--- /dev/null
+--- a/build.gradle 2021-09-20 17:46:04.088152106 +0100
++++ b/build.gradle 2021-09-20 17:46:09.180302062 +0100
+@@ -2,16 +2,6 @@
+ * 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.internal.generator.PropertiesPersistableConfigurationObject
+-import org.gradle.api.internal.PropertiesTransformer
+-import org.gradle.util.ConfigureUtil
+-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
+ import com.vladsch.flexmark.util.ast.Node
+ import com.vladsch.flexmark.html.HtmlRenderer
+ import com.vladsch.flexmark.parser.Parser
+@@ -24,34 +14,17 @@
+ import com.vladsch.flexmark.ext.toc.TocExtension
+
+ buildscript {
+- repositories {
+- mavenCentral()
+- mavenLocal()
+- }
+ dependencies {
+ classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
+ }
+ }
+
+-
+ plugins {
+ id 'java'
+ id 'application'
+- id 'eclipse'
+- id "com.diffplug.gradle.spotless" version "3.28.0"
+- id 'com.github.johnrengelman.shadow' version '4.0.3'
+- id 'com.install4j.gradle' version '8.0.10'
+- id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+ id 'com.palantir.git-version' version '0.12.3'
+ }
+
+-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()
+@@ -96,19 +69,11 @@
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+- getdownChannelName = CHANNEL.toLowerCase()
+- // default to "default". Currently only has different cosmetics for "develop", "release", "default"
+- propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+- // Import channel_properties
++ propertiesChannelName = "release"
+ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+ channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ overrideProperties(channelGradleProperties, false)
+- // local build environment properties
+- // can be "projectDir/local.properties"
+- overrideProperties("${projectDir}/local.properties", true)
+- // or "../projectDir_local.properties"
+- overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
+-
++
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+@@ -128,41 +93,6 @@
+ 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")
+- }
+-
+- J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+- if (J2S_ENABLED) {
+- println("J2S ENABLED")
+- }
+- /* *-/
+- System.properties.sort { it.key }.each {
+- key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
+- }
+- /-* *-/
+- if (false && IN_ECLIPSE) {
+- jalviewDir = jalviewDirAbsolutePath
+- }
+- */
+-
+- // datestamp
+- buildDate = new Date().format("yyyyMMdd")
+
+ // essentials
+ bareSourceDir = string(source_dir)
+@@ -173,214 +103,18 @@
+
+ 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("${cloverBuildDir}/clover.db")
+-
+- testSourceDir = useClover ? cloverTestInstrDir : testDir
+- testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
+-
+- getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
+- buildDist = true
+- buildProperties = null
+-
+- // the following values might be overridden by the CHANNEL switch
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
+- getdownAppDistDir = getdown_app_dir_alt
+- getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
++ useClover = false
++
++ resourceClassesDir = classesDir
++
++ testSourceDir = testDir
++ testClassesDir = "${jalviewDir}/${test_output_dir}"
++
++ buildProperties = string("${classesDir}/${build_properties_file}")
+ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
+- reportRsyncCommand = false
+- jvlChannelName = CHANNEL.toLowerCase()
+- install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
+- install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+- install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
+- install4jInstallerName = "${jalview_name} Non-Release Installer"
+- install4jExecutableName = install4j_executable_name
+- install4jExtraScheme = "jalviewx"
+- install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
+- install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
+- install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
+- install4jBackground = string("${install4j_images_dir}/${install4j_background}")
+- 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 += "_${getdownChannelName}"
+- // automatically add the test group Not-bamboo for exclusion
+- if ("".equals(testng_excluded_groups)) {
+- testng_excluded_groups = "Not-bamboo"
+- }
+- install4jExtraScheme = "jalviewb"
+- break
+
+- case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
+- getdownAppDistDir = getdown_app_dir_release
+- reportRsyncCommand = true
+- install4jSuffix = ""
+- install4jInstallerName = "${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}/${getdown_launcher_local}")
+- install4jSuffix = "Archive"
+- install4jExtraScheme = "jalviewa"
+- break
+-
+- case "DEVELOP":
+- reportRsyncCommand = true
+- getdownSetAppBaseProperty = true
+- // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+- JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
+-
+- install4jSuffix = "Develop"
+- install4jExtraScheme = "jalviewd"
+- install4jInstallerName = "${jalview_name} Develop Installer"
+- break
+-
+- case "TEST-RELEASE":
+- reportRsyncCommand = true
+- // Don't ignore transpile errors for release build
+- if (jalviewjs_ignore_transpile_errors.equals("true")) {
+- jalviewjs_ignore_transpile_errors = "false"
+- println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+- }
+- JALVIEW_VERSION = JALVIEW_VERSION+"-test"
+- install4jSuffix = "Test"
+- install4jExtraScheme = "jalviewt"
+- install4jInstallerName = "${jalview_name} Test Installer"
+- break
+-
+- case ~/^SCRATCH(|-[-\w]*)$/:
+- getdownChannelName = CHANNEL
+- JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
+-
