+ inputs.dir(sourceSets.main.java.outputDir)
+ 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": applicationName
+ }
+
+ duplicatesStrategy "INCLUDE"
+
+ 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 getdownResourceDir = getdownResourceDir
+ def getdownResourceFilenames = []
+
+ doFirst {
+ // clean the getdown website and files dir before creating getdown folders
+ delete getdownAppBaseDir
+ delete getdownFilesDir
+
+ copy {
+ from buildProperties
+ rename(file(buildProperties).getName(), getdown_build_properties)
+ into getdownAppDir
+ }
+ getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
+
+ copy {
+ from channelPropsFile
+ into getdownAppBaseDir
+ }
+ getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
+
+ // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
+ 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", applicationName)
+
+ // start with appbase
+ getdownTextLines += "appbase = ${getdownAppBase}"
+ props.each{ prop, val ->
+ if (prop.startsWith("getdown_txt_") && val != null) {
+ if (prop.startsWith("getdown_txt_multi_")) {
+ def key = prop.substring(18)
+ val.split(",").each{ v ->
+ def line = "${key} = ${v}"
+ getdownTextLines += line
+ }
+ } else {
+ // file values rationalised
+ if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
+ def r = null
+ if (val.indexOf('/') == 0) {
+ // absolute path
+ r = file(val)
+ } else if (val.indexOf('/') > 0) {
+ // relative path (relative to jalviewDir)
+ r = file( "${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}"
+ getdownTextLines += line
+ }
+ }
+ }
+ }
+
+ getdownWebsiteResourceFilenames.each{ filename ->
+ getdownTextLines += "resource = ${filename}"
+ }
+ getdownResourceFilenames.each{ filename ->
+ copy {
+ from filename
+ into getdownResourceDir
+ }
+ }
+
+ def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+ getdownWrapperScripts.each{ script ->
+ def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+ if (s.exists()) {
+ copy {
+ from s
+ into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
+ }
+ getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
+ }
+ }
+
+ 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
+ }
+ }
+ def jalviewJar = jar.archiveFileName.getOrNull()
+ // put jalview.jar first for CLASSPATH and .properties files reasons
+ codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
+ def name = f.getName()
+ def line = "code = ${getdownAppDistDir}/${name}"
+ getdownTextLines += 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}"
+ getdownTextLines += 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.
+ //getdownTextLines += "class = " + file(getdownLauncher).getName()
+ getdownTextLines += "resource = ${getdown_launcher_new}"
+ getdownTextLines += "class = ${main_class}"
+ // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
+ if (getdownSetAppBaseProperty) {
+ getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
+ getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
+ }
+
+ def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
+ getdownTxt.write(getdownTextLines.join("\n"))
+
+ getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+ def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
+ launchJvl.write("appbase=${getdownAppBase}")
+
+ // files going into the getdown website dir: getdown-launcher.jar
+ copy {
+ from getdownLauncher
+ rename(file(getdownLauncher).getName(), getdown_launcher_new)
+ into getdownAppBaseDir
+ }
+
+ // 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 getdownAppBaseDir
+ }
+
+ // files going into the getdown website dir: ./install dir and files
+ if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
+ copy {
+ from getdownTxt
+ 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 getdownTxt
+ from launchJvl
+ from getdownLauncher
+ from "${getdownAppBaseDir}/${getdown_build_properties}"
+ from "${getdownAppBaseDir}/${channel_props}"
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownFilesDir
+ }
+
+ // and ./resource (not all downloaded by getdown)
