* For properties set within build.gradle, use camelCaseNoSpace.
*/
import org.apache.tools.ant.filters.ReplaceTokens
-
-
+import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.eclipse.model.Output
+import org.gradle.plugins.ide.eclipse.model.Library
+import java.security.MessageDigest
+import groovy.transform.ExternalizeMethods
+import groovy.util.XmlParser
+import groovy.xml.XmlUtil
+
+
+buildscript {
+ repositories {
+ mavenCentral()
+ mavenLocal()
+ }
+}
plugins {
id 'java'
+ id 'application'
+ id 'eclipse'
+ id 'com.github.johnrengelman.shadow' version '4.0.3'
+ id 'com.install4j.gradle' version '8.0.4'
+ id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
}
+repositories {
+ jcenter()
+ mavenCentral()
+ mavenLocal()
+}
// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
jalviewDirRelativePath = jalviewDir
+ // local build environment properties
+ // can be "projectDir/local.properties"
+ def localProps = "${projectDir}/local.properties"
+ def propsFile = null;
+ if (file(localProps).exists()) {
+ propsFile = localProps
+ }
+ // or "../projectDir_local.properties"
+ def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
+ if (file(dirLocalProps).exists()) {
+ propsFile = dirLocalProps
+ }
+ if (propsFile != null) {
+ try {
+ def p = new Properties()
+ def localPropsFIS = new FileInputStream(propsFile)
+ p.load(localPropsFIS)
+ localPropsFIS.close()
+ p.each {
+ key, val ->
+ def oldval = findProperty(key)
+ setProperty(key, val)
+ if (oldval != null) {
+ println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ } else {
+ println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ }
+ }
+ } catch (Exception e) {
+ System.out.println("Exception reading local.properties")
+ }
+ }
////
// Import releaseProps from the RELEASE file
JALVIEW_VERSION = releaseProps.get("jalview.version")
}
+ // this property set when running Eclipse headlessly
+ j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
+ // this property set by Eclipse
+ eclipseApplicationProperty = string("eclipse.application")
+ // CHECK IF RUNNING FROM WITHIN ECLIPSE
+ def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
+ IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
+ // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
+ if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
+ println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
+ IN_ECLIPSE = false
+ }
+ if (IN_ECLIPSE) {
+ println("WITHIN ECLIPSE IDE")
+ } else {
+ println("HEADLESS BUILD")
+ }
+ /* *-/
+ System.properties.sort { it.key }.each {
+ key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
+ }
+ /-* *-/
+ if (false && IN_ECLIPSE) {
+ jalviewDir = jalviewDirAbsolutePath
+ }
+ */
// essentials
bareSourceDir = string(source_dir)
classesDir = string("${jalviewDir}/${classes_dir}")
-
- resourceClassesDir = classesDir
-
- testSourceDir = testDir
- testClassesDir = "${jalviewDir}/${test_output_dir}"
-
+ // clover
+ useClover = clover.equals("true")
+ cloverBuildDir = "${buildDir}/clover"
+ cloverInstrDir = file("${cloverBuildDir}/clover-instr")
+ cloverClassesDir = file("${cloverBuildDir}/clover-classes")
+ cloverReportDir = file("${buildDir}/reports/clover")
+ cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
+ cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
+ //cloverTestClassesDir = cloverClassesDir
+ cloverDb = string("${cloverBuildDir}/clover.db")
+
+ resourceClassesDir = useClover ? cloverClassesDir : classesDir
+
+ testSourceDir = useClover ? cloverTestInstrDir : testDir
+ testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
+
+ getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
+ buildDist = true
+
+ // the following values might be overridden by the CHANNEL switch
+ getdownChannelName = CHANNEL.toLowerCase()
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
+ getdownAppDistDir = getdown_app_dir_alt
buildProperties = string("${classesDir}/${build_properties_file}")
+ reportRsyncCommand = false
+ jvlChannelName = CHANNEL.toLowerCase()
+ install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
+ install4jDSStore = "DS_Store-NON-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
+ install4jInstallerName = "${jalview_name} Non-Release Installer"
+ install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+ install4jExtraScheme = "jalviewx"
+ switch (CHANNEL) {
+