+- getdownDir = string("${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"
+- install4jExtraScheme = "jalviewt"
+- install4jInstallerName = "${jalview_name} Test Installer"
+- break
+-
+- case [ "LOCAL", "JALVIEWJS" ]:
+- JALVIEW_VERSION = "TEST"
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownLauncher = string("${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) {
+- // revert to LOCAL if empty string
+- if (string(getdown_appbase_override) == "") {
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- } else if (string(getdown_appbase_override).startsWith("file://")) {
+- getdownAppBase = string(getdown_appbase_override)
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- } else {
+- getdownAppBase = string(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()
+-
+- getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
+- 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}/${j11modDir}", include: ["*.jar"])
+- modules_runtimeClasspath = modules_compileClasspath
+- */
++ install4jApplicationName = "${jalview_name}"
++
+ def details = versionDetails()
+ gitHash = details.gitHash
+ gitBranch = details.branchName
+@@ -396,71 +130,16 @@
+ libDistDir = j8libDir
+ 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
+ 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}/${install4jConfFileName}")
+- install4jHomeDir = install4j_home_dir
+- if (install4jHomeDir.startsWith("~/")) {
+- install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
+- }
+-
+ resourceBuildDir = string("${buildDir}/resources")
+ resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+ helpBuildDir = string("${resourceBuildDir}/help_build")
+@@ -474,31 +153,6 @@
+ helpSourceDir = string("${helpParentDir}/${help_dir}")
+ helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
+
+-
+- 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}/${jalviewjs_j2s_settings}")
+- jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
+- jalviewjsJ2sProps = null
+- jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+-
+- eclipseWorkspace = null
+- eclipseBinary = string("")
+- eclipseVersion = string("")
+- eclipseDebug = false
+ // ENDEXT
+ }
+
+@@ -517,27 +171,12 @@
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+- runtimeClasspath = compileClasspath
+- runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+- }
+-
+- clover {
+- java {
+- srcDirs cloverInstrDir
+- outputDir = cloverClassesDir
+- }
+
+- resources {
+- srcDirs = sourceSets.main.resources.srcDirs
+- }
+-
+- compileClasspath = files( sourceSets.clover.java.outputDir )
+- //compileClasspath += files( testClassesDir )
++ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+- compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+- compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+
+ runtimeClasspath = compileClasspath
++ runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+ }
+
+ test {
+@@ -557,453 +196,41 @@
+ runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.test.resources.srcDirs)
+ }
+-
+-}
+-
+-
+-// eclipse project and settings files creation, also used by buildship
+-eclipse {
+- project {
+- name = eclipse_project_name
+-
+- natures 'org.eclipse.jdt.core.javanature',
+- 'org.eclipse.jdt.groovy.core.groovyNature',
+- 'org.eclipse.buildship.core.gradleprojectnature'
+-
+- buildCommand 'org.eclipse.jdt.core.javabuilder'
+- buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+- }
+-
+- classpath {
+- //defaultOutputDir = sourceSets.main.java.outputDir
+- configurations.each{ c->
+- if (c.isCanBeResolved()) {
+- minusConfigurations += [c]
+- }
+- }
+-
+- plusConfigurations = [ ]
+- file {
+-
+- whenMerged { cp ->
+- def removeTheseToo = []
+- HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
+- cp.entries.each { entry ->
+- // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+- // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+- // we add the resources and help/help dirs in as libs afterwards (see below)
+- if (entry.kind == 'src') {
+- if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
+- removeTheseToo += entry
+- } else {
+- alreadyAddedSrcPath.putAt(entry.path, true)
+- }
+- }
+-
+- }
+- cp.entries.removeAll(removeTheseToo)
+-
+- //cp.entries += new Output("${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<String, Boolean> 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)
+- }
+- }
+- // codestyle file -- overrides previous formatter prefs
+- def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
+- if (csFile.exists()) {
+- XmlParser parser = new XmlParser()
+- def profiles = parser.parse(csFile)
+- def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
+- if (profile != null) {
+- profile.'setting'.each { s ->
+- def id = s.'@id'
+- def value = s.'@value'
+- if (id != null && value != null) {
+- props.putAt(id, value)
+- }
+- }
+- }
+- }
+- }
+- }
+-
+- } // jdt
+-
+- if (IN_ECLIPSE) {
+- // Don't want these to be activated if in headless build
+- synchronizationTasks "eclipseSynchronizationTask"
+- //autoBuildTasks "eclipseAutoBuildTask"
+-
+- }
+-}
+-
+-
+-/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
+-// Class to allow updating arbitrary properties files
+-class PropertiesFile extends PropertiesPersistableConfigurationObject {
+- public PropertiesFile(PropertiesTransformer t) { super(t); }
+- @Override protected void load(Properties properties) { }
+- @Override protected void store(Properties properties) { }
+- @Override protected String getDefaultResourceName() { return ""; }
+- // This is necessary, because PropertiesPersistableConfigurationObject fails
+- // if no default properties file exists.