+ copy {
+ from getdownResourceDir
+ into "${getdownFilesDir}/${getdown_resource_dir}"
+ }
+ }
+
+ if (buildDist) {
+ inputs.dir("${jalviewDir}/${package_dir}")
+ }
+ outputs.dir(getdownAppBaseDir)
+ 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 getdownAppBaseDir
+ inputs.dir(getdownAppBaseDir)
+ outputs.file("${getdownAppBaseDir}/digest2.txt")
+}
+
+
+task getdown() {
+ group = "distribution"
+ description = "Create the minimal and full getdown app folder for installers and website and create digest file"
+ dependsOn getdownDigest
+ doLast {
+ if (reportRsyncCommand) {
+ def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
+ def toDir = "${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
+ }
+ }
+ }
+ }
+}
+
+
+task getdownArchiveBuild() {
+ group = "distribution"
+ description = "Put files in the archive dir to go on the website"
+
+ dependsOn getdownWebsite
+
+ def v = "v${JALVIEW_VERSION_UNDERSCORES}"
+ def vDir = "${getdownArchiveDir}/${v}"
+ getdownFullArchiveDir = "${vDir}/getdown"
+ getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
+
+ def vAltDir = "alt_${v}"
+ def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
+
+ doFirst {
+ // cleanup old "old" dir
+ delete getdownArchiveDir
+
+ def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
+ getdownArchiveTxt.getParentFile().mkdirs()
+ def getdownArchiveTextLines = []
+ def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
+
+ // the libdir
+ copy {
+ from "${getdownAppBaseDir}/${getdownAppDistDir}"
+ into "${getdownFullArchiveDir}/${vAltDir}"
+ }
+
+ getdownTextLines.each { line ->
+ line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
+ line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
+ line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
+ line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
+ line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
+ line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
+ // remove the existing resource = resource/ or bin/ lines
+ if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
+ getdownArchiveTextLines += line
+ }
+ }
+
+ // the resource dir -- add these files as resource lines in getdown.txt
+ copy {
+ from "${archiveImagesDir}"
+ into "${getdownFullArchiveDir}/${getdown_resource_dir}"
+ eachFile { file ->
+ getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
+ }
+ }
+
+ getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
+
+ def vLaunchJvl = file(getdownVersionLaunchJvl)
+ vLaunchJvl.getParentFile().mkdirs()
+ vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
+ def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
+ def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
+ // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
+ //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
+ java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
+
+ // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
+ copy {
+ from getdownLauncher
+ from "${getdownAppBaseDir}/${getdownLaunchJvl}"
+ from "${getdownAppBaseDir}/${getdown_launcher_new}"
+ from "${getdownAppBaseDir}/${channel_props}"
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownFullArchiveDir
+ }
+
+ }
+}
+
+task getdownArchiveDigest(type: JavaExec) {
+ group = "distribution"
+ description = "Digest the getdown archive folder"
+
+ dependsOn getdownArchiveBuild
+
+ doFirst {
+ classpath = files(getdownLauncher)
+ args getdownFullArchiveDir
+ }
+ main = "com.threerings.getdown.tools.Digester"
+ inputs.dir(getdownFullArchiveDir)
+ outputs.file("${getdownFullArchiveDir}/digest2.txt")
+}
+
+task getdownArchive() {
+ group = "distribution"
+ description = "Build the website archive dir with getdown digest"
+
+ dependsOn getdownArchiveBuild
+ dependsOn getdownArchiveDigest
+}
+
+tasks.withType(JavaCompile) {
+ options.encoding = 'UTF-8'
+}
+
+
+clean {
+ doFirst {
+ delete getdownAppBaseDir
+ delete getdownFilesDir
+ delete getdownArchiveDir
+ }
+}
+
+
+install4j {
+ if (file(install4jHomeDir).exists()) {
+ // good to go!
+ } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
+ install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+ } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
+ install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
+ }
+ installDir(file(install4jHomeDir))
+
+ mediaTypes = Arrays.asList(install4j_media_types.split(","))
+}
+
+
+task copyInstall4jTemplate {
+ def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+ def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+ inputs.file(install4jTemplateFile)
+ inputs.file(install4jFileAssociationsFile)
+ inputs.property("CHANNEL", { CHANNEL })
+ outputs.file(install4jConfFile)
+
+ doLast {
+ def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
+
+ // turn off code signing if no OSX_KEYPASS
+ if (OSX_KEYPASS == "") {
+ install4jConfigXml.'**'.codeSigning.each { codeSigning ->
+ codeSigning.'@macEnabled' = "false"
+ }
+ install4jConfigXml.'**'.windows.each { windows ->
+ windows.'@runPostProcessor' = "false"
+ }
+ }
+
+ // disable install screen for OSX dmg (for 2.11.2.0)
+ install4jConfigXml.'**'.macosArchive.each { macosArchive ->
+ macosArchive.attributes().remove('executeSetupApp')
+ macosArchive.attributes().remove('setupAppId')
+ }
+
+ // turn off checksum creation for LOCAL channel
+ def e = install4jConfigXml.application[0]
+ e.'@createChecksums' = string(install4jCheckSums)
+
+ // put file association actions where placeholder action is
+ def install4jFileAssociationsText = install4jFileAssociationsFile.text
+ def fileAssociationActions = new XmlParser().parseText("<actions>${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 cleanInstallersDataFiles {
+ def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
+ def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
+ def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
+ doFirst {
+ delete installersOutputTxt
+ delete installersSha256
+ delete hugoDataJsonFile
+ }
+}
+
+task installerFiles(type: com.install4j.gradle.Install4jTask) {
+ group = "distribution"
+ description = "Create the install4j installers"
+ dependsOn getdown
+ dependsOn copyInstall4jTemplate
+ dependsOn cleanInstallersDataFiles
+
+ projectFile = install4jConfFile
+
+ // create an md5 for the input files to use as version for install4j conf file
+ def digest = MessageDigest.getInstance("MD5")
+ digest.update(
+ (file("${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}"
+
+ variables = [
+ 'JALVIEW_NAME': jalview_name,
+ 'JALVIEW_APPLICATION_NAME': applicationName,
+ '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_CHANNEL_DIR': getdownChannelDir,
+ '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(getdownAppBaseDir)
+ inputs.file(install4jConfFile)
+ inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
+ inputs.dir(macosJavaVMDir)
+ inputs.dir(windowsJavaVMDir)
+ outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
+}
+
+def getDataHash(File myFile) {
+ HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
+ return myFile.exists()
+ ? [
+ "file" : myFile.getName(),
+ "filesize" : myFile.length(),
+ "sha256" : hash.toString()
+ ]
+ : null
+}
+
+def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
+ def hash = [
+ "channel" : getdownChannelName,
+ "date" : getDate("yyyy-MM-dd HH:mm:ss"),
+ "git-commit" : "${gitHash} [${gitBranch}]",
+ "version" : JALVIEW_VERSION
+ ]
+ // install4j installer files
+ if (installersOutputTxt.exists()) {
+ def idHash = [:]
+ installersOutputTxt.readLines().each { def line ->
+ if (line.startsWith("#")) {
+ return;
+ }
+ line.replaceAll("\n","")
+ def vals = line.split("\t")
+ def filename = vals[3]
+ def filesize = file(filename).length()
+ filename = filename.replaceAll(/^.*\//, "")
+ hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
+ idHash."${filename}" = vals[0]
+ }
+ if (install4jCheckSums && installersSha256.exists()) {
+ installersSha256.readLines().each { def line ->
+ if (line.startsWith("#")) {
+ return;
+ }
+ line.replaceAll("\n","")
+ def vals = line.split(/\s+\*?/)
+ def filename = vals[1]
+ def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
+ }
+ }
+ }
+
+ [
+ "JAR": shadowJar.archiveFile, // executable JAR
+ "JVL": getdownVersionLaunchJvl, // version JVL
+ "SOURCE": sourceDist.archiveFile // source TGZ
+ ].each { key, value ->
+ def file = file(value)
+ if (file.exists()) {
+ def fileHash = getDataHash(file)
+ if (fileHash != null) {
+ hash."${key}" = fileHash;
+ }
+ }
+ }
+ return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
+}
+
+task staticMakeInstallersJsonFile {
+ doFirst {
+ def output = findProperty("i4j_output")
+ def sha256 = findProperty("i4j_sha256")
