/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names. * For properties set within build.gradle, use camelCaseNoSpace. */ import org.apache.tools.ant.filters.ReplaceTokens 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() } } plugins { id 'java' id 'application' id 'eclipse' id 'com.github.johnrengelman.shadow' version '4.0.3' 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() } // 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 == null ? "" : o.toString() } ext { jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() jalviewDirRelativePath = jalviewDir // local build environment properties // can be "projectDir/local.properties" def localProps = "${projectDir}/local.properties" def propsFile = null; if (file(localProps).exists()) { propsFile = localProps } // or "../projectDir_local.properties" def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties" if (file(dirLocalProps).exists()) { propsFile = dirLocalProps } if (propsFile != null) { try { def p = new Properties() def localPropsFIS = new FileInputStream(propsFile) p.load(localPropsFIS) localPropsFIS.close() p.each { key, val -> def oldval = findProperty(key) setProperty(key, val) if (oldval != null) { println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") } else { println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'") } } } catch (Exception e) { System.out.println("Exception reading local.properties") } } //// // 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 eclipseApplicationProperty = string("eclipse.application") // CHECK IF RUNNING FROM WITHIN ECLIPSE def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty] IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.") // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET if (System.properties[j2sHeadlessBuildProperty].equals("true")) { println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'") IN_ECLIPSE = false } if (IN_ECLIPSE) { println("WITHIN ECLIPSE IDE") } else { println("HEADLESS BUILD") } /* *-/ System.properties.sort { it.key }.each { key, val -> println("SYSTEM PROPERTY ${key}='${val}'") } /-* *-/ if (false && IN_ECLIPSE) { jalviewDir = jalviewDirAbsolutePath } */ // essentials bareSourceDir = string(source_dir) sourceDir = string("${jalviewDir}/${bareSourceDir}") resourceDir = string("${jalviewDir}/${resource_dir}") bareTestSourceDir = string(test_source_dir) testDir = string("${jalviewDir}/${bareTestSourceDir}") classesDir = string("${jalviewDir}/${classes_dir}") // clover useClover = clover.equals("true") cloverBuildDir = "${buildDir}/clover" cloverInstrDir = file("${cloverBuildDir}/clover-instr") cloverClassesDir = file("${cloverBuildDir}/clover-classes") cloverReportDir = file("${buildDir}/reports/clover") cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr") cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes") //cloverTestClassesDir = cloverClassesDir cloverDb = string("${cloverBuildDir}/clover.db") resourceClassesDir = useClover ? cloverClassesDir : classesDir testSourceDir = useClover ? cloverTestInstrDir : testDir testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}" getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") buildDist = true // 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 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}") getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") jvlChannelName += "_${getdownChannelName}" // automatically add the test group Not-bamboo for exclusion if ("".equals(testng_excluded_groups)) { testng_excluded_groups = "Not-bamboo" } install4jExtraScheme = "jalviewb" break case "RELEASE": getdownAppDistDir = getdown_app_dir_release reportRsyncCommand = true install4jSuffix = "" install4jDSStore = "DS_Store" install4jDMGBackgroundImage = "jalview_dmg_background.png" install4jInstallerName = "${jalview_name} Installer" break case "ARCHIVE": getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = string("${getdown_channel_base}/${getdownDir}") if (!file("${ARCHIVEDIR}/${package_dir}").exists()) { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { package_dir = string("${ARCHIVEDIR}/${package_dir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true install4jExtraScheme = "jalviewa" break case "ARCHIVELOCAL": getdownChannelName = string("archive/${JALVIEW_VERSION}") getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = file(getdownWebsiteDir).toURI().toString() if (!file("${ARCHIVEDIR}/${package_dir}").exists()) { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { package_dir = string("${ARCHIVEDIR}/${package_dir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") install4jSuffix = "Archive" install4jExtraScheme = "jalviewa" break case "DEVELOP": reportRsyncCommand = true // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version JALVIEW_VERSION=JALVIEW_VERSION+"-develop" install4jSuffix = "Develop" install4jDSStore = "DS_Store-DEVELOP" install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png" install4jExtraScheme = "jalviewd" install4jInstallerName = "${jalview_name} Develop Installer" break case "TEST-RELEASE": 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 = "${jalview_name} Test Installer" break case ~/^SCRATCH(|-[-\w]*)$/: 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": getdownAppBase = file(getdownWebsiteDir).toURI().toString() getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") install4jExtraScheme = "jalviewl" break default: // something wrong specified throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") break } // override getdownAppBase if requested if (findProperty("getdown_appbase_override") != null) { getdownAppBase = string(getProperty("getdown_appbase_override")) println("Overriding getdown appbase with '${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}") getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/") getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}") /* compile without modules -- using classpath libraries modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) modules_runtimeClasspath = modules_compileClasspath */ gitHash = string("") gitBranch = string("") println("Using a ${CHANNEL} profile.") additional_compiler_args = [] // configure classpath/args for j8/j11 compilation if (JAVA_VERSION.equals("1.8")) { JAVA_INTEGER_VERSION = string("8") //libDir = j8libDir libDir = j11libDir libDistDir = j8libDir digestonlyDir = j8digestonlyDir compile_source_compatibility = 1.8 compile_target_compatibility = 1.8 // these are getdown.txt properties defined dependent on the JAVA_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 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location")) // this property is for the Java library used in eclipse eclipseJavaRuntimeName = string("JavaSE-1.8") } else if (JAVA_VERSION.equals("11")) { JAVA_INTEGER_VERSION = string("11") libDir = j11libDir libDistDir = j11libDir digestonlyDir = j11digestonlyDir compile_source_compatibility = 11 compile_target_compatibility = 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, '--add-modules', j11modules ] */ } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) { JAVA_INTEGER_VERSION = JAVA_VERSION libDir = j11libDir libDistDir = j11libDir compile_source_compatibility = JAVA_VERSION compile_target_compatibility = JAVA_VERSION 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, '--add-modules', j11modules ] */ } else { throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview") } // for install4j JAVA_MIN_VERSION = JAVA_VERSION JAVA_MAX_VERSION = JAVA_VERSION 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-install4j-conf.install4j") install4jConfFile = file("${install4jDir}/${install4jConfFileName}") install4jHomeDir = install4j_home_dir if (install4jHomeDir.startsWith("~/")) { install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1) } buildingHTML = string("${jalviewDir}/${doc_dir}/building.html") helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm") helpParentDir = string("${jalviewDir}/${help_parent_dir}") helpSourceDir = string("${helpParentDir}/${help_dir}") relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs") jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}") if (IN_ECLIPSE) { jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir) } else { jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js") } jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib") jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs") jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core") jalviewjsJalviewCoreHtmlFile = string("") jalviewjsJalviewCoreName = string(jalviewjs_core_name) jalviewjsCoreClasslists = [] jalviewjsJalviewTemplateName = string(jalviewjs_name) jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}") jalviewjsJ2sProps = null eclipseWorkspace = null eclipseBinary = string("") eclipseVersion = string("") eclipseDebug = false // ENDEXT } sourceSets { main { java { srcDirs sourceDir outputDir = file(classesDir) } resources { srcDirs resourceDir srcDirs += helpParentDir } jar.destinationDir = file("${jalviewDir}/${package_dir}") compileClasspath = files(sourceSets.main.java.outputDir) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath } clover { java { srcDirs cloverInstrDir outputDir = cloverClassesDir } resources { srcDirs = sourceSets.main.resources.srcDirs } compileClasspath = files( sourceSets.clover.java.outputDir ) //compileClasspath += files( testClassesDir ) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath } test { java { srcDirs testSourceDir outputDir = file(testClassesDir) } resources { srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs } compileClasspath = files( sourceSets.test.java.outputDir ) compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath } } // eclipse project and settings files creation, also used by buildship eclipse { project { name = eclipse_project_name natures 'org.eclipse.jdt.core.javanature', 'org.eclipse.jdt.groovy.core.groovyNature', 'org.eclipse.buildship.core.gradleprojectnature' buildCommand 'org.eclipse.jdt.core.javabuilder' buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder' } classpath { //defaultOutputDir = sourceSets.main.java.outputDir def removeThese = [] configurations.each{ if (it.isCanBeResolved()) { removeThese += it } } minusConfigurations += removeThese plusConfigurations = [ ] file { whenMerged { cp -> def removeTheseToo = [] HashMap alreadyAddedSrcPath = new HashMap<>(); cp.entries.each { entry -> // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test". // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover // we add the resources and help/help dirs in as libs afterwards (see below) if (entry.kind == 'src') { if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) { removeTheseToo += entry } else { alreadyAddedSrcPath.putAt(entry.path, true) } } } cp.entries.removeAll(removeTheseToo) //cp.entries += new Output("${eclipse_bin_dir}/main") if (file(helpParentDir).isDirectory()) { cp.entries += new Library(fileReference(helpParentDir)) } if (file(resourceDir).isDirectory()) { cp.entries += new Library(fileReference(resourceDir)) } HashMap alreadyAddedLibPath = new HashMap<>(); 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 return false // groovy "continue" in .any closure } def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { // make relative path itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) } if (alreadyAddedLibPath.get(itPath)) { //println("Not adding duplicate entry "+itPath) } else { //println("Adding entry "+itPath) cp.entries += new Library(fileReference(itPath)) alreadyAddedLibPath.put(itPath, true) } } sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //no longer want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath return false // groovy "continue" in .any closure } def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) } if (alreadyAddedLibPath.get(itPath)) { // don't duplicate } else { def lib = new Library(fileReference(itPath)) lib.entryAttributes["test"] = "true" cp.entries += lib alreadyAddedLibPath.put(itPath, true) } } } // whenMerged } // file containers 'org.eclipse.buildship.core.gradleclasspathcontainer' } // classpath jdt { // for the IDE, use java 11 compatibility sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility javaRuntimeName = eclipseJavaRuntimeName // add in jalview project specific properties/preferences into eclipse core preferences file { withProperties { props -> def jalview_prefs = new Properties() def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}") jalview_prefs.load(ins) ins.close() jalview_prefs.forEach { t, v -> if (props.getAt(t) == null) { props.putAt(t, v) } } } } } // jdt if (IN_ECLIPSE) { // Don't want these to be activated if in headless build synchronizationTasks "eclipseSynchronizationTask" autoBuildTasks "eclipseAutoBuildTask" } } // clover bits task cleanClover { doFirst { delete cloverBuildDir delete cloverReportDir } } task cloverInstrJava(type: JavaExec) { group = "Verification" description = "Create clover instrumented source java files" dependsOn cleanClover inputs.files(sourceSets.main.allJava) outputs.dir(cloverInstrDir) //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) classpath = sourceSets.clover.compileClasspath main = "com.atlassian.clover.CloverInstr" def argsList = [ "--encoding", "UTF-8", "--initstring", cloverDb, "--destdir", cloverInstrDir.getPath(), ] def srcFiles = sourceSets.main.allJava.files argsList.addAll( srcFiles.collect( { file -> file.absolutePath } ) ) args argsList.toArray() doFirst { delete cloverInstrDir println("Clover: About to instrument "+srcFiles.size() +" files") } } task cloverInstrTests(type: JavaExec) { group = "Verification" description = "Create clover instrumented source test files" dependsOn cleanClover inputs.files(testDir) outputs.dir(cloverTestInstrDir) classpath = sourceSets.clover.compileClasspath main = "com.atlassian.clover.CloverInstr" def argsList = [ "--encoding", "UTF-8", "--initstring", cloverDb, "--srcdir", testDir, "--destdir", cloverTestInstrDir.getPath(), ] args argsList.toArray() doFirst { delete cloverTestInstrDir println("Clover: About to instrument test files") } } task cloverInstr { group = "Verification" description = "Create clover instrumented all source files" dependsOn cloverInstrJava dependsOn cloverInstrTests } cloverClasses.dependsOn cloverInstr task cloverConsoleReport(type: JavaExec) { group = "Verification" description = "Creates clover console report" onlyIf { file(cloverDb).exists() } inputs.dir cloverClassesDir classpath = sourceSets.clover.runtimeClasspath main = "com.atlassian.clover.reporters.console.ConsoleReporter" if (cloverreport_mem.length() > 0) { maxHeapSize = cloverreport_mem } if (cloverreport_jvmargs.length() > 0) { jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } def argsList = [ "--alwaysreport", "--initstring", cloverDb, "--unittests" ] args argsList.toArray() } task cloverHtmlReport(type: JavaExec) { group = "Verification" description = "Creates clover HTML report" onlyIf { file(cloverDb).exists() } def cloverHtmlDir = cloverReportDir inputs.dir cloverClassesDir outputs.dir cloverHtmlDir classpath = sourceSets.clover.runtimeClasspath main = "com.atlassian.clover.reporters.html.HtmlReporter" if (cloverreport_mem.length() > 0) { maxHeapSize = cloverreport_mem } if (cloverreport_jvmargs.length() > 0) { jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } def argsList = [ "--alwaysreport", "--initstring", cloverDb, "--outputdir", cloverHtmlDir ] if (cloverreport_html_options.length() > 0) { argsList += cloverreport_html_options.split(" ") } args argsList.toArray() } task cloverXmlReport(type: JavaExec) { group = "Verification" description = "Creates clover XML report" onlyIf { file(cloverDb).exists() } def cloverXmlFile = "${cloverReportDir}/clover.xml" inputs.dir cloverClassesDir outputs.file cloverXmlFile classpath = sourceSets.clover.runtimeClasspath main = "com.atlassian.clover.reporters.xml.XMLReporter" if (cloverreport_mem.length() > 0) { maxHeapSize = cloverreport_mem } if (cloverreport_jvmargs.length() > 0) { jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } def argsList = [ "--alwaysreport", "--initstring", cloverDb, "--outfile", cloverXmlFile ] if (cloverreport_xml_options.length() > 0) { argsList += cloverreport_xml_options.split(" ") } args argsList.toArray() } task cloverReport { group = "Verification" description = "Creates clover reports" dependsOn cloverXmlReport dependsOn cloverHtmlReport } 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 } // end clover bits compileJava { doFirst { sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility options.compilerArgs = additional_compiler_args print ("Setting target compatibility to "+targetCompatibility+"\n") } } compileTestJava { doFirst { sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility options.compilerArgs = additional_compiler_args print ("Setting target compatibility to "+targetCompatibility+"\n") } } clean { doFirst { delete sourceSets.main.java.outputDir } } cleanTest { dependsOn cleanClover doFirst { delete sourceSets.test.java.outputDir } } // format is a string like date.format("dd MMMM yyyy") def getDate(format) { def date = new Date() return date.format(format) } task setGitVals { def hashStdOut = new ByteArrayOutputStream() exec { commandLine "git", "rev-parse", "--short", "HEAD" standardOutput = hashStdOut ignoreExitValue true } def branchStdOut = new ByteArrayOutputStream() exec { commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" standardOutput = branchStdOut ignoreExitValue true } gitHash = hashStdOut.toString().trim() gitBranch = branchStdOut.toString().trim() outputs.upToDateWhen { false } } task createBuildProperties(type: WriteProperties) { dependsOn setGitVals inputs.dir(sourceDir) inputs.dir(resourceDir) file(buildProperties).getParentFile().mkdirs() outputFile (buildProperties) // taking time specific comment out to allow better incremental builds comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") property "VERSION", JALVIEW_VERSION property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" outputs.file(outputFile) } task cleanBuildingHTML(type: Delete) { doFirst { delete