+- @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
+-}
+-
+-// Task to update arbitrary properties files (set outputFile)
+-class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
+- private final PropertiesFileContentMerger file;
+- public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
+- protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
+- protected void configure(PropertiesFile props) {
+- file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
+- }
+- public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
+-}
+-
+-task eclipseUIPreferences(type: PropertiesFileTask) {
+- description = "Generate Eclipse additional settings"
+- def filename = "org.eclipse.jdt.ui.prefs"
+- outputFile = "$projectDir/.settings/${filename}" as File
+- file {
+- withProperties {
+- it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
++ /* test {
++ java {
++ srcDirs testSourceDir
++ outputDir = file(testClassesDir)
+ }
+- }
+-}
+
+-task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
+- description = "Generate Eclipse additional settings"
+- def filename = "org.eclipse.jdt.groovy.core.prefs"
+- outputFile = "$projectDir/.settings/${filename}" as File
+- file {
+- withProperties {
+- it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
++ resources {
++ srcDirs = sourceSets.main.resources.srcDirs
+ }
+- }
+-}
+-
+-task eclipseAllPreferences {
+- dependsOn eclipseJdt
+- dependsOn eclipseUIPreferences
+- dependsOn eclipseGroovyCorePreferences
+-}
+-
+-eclipseUIPreferences.mustRunAfter eclipseJdt
+-eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
+-
+-/* end of eclipse preferences hack */
+-
+-
+-// 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 = "${cloverReportDir}/clover.xml"
+- inputs.dir cloverClassesDir
+- outputs.file cloverXmlFile
+-
+- classpath = sourceSets.clover.runtimeClasspath
+- main = "com.atlassian.clover.reporters.xml.XMLReporter"
+-
+- if (cloverreport_mem.length() > 0) {
+- maxHeapSize = cloverreport_mem
+- }
+- if (cloverreport_jvmargs.length() > 0) {
+- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+- }
+-
+- def argsList = [
+- "--alwaysreport",
+- "--initstring",
+- cloverDb,
+- "--outfile",
+- cloverXmlFile
+- ]
+-
+- if (cloverreport_xml_options.length() > 0) {
+- argsList += cloverreport_xml_options.split(" ")
+- }
+
+- args argsList.toArray()
+-}
+-
+-
+-task cloverReport {
+- group = "Verification"
+- description = "Creates clover reports"
+-
+- dependsOn cloverXmlReport
+- dependsOn cloverHtmlReport
+-}
+-
+-
+-compileCloverJava {
++ compileClasspath = files( sourceSets.test.java.outputDir )
++ compileClasspath += sourceSets.main.compileClasspath
++ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["** REMOVE_THIS_GAP /*.jar"])
+
+- doFirst {
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- options.compilerArgs += additional_compiler_args
+- print ("Setting target compatibility to "+targetCompatibility+"\n")
++ runtimeClasspath = compileClasspath
+ }
+- //classpath += configurations.cloverRuntime
++*/
+ }
+-// end clover bits
+
+
+ compileJava {
+- // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+- options.encoding = "UTF-8"
+ doFirst {
+ print ("Setting target compatibility to "+compile_target_compatibility+"\n")
+ }
+-
+ }
+
+
+ compileTestJava {
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- options.compilerArgs = additional_compiler_args
+ doFirst {
++ sourceCompatibility = compile_source_compatibility
++ targetCompatibility = compile_target_compatibility
++ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ }
+@@ -1017,7 +244,6 @@
+
+
+ cleanTest {
+- dependsOn cleanClover
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ }
+@@ -1306,12 +532,7 @@
+ //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+ test {
+ dependsOn prepare
+-
+- if (useClover) {
+- dependsOn cloverClasses
+- } else { //?
+- dependsOn compileJava //?
+- }
++ dependsOn compileJava //?
+
+ useTestNG() {
+ includeGroups testng_groups
+@@ -1323,6 +544,7 @@
+ maxHeapSize = "1024m"
+
+ workingDir = jalviewDir
++ //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+@@ -1338,9 +560,6 @@
+ jvmArgs += additional_compiler_args
+
+ doFirst {
+- if (useClover) {
+- println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+- }
+ }
+ }
+
+@@ -1420,1752 +639,7 @@
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+- outputs.file("${outputDir}/${archiveFileName}")
+-}
+-
+-
+-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) {
+- dependsOn jar
+- from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
+- into "${jalviewDir}/${package_dir}"
+- preserve {
+- include jar.archiveFileName.getOrNull()
+- }
+-}
+-
+-
+-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"
+- description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
+- if (buildDist) {
+- dependsOn makeDist
+- }
+- from ("${jalviewDir}/${libDistDir}") {
+- include("*.jar")
+- }
+- manifest {
+- attributes "Implementation-Version": JALVIEW_VERSION,
+- "Application-Name": install4jApplicationName
+- }
+- 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(file(buildProperties).getName(), 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)
+- }
+- if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
+- props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
+- props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
+- props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
+- props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+- props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+- props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
+- }
+-
+- 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 = ${filename}\n"
+- }
+- getdownResourceFilenames.each{ filename ->
+- copy {
+- from filename
+- into getdownResourceDir
+- }
+- }
+-
+- def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+- getdownWrapperScripts.each{ script ->
+- def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+- if (s.exists()) {
+- copy {
+- from s
+- into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+- }
+- getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+- }
+- }
+-
+- 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
+- }
+- }
+-
+- // 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 = ${main_class}\n"
+- // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
+- if (getdownSetAppBaseProperty) {
+- getdownTextString += "jvmarg = -Dgetdowndistdir=${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}")
+-
+- // files going into the getdown website dir: getdown-launcher.jar
+- copy {
+- from getdownLauncher
+- rename(file(getdownLauncher).getName(), getdown_launcher_new)
+- into getdownWebsiteDir
+- }
+-
