { delete sourceSets.main.java.outputDir @@ -634,9 +771,9 @@ clean { cleanTest { + dependsOn cleanClover doFirst { delete sourceSets.test.java.outputDir - delete cloverInstrDir } } @@ -707,7 +844,8 @@ task convertBuildingMD(type: Exec) { } def hostname = "hostname".execute().text.trim() - if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) { + def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" + if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) { pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" } @@ -746,7 +884,7 @@ task syncDocs(type: Sync) { task copyHelp(type: Copy) { def inputDir = helpSourceDir - def outputDir = "${classesDir}/${helpDir}" + def outputDir = "${classesDir}/${help_dir}" from(inputDir) { exclude '**/*.gif' exclude '**/*.jpg' @@ -811,12 +949,25 @@ test { useTestNG() { includeGroups testngGroups + excludeGroups testngExcludedGroups preserveOrder true useDefaultListeners=true } + maxHeapSize = "1024m" + workingDir = jalviewDir //systemProperties 'clover.jar' System.properties.clover.jar + def testLaf = project.findProperty("test_laf") + if (testLaf != null) { + println("Setting Test LaF to '${testLaf}'") + systemProperty "laf", testLaf + } + def testHiDPIScale = project.findProperty("test_HiDPIScale") + if (testHiDPIScale != null) { + println("Setting Test HiDPI Scale to '${testHiDPIScale}'") + systemProperty "sun.java2d.uiScale", testHiDPIScale + } sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility jvmArgs += additional_compiler_args @@ -828,7 +979,7 @@ task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" - workingDir = "${classesDir}/${helpDir}" + workingDir = "${classesDir}/${help_dir}" def argDir = "html" args = [ argDir ] inputs.dir("${workingDir}/${argDir}") @@ -864,8 +1015,7 @@ task linkCheck(type: JavaExec) { classpath = files("${jalviewDir}/${utilsDir}") main = "HelpLinksChecker" workingDir = jalviewDir - def help = "${classesDir}/${helpDir}" - args = [ "${classesDir}/${helpDir}", "-nointernet" ] + args = [ "${classesDir}/${help_dir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append def errFOS = outFOS @@ -876,13 +1026,13 @@ task linkCheck(type: JavaExec) { outFOS, errorOutput) - inputs.dir("${classesDir}/${helpDir}") + inputs.dir("${classesDir}/${help_dir}") outputs.file(helpLinksCheckerOutFile) } // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" -ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}" +ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}" ant.importBuild "${utilsDir}/publishHelp.xml" @@ -981,7 +1131,6 @@ task getdownWebsite() { def getdownWebsiteResourceFilenames = [] def getdownTextString = "" def getdownResourceDir = getdownResourceDir - def getdownAppDir = getdownAppDir def getdownResourceFilenames = [] doFirst { @@ -994,19 +1143,25 @@ task getdownWebsite() { rename(build_properties_file, getdown_build_properties) into getdownAppDir } - getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}" + getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" - // go through properties looking for getdown_txt_... + // set some getdown_txt_ properties then go through all properties looking for getdown_txt_... def props = project.properties.sort { it.key } - if (getdown_alt_java_min_version.length() > 0) { - props.put("getdown_txt_java_min_version", getdown_alt_java_min_version) + if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) { + props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion) } - if (getdown_alt_java_max_version.length() > 0) { - props.put("getdown_txt_java_max_version", getdown_alt_java_max_version) + if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) { + props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion) } - props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location) + if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) { + props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) + } + + props.put("getdown_txt_title", jalview_name) + props.put("getdown_txt_ui.name", install4jApplicationName) - props.put("getdown_txt_appbase", getdown_app_base) + // start with appbase + getdownTextString += "appbase = ${getdownAppBase}\n" props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { if (prop.startsWith("getdown_txt_multi_")) { @@ -1061,7 +1216,7 @@ task getdownWebsite() { } codeFiles.sort().each{f -> def name = f.getName() - def line = "code = ${getdown_app_dir}/${name}\n" + def line = "code = ${getdownAppDistDir}/${name}\n" getdownTextString += line copy { from f.getPath() @@ -1093,8 +1248,9 @@ task getdownWebsite() { def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) - def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}") - launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) + def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl" + def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}") + launchJvl.write("appbase=${getdownAppBase}") copy { from getdownLauncher @@ -1129,7 +1285,7 @@ task getdownWebsite() { copy { from getdown_txt - from launch_jvl + from launchJvl from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { @@ -1152,12 +1308,30 @@ task getdownWebsite() { } +// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir +task getdownDigestDir(type: JavaExec) { + group "Help" + description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..." + + def digestDirPropertyName = "DIGESTDIR" + doFirst { + classpath = files(getdownLauncher) + def digestDir = findProperty(digestDirPropertyName) + if (digestDir == null) { + throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest") + } + args digestDir + } + main = "com.threerings.getdown.tools.Digester" +} + + task getdownDigest(type: JavaExec) { group = "distribution" description = "Digest the getdown website folder" dependsOn getdownWebsite doFirst { - classpath = files("${getdownWebsiteDir}/${getdown_launcher}") + classpath = files(getdownLauncher) } main = "com.threerings.getdown.tools.Digester" args getdownWebsiteDir @@ -1208,88 +1382,85 @@ install4j { installDir(file(install4jHomeDir)) mediaTypes = Arrays.asList(install4j_media_types.split(",")) - if (install4j_faster.equals("true")) { - faster = true - } } -task copyInstall4jTemplate(type: Copy) { - from (install4jDir) { - include install4j_template - rename (install4j_template, install4jConfFileName) - filter(ReplaceTokens, - beginToken: '', - endToken: '', - tokens: [ - '1111111111': JAVA_MIN_VERSION, - '9999999999': JAVA_MAX_VERSION - ] - ) - filter(ReplaceTokens, - beginToken: '$$', - endToken: '$$', - tokens: [ - 'JAVA_VERSION': JAVA_VERSION, - 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, - 'VERSION': JALVIEW_VERSION, - 'MACOS_JAVA_VM_DIR': macosJavaVMDir, - 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, - 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, - 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, - 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4j_info_plist_file_associations, - 'COPYRIGHT_MESSAGE': install4j_copyright_message, - 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id, - 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, - 'GETDOWN_DIST_DIR': getdown_app_dir, - 'GETDOWN_ALT_DIR': getdown_app_dir_alt, - 'GETDOWN_INSTALL_DIR': getdown_install_dir - ] - ) +task copyInstall4jTemplate { + def install4jTemplateFile = file("${install4jDir}/${install4j_template}") + def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}") + inputs.file(install4jTemplateFile) + inputs.file(install4jFileAssociationsFile) + inputs.property("CHANNEL", { CHANNEL }) + outputs.file(install4jConfFile) + + doLast { + def install4jConfigXml = new XmlParser().parse(install4jTemplateFile) + + // turn off code signing if no OSX_KEYPASS if (OSX_KEYPASS == "") { - filter(ReplaceTokens, - beginToken: 'codeSigning macEnabled="', - endToken: '"', - tokens: [ - 'true': 'codeSigning macEnabled="false"' - ] - ) - filter(ReplaceTokens, - beginToken: 'runPostProcessor="true" ', - endToken: 'Processor', - tokens: [ - 'post': 'runPostProcessor="false" postProcessor' - ] - ) + install4jConfigXml.'**'.codeSigning.each { codeSigning -> + codeSigning.'@macEnabled' = "false" + } + install4jConfigXml.'**'.windows.each { windows -> + windows.'@runPostProcessor' = "false" + } } - } - into install4jDir - inputs.file("${install4jDir}/${install4j_template}") - inputs.file("${install4jDir}/${install4j_installer_file_associations}") - inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") - outputs.files(install4jConfFile) - doLast { - // include file associations in installer - def installerFileAssociationsXml = file("${install4jDir}/${install4j_installer_file_associations}").