--- /dev/null
+import org.apache.tools.ant.filters.ReplaceTokens
+//import org.apache.tools.ant.filters.ReplaceRegexp
+import org.gradle.internal.os.OperatingSystem
+
+buildscript {
+ dependencies {
+ classpath 'org.openclover:clover:4.3.1'
+ classpath 'org.apache.commons:commons-compress:1.18'
+ }
+}
+
+plugins {
+ id 'java'
+ id 'application'
+ id 'eclipse'
+ id 'com.github.johnrengelman.shadow' version '4.0.3'
+ id 'com.install4j.gradle' version '7.0.9'
+}
+
+repositories {
+ jcenter()
+ mavenCentral()
+ mavenLocal()
+ flatDir {
+ dirs gradlePluginsDir
+ }
+}
+
+mainClassName = launcherClass
+def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
+def classes = "$jalviewDir/$classesDir"
+
+if (clover.equals("true")) {
+ use_clover = true
+ classes = "$buildDir/$cloverClassesDir"
+} else {
+ use_clover = false
+ classes = "$jalviewDir/$classesDir"
+}
+
+// configure classpath/args for j8/j11 compilation
+
+def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+def libDir
+def libDistDir
+def compile_source_compatibility
+def compile_target_compatibility
+
+ext {
+ // where the getdown channel will be built.
+ // TODO: consider allowing this expression to be overrriden by -P arg
+ getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + '/'
+ getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
+ getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+ getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
+ getdownLauncher = jalviewDir + '/' + getdown_launcher
+ getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
+ def getdownChannel = getdown_channel_name
+ if (getdown_channel_name.equals("COMMIT")) {
+ getdownChannel = getGitHash()
+ }
+ getdown_app_base = getdown_channel_base+"/"+getdownChannel+"/"+JAVA_VERSION+"/"
+ modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
+ modules_runtimeClasspath = modules_compileClasspath
+}
+
+def JAVA_INTEGER_VERSION
+def additional_compiler_args = []
+// these are getdown.txt properties defined dependent on the JAVA_VERSION
+def getdown_alt_java_min_version
+// this property is assigned below and expanded to multiple lines in the getdown task
+def getdown_alt_multi_java_location
+if (JAVA_VERSION.equals("1.8")) {
+ JAVA_INTEGER_VERSION = "8"
+ libDir = j11libDir
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+ getdown_alt_java_min_version = getdown_alt_java8_min_version
+ getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
+} else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = "11"
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+ getdown_alt_java_min_version = getdown_alt_java11_min_version
+ getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+ additional_compiler_args += [
+ '--module-path', ext.modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+} else {
+ throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
+}
+
+sourceSets {
+
+ main {
+ java {
+ srcDirs "$jalviewDir/$sourceDir"
+ outputDir = file("$classes")
+ }
+
+ resources {
+ srcDirs "$jalviewDir/$resourceDir"
+ srcDirs "$jalviewDir/$libDistDir"
+ }
+
+ jar.destinationDir = file("$jalviewDir/$packageDir")
+
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+ clover {
+ java {
+ srcDirs = [ cloverInstrDir ]
+ outputDir = file("${buildDir}/${cloverClassesDir}")
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+ compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
+ compileClasspath += files(sourceSets.main.java.outputDir)
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+
+ test {
+ java {
+ srcDirs "$jalviewDir/$testSourceDir"
+ outputDir = file("$jalviewDir/$testOutputDir")
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+
+ compileClasspath = files( sourceSets.test.java.outputDir )
+
+ if (use_clover) {
+ compileClasspath += sourceSets.clover.compileClasspath
+ } else {