+ case "BUILD":
+ // TODO: get bamboo build artifact URL for getdown artifacts
+ getdown_channel_base = bamboo_channelbase
+ getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
+ getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
+ jvlChannelName += "_${getdownChannelName}"
+ // automatically add the test group Not-bamboo for exclusion
+ if ("".equals(testng_excluded_groups)) {
+ testng_excluded_groups = "Not-bamboo"
+ }
+ install4jExtraScheme = "jalviewb"
+ break
+
+ case "RELEASE":
+ getdownAppDistDir = getdown_app_dir_release
+ reportRsyncCommand = true
+ install4jSuffix = ""
+ install4jDSStore = "DS_Store"
+ install4jDMGBackgroundImage = "jalview_dmg_background.png"
+ install4jInstallerName = "${jalview_name} Installer"
+ break
+
+ case "ARCHIVE":
+ getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
+ } else {
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+ buildDist = false
+ }
+ reportRsyncCommand = true
+ install4jExtraScheme = "jalviewa"
+ break
+
+ case "ARCHIVELOCAL":
+ getdownChannelName = string("archive/${JALVIEW_VERSION}")
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
+ } else {
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+ buildDist = false
+ }
+ reportRsyncCommand = true
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jSuffix = "Archive"
+ install4jExtraScheme = "jalviewa"
+ break
+
+ case "DEVELOP":
+ reportRsyncCommand = true
+
+ // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+ JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
+
+ install4jSuffix = "Develop"
+ install4jDSStore = "DS_Store-DEVELOP"
+ install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
+ install4jExtraScheme = "jalviewd"
+ install4jInstallerName = "${jalview_name} Develop Installer"
+ break
+
+ case "TEST-RELEASE":
+ reportRsyncCommand = true
+
+ // TEST-RELEASE is usually associated with a Jalview release series so set the version
+ JALVIEW_VERSION=JALVIEW_VERSION+"-test"
+
+ install4jSuffix = "Test"
+ install4jDSStore = "DS_Store-TEST-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
+ break
+
+ case ~/^SCRATCH(|-[-\w]*)$/:
+ getdownChannelName = CHANNEL
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+ reportRsyncCommand = true
+ install4jSuffix = "Scratch"
+ break
+
+ case "TEST-LOCAL":
+ if (!file("${LOCALDIR}").exists()) {
+ throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
+ } else {
+ getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ }
+ JALVIEW_VERSION = "TEST"
+ install4jSuffix = "Test-Local"
+ install4jDSStore = "DS_Store-TEST-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
+ break
+
+ case "LOCAL":
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jExtraScheme = "jalviewl"
+ break
+
+ default: // something wrong specified
+ throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
+ break
+
+ }
+ // override getdownAppBase if requested
+ if (findProperty("getdown_appbase_override") != null) {
+ getdownAppBase = string(getProperty("getdown_appbase_override"))
+ println("Overriding getdown appbase with '${getdownAppBase}'")
+ }
+ // sanitise file name for jalview launcher file for this channel
+ jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
+ // install4j application and folder names
+ if (install4jSuffix == "") {
+ install4jApplicationName = "${jalview_name}"
+ install4jBundleId = "${install4j_bundle_id}"
+ install4jWinApplicationId = install4j_release_win_application_id
+ } else {
+ install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+ install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
+ // add int hash of install4jSuffix to the last part of the application_id
+ def id = install4j_release_win_application_id
+ def idsplitreverse = id.split("-").reverse()
+ idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
+ install4jWinApplicationId = idsplitreverse.reverse().join("-")
+ }
+ // sanitise folder and id names
+ // install4jApplicationFolder = e.g. "Jalview Build"
+ install4jApplicationFolder = install4jApplicationName
+ .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
+ .replaceAll("_+", "_") // collapse __
+ install4jInternalId = install4jApplicationName
+ .replaceAll(" ","_")
+ .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+ .replaceAll("_+", "") // collapse __
+ //.replaceAll("_*-_*", "-") // collapse _-_
+ install4jUnixApplicationFolder = install4jApplicationName