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerFileAssociationsXml, - file: install4jConfFile - ) - /* - // include uninstaller applescript app files in dmg - def installerDMGUninstallerXml = file("$install4jDir/$install4j_DMG_uninstaller_app_files").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerDMGUninstallerXml, - file: install4jConfFile - ) - */ + // turn off checksum creation for LOCAL channel + def e = install4jConfigXml.application[0] + if (CHANNEL == "LOCAL") { + e.'@createChecksums' = "false" + } else { + e.'@createChecksums' = "true" + } + + // put file association actions where placeholder action is + def install4jFileAssociationsText = install4jFileAssociationsFile.text + def fileAssociationActions = new XmlParser().parseText("${install4jFileAssociationsText}") + install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true + if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') { + def parent = a.parent() + parent.remove(a) + fileAssociationActions.each { faa -> + parent.append(faa) + } + // don't need to continue in .any loop once replacements have been made + return true + } + } + + // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else + // NB we're deleting the /other/ one! + // Also remove the examples subdir from non-release versions + def customizedIdToDelete = "PROGRAM_GROUP_RELEASE" + // 2.11.1.0 NOT releasing with the Examples folder in the Program Group + if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel + customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE" + } else { + // remove the examples subdir from Full File Set + def files = install4jConfigXml.files[0] + def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" } + def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' } + def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' } + def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" } + dirEntry.parent().remove(dirEntry) + } + install4jConfigXml.'**'.action.any { a -> + if (a.'@customizedId' == customizedIdToDelete) { + def parent = a.parent() + parent.remove(a) + return true + } + } + + // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores + if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) { + def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" } + symlink.parent().remove(symlink) + } + + // write install4j file + install4jConfFile.text = XmlUtil.serialize(install4jConfigXml) } } @@ -1304,15 +1475,82 @@ clean { task installers(type: com.install4j.gradle.Install4jTask) { group = "distribution" description = "Create the install4j installers" + dependsOn setGitVals dependsOn getdown dependsOn copyInstall4jTemplate - projectFile = file(install4jConfFile) - variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH] - destination = "${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}" + + projectFile = install4jConfFile + + // create an md5 for the input files to use as version for install4j conf file + def digest = MessageDigest.getInstance("MD5") + digest.update( + (file("${install4jDir}/${install4j_template}").text + + file("${install4jDir}/${install4j_info_plist_file_associations}").text + + file("${install4jDir}/${install4j_installer_file_associations}").text).bytes) + def filesMd5 = new BigInteger(1, digest.digest()).toString(16) + if (filesMd5.length() >= 8) { + filesMd5 = filesMd5.substring(0,8) + } + def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}" + // make install4jBuildDir relative to jalviewDir + def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}" + + variables = [ + 'JALVIEW_NAME': jalview_name, + 'JALVIEW_APPLICATION_NAME': install4jApplicationName, + 'JALVIEW_DIR': "../..", + 'OSX_KEYSTORE': OSX_KEYSTORE, + 'JSIGN_SH': JSIGN_SH, + 'JRE_DIR': getdown_app_dir_java, + 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion, + 'JALVIEW_VERSION': JALVIEW_VERSION, + 'JAVA_MIN_VERSION': JAVA_MIN_VERSION, + 'JAVA_MAX_VERSION': JAVA_MAX_VERSION, + 'JAVA_VERSION': JAVA_VERSION, + 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, + 'VERSION': JALVIEW_VERSION, + 'MACOS_JAVA_VM_DIR': macosJavaVMDir, + 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, + 'LINUX_JAVA_VM_DIR': linuxJavaVMDir, + 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, + 