+- // files going into the getdown website dir: getdown-launcher(-local).jar
+- copy {
+- from getdownLauncher
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownWebsiteDir
+- }
+-
+- // files going into the getdown website dir: ./install dir and files
+- 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
+- }
+-
+- // and make a copy in the getdown files dir (these are not downloaded by getdown)
+- copy {
+- from getdownInstallDir
+- into getdownFilesInstallDir
+- }
+- }
+-
+- // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
+- 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
+- }
+-
+- // and ./resources (not all downloaded by getdown)
+- 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
+- }
+- }
+- }
+- }
+-}
+-
+-
+-tasks.withType(JavaCompile) {
+- options.encoding = 'UTF-8'
+-}
+-
+-
+-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("<actions>${install4jFileAssociationsText}</actions>")
+- 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
+- }
+- }
+-
+- // 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 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,
+- 'OSX_APPLEID': OSX_APPLEID,
+- 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
+- '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_DMG_DS_STORE': install4jDMGDSStore,
+- 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+- 'WRAPPER_LINK': getdownWrapperLink,
+- 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+- 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+- 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
+- '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,
+- 'MAC_ICONS_FILE': install4jMacIconsFile,
+- 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
+- 'PNG_ICON_FILE': install4jPngIconFile,
+- 'BACKGROUND': install4jBackground,
+-
+- ]
+-
+- //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
+- disableNotarization = true
+- }
+-
+- if (OSX_KEYPASS) {
+- macKeystorePassword = OSX_KEYPASS
+- }
+-
+- if (OSX_ALTOOLPASS) {
+- appleIdPassword = OSX_ALTOOLPASS
+- disableNotarization = false
+- } else {
+- disableNotarization = true
+- }
+-
+- doFirst {
+- println("Using projectFile "+projectFile)
+- if (!disableNotarization) { println("Will notarize OSX App DMG") }
+- }
+- //verbose=true
+-
+- 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}/${JAVA_VERSION}")
+-}
+-
+-
+-spotless {
+- java {
+- eclipse().configFile(eclipse_codestyle_file)
+- }
+-}
+-
+-
+-task sourceDist(type: Tar) {
+- group "distribution"
+- description "Create a source .tar.gz file for distribution"
+-
+- dependsOn createBuildProperties
+- dependsOn convertMdFiles
+-
+- def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+- def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
+- archiveFileName = outputFileName
+-
+- compression Compression.GZIP
+-
+- into project.name
+-
+- def EXCLUDE_FILES=[
+- "build/*",
+- "bin/*",
+- "test-output/",
+- "test-reports",
+- "tests",
+- "clover*/*",
+- ".*",
+- "benchmarking/*",
+- "**/.*",
+- "*.class",
+- "**/*.class","$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 ("${j11modDir}/**/*.jar")
+- }
+- from(jalviewDir) {
+- include(INCLUDE_FILES)
+- }
+-// from (jalviewDir) {
+-// // explicit includes for stuff that seemed to not get included
+-// include(fileTree("test/**/*."))
+-// exclude(EXCLUDE_FILES)
+-// exclude(PROCESS_FILES)
+-// }
+-
+- from(file(buildProperties).getParent()) {
+- include(file(buildProperties).getName())
+- rename(file(buildProperties).getName(), "build_properties")
+- filter({ line ->
+- line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+- })
+- }
+-
+-}
+-
+-
+-task helppages {
+- dependsOn copyHelp
+- dependsOn pubhtmlhelp
+-
+- inputs.dir("${helpBuildDir}/${help_dir}")
+- outputs.dir("${buildDir}/distributions/${help_dir}")
+-}
+-
+-
+-task j2sSetHeadlessBuild {
+- doFirst {
+- IN_ECLIPSE = false
+- }
+-}
+-
+-
+-task jalviewjsEnableAltFileProperty(type: WriteProperties) {
+- group "jalviewjs"
+- description "Enable the alternative J2S Config file for headless build"
+-
+- outputFile = jalviewjsJ2sSettingsFileName
+- def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
+- def j2sProps = new Properties()
+- if (j2sPropsFile.exists()) {
+- try {
+- def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
+- j2sProps.load(j2sPropsFileFIS)
+- j2sPropsFileFIS.close()
+-
+- j2sProps.each { prop, val ->
+- property(prop, val)
+- }
+- } catch (Exception e) {
+- println("Exception reading ${jalviewjsJ2sSettingsFileName}")
+- e.printStackTrace()
+- }
+- }
+- if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
+- property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
+- }
+-}
+-
+-
+-task jalviewjsSetEclipseWorkspace {
+- def propKey = "jalviewjs_eclipse_workspace"
+- def propVal = null
+- if (project.hasProperty(propKey)) {
+- propVal = project.getProperty(propKey)
+- if (propVal.startsWith("~/")) {
+- propVal = System.getProperty("user.home") + propVal.substring(1)
+- }
+- }
+- def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+- def propsFile = file(propsFileName)
+- def eclipseWsDir = propVal
+- def props = new Properties()
+-
+- def writeProps = true
+- if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+- def ins = new FileInputStream(propsFileName)
+- props.load(ins)
+- ins.close()
+- if (props.getProperty(propKey, null) != null) {
+- eclipseWsDir = props.getProperty(propKey)
+- writeProps = false
+- }
+- }
+-
+- if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
+- def tempDir = File.createTempDir()
+- eclipseWsDir = tempDir.getAbsolutePath()
+- writeProps = true
+- }
+- eclipseWorkspace = file(eclipseWsDir)
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+-
+- if (writeProps) {
+- props.setProperty(propKey, eclipseWsDir)
+- propsFile.parentFile.mkdirs()
+- def bytes = new ByteArrayOutputStream()
+- props.store(bytes, null)
+- def propertiesString = bytes.toString()
+- propsFile.text = propertiesString
+- print("NEW ")
+- } else {
+- print("EXISTING ")
+- }
+-
+- println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+- }
+-
+- //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
+- outputs.file(propsFileName)
+- outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
+-}
+-
+-
+-task jalviewjsEclipsePaths {
+- def eclipseProduct
+-
+- def eclipseRoot = jalviewjs_eclipse_root
+- if (eclipseRoot.startsWith("~/")) {
+- eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+- }
+- if (OperatingSystem.current().isMacOsX()) {
+- eclipseRoot += "/Eclipse.app"
+- eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
+- eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
+- } else if (OperatingSystem.current().isWindows()) { // check these paths!!