+ .replaceAll(" ","_")
+ .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+ .replaceAll("_+", "_") // collapse __
+ .replaceAll("_*-_*", "-") // collapse _-_
+ .toLowerCase()
+
+ getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
+ //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
+ getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
+ getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
+ getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
+ getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
+ /* compile without modules -- using classpath libraries
+ modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
+ modules_runtimeClasspath = modules_compileClasspath
+ */
gitHash = string("")
gitBranch = string("")
//libDir = j8libDir
libDir = j11libDir
libDistDir = j8libDir
+ digestonlyDir = j8digestonlyDir
compile_source_compatibility = 1.8
compile_target_compatibility = 1.8
+ // these are getdown.txt properties defined dependent on the JAVA_VERSION
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
+ // this property is assigned below and expanded to multiple lines in the getdown task
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
+ // this property is for the Java library used in eclipse
+ eclipseJavaRuntimeName = string("JavaSE-1.8")
} else if (JAVA_VERSION.equals("11")) {
JAVA_INTEGER_VERSION = string("11")
libDir = j11libDir
libDistDir = j11libDir
+ digestonlyDir = j11digestonlyDir
compile_source_compatibility = 11
compile_target_compatibility = 11
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+ eclipseJavaRuntimeName = string("JavaSE-11")
+ /* compile without modules -- using classpath libraries
+ additional_compiler_args += [
+ '--module-path', modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ */
} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
JAVA_INTEGER_VERSION = JAVA_VERSION
libDir = j11libDir
libDistDir = j11libDir
compile_source_compatibility = JAVA_VERSION
compile_target_compatibility = JAVA_VERSION
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+ eclipseJavaRuntimeName = string("JavaSE-11")
+ /* compile without modules -- using classpath libraries
+ additional_compiler_args += [
+ '--module-path', modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ */
} else {
throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
}
+ // for install4j
+ JAVA_MIN_VERSION = JAVA_VERSION
+ JAVA_MAX_VERSION = JAVA_VERSION
+ def jreInstallsDir = string(jre_installs_dir)
+ if (jreInstallsDir.startsWith("~/")) {
+ jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
+ }
+ macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
+ macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
+ windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
+ windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
+ linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
+ linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
+ install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
+ install4jConfFileName = string("jalview-install4j-conf.install4j")
+ install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
+ install4jHomeDir = install4j_home_dir
+ if (install4jHomeDir.startsWith("~/")) {
+ install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
+ }
+
buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
helpSourceDir = string("${helpParentDir}/${help_dir}")
+ relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+ jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
+ jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
+ if (IN_ECLIPSE) {
+ jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
+ } else {
+ jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
+ }
+ jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
+ jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
+ jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
+ jalviewjsJalviewCoreHtmlFile = string("")
+ jalviewjsJalviewCoreName = string(jalviewjs_core_name)
+ jalviewjsCoreClasslists = []
+ jalviewjsJalviewTemplateName = string(jalviewjs_name)
+ jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+ jalviewjsJ2sProps = null
+
+ eclipseWorkspace = null
+ eclipseBinary = string("")
+ eclipseVersion = string("")
+ eclipseDebug = false
// ENDEXT
}
runtimeClasspath = compileClasspath
}
+ clover {