+ def json = findProperty("i4j_json")
+ if (output == null || sha256 == null || json == null) {
+ throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
+ }
+ writeDataJsonFile(file(output), file(sha256), file(json))
+ }
+}
+
+task installers {
+ dependsOn installerFiles
+}
+
+
+spotless {
+ java {
+ eclipse().configFile(eclipse_codestyle_file)
+ }
+}
+
+task createSourceReleaseProperties(type: WriteProperties) {
+ group = "distribution"
+ description = "Create the source RELEASE properties file"
+
+ def sourceTarBuildDir = "${buildDir}/sourceTar"
+ def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
+ outputFile (sourceReleasePropertiesFile)
+
+ doFirst {
+ releaseProps.each{ key, val -> property key, val }
+ property "git.branch", gitBranch
+ property "git.hash", gitHash
+ }
+
+ outputs.file(outputFile)
+}
+
+task sourceDist(type: Tar) {
+ group "distribution"
+ description "Create a source .tar.gz file for distribution"
+
+ dependsOn createBuildProperties
+ dependsOn convertMdFiles
+ dependsOn eclipseAllPreferences
+ dependsOn createSourceReleaseProperties
+
+
+ def outputFileName = "${project.name}_${JALVIEW_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",
+ "RELEASE",
+ ]
+ def PROCESS_FILES=[
+ "AUTHORS",
+ "CITATION",
+ "FEATURETODO",
+ "JAVA-11-README",
+ "FEATURETODO",
+ "LICENSE",
+ "**/README",
+ "THIRDPARTYLIBS",
+ "TESTNG",
+ "build.gradle",
+ "gradle.properties",
+ "**/*.java",
+ "**/*.html",
+ "**/*.xml",
+ "**/*.gradle",
+ "**/*.groovy",
+ "**/*.properties",
+ "**/*.perl",
+ "**/*.sh",
+ ]
+ def INCLUDE_FILES=[
+ ".classpath",
+ ".settings/org.eclipse.buildship.core.prefs",
+ ".settings/org.eclipse.jdt.core.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)
+ // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
+ //exclude (getdown_website_dir)
+ //exclude (getdown_archive_dir)
+
+ // exluding these as not using jars as modules yet
+ exclude ("${j11modDir}/**/*.jar")
+ }
+ from(jalviewDir) {
+ include(INCLUDE_FILES)
+ }
+// from (jalviewDir) {
+// // explicit includes for stuff that seemed to not get included
+// include(fileTree("test/**/*."))
+// exclude(EXCLUDE_FILES)
+// exclude(PROCESS_FILES)
+// }
+
+ from(file(buildProperties).getParent()) {
+ include(file(buildProperties).getName())
+ rename(file(buildProperties).getName(), "build_properties")
+ filter({ line ->
+ line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+ })
+ }
+
+ def sourceTarBuildDir = "${buildDir}/sourceTar"
+ from(sourceTarBuildDir) {
+ // this includes the appended RELEASE properties file
+ }
+}
+
+task dataInstallersJson {
+ group "website"
+ description "Create the installers-VERSION.json data file for installer files created"
+
+ mustRunAfter installers
+ mustRunAfter shadowJar
+ mustRunAfter sourceDist
+ mustRunAfter getdownArchive
+
+ def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
+ def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
+
+ if (installersOutputTxt.exists()) {
+ inputs.file(installersOutputTxt)
+ }
+ if (install4jCheckSums && installersSha256.exists()) {
+ inputs.file(installersSha256)
+ }
+ [
+ shadowJar.archiveFile, // executable JAR
+ getdownVersionLaunchJvl, // version JVL
+ sourceDist.archiveFile // source TGZ
+ ].each { fileName ->
+ if (file(fileName).exists()) {
+ inputs.file(fileName)
+ }
+ }
+
+ outputs.file(hugoDataJsonFile)
+
+ doFirst {
+ writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
+ }
+}
+
+task helppages {
+ group "help"
+ description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
+
+ 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 "**"
+ }
+
+ // should this be exclude really ?
+ duplicatesStrategy "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}/${jalviewjs_closure_compiler}"])
+ main = "com.google.javascript.jscomp.CommandLineRunner"
+ jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+ args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+ maxHeapSize = "2g"
+
+ msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+ println(msg)
+ logOutFile.append(msg+"\n")
+
+ if (logOutConsole) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr),
+ System.err)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr)
+ }
+ }
+ msg = "--"
+ println(msg)
+ logOutFile.append(msg+"\n")
+}
+
+
+task jalviewjsBuildAllCores {
+ group "JalviewJS"
+ description "Build the core js lib closures listed in the classlists dir"
+ dependsOn jalviewjsTranspile
+ dependsOn jalviewjsTransferUnzipSwingJs
+
+ def j2sDir = "${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
+}
+
+
+task jalviewjs {
+ group "JalviewJS"
+ description "Build the site"
+ dependsOn jalviewjsBuildSite