+- if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+- eclipseRoot += "/eclipse"
+- }
+- eclipseBinary = "${eclipseRoot}/eclipse.exe"
+- eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+- } else { // linux or unix
+- if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+- eclipseRoot += "/eclipse"
+-println("eclipseDir exists")
+- }
+- eclipseBinary = "${eclipseRoot}/eclipse"
+- eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+- }
+-
+- eclipseVersion = "4.13" // default
+- def assumedVersion = true
+- if (file(eclipseProduct).exists()) {
+- def fis = new FileInputStream(eclipseProduct)
+- def props = new Properties()
+- props.load(fis)
+- eclipseVersion = props.getProperty("version")
+- fis.close()
+- assumedVersion = false
+- }
+-
+- def propKey = "eclipse_debug"
+- eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+-
+- if (!assumedVersion) {
+- println("ECLIPSE VERSION=${eclipseVersion}")
+- }
+- }
+-}
+-
+-
+-task printProperties {
+- group "Debug"
+- description "Output to console all System.properties"
+- doFirst {
+- System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
+- }
+-}
+-
+-
+-task eclipseSetup {
+- dependsOn eclipseProject
+- dependsOn eclipseClasspath
+- dependsOn eclipseJdt
+-}
+-
+-
+-// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
+-task jalviewjsEclipseCopyDropins(type: Copy) {
+- dependsOn jalviewjsEclipsePaths
+-
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+- inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+-
+- from inputFiles
+- into outputDir
+-}
+-
+-
+-// this eclipse -clean doesn't actually work
+-task jalviewjsCleanEclipse(type: Exec) {
+- dependsOn eclipseSetup
+- dependsOn jalviewjsEclipsePaths
+- dependsOn jalviewjsEclipseCopyDropins
+-
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += "-l"
+-
+- def inputString = """exit
+-y
+-"""
+- def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
+- standardInput = inputByteStream
+-}
+-
+-/* not really working yet
+-jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
+-*/
+-
+-
+-task jalviewjsTransferUnzipSwingJs {
+- def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
+-
+- doLast {
+- copy {
+- from zipTree(file_zip)
+- into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+- }
+- }
+-
+- inputs.file file_zip
+- outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+-}
+-
+-
+-task jalviewjsTransferUnzipLib {
+- def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+-
+- doLast {
+- zipFiles.each { file_zip ->
+- copy {
+- from zipTree(file_zip)
+- into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+- }
+- }
+- }
+-
+- inputs.files zipFiles
+- outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+-}
+-
+-
+-task jalviewjsTransferUnzipAllLibs {
+- dependsOn jalviewjsTransferUnzipSwingJs
+- dependsOn jalviewjsTransferUnzipLib
+-}
+-
+-
+-task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+- group "JalviewJS"
+- description "Create the alternative j2s file from the j2s.* properties"
+-
+- jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+- def siteDirProperty = "j2s.site.directory"
+- def setSiteDir = false
+- jalviewjsJ2sProps.each { prop, val ->
+- if (val != null) {
+- if (prop == siteDirProperty) {
+- if (!(val.startsWith('/') || val.startsWith("file://") )) {
+- val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
+- }
+- setSiteDir = true
+- }
+- property(prop,val)
+- }
+- if (!setSiteDir) { // default site location, don't override specifically set property
+- property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
+- }
+- }
+- outputFile = jalviewjsJ2sAltSettingsFileName
+-
+- if (! IN_ECLIPSE) {
+- inputs.properties(jalviewjsJ2sProps)
+- outputs.file(jalviewjsJ2sAltSettingsFileName)
+- }
+-}
+-
+-
+-task jalviewjsEclipseSetup {
+- dependsOn jalviewjsEclipseCopyDropins
+- dependsOn jalviewjsSetEclipseWorkspace
+- dependsOn jalviewjsCreateJ2sSettings
+-}
+-
+-
+-task jalviewjsSyncAllLibs (type: Sync) {
+- dependsOn jalviewjsTransferUnzipAllLibs
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+- inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncResources (type: Sync) {
+- dependsOn buildResources
+-
+- def inputFiles = fileTree(dir: resourcesBuildDir)
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncSiteResources (type: Sync) {
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncBuildProperties (type: Sync) {
+- dependsOn createBuildProperties
+- def inputFiles = [file(buildProperties)]
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsProjectImport(type: Exec) {
+- dependsOn eclipseSetup
+- dependsOn jalviewjsEclipsePaths
+- dependsOn jalviewjsEclipseSetup
+-
+- doFirst {
+- // do not run a headless import when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+- }
+-
+- //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+- def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+- if (!IN_ECLIPSE) {
+- args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+- args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
+- }
+-
+- inputs.file("${jalviewDir}/.project")
+- outputs.upToDateWhen {
+- file(projdir).exists()
+- }
+-}
+-
+
+-task jalviewjsTranspile(type: Exec) {
+- dependsOn jalviewjsEclipseSetup
+- dependsOn jalviewjsProjectImport
+- dependsOn jalviewjsEclipsePaths
+- if (!IN_ECLIPSE) {
+- dependsOn jalviewjsEnableAltFileProperty
+- }
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+- }
+-
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+- if (!IN_ECLIPSE) {
+- args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+- args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