+ compileClasspath += files(sourceSets.main.java.outputDir)
+ }
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += files( sourceSets.main.resources.srcDirs)
+ compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+}
+
+// clover bits
+dependencies {
+ if (use_clover) {
+ cloverCompile 'org.openclover:clover:4.3.1'
+ testCompile 'org.openclover:clover:4.3.1'
+ }
+}
+
+configurations {
+ cloverRuntime
+ cloverRuntime.extendsFrom cloverCompile
+}
+
+eclipse {
+ project {
+ name = "Jalview with gradle build"
+
+ natures 'org.eclipse.jdt.core.javanature',
+ 'org.eclipse.jdt.groovy.core.groovyNature',
+ 'org.eclipse.buildship.core.gradleprojectnature'
+
+ buildCommand 'org.eclipse.jdt.core.javabuilder'
+ buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+ }
+
+ classpath {
+ //defaultOutputDir = sourceSets.main.java.outputDir
+ def removeThese = []
+ configurations.each{ if (it.isCanBeResolved()) {
+ removeThese += it
+ }
+ }
+ containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+
+ minusConfigurations += removeThese
+ plusConfigurations = [ ]
+ file {
+
+ whenMerged { cp ->
+ def removeTheseToo = []
+ HashMap<String, Boolean> addedSrcPath = new HashMap<>();
+ cp.entries.each { entry ->
+ if (entry.kind == 'src') {
+ if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+ removeTheseToo += entry
+ } else {
+ addedSrcPath.putAt(entry.path, true)
+ }
+ }
+ }
+ cp.entries.removeAll(removeTheseToo)
+ }
+
+ withXml {
+ def node = it.asNode()
+ def srcTestAttributes
+ node.children().each{ cpe ->
+ def attributes = cpe.attributes()
+ if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
+ srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
+ return
+ }
+ }
+ def addTestAttribute = true
+ srcTestAttributes.each{a ->
+ if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
+ addTestAttribute = false
+ }
+ }
+ if (addTestAttribute) {
+ srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
+ }
+
+ node.appendNode('classpathentry', [kind:"output", path:"bin/main"])
+ node.appendNode('classpathentry', [kind:"lib", path:helpParentDir])
+ node.appendNode('classpathentry', [kind:"lib", path:resourceDir])
+ HashMap<String, Boolean> addedLibPath = new HashMap<>();
+ def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath
+ sourceSets.main.compileClasspath.each{
+ //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
+ //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
+ //println("Not adding directory "+it)
+ return
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (addedLibPath.get(itPath)) {
+ //println("Not adding duplicate entry "+itPath)
+ } else {
+ //println("Adding entry "+itPath)
+ node.appendNode('classpathentry', [kind:"lib", path:itPath])
+ addedLibPath.put(itPath, true)
+ }
+ }
+ sourceSets.test.compileClasspath.each{
+ //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
+ //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
+ //println("Not adding directory "+it)
+ return
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (addedLibPath.get(itPath)) {
+ //println("Not adding duplicate entry "+itPath)
+ } else {
+ //println("Adding entry "+itPath)
+ node.appendNode('classpathentry', [kind:"lib", path:itPath])
+ .appendNode('attributes')
+ .appendNode('attribute', [name:"test", value:"true"])
+ addedLibPath.put(itPath, true)
+ }
+ }
+ }
+
+ }
+ }
+
+ jdt {
+ // for the IDE, use java 11 compatibility
+ sourceCompatibility = 11
+ targetCompatibility = 11
+ javaRuntimeName = "JavaSE-11"
+
+ file {
+ withProperties { props ->
+ def jalview_prefs = new Properties()
+ def ins = new FileInputStream(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)
+ }
+ }
+ }
+ }
+ }
+
+}
+
+task cloverInstr() {
+ // only instrument source, we build test classes as normal
+ inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+ outputs.dir cloverInstrDir
+
+ doFirst {
+ delete cloverInstrDir
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-d", "${buildDir}/${cloverSourcesInstrDir}"]
+ argsList.addAll(inputs.files.files.collect({ file ->
+ file.absolutePath
+ }))
+ String[] args = argsList.toArray()
+ println("About to instrument "+args.length +" files")
+ com.atlassian.clover.CloverInstr.mainImpl(args)
+ }
+}
+
+
+task cloverReport {
+ group = "Verification"
+ description = "Createst the Clover report"
+ inputs.dir "${buildDir}/clover"
+ outputs.dir "${reportsDir}/clover"
+ onlyIf {
+ file("${buildDir}/clover/clover.db").exists()
+ }
+ doFirst {
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover"]
+ String[] args = argsList.toArray()
+ com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+ // and generate ${reportsDir}/clover/clover.xml
+ args = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover/clover.xml"].toArray()
+ com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+ }
+}
+
+// end clover bits
+
+
+compileJava {
+
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+
+}
+
+compileTestJava {
+ if (use_clover) {
+ dependsOn compileCloverJava
+ classpath += configurations.cloverRuntime
+ } else {
+ classpath += sourceSets.main.runtimeClasspath
+ }
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+}
+
+
+compileCloverJava {
+
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs += additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ classpath += configurations.cloverRuntime
+}
+
+clean {
+ delete sourceSets.main.java.outputDir
+}
+
+cleanTest {
+ delete sourceSets.test.java.outputDir
+ delete cloverInstrDir
+}
+
+def getDate(format) {
+ def date = new Date()
+ //return date.format("dd MMMM yyyy")
+ return date.format(format)
+}
+
+def getGitHash() {
+ def stdout = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--short", "HEAD"
+ standardOutput = stdout
+ workingDir = jalviewDir
+ }
+ return stdout.toString().trim()
+}
+
+def getGitBranch() {
+ def stdout = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
+ standardOutput = stdout
+ workingDir = jalviewDir
+ }
+ return stdout.toString().trim()
+}
+
+task createBuildProperties(type: WriteProperties) {
+ inputs.dir("$jalviewDir/$sourceDir")
+ inputs.dir("$jalviewDir/$resourceDir")
+ outputFile "$classes/$buildPropertiesFile"
+ /* taking time/date specific comment out to allow better incremental builds */
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("dd MMMM yyyy")
+ property "VERSION", JALVIEW_VERSION
+ property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
+ outputs.file(outputFile)
+ outputs.dir("$classes")
+}
+
+task syncDocs(type: Sync) {
+ def syncDir = "$classes/$docDir"
+ from fileTree("$jalviewDir/$docDir")
+ into syncDir
+
+}
+
+def helpFile = "$classes/$helpDir/help.jhm"
+
+task copyHelp(type: Copy) {
+ def inputDir = "$jalviewDir/$helpParentDir/$helpDir"
+ def outputDir = "$classes/$helpDir"
+ from(inputDir) {
+ exclude '**/*.gif'
+ exclude '**/*.jpg'
+ exclude '**/*.png'
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION])
+ }
+ from(inputDir) {
+ include '**/*.gif'
+ include '**/*.jpg'
+ include '**/*.png'
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.files(helpFile)
+ outputs.dir(outputDir)
+}
+
+task syncLib(type: Sync) {
+ def syncDir = "$classes/$libDistDir"
+ from fileTree("$jalviewDir/$libDistDir")
+ into syncDir
+}
+
+task syncResources(type: Sync) {
+ from "$jalviewDir/$resourceDir"
+ include "**/*.*"
+ exclude "install4j"
+ into "$classes"
+ preserve {
+ include "**"
+ }
+}
+
+task prepare {
+ dependsOn syncResources
+ dependsOn syncDocs
+ dependsOn copyHelp
+}
+
+
+//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+test {
+ dependsOn prepare
+ dependsOn compileJava
+ if (use_clover) {
+ dependsOn cloverInstr
+ }
+
+ print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+
+ useTestNG() {