+ java {
+ srcDirs cloverInstrDir
+ outputDir = cloverClassesDir
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+
+ compileClasspath = files( sourceSets.clover.java.outputDir )
+ //compileClasspath += files( testClassesDir )
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+
test {
java {
srcDirs testSourceDir
}
resources {
- srcDirs = sourceSets.main.resources.srcDirs
+ srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
}
compileClasspath = files( sourceSets.test.java.outputDir )
- compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
}
+// eclipse project and settings files creation, also used by buildship
+eclipse {
+ project {
+ name = eclipse_project_name
+
+ natures 'org.eclipse.jdt.core.javanature',
+ 'org.eclipse.jdt.groovy.core.groovyNature',
+ 'org.eclipse.buildship.core.gradleprojectnature'
+
+ buildCommand 'org.eclipse.jdt.core.javabuilder'
+ buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+ }
+
+ classpath {
+ //defaultOutputDir = sourceSets.main.java.outputDir
+ def removeThese = []
+ configurations.each{
+ if (it.isCanBeResolved()) {
+ removeThese += it
+ }
+ }
+
+ minusConfigurations += removeThese
+ plusConfigurations = [ ]
+ file {
+
+ whenMerged { cp ->
+ def removeTheseToo = []
+ HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
+ cp.entries.each { entry ->
+ // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+ // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+ // we add the resources and help/help dirs in as libs afterwards (see below)
+ if (entry.kind == 'src') {
+ if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
+ removeTheseToo += entry
+ } else {
+ alreadyAddedSrcPath.putAt(entry.path, true)
+ }
+ }
+
+ }
+ cp.entries.removeAll(removeTheseToo)
+
+ //cp.entries += new Output("${eclipse_bin_dir}/main")
+ if (file(helpParentDir).isDirectory()) {
+ cp.entries += new Library(fileReference(helpParentDir))
+ }
+ if (file(resourceDir).isDirectory()) {
+ cp.entries += new Library(fileReference(resourceDir))
+ }
+
+ HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
+
+ sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+ //don't want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath, especially if they don't exist
+ return false // groovy "continue" in .any closure
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
+ // make relative path
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ //println("Not adding duplicate entry "+itPath)
+ } else {
+ //println("Adding entry "+itPath)
+ cp.entries += new Library(fileReference(itPath))
+ alreadyAddedLibPath.put(itPath, true)
+ }
+ }
+
+ sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+ //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath
+ return false // groovy "continue" in .any closure
+ }
+
+ def itPath = it.toString()
+ if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ // don't duplicate
+ } else {
+ def lib = new Library(fileReference(itPath))
+ lib.entryAttributes["test"] = "true"
+ cp.entries += lib
+ alreadyAddedLibPath.put(itPath, true)
+ }
+ }
+
+ } // whenMerged
+
+ } // file
+
+ containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+
+ } // classpath
+
+ jdt {
+ // for the IDE, use java 11 compatibility
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ javaRuntimeName = eclipseJavaRuntimeName
+
+ // add in jalview project specific properties/preferences into eclipse core preferences
+ file {
+ withProperties { props ->
+ def jalview_prefs = new Properties()
+ def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
+ jalview_prefs.load(ins)
+ ins.close()
+ jalview_prefs.forEach { t, v ->
+ if (props.getAt(t) == null) {
+ props.putAt(t, v)
+ }
+ }
+ }
+ }
+
+ } // jdt
+
+ if (IN_ECLIPSE) {
+ // Don't want these to be activated if in headless build
+ synchronizationTasks "eclipseSynchronizationTask"
+ autoBuildTasks "eclipseAutoBuildTask"
+
+ }
+}
+
+
+// clover bits
+
+
+task cleanClover {
+ doFirst {
+ delete cloverBuildDir
+ delete cloverReportDir
+ }
+}
+
+
+task cloverInstrJava(type: JavaExec) {
+ group = "Verification"
+ description = "Create clover instrumented source java files"
+
+ dependsOn cleanClover
+
+ inputs.files(sourceSets.main.allJava)
+ outputs.dir(cloverInstrDir)
+
+ //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+ classpath = sourceSets.clover.compileClasspath
+ main = "com.atlassian.clover.CloverInstr"