+- }
+-
+- def stdout
+- def stderr
+- doFirst {
+- stdout = new ByteArrayOutputStream()
+- stderr = new ByteArrayOutputStream()
+-
+- def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+- def logOutFile = file(logOutFileName)
+- logOutFile.createNewFile()
+- logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+-BINARY: ${eclipseBinary}
+-VERSION: ${eclipseVersion}
+-WORKSPACE: ${eclipseWorkspace}
+-DEBUG: ${eclipseDebug}
+-----
+-"""
+- def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+- // combine stdout and stderr
+- def logErrFOS = logOutFOS
+-
+- if (jalviewjs_j2s_to_console.equals("true")) {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout),
+- System.out)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr),
+- System.err)
+- } else {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr)
+- }
+- }
+-
+- doLast {
+- if (stdout.toString().contains("Error processing ")) {
+- // j2s did not complete transpile
+- //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- if (jalviewjs_ignore_transpile_errors.equals("true")) {
+- println("IGNORING TRANSPILE ERRORS")
+- println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- } else {
+- throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- }
+- }
+- }
+-
+- inputs.dir("${jalviewDir}/${sourceDir}")
+- outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+- outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+-}
+-
+-
+-def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+-
+- def stdout = new ByteArrayOutputStream()
+- def stderr = new ByteArrayOutputStream()
+-
+- def coreFile = file(jsfile)
+- def msg = ""
+- msg = "Creating core for ${name}...\nGenerating ${jsfile}"
+- println(msg)
+- logOutFile.createNewFile()
+- logOutFile.append(msg+"\n")
+-
+- def coreTop = file(prefixFile)
+- def coreBottom = file(suffixFile)
+- coreFile.getParentFile().mkdirs()
+- coreFile.createNewFile()
+- coreFile.write( coreTop.getText("UTF-8") )
+- list.each {
+- f ->
+- if (f.exists()) {
+- def t = f.getText("UTF-8")
+- t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
+- coreFile.append( t )
+- } else {
+- msg = "...file '"+f.getPath()+"' does not exist, skipping"
+- println(msg)
+- logOutFile.append(msg+"\n")
+- }
+- }
+- coreFile.append( coreBottom.getText("UTF-8") )
+-
+- msg = "Generating ${zjsfile}"
+- println(msg)
+- logOutFile.append(msg+"\n")
+- def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+- def logErrFOS = logOutFOS
+-
+- javaexec {
+- classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
+- main = "com.google.javascript.jscomp.CommandLineRunner"
+- jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+- args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+- maxHeapSize = "2g"
+-
+- msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+- println(msg)
+- logOutFile.append(msg+"\n")
+-
+- if (logOutConsole) {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout),
+- standardOutput)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr),
+- errorOutput)
+- } else {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr)
+- }
+- }
+- msg = "--"
+- println(msg)
+- logOutFile.append(msg+"\n")
+-}
+-
+-
+-task jalviewjsBuildAllCores {
+- group "JalviewJS"
+- description "Build the core js lib closures listed in the classlists dir"
+- dependsOn jalviewjsTranspile
+- dependsOn jalviewjsTransferUnzipSwingJs
+-
+- def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+- def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+- def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
+- def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+- def prefixFile = "${jsDir}/core/coretop2.js"
+- def suffixFile = "${jsDir}/core/corebottom2.js"
+-
+- inputs.file prefixFile
+- inputs.file suffixFile
+-
+- def classlistFiles = []
+- // add the classlists found int the jalviewjs_classlists_dir
+- fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
+- file ->
+- def name = file.getName() - ".txt"
+- classlistFiles += [
+- 'file': file,
+- 'name': name
+- ]
+- }
+-
+- // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+- //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+- classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
+-
+- jalviewjsCoreClasslists = []
+-
+- classlistFiles.each {
+- hash ->
+-
+- def file = hash['file']
+- if (! file.exists()) {
+- //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+- return false // this is a "continue" in groovy .each closure
+- }
+- def name = hash['name']
+- if (name == null) {
+- name = file.getName() - ".txt"
+- }
+-
+- def filelist = []
+- file.eachLine {
+- line ->
+- filelist += line
+- }
+- def list = fileTree(dir: j2sDir, includes: filelist)
+-
+- def jsfile = "${outputDir}/core${name}.js"
+- def zjsfile = "${outputDir}/core${name}.z.js"
+-
+- jalviewjsCoreClasslists += [
+- 'jsfile': jsfile,
+- 'zjsfile': zjsfile,
+- 'list': list,
+- 'name': name
+- ]
+-
+- inputs.file(file)
+- inputs.files(list)
+- outputs.file(jsfile)
+- outputs.file(zjsfile)
+- }
+-
+- // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+- def stevesoftClasslistName = "_stevesoft"
+- def stevesoftClasslist = [
+- 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+- 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+- 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+- 'name': stevesoftClasslistName
+- ]
+- jalviewjsCoreClasslists += stevesoftClasslist
+- inputs.files(stevesoftClasslist['list'])
+- outputs.file(stevesoftClasslist['jsfile'])
+- outputs.file(stevesoftClasslist['zjsfile'])