buildingHTML } } task convertBuildingMD(type: Exec) { dependsOn cleanBuildingHTML def buildingMD = "${jalviewDir}/${doc_dir}/building.md" def css = "${jalviewDir}/${doc_dir}/github.css" def pandoc = null pandoc_exec.split(",").each { if (file(it.trim()).exists()) { pandoc = it.trim() return true } } def hostname = "hostname".execute().text.trim() def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) { pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" } doFirst { if (pandoc != null && file(pandoc).exists()) { commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD } else { println("Cannot find pandoc. Skipping convert building.md to HTML") throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML") } } ignoreExitValue true inputs.file(buildingMD) inputs.file(css) outputs.file(buildingHTML) } clean { doFirst { delete buildingHTML } } task syncDocs(type: Sync) { dependsOn convertBuildingMD def syncDir = "${resourceClassesDir}/${doc_dir}" from fileTree("${jalviewDir}/${doc_dir}") into syncDir } task copyHelp(type: Copy) { def inputDir = helpSourceDir def outputDir = "${resourceClassesDir}/${help_dir}" from(inputDir) { exclude '**/*.gif' exclude '**/*.jpg' exclude '**/*.png' filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: [ 'Version-Rel': JALVIEW_VERSION, 'Year-Rel': getDate("yyyy") ] ) } from(inputDir) { include '**/*.gif' include '**/*.jpg' include '**/*.png' } into outputDir inputs.dir(inputDir) outputs.files(helpFile) outputs.dir(outputDir) } task syncLib(type: Sync) { def syncDir = "${resourceClassesDir}/${libDistDir}" from fileTree("${jalviewDir}/${libDistDir}") into syncDir } task syncResources(type: Sync) { from resourceDir include "**/*.*" into "${resourceClassesDir}" preserve { include "**" } } task prepare { dependsOn syncResources dependsOn syncDocs dependsOn copyHelp } //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir test { dependsOn prepare //dependsOn compileJava ////? DELETE if (useClover) { dependsOn cloverClasses } else { //? dependsOn compileJava //? } useTestNG() { includeGroups testng_groups excludeGroups testng_excluded_groups preserveOrder true useDefaultListeners=true } maxHeapSize = "1024m" workingDir = jalviewDir //systemProperties 'clover.jar' System.properties.clover.jar def testLaf = project.findProperty("test_laf") if (testLaf != null) { println("Setting Test LaF to '${testLaf}'") systemProperty "laf", testLaf } def testHiDPIScale = project.findProperty("test_HiDPIScale") if (testHiDPIScale != null) { println("Setting Test HiDPI Scale to '${testHiDPIScale}'") systemProperty "sun.java2d.uiScale", testHiDPIScale } sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility jvmArgs += additional_compiler_args doFirst { if (useClover) { println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover") } } } task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" workingDir = "${classesDir}/${help_dir}" def argDir = "html" args = [ argDir ] inputs.dir("${workingDir}/${argDir}") outputs.dir("${classesDir}/doc") outputs.dir("${classesDir}/help") outputs.file("${workingDir}/JavaHelpSearch/DOCS") outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") outputs.file("${workingDir}/JavaHelpSearch/POSITIONS") outputs.file("${workingDir}/JavaHelpSearch/SCHEMA") outputs.file("${workingDir}/JavaHelpSearch/TMAP") } task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utils_dir}") destinationDir = file("${jalviewDir}/${utils_dir}") source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class") outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class") } task linkCheck(type: JavaExec) { dependsOn prepare, compileLinkCheck def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out") classpath = files("${jalviewDir}/${utils_dir}") main = "HelpLinksChecker" workingDir = jalviewDir args = [ "${classesDir}/${help_dir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append def errFOS = outFOS standardOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, standardOutput) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, errorOutput) inputs.dir("${classesDir}/${help_dir}") outputs.file(helpLinksCheckerOutFile) } // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}" ant.importBuild "${utils_dir}/publishHelp.xml" task cleanPackageDir(type: Delete) { doFirst { delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar") } } jar { dependsOn linkCheck dependsOn buildIndices dependsOn createBuildProperties manifest { attributes "Main-Class": main_class, "Permissions": "all-permissions", "Application-Name": "Jalview Desktop", "Codebase": application_codebase } destinationDir = file("${jalviewDir}/${package_dir}") archiveName = rootProject.name+".jar" exclude "cache*/**" exclude "*.jar" exclude "*.jar.