+
+ def argsList = [
+ "--encoding",
+ "UTF-8",
+ "--initstring",
+ cloverDb,
+ "--destdir",
+ cloverInstrDir.getPath(),
+ ]
+ def srcFiles = sourceSets.main.allJava.files
+ argsList.addAll(
+ srcFiles.collect(
+ { file -> file.absolutePath }
+ )
+ )
+ args argsList.toArray()
+
+ doFirst {
+ delete cloverInstrDir
+ println("Clover: About to instrument "+srcFiles.size() +" files")
+ }
+}
+
+
+task cloverInstrTests(type: JavaExec) {
+ group = "Verification"
+ description = "Create clover instrumented source test files"
+
+ dependsOn cleanClover
+
+ inputs.files(testDir)
+ outputs.dir(cloverTestInstrDir)
+
+ classpath = sourceSets.clover.compileClasspath
+ main = "com.atlassian.clover.CloverInstr"
+
+ def argsList = [
+ "--encoding",
+ "UTF-8",
+ "--initstring",
+ cloverDb,
+ "--srcdir",
+ testDir,
+ "--destdir",
+ cloverTestInstrDir.getPath(),
+ ]
+ args argsList.toArray()
+
+ doFirst {
+ delete cloverTestInstrDir
+ println("Clover: About to instrument test files")
+ }
+}
+
+
+task cloverInstr {
+ group = "Verification"
+ description = "Create clover instrumented all source files"
+
+ dependsOn cloverInstrJava
+ dependsOn cloverInstrTests
+}
+
+
+cloverClasses.dependsOn cloverInstr
+
+
+task cloverConsoleReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover console report"
+
+ onlyIf {
+ file(cloverDb).exists()
+ }
+
+ inputs.dir cloverClassesDir
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.console.ConsoleReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+ }
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--unittests"
+ ]
+
+ args argsList.toArray()
+}
+
+
+task cloverHtmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover HTML report"
+
+ onlyIf {
+ file(cloverDb).exists()
+ }
+
+ def cloverHtmlDir = cloverReportDir
+ inputs.dir cloverClassesDir
+ outputs.dir cloverHtmlDir
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+ }
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--outputdir",
+ cloverHtmlDir
+ ]
+
+ if (cloverreport_html_options.length() > 0) {
+ argsList += cloverreport_html_options.split(" ")
+ }
+
+ args argsList.toArray()
+}
+
+
+task cloverXmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover XML report"
+
+ onlyIf {
+ file(cloverDb).exists()
+ }
+
+ def cloverXmlFile = "${cloverReportDir}/clover.xml"
+ inputs.dir cloverClassesDir
+ outputs.file cloverXmlFile
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.xml.XMLReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+ }
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--outfile",
+ cloverXmlFile
+ ]
+
+ if (cloverreport_xml_options.length() > 0) {
+ argsList += cloverreport_xml_options.split(" ")
+ }
+
+ args argsList.toArray()
+}
+
+
+task cloverReport {
+ group = "Verification"
+ description = "Creates clover reports"
+
+ dependsOn cloverXmlReport
+ dependsOn cloverHtmlReport
+}
+
+
+compileCloverJava {
+
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs += additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ //classpath += configurations.cloverRuntime
+}
+// end clover bits
compileJava {
cleanTest {
+ dependsOn cleanClover
doFirst {
delete sourceSets.test.java.outputDir
}
}
+task syncLib(type: Sync) {
+ def syncDir = "${resourceClassesDir}/${libDistDir}"
+ from fileTree("${jalviewDir}/${libDistDir}")
+ into syncDir
+}
+
+
task syncResources(type: Sync) {
from resourceDir
include "**/*.*"
dependsOn prepare
//dependsOn compileJava ////? DELETE
- dependsOn compileJava //?
+ if (useClover) {
+ dependsOn cloverClasses
+ } else { //?
+ dependsOn compileJava //?
+ }
useTestNG() {
includeGroups testng_groups
jvmArgs += additional_compiler_args
doFirst {
+ if (useClover) {
+ println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+ }
}
}
inputs.dir(classesDir)
outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
}
+
+
+task copyJars(type: Copy) {
+ from fileTree(dir: classesDir, include: "**/*.jar").files
+ into "${jalviewDir}/${package_dir}"
+}
+
+
+// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
+task syncJars(type: Sync) {
+ from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
+ into "${jalviewDir}/${package_dir}"
+ preserve {
+ include jar.archiveName
+ }
+}
+
+
+task makeDist {
+ group = "build"
+ description = "Put all required libraries in dist"
+ // order of "cleanPackageDir", "copyJars", "jar" important!