+-
+- // _all core
+- def allClasslistName = "_all"
+- def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+- allJsFiles += fileTree(
+- dir: libJ2sDir,
+- include: "**/*.js",
+- excludes: [
+- // these exlusions are files that the closure-compiler produces errors for. Should fix them
+- "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+- "**/org/jmol/export/JSExporter.js"
+- ]
+- )
+- allJsFiles += fileTree(
+- dir: swingJ2sDir,
+- include: "**/*.js",
+- excludes: [
+- // these exlusions are files that the closure-compiler produces errors for. Should fix them
+- "**/sun/misc/Unsafe.js",
+- "**/swingjs/jquery/jquery-editable-select.js",
+- "**/swingjs/jquery/j2sComboBox.js",
+- "**/sun/misc/FloatingDecimal.js"
+- ]
+- )
+- def allClasslist = [
+- 'jsfile': "${outputDir}/core${allClasslistName}.js",
+- 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+- 'list': allJsFiles,
+- 'name': allClasslistName
+- ]
+- // not including this version of "all" core at the moment
+- //jalviewjsCoreClasslists += allClasslist
+- inputs.files(allClasslist['list'])
+- outputs.file(allClasslist['jsfile'])
+- outputs.file(allClasslist['zjsfile'])
+-
+- doFirst {
+- def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+- logOutFile.getParentFile().mkdirs()
+- logOutFile.createNewFile()
+- logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+-
+- jalviewjsCoreClasslists.each {
+- jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+- }
+- }
+-
+-}
+-
+-
+-def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+- copy {
+- from inputFile
+- into file(outputFile).getParentFile()
+- rename { filename ->
+- if (filename.equals(inputFile.getName())) {
+- return file(outputFile).getName()
+- }
+- return null
+- }
+- filter(ReplaceTokens,
+- beginToken: '_',
+- endToken: '_',
+- tokens: [
+- 'MAIN': '"'+main_class+'"',
+- 'CODE': "null",
+- 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+- 'COREKEY': jalviewjs_core_key,
+- 'CORENAME': coreName
+- ]
+- )
+- }
+-}
+-
+-
+-task jalviewjsPublishCoreTemplates {
+- dependsOn jalviewjsBuildAllCores
+- def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+- def inputFile = file(inputFileName)
+- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+-
+- def outputFiles = []
+- jalviewjsCoreClasslists.each { cl ->
+- def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+- cl['outputfile'] = outputFile
+- outputFiles += outputFile
+- }
+-
+- doFirst {
+- jalviewjsCoreClasslists.each { cl ->
+- jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+- }
+- }
+- inputs.file(inputFile)
+- outputs.files(outputFiles)
+-}
+-
+-
+-task jalviewjsSyncCore (type: Sync) {
+- dependsOn jalviewjsBuildAllCores
+- dependsOn jalviewjsPublishCoreTemplates
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-// this Copy version of TransferSiteJs will delete anything else in the target dir
+-task jalviewjsCopyTransferSiteJs(type: Copy) {
+- dependsOn jalviewjsTranspile
+- from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- into "${jalviewDir}/${jalviewjsSiteDir}"
+-}
+-
+-
+-// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+-task jalviewjsSyncTransferSiteJs(type: Sync) {
+- from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- include "**/*.*"
+- into "${jalviewDir}/${jalviewjsSiteDir}"
+- preserve {
+- include "**"
+- }
+-}
+-
+-
+-jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+-
+-jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+-
+-
+-task jalviewjsPrepareSite {
+- group "JalviewJS"
+- description "Prepares the website folder including unzipping files and copying resources"
+- dependsOn jalviewjsSyncAllLibs
+- dependsOn jalviewjsSyncResources
+- dependsOn jalviewjsSyncSiteResources
+- dependsOn jalviewjsSyncBuildProperties
+- dependsOn jalviewjsSyncCore
+-}
+-
+-
+-task jalviewjsBuildSite {
+- group "JalviewJS"
+- description "Builds the whole website including transpiled code"
+- dependsOn jalviewjsCopyTransferSiteJs
+- dependsOn jalviewjsPrepareSite
+-}
+-
+-
+-task cleanJalviewjsTransferSite {
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+- }
+-}
+-
+-
+-task cleanJalviewjsSite {
+- dependsOn cleanJalviewjsTransferSite
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsSiteDir}"
+- }
+-}
+-
+-
+-task jalviewjsSiteTar(type: Tar) {
+- group "JalviewJS"
+- description "Creates a tar.gz file for the website"
+- dependsOn jalviewjsBuildSite
+- def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
+- archiveFileName = outputFilename
+-
+- compression Compression.GZIP
+-
+- from "${jalviewDir}/${jalviewjsSiteDir}"
+- into jalviewjs_site_dir // this is inside the tar file
+-
+- inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
+-}
+-
+-
+-task jalviewjsServer {
+- group "JalviewJS"
+- def filename = "jalviewjsTest.html"
+- description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
+- def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
+- doLast {
+-
+- def factory
+- try {
+- def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+- factory = f.newInstance()
+- } catch (ClassNotFoundException e) {
+- throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+- }
+- def port = Integer.valueOf(jalviewjs_server_port)
+- def start = port
+- def running = false
+- def url
+- def jalviewjsServer
+- while(port < start+1000 && !running) {
+- try {
+- def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
+- jalviewjsServer = factory.start(doc_root, port)
+- running = true
+- url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
+- println("SERVER STARTED with document root ${doc_root}.")