*" exclude "**/*.jar" exclude "**/*.jar.*" inputs.dir(classesDir) outputs.file("${jalviewDir}/${package_dir}/${archiveName}") } task copyJars(type: Copy) { from fileTree(dir: classesDir, include: "**/*.jar").files into "${jalviewDir}/${package_dir}" } // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well task syncJars(type: Sync) { from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files into "${jalviewDir}/${package_dir}" preserve { include jar.archiveName } } task makeDist { group = "build" description = "Put all required libraries in dist" // order of "cleanPackageDir", "copyJars", "jar" important! jar.mustRunAfter cleanPackageDir syncJars.mustRunAfter cleanPackageDir dependsOn cleanPackageDir dependsOn syncJars dependsOn jar outputs.dir("${jalviewDir}/${package_dir}") } task cleanDist { dependsOn cleanPackageDir dependsOn cleanTest dependsOn clean } shadowJar { group = "distribution" if (buildDist) { dependsOn makeDist } from ("${jalviewDir}/${libDistDir}") { include("*.jar") } manifest { attributes 'Implementation-Version': JALVIEW_VERSION } mainClassName = shadow_jar_main_class mergeServiceFiles() classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION minimize() } task getdownWebsite() { group = "distribution" description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer" if (buildDist) { dependsOn makeDist } def getdownWebsiteResourceFilenames = [] def getdownTextString = "" def getdownResourceDir = getdownResourceDir def getdownResourceFilenames = [] doFirst { // clean the getdown website and files dir before creating getdown folders delete getdownWebsiteDir delete getdownFilesDir copy { from buildProperties rename(build_properties_file, getdown_build_properties) into getdownAppDir } getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" // set some getdown_txt_ properties then go through all properties looking for getdown_txt_... def props = project.properties.sort { it.key } if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) { props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion) } if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) { props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion) } 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) // start with appbase getdownTextString += "appbase = ${getdownAppBase}\n" props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { if (prop.startsWith("getdown_txt_multi_")) { def key = prop.substring(18) val.split(",").each{ v -> def line = "${key} = ${v}\n" getdownTextString += line } } else { // file values rationalised if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) { def r = null if (val.indexOf('/') == 0) { // absolute path r = file(val) } else if (val.indexOf('/') > 0) { // relative path (relative to jalviewDir) r = file( "${jalviewDir}/${val}" ) } if (r.exists()) { val = "${getdown_resource_dir}/" + r.getName() getdownWebsiteResourceFilenames += val getdownResourceFilenames += r.getPath() } } if (! prop.startsWith("getdown_txt_resource")) { def line = prop.substring(12) + " = ${val}\n" getdownTextString += line } } } } getdownWebsiteResourceFilenames.each{ filename -> getdownTextString += "resource = ${filename}\n" } getdownResourceFilenames.each{ filename -> copy { from filename into getdownResourceDir } } def codeFiles = [] fileTree(file(package_dir)).each{ f -> if (f.isDirectory()) { def files = fileTree(dir: f, include: ["*"]).getFiles() codeFiles += files } else if (f.exists()) { codeFiles += f } } codeFiles.sort().each{f -> def name = f.getName() def line = "code = ${getdownAppDistDir}/${name}\n" getdownTextString += line copy { from f.getPath() into getdownAppDir } } fileTree(dir: digestonlyDir, include: ["*"]).getFiles().sort().each{f -> def name = f.getName() def line = "digestonly = ${getdownAppDistDir}/${name}\n" getdownTextString += line copy { from f.getPath() into getdownAppDir } } // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist /* if (JAVA_VERSION.equals("11")) { def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles() j11libFiles.sort().each{f -> def name = f.getName() def line = "code = ${getdown_j11lib_dir}/${name}\n" getdownTextString += line copy { from f.getPath() into getdownJ11libDir } } } */ // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated. //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n" getdownTextString += "resource = ${getdown_launcher_new}\n" getdownTextString += "class = ${main_class}\n" /* NOT setting these properties so that getdownappbase and getdowndistdir will default to release version * getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n" * getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n" */ def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) 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 rename(file(getdownLauncher).getName(), getdown_launcher_new) into getdownWebsiteDir } copy { from getdownLauncher if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownWebsiteDir } if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { copy { from getdown_txt from getdownLauncher from "${getdownAppDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownInstallDir } copy { from getdownInstallDir into getdownFilesInstallDir } } copy { from getdown_txt from launchJvl from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownFilesDir } copy { from getdownResourceDir into "${getdownFilesDir}/${getdown_resource_dir}" } } if (buildDist) { inputs.dir("${jalviewDir}/${package_dir}") } outputs.dir(getdownWebsiteDir) outputs.dir(getdownFilesDir) } // 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(getdownLauncher) } main = "com.threerings.getdown.tools.Digester" args getdownWebsiteDir inputs.dir(getdownWebsiteDir) outputs.file("${getdownWebsiteDir}/digest2.txt") } task getdown() { group = "distribution" description = "Create the minimal and full getdown app folder for installers and website and create digest file" dependsOn getdownDigest doLast { if (reportRsyncCommand) { def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/') def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/') println "LIKELY RSYNC COMMAND:" println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'" if (RUNRSYNC == "true") { exec { commandLine "mkdir", "-p", toDir } exec { commandLine "rsync", "-avh", "--delete", fromDir, toDir } } } } } clean { doFirst { delete getdownWebsiteDir delete getdownFilesDir } } install4j { if (file(install4jHomeDir).exists()) { // good to go! } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) { install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) { install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app" } installDir(file(install4jHomeDir)) mediaTypes = Arrays.asList(install4j_media_types.split(",")) } 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 == "") { install4jConfigXml.'**'.codeSigning.each { codeSigning -> codeSigning.'@macEnabled' = "false" } install4jConfigXml.'**'.windows.each { windows -> windows.'@runPostProcessor' = "false" } } // 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) } } clean { doFirst { delete install4jConfFile } } task installers(type: com.install4j.gradle.Install4jTask) { group = "distribution" description = "Create the install4j installers" dependsOn setGitVals dependsOn getdown dependsOn copyInstall4jTemplate 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 } doFirst { println("Using projectFile "+projectFile) } 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}/${JAVA_VERSION}") } task sourceDist(type: Tar) { def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09] try { archiveFileName = outputFileName } catch (Exception e) { archiveName = outputFileName } compression Compression.GZIP into project.name def EXCLUDE_FILES=[ "build/*", "bin/*", "test-output/", "test-reports", "tests", "clover*/*", ".*", "benchmarking/*", "**/.*", "*.class", "**/*.class","$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) include (PROCESS_FILES) filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: [ 'Version-Rel': JALVIEW_VERSION, 'Year-Rel': getDate("yyyy") ] ) } from(jalviewDir) { exclude (EXCLUDE_FILES) exclude (PROCESS_FILES) exclude ("appletlib") exclude ("**/*locales") exclude ("*locales/**") exclude ("utils/InstallAnywhere") exclude (getdown_files_dir) exclude (getdown_website_dir) // exluding these as not using jars as modules yet exclude ("$j11modDir/**/*.jar") } from(jalviewDir) { include(INCLUDE_FILES) } // from (jalviewDir) { // // explicit includes for stuff that seemed to not get included // include(fileTree("test/**/*.")) // exclude(EXCLUDE_FILES) // exclude(PROCESS_FILES) // } } task helppages { dependsOn copyHelp dependsOn pubhtmlhelp inputs.dir("${classesDir}/${help_dir}") outputs.dir("${buildDir}/distributions/${help_dir}") } // LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE task eclipseAutoBuildTask {} task eclipseSynchronizationTask {}