+ includeGroups testngGroups
+ preserveOrder true
+ useDefaultListeners=true
+ }
+
+ workingDir = jalviewDir
+ //systemProperties 'clover.jar' System.properties.clover.jar
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ jvmArgs += additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+}
+
+task buildIndices(type: JavaExec) {
+ dependsOn copyHelp
+ classpath = sourceSets.main.compileClasspath
+ main = "com.sun.java.help.search.Indexer"
+ workingDir = "$classes/$helpDir"
+ def argDir = "html"
+ args = [ argDir ]
+ inputs.dir("$workingDir/$argDir")
+
+ outputs.dir("$classes/doc")
+ outputs.dir("$classes/help")
+ outputs.file("$workingDir/JavaHelpSearch/DOCS")
+ outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB")
+ outputs.file("$workingDir/JavaHelpSearch/OFFSETS")
+ outputs.file("$workingDir/JavaHelpSearch/POSITIONS")
+ outputs.file("$workingDir/JavaHelpSearch/SCHEMA")
+ outputs.file("$workingDir/JavaHelpSearch/TMAP")
+}
+
+task compileLinkCheck(type: JavaCompile) {
+ options.fork = true
+ classpath = files("$jalviewDir/$utilsDir")
+ destinationDir = file("$jalviewDir/$utilsDir")
+ source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+ outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
+ outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
+}
+
+def helplinkscheckeroutputfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+task linkCheck(type: JavaExec) {
+ dependsOn prepare, compileLinkCheck
+ classpath = files("$jalviewDir/$utilsDir")
+ main = "HelpLinksChecker"
+ workingDir = jalviewDir
+ def help = "$classes/$helpDir"
+ args = [ "$classes/$helpDir", "-nointernet" ]
+ //args = [ "$classesDir/$helpDir", "-nointernet" ]
+
+ doFirst {
+ helplinkscheckeroutputfile.createNewFile()
+ standardOutput new FileOutputStream(helplinkscheckeroutputfile, false)
+ }
+
+ outputs.file(helplinkscheckeroutputfile)
+}
+
+task cleanPackageDir(type: Delete) {
+ delete fileTree("$jalviewDir/$packageDir").include("*.jar")
+}
+
+jar {
+ dependsOn linkCheck
+ dependsOn buildIndices
+ dependsOn createBuildProperties
+
+ manifest {
+ attributes "Main-Class": mainClass,
+ "Permissions": "all-permissions",
+ "Application-Name": "Jalview Desktop",
+ "Codebase": application_codebase
+ }
+
+ destinationDir = file("$jalviewDir/$packageDir")
+ archiveName = rootProject.name+".jar"
+
+ exclude "cache*/**"
+ exclude "*.jar"
+ exclude "*.jar.*"
+ exclude "**/*.jar"
+ exclude "**/*.jar.*"
+
+ inputs.dir("$classes")
+ outputs.file("$jalviewDir/$packageDir/$archiveName")
+}
+
+task copyJars(type: Copy) {
+ from fileTree("$classes").include("**/*.jar").include("*.jar").files
+ into "$jalviewDir/$packageDir"
+}
+
+// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
+task syncJars(type: Sync) {
+ from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files
+ into "$jalviewDir/$packageDir"
+ preserve {
+ include jar.archiveName
+ }
+}
+
+task makeDist {
+ group = "build"
+ description = "Put all required libraries in dist"
+ // order of "cleanPackageDir", "copyJars", "jar" important!
+ jar.mustRunAfter cleanPackageDir
+ syncJars.mustRunAfter cleanPackageDir
+ dependsOn cleanPackageDir
+ dependsOn syncJars
+ dependsOn jar
+ outputs.dir("$jalviewDir/$packageDir")
+}
+
+task cleanDist {
+ dependsOn cleanPackageDir
+ dependsOn cleanTest
+ dependsOn clean
+}
+
+shadowJar {
+ dependsOn makeDist
+ from ("$jalviewDir/$libDistDir") {
+ include("*.jar")
+ }
+ mainClassName = shadowJarMainClass
+ mergeServiceFiles()
+ classifier = "all-"+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"
+ dependsOn makeDist
+ def getdownWebsiteResourceFilenames = []
+ def getdownTextString = ""
+ def getdownResourceDir = project.ext.getdownResourceDir
+ def getdownAppDir = project.ext.getdownAppDir
+ def getdownResourceFilenames = []
+ doFirst {
+ // go through properties looking for getdown_txt_...
+ def props = project.properties.sort { it.key }
+ props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+ props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+
+ if (getdown_local == "true") {
+ getdown_app_base = "file://"+file(getdownWebsiteDir).getAbsolutePath()
+ }
+ props.put("getdown_txt_appbase", getdown_app_base)
+ 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) {
+ 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()
+ }
+ }
+ def line = prop.substring(12) + " = " + val + "\n"
+ getdownTextString += line
+ }
+ }
+ }
+
+ getdownWebsiteResourceFilenames.each{ filename ->
+ getdownTextString += "resource = "+filename+"\n"
+ }
+ getdownResourceFilenames.each{ filename ->
+ copy {
+ from filename
+ into project.ext.getdownResourceDir
+ }
+ }
+
+ def codeFiles = []
+ makeDist.outputs.files.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 line = "code = " + getdown_app_dir + '/' + f.getName() + "\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into project.ext.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 line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into project.ext.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 = " + file(getdownLauncher).getName() + "\n"
+ getdownTextString += "class = " + mainClass + "\n"
+
+ def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
+ getdown_txt.write(getdownTextString)
+
+ copy {
+ from getdown_txt
+ into project.ext.getdownFilesDir
+ }
+
+ copy {
+ from getdownLauncher
+ into project.ext.getdownFilesDir
+ }
+
+ copy {
+ from getdownLauncher
+ into project.ext.getdownWebsiteDir
+ }
+
+ copy {
+ from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image')
+ from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background')
+ from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
+ from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon')
+ from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon')
+ into project.ext.getdownFilesDir + '/' + getdown_resource_dir
+ }
+ }
+
+ inputs.dir(jalviewDir + '/' + packageDir)
+ outputs.dir(project.ext.getdownWebsiteDir)
+ outputs.dir(project.ext.getdownFilesDir)
+}
+
+task getdownDigest(type: JavaExec) {
+ group = "distribution"
+ description = "Digest the getdown website folder"
+ dependsOn getdownWebsite
+ classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher)
+ main = "com.threerings.getdown.tools.Digester"
+ args project.ext.getdownWebsiteDir
+ inputs.dir(project.ext.getdownWebsiteDir)
+ outputs.file(project.ext.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
+}
+
+clean {
+ delete project.ext.getdownWebsiteDir
+ delete project.ext.getdownFilesDir
+}
+
+install4j {
+ def install4jHomeDir = "/opt/install4j"
+ def hostname = "hostname".execute().text.trim()
+ if (hostname.equals("jv-bamboo")) {
+ install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+ } else if (OperatingSystem.current().isMacOsX()) {
+ install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app'
+ if (! file(install4jHomeDir).exists()) {
+ install4jHomeDir = System.getProperty("user.home")+install4jHomeDir
+ }
+ } else if (OperatingSystem.current().isLinux()) {
+ install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+ }
+ installDir = file(install4jHomeDir)
+ mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
+ if (install4jFaster.equals("true")) {
+ faster = true
+ }
+}
+
+def install4jConf
+def macosJavaVMDir
+def macosJavaVMTgz
+def windowsJavaVMDir
+def windowsJavaVMTgz
+def install4jDir = "$jalviewDir/$install4jResourceDir"
+def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
+install4jConf = "$install4jDir/$install4jConfFile"
+
+task copyInstall4jTemplate(type: Copy) {
+ macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre"
+ macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
+ windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre"
+ windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
+ from (install4jDir) {
+ include install4jTemplate
+ rename (install4jTemplate, install4jConfFile)
+ filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
+ tokens: [
+ 'JAVA_VERSION': JAVA_VERSION,
+ 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+ 'VERSION': JALVIEW_VERSION,
+ 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+ 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+ 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+ 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+ 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
+ 'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
+ 'MACOS_BUNDLE_ID': install4jMacOSBundleId
+ ]
+ )
+ if (OSX_KEYPASS=="") {
+ filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
+ filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
+ }
+ }
+ into install4jDir
+ outputs.files(install4jConf)
+
+ doLast {
+ def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
+ ant.replaceregexp(
+ byline: false,
+ flags: "s",
+ match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
+ //match: '<action.*?EXTENSIONS_REPLACED_BY_GRADLE.*?</action>',
+ replace: installerFileAssociationsXml,
+ file: install4jConf
+ )
+ }
+}
+
+task installers(type: com.install4j.gradle.Install4jTask) {
+ group = "distribution"
+ description = "Create the install4j installers"
+ dependsOn getdown
+ dependsOn copyInstall4jTemplate
+ projectFile = file(install4jConf)
+ println("Using projectFile "+projectFile)
+ variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
+ destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
+ buildSelected = true
+
+ if (OSX_KEYPASS) {
+ macKeystorePassword=OSX_KEYPASS
+
+ }
+
+ inputs.dir(project.ext.getdownWebsiteDir)
+ inputs.file(install4jConf)
+ inputs.dir(macosJavaVMDir)
+ inputs.dir(windowsJavaVMDir)
+ outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
+}
+
+clean {
+ delete install4jConf
+}
git://source.jalview.org / jalview.git / blobdiff