+- println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
+- println("For debug: "+url+"?j2sdebug")
+- println("For verbose: "+url+"?j2sverbose")
+- } catch (Exception e) {
+- port++;
+- }
+- }
+- def htmlText = """
+- <p><a href="${url}">JalviewJS Test. <${url}></a></p>
+- <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
+- <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
+- """
+- jalviewjsCoreClasslists.each { cl ->
+- def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+- htmlText += """
+- <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
+- """
+- println("For core ${cl.name}: "+urlcore)
+- }
+-
+- file(htmlFile).text = htmlText
+- }
+-
+- outputs.file(htmlFile)
+- outputs.upToDateWhen({false})
+-}
+-
+-
+-task cleanJalviewjsAll {
+- group "JalviewJS"
+- description "Delete all configuration and build artifacts to do with JalviewJS build"
+- dependsOn cleanJalviewjsSite
+- dependsOn jalviewjsEclipsePaths
+-
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsBuildDir}"
+- delete "${jalviewDir}/${eclipse_bin_dir}"
+- if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
+- delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+- }
+- delete jalviewjsJ2sAltSettingsFileName
+- }
+-
+- outputs.upToDateWhen( { false } )
+-}
+-
+-
+-task jalviewjsIDE_checkJ2sPlugin {
+- group "00 JalviewJS in Eclipse"
+- description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+-
+- doFirst {
+- def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def j2sPluginFile = file(j2sPlugin)
+- def eclipseHome = System.properties["eclipse.home.location"]
+- if (eclipseHome == null || ! IN_ECLIPSE) {
+- throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+- }
+- def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
+- def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
+- if (altPluginsDir != null && file(altPluginsDir).exists()) {
+- eclipseJ2sPluginDirs += altPluginsDir
+- }
+- def foundPlugin = false
+- def j2sPluginFileName = j2sPluginFile.getName()
+- def eclipseJ2sPlugin
+- def eclipseJ2sPluginFile
+- eclipseJ2sPluginDirs.any { dir ->
+- eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
+- eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+- if (eclipseJ2sPluginFile.exists()) {
+- foundPlugin = true
+- return true
+- }
+- }
+- if (!foundPlugin) {
+- def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
+- System.err.println(msg)
+- throw new StopExecutionException(msg)
+- }
+-
+- def digest = MessageDigest.getInstance("MD5")
+-
+- digest.update(j2sPluginFile.text.bytes)
+- def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+-
+- digest.update(eclipseJ2sPluginFile.text.bytes)
+- def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+-
+- if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+- def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+- System.err.println(msg)
+- throw new StopExecutionException(msg)
+- } else {
+- def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
+- println(msg)
+- }
+- }
+-}
+-
+-task jalviewjsIDE_copyJ2sPlugin {
+- group "00 JalviewJS in Eclipse"
+- description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
+-
+- doFirst {
+- def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def j2sPluginFile = file(j2sPlugin)
+- def eclipseHome = System.properties["eclipse.home.location"]
+- if (eclipseHome == null || ! IN_ECLIPSE) {
+- throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
+- }
+- def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+- def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+- def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
+- System.err.println(msg)
+- copy {
+- from j2sPlugin
+- eclipseJ2sPluginFile.getParentFile().mkdirs()
+- into eclipseJ2sPluginFile.getParent()
+- }
+- }
+-}
+-
+-
+-task jalviewjsIDE_j2sFile {
+- group "00 JalviewJS in Eclipse"
+- description "Creates the .j2s file"
+- dependsOn jalviewjsCreateJ2sSettings
+-}
+-
+-
+-task jalviewjsIDE_SyncCore {
+- group "00 JalviewJS in Eclipse"
+- description "Build the core js lib closures listed in the classlists dir and publish core html from template"
+- dependsOn jalviewjsSyncCore
+-}
+-
+-
+-task jalviewjsIDE_SyncSiteAll {
+- dependsOn jalviewjsSyncAllLibs
+- dependsOn jalviewjsSyncResources
+- dependsOn jalviewjsSyncSiteResources
+- dependsOn jalviewjsSyncBuildProperties
+-}
+-
+-
+-cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+-
+-
+-task jalviewjsIDE_PrepareSite {
+- group "00 JalviewJS in Eclipse"
+- description "Sync libs and resources to site dir, but not closure cores"
+-
+- dependsOn jalviewjsIDE_SyncSiteAll
+- //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
+-}
+-
+-
+-task jalviewjsIDE_AssembleSite {
+- group "00 JalviewJS in Eclipse"
+- description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
+- dependsOn jalviewjsPrepareSite
+-}
+-
+-
+-task jalviewjsIDE_SiteClean {
+- group "00 JalviewJS in Eclipse"
+- description "Deletes the Eclipse transpiled site"
+- dependsOn cleanJalviewjsSite
+-}
+-
+-
+-task jalviewjsIDE_Server {
+- group "00 JalviewJS in Eclipse"
+- description "Starts a webserver on localhost to test the website"
+- dependsOn jalviewjsServer
+-}
+-
+-
+-// buildship runs this at import or gradle refresh
+-task eclipseSynchronizationTask {
+- //dependsOn eclipseSetup
+- dependsOn createBuildProperties
+- if (J2S_ENABLED) {
+- dependsOn jalviewjsIDE_j2sFile
+- dependsOn jalviewjsIDE_checkJ2sPlugin
+- dependsOn jalviewjsIDE_PrepareSite
+- }
+-}
+-
+-
+-// buildship runs this at build time or project refresh
+-task eclipseAutoBuildTask {
+- //dependsOn jalviewjsIDE_checkJ2sPlugin
+- //dependsOn jalviewjsIDE_PrepareSite
++ outputs.file("${outputDir}/${archiveFileName}")
+ }
+
+-
+-task jalviewjs {
+- group "JalviewJS"
+- description "Build the site"
+- dependsOn jalviewjsBuildSite
+-}
git://source.jalview.org / jalview.git / commitdiff