+ jar.mustRunAfter cleanPackageDir
+ syncJars.mustRunAfter cleanPackageDir
+ dependsOn cleanPackageDir
+ dependsOn syncJars
+ dependsOn jar
+ outputs.dir("${jalviewDir}/${package_dir}")
+}
+
+
+task cleanDist {
+ dependsOn cleanPackageDir
+ dependsOn cleanTest
+ dependsOn clean
+}
+
+shadowJar {
+ group = "distribution"
+ if (buildDist) {
+ dependsOn makeDist
+ }
+ from ("${jalviewDir}/${libDistDir}") {
+ include("*.jar")
+ }
+ manifest {
+ attributes 'Implementation-Version': JALVIEW_VERSION
+ }
+ mainClassName = shadow_jar_main_class
+ mergeServiceFiles()
+ classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+ minimize()
+}
+
+
+task getdownWebsite() {
+ group = "distribution"
+ description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+ if (buildDist) {
+ dependsOn makeDist
+ }
+
+ def getdownWebsiteResourceFilenames = []
+ def getdownTextString = ""
+ def getdownResourceDir = getdownResourceDir
+ def getdownResourceFilenames = []
+
+ doFirst {
+ // clean the getdown website and files dir before creating getdown folders
+ delete getdownWebsiteDir
+ delete getdownFilesDir
+
+ copy {
+ from buildProperties
+ rename(build_properties_file, getdown_build_properties)
+ into getdownAppDir
+ }
+ getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
+
+ // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
+ def props = project.properties.sort { it.key }
+ if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
+ props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
+ }
+ if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
+ props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
+ }
+ if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
+ props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
+ }
+
+ props.put("getdown_txt_title", jalview_name)
+ props.put("getdown_txt_ui.name", install4jApplicationName)
+
+ // start with appbase
+ getdownTextString += "appbase = ${getdownAppBase}\n"
+ props.each{ prop, val ->
+ if (prop.startsWith("getdown_txt_") && val != null) {
+ if (prop.startsWith("getdown_txt_multi_")) {
+ def key = prop.substring(18)
+ val.split(",").each{ v ->
+ def line = "${key} = ${v}\n"
+ getdownTextString += line
+ }
+ } else {
+ // file values rationalised
+ if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
+ def r = null
+ if (val.indexOf('/') == 0) {
+ // absolute path
+ r = file(val)
+ } else if (val.indexOf('/') > 0) {
+ // relative path (relative to jalviewDir)
+ r = file( "${jalviewDir}/${val}" )
+ }
+ if (r.exists()) {
+ val = "${getdown_resource_dir}/" + r.getName()
+ getdownWebsiteResourceFilenames += val
+ getdownResourceFilenames += r.getPath()
+ }
+ }
+ if (! prop.startsWith("getdown_txt_resource")) {
+ def line = prop.substring(12) + " = ${val}\n"
+ getdownTextString += line
+ }
+ }
+ }
+ }
+
+ getdownWebsiteResourceFilenames.each{ filename ->
+ getdownTextString += "resource = ${filename}\n"
+ }
+ getdownResourceFilenames.each{ filename ->
+ copy {
+ from filename
+ into getdownResourceDir
+ }
+ }
+
+ def codeFiles = []
+ fileTree(file(package_dir)).each{ f ->
+ if (f.isDirectory()) {
+ def files = fileTree(dir: f, include: ["*"]).getFiles()
+ codeFiles += files
+ } else if (f.exists()) {
+ codeFiles += f
+ }
+ }
+ codeFiles.sort().each{f ->
+ def name = f.getName()
+ def line = "code = ${getdownAppDistDir}/${name}\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into getdownAppDir
+ }
+ }
+
+ fileTree(dir: digestonlyDir, include: ["*"]).getFiles().sort().each{f ->
+ def name = f.getName()
+ def line = "digestonly = ${getdownAppDistDir}/${name}\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into getdownAppDir
+ }
+ }
+
+ // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+ /*
+ if (JAVA_VERSION.equals("11")) {
+ def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
+ j11libFiles.sort().each{f ->
+ def name = f.getName()
+ def line = "code = ${getdown_j11lib_dir}/${name}\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into getdownJ11libDir
+ }
+ }
+ }
+ */
+
+ // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
+ //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
+ getdownTextString += "resource = ${getdown_launcher_new}\n"
+ getdownTextString += "class = ${main_class}\n"
+ /* NOT setting these properties so that getdownappbase and getdowndistdir will default to release version
+ * getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
+ * getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+ */
+
+ def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
+ getdown_txt.write(getdownTextString)
+
+ def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+ def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+ launchJvl.write("appbase=${getdownAppBase}")
+
+ copy {
+ from getdownLauncher
+ rename(file(getdownLauncher).getName(), getdown_launcher_new)