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, + 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, + 'COPYRIGHT_MESSAGE': install4j_copyright_message, + 'BUNDLE_ID': install4jBundleId, + 'INTERNAL_ID': install4jInternalId, + 'WINDOWS_APPLICATION_ID': install4jWinApplicationId, + 'MACOS_DS_STORE': install4jDSStore, + 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage, + 'INSTALLER_NAME': install4jInstallerName, + 'INSTALL4J_UTILS_DIR': install4j_utils_dir, + 'GETDOWN_WEBSITE_DIR': getdown_website_dir, + 'GETDOWN_FILES_DIR': getdown_files_dir, + 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, + 'GETDOWN_DIST_DIR': getdownAppDistDir, + 'GETDOWN_ALT_DIR': getdown_app_dir_alt, + 'GETDOWN_INSTALL_DIR': getdown_install_dir, + 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations, + 'BUILD_DIR': install4jBuildDir, + 'APPLICATION_CATEGORIES': install4j_application_categories, + 'APPLICATION_FOLDER': install4jApplicationFolder, + 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder, + 'EXECUTABLE_NAME': install4jExecutableName, + 'EXTRA_SCHEME': install4jExtraScheme, + ] + + //println("INSTALL4J VARIABLES:") + //variables.each{k,v->println("${k}=${v}")} + + destination = "${jalviewDir}/${install4jBuildDir}" buildSelected = true + if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) { + faster = true + disableSigning = true + } + if (OSX_KEYPASS) { - macKeystorePassword=OSX_KEYPASS + macKeystorePassword = OSX_KEYPASS } doFirst { @@ -1321,13 +1559,14 @@ task installers(type: com.install4j.gradle.Install4jTask) { inputs.dir(getdownWebsiteDir) inputs.file(install4jConfFile) + inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") inputs.dir(macosJavaVMDir) inputs.dir(windowsJavaVMDir) outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}") } -task sourceDist (type: Tar) { +task sourceDist(type: Tar) { def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" @@ -1342,33 +1581,47 @@ task sourceDist (type: Tar) { into project.name - def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*" - ,".*" - ,"benchmarking/*" - ,"**/.*" - ,"*.class" - ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales" - ,"*locales/**", - ,"utils/InstallAnywhere"] - def PROCESS_FILES=[ "AUTHORS", - "CITATION", - "FEATURETODO", - "JAVA-11-README", - "FEATURETODO", - "LICENSE", - "**/README", - "RELEASE", - "THIRDPARTYLIBS","TESTNG", - "build.gradle", - "gradle.properties", - "**/*.java", - "**/*.html", - "**/*.xml", - "**/*.gradle", - "**/*.groovy", - "**/*.properties", - "**/*.perl", - "**/*.sh"] + def EXCLUDE_FILES=[ + "build/*", + "bin/*", + "test-output/", + "test-reports", + "tests", + "clover*/*", + ".*", + "benchmarking/*", + "**/.*", + "*.class", + "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales", + "*locales/**", + "utils/InstallAnywhere", + "**/*.log", + ] + def PROCESS_FILES=[ + "AUTHORS", + "CITATION", + "FEATURETODO", + "JAVA-11-README", + "FEATURETODO", + "LICENSE", + "**/README", + "RELEASE", + "THIRDPARTYLIBS", + "TESTNG", + "build.gradle", + "gradle.properties", + "**/*.java", + "**/*.html", + "**/*.xml", + "**/*.gradle", + "**/*.groovy", + "**/*.properties", + "**/*.perl", + "**/*.sh", + ] + def INCLUDE_FILES=[ + ".settings/org.eclipse.jdt.core.jalview.prefs", + ] from(jalviewDir) { exclude (EXCLUDE_FILES) @@ -1394,23 +1647,28 @@ task sourceDist (type: Tar) { exclude (getdown_website_dir) // exluding these as not using jars as modules yet - exclude ("${j11modDir}/**/*.jar") - } - // from (jalviewDir) { - // // explicit includes for stuff that seemed to not get included - // include(fileTree("test/**/*.")) - // exclude(EXCLUDE_FILES) - // exclude(PROCESS_FILES) - // } + exclude ("$j11modDir/**/*.jar") + } + from(jalviewDir) { + include(INCLUDE_FILES) + } +// from (jalviewDir) { +// // explicit includes for stuff that seemed to not get included +// include(fileTree("test/**/*.")) +// exclude(EXCLUDE_FILES) +// exclude(PROCESS_FILES) +// } } -task helppages { +task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("${classesDir}/${helpDir}") - outputs.dir("${buildDir}/distributions/${helpDir}") + inputs.dir("${classesDir}/${help_dir}") + outputs.dir("${buildDir}/distributions/${help_dir}") } // LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE +task eclipseAutoBuildTask {} +task eclipseSynchronizationTask {}