+
+task sourceDist (type: Tar) {
+
+ def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+ def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
+ try {
+ archiveFileName = outputFileName
+ } catch (Exception e) {
+ archiveName = outputFileName
+ }
+
+ compression Compression.GZIP
+
+ into project.name
+
+ def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
+ ,".*"
+ ,"benchmarking/*"
+ ,"**/.*"
+ ,"*.class"
+ ,"**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales"
+ ,"*locales/**",
+ ,"utils/InstallAnywhere"]
+ 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"]
+
+ 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 ("$j11modDir/**/*.jar")
+}
+// from (jalviewDir) {
+// // explicit includes for stuff that seemed to not get included
+// include(fileTree("test/**/*."))
+// exclude(EXCLUDE_FILES)
+// exclude(PROCESS_FILES)
+// }
+}
+
+task helppages {
+ dependsOn copyHelp
+ dependsOn pubhtmlhelp
+
+ inputs.dir("$classes/$helpDir")
+ outputs.dir("$helpOutputDir")
+}
+
+def jalviewjsBuildDir
+def jalviewjsSiteDir
+def jalviewjsTransferSiteDir
+task jalviewjsSitePath {
+ if (jalviewjs_site_dir.startsWith("/")) {
+ jalviewjsSiteDir = jalviewjs_site_dir
+ } else {
+ def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+ jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
+ jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir
+ }
+ jalviewjsTransferSiteDir = jalviewjsBuildDir + "/tmp/site"
+}
+
+def eclipseWorkspace
+task jalviewjsSetEclipseWorkspace {
+ def propKey = "jalviewjs_eclipse_workspace"
+ def propsFile = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+ def props = new Properties()
+ def eclipseWsDir
+ def propVal = null
+ if (project.hasProperty(propKey)) {
+ propVal = project.getProperty(propKey)
+ eclipseWsDir = propVal
+ }
+ if ((eclipseWsDir == null || !file(eclipseWsDir).exists()) && file(propsFile).exists()) {
+ def ins = new FileInputStream(propsFile)
+ props.load(ins)
+ ins.close()
+ eclipseWsDir = props.getProperty(propKey)
+ }
+ if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
+ def tempDir = File.createTempDir()
+ eclipseWsDir = tempDir.getAbsolutePath()
+ props.setProperty(propKey, eclipseWsDir)
+ def outs = new FileOutputStream(propsFile)
+ props.store(outs, null)
+ outs.close()
+ }
+
+ eclipseWorkspace = file(eclipseWsDir)
+
+ println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+
+ inputs.property(propKey, propVal)
+ outputs.file(propsFile)
+}
+
+
+task jalviewjsUnzipFiles {
+ dependsOn jalviewjsSitePath
+
+ def zipFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_libjs_dir).include("*.zip")
+ zipFiles += jalviewjs_utils_dir+"/"+jalviewjs_swingjs_zip
+
+ doLast {
+ zipFiles.each { file_zip ->
+ copy {
+ from zipTree(file_zip)
+ into jalviewjsSiteDir
+ }
+ }
+ }
+
+ inputs.files zipFiles
+ outputs.dir jalviewjsSiteDir
+}
+
+def eclipseDropinsDir
+def eclipseBinary
+task jalviewjsEclipsePaths {
+ def eclipseRoot
+ eclipseRoot = jalviewjs_eclipse_root
+ if (eclipseRoot.startsWith("~")) {
+ eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+ }
+ if (OperatingSystem.current().isMacOsX()) {
+ eclipseRoot += "/Eclipse.app"
+ eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins"
+ eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse"
+ } else if (OperatingSystem.current().isWindows()) { // check these paths!!
+ eclipseDropinsDir = eclipseRoot+"/dropins"
+ eclipseBinary = eclipseRoot+"/eclipse"
+ } else { // linux or unix
+ eclipseDropinsDir = eclipseRoot+"/dropins"
+ eclipseBinary = eclipseRoot+"/eclipse"
+ }
+}
+
+task jalviewjsEclipseCopyDropins {
+ dependsOn jalviewjsEclipsePaths
+ def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir, include: "*.jar")
+ def outputDir = eclipseDropinsDir
+
+ inputs.files inputFiles
+ inputFiles.each { file ->
+ outputs.file(outputDir+"/"+file.name)
+ }
+
+ doLast {
+ def outputFiles = []
+ inputFiles.each { file ->
+ copy {
+ from file
+ into outputDir
+ }
+ }
+ }
+}
+
+task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+ dependsOn jalviewjsSitePath
+ outputFile (jalviewDir+"/"+jalviewjs_j2s_settings)
+ def props = project.properties.sort { it.key }
+ def siteDirProperty = "j2s.site.directory"
+ def setSiteDir = false
+ props.each { prop, val ->
+ if (prop.startsWith("j2s.") && val != null) {
+ if (prop == siteDirProperty) {
+ if (!(val.startsWith("/") || val.startsWith("file://") )) {
+ val = jalviewjsTransferSiteDir+"/"+val
+ }
+ setSiteDir = true
+ }
+ property(prop,val)
+ }
+ if (!setSiteDir) {
+ property(siteDirProperty,jalviewjsTransferSiteDir)
+ }
+ }
+ outputs.file(outputFile)
+}
+
+task jalviewjsEclipseSetup {
+ dependsOn jalviewjsEclipseCopyDropins
+ dependsOn jalviewjsSetEclipseWorkspace
+ dependsOn jalviewjsCreateJ2sSettings
+}
+
+task jalviewjsCopyResources (type: Copy) {
+ dependsOn jalviewjsSitePath
+ def inputFiles = fileTree(dir: jalviewjs_resource_dir)
+ def outputDir = jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += outputDir+"/"+filename
+ null
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+task jalviewjsCopySiteResources (type: Copy) {
+ dependsOn jalviewjsSitePath
+ def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_site_resource_dir)
+ def outputDir = jalviewjsSiteDir
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += outputDir+"/"+filename
+ null
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+task cleanJalviewjs {
+ //delete jalviewjsBuildDir
+ //delete jalviewDir+"/"+eclipse_bin_dir
+ //delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+ //delete jalviewDir+"/"+jalviewjs_j2s_settings
+}
+
+task jalviewjsProjectImport(type: Exec) {
+ // work out how to do this!
+ dependsOn eclipseProject
+ dependsOn eclipseClasspath
+ dependsOn eclipseJdt
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseSetup
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+
+ def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+ inputs.file(jalviewDir+"/.project")
+ outputs.dir(projdir)
+ outputs.upToDateWhen { file(projdir).exists() }
+}
+
+task jalviewjsTranspile(type: Exec) {
+ dependsOn jalviewjsEclipseSetup
+ dependsOn jalviewjsProjectImport
+ dependsOn jalviewjsEclipsePaths
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ])
+
+ def stdout
+ def stderr
+ doFirst {
+ stdout = new ByteArrayOutputStream()
+ stderr = new ByteArrayOutputStream()
+
+ if (jalviewjs_j2s_to_console.equals("true")) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"),
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"),
+ stderr),
+ errorOutput)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"),
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"),
+ stderr)
+ }
+ }
+ doLast {
+ if (stdout.toString().contains("Error processing ")) {
+ // j2s did not complete transpile
+ throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log files '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}' and '${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}'\n")
+ }
+ }
+
+ inputs.dir(sourceDir)
+ outputs.dir(eclipse_bin_dir+"/main")
+ outputs.dir(jalviewjsTransferSiteDir)
+
+}
+
+task jalviewjsCopyTransferSite(type: Copy) {
+ dependsOn jalviewjsTranspile
+ from jalviewjsTransferSiteDir
+ into jalviewjsSiteDir
+}
+
+jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite
+
+task jalviewjsPrepareSite {
+ group "JalviewJS"
+ description "Prepares the website folder including unzipping files and copying resources"
+ dependsOn jalviewjsSitePath
+ dependsOn jalviewjsUnzipFiles
+ dependsOn jalviewjsCopyResources
+ dependsOn jalviewjsCopySiteResources
+}
+
+task jalviewjsBuildSite {
+ group "JalviewJS"
+ description "Builds the whole website including transpiled code"
+ dependsOn jalviewjsCopyTransferSite
+ dependsOn jalviewjsPrepareSite
+}
+
+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"
+ try {
+ archiveFileName = outputFilename
+ } catch (Exception e) {
+ archiveName = outputFilename
+ }
+
+ compression Compression.GZIP
+
+ from jalviewjsSiteDir
+ into jalviewjs_site_dir // this is inside the tar file
+
+ inputs.dir(jalviewjsSiteDir)
+}
+
+task jalviewjsServer {
+ group "JalviewJS"
+ description "Starts a webserver on localhost to test the website"
+ dependsOn jalviewjsSitePath
+ doLast {
+
+ SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+ def port = Integer.valueOf(jalviewjs_server_port)
+ def start = port
+ def running = false
+ while(port < start+1000 && !running) {
+ try {
+ def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir)
+ jalviewjsServer = factory.start(doc_root, port)
+ running = true
+ println("SERVER STARTED with document root ${doc_root}.")
+ println("Go to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run gradle --stop to stop (kills all gradle daemons).")
+ println("For debug: "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+"?j2sdebug")
+ } catch (Exception e) {
+ port++;
+ }
+ }
+
+ }
+
+}
+
+task jalviewjs {
+ group "JalviewJS"
+ description "Build the site"
+ dependsOn jalviewjsBuildSite
+}
+
+