+ into getdownWebsiteDir
+ }
+
+ copy {
+ from getdownLauncher
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownWebsiteDir
+ }
+
+ if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
+ copy {
+ from getdown_txt
+ from getdownLauncher
+ from "${getdownAppDir}/${getdown_build_properties}"
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownInstallDir
+ }
+
+ copy {
+ from getdownInstallDir
+ into getdownFilesInstallDir
+ }
+ }
+
+ copy {
+ from getdown_txt
+ from launchJvl
+ from getdownLauncher
+ from "${getdownWebsiteDir}/${getdown_build_properties}"
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownFilesDir
+ }
+
+ copy {
+ from getdownResourceDir
+ into "${getdownFilesDir}/${getdown_resource_dir}"
+ }
+ }
+
+ if (buildDist) {
+ inputs.dir("${jalviewDir}/${package_dir}")
+ }
+ outputs.dir(getdownWebsiteDir)
+ outputs.dir(getdownFilesDir)
+}
+
+
+// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
+task getdownDigestDir(type: JavaExec) {
+ group "Help"
+ description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
+
+ def digestDirPropertyName = "DIGESTDIR"
+ doFirst {
+ classpath = files(getdownLauncher)
+ def digestDir = findProperty(digestDirPropertyName)
+ if (digestDir == null) {
+ throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
+ }
+ args digestDir
+ }
+ main = "com.threerings.getdown.tools.Digester"
+}
+
+
+task getdownDigest(type: JavaExec) {
+ group = "distribution"
+ description = "Digest the getdown website folder"
+ dependsOn getdownWebsite
+ doFirst {
+ classpath = files(getdownLauncher)
+ }
+ main = "com.threerings.getdown.tools.Digester"
+ args getdownWebsiteDir
+ inputs.dir(getdownWebsiteDir)
+ outputs.file("${getdownWebsiteDir}/digest2.txt")
+}
+
+
+task getdown() {
+ group = "distribution"
+ description = "Create the minimal and full getdown app folder for installers and website and create digest file"
+ dependsOn getdownDigest
+ doLast {
+ if (reportRsyncCommand) {
+ def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+ def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
+ println "LIKELY RSYNC COMMAND:"
+ println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
+ if (RUNRSYNC == "true") {
+ exec {
+ commandLine "mkdir", "-p", toDir
+ }
+ exec {
+ commandLine "rsync", "-avh", "--delete", fromDir, toDir
+ }
+ }
+ }
+ }
+}
+
+
+clean {
+ doFirst {
+ delete getdownWebsiteDir
+ delete getdownFilesDir
+ }
+}
+
+
+install4j {
+ if (file(install4jHomeDir).exists()) {
+ // good to go!
+ } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
+ install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+ } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
+ install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
+ }
+ installDir(file(install4jHomeDir))
+
+ mediaTypes = Arrays.asList(install4j_media_types.split(","))
+}
+
+
+task copyInstall4jTemplate {
+ def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+ def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+ inputs.file(install4jTemplateFile)
+ inputs.file(install4jFileAssociationsFile)
+ inputs.property("CHANNEL", { CHANNEL })
+ outputs.file(install4jConfFile)
+
+ doLast {
+ def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
+
+ // turn off code signing if no OSX_KEYPASS
+ if (OSX_KEYPASS == "") {
+ install4jConfigXml.'**'.codeSigning.each { codeSigning ->
+ codeSigning.'@macEnabled' = "false"
+ }
+ install4jConfigXml.'**'.windows.each { windows ->
+ windows.'@runPostProcessor' = "false"
+ }
+ }
+
+ // turn off checksum creation for LOCAL channel
+ def e = install4jConfigXml.application[0]
+ if (CHANNEL == "LOCAL") {
+ e.'@createChecksums' = "false"
+ } else {
+ e.'@createChecksums' = "true"
+ }
+
+ // put file association actions where placeholder action is
+ def install4jFileAssociationsText = install4jFileAssociationsFile.text
+ def fileAssociationActions = new XmlParser().parseText("<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
+ }
+ }
+
+ // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
+ if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
+ def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
+ symlink.parent().remove(symlink)
+ }
+
+ // write install4j file
+ install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
+ }
+}
+
+
+clean {
+ doFirst {
+ delete install4jConfFile
+ }
+}
+
+
+task installers(type: com.install4j.gradle.Install4jTask) {
+ group = "distribution"
+ description = "Create the install4j installers"
+ dependsOn setGitVals
+ dependsOn getdown
+ dependsOn copyInstall4jTemplate
+
+ projectFile = install4jConfFile
+
+ // create an md5 for the input files to use as version for install4j conf file
+ def digest = MessageDigest.getInstance("MD5")
+ digest.update(
+ (file("${install4jDir}/${install4j_template}").text +
+ file("${install4jDir}/${install4j_info_plist_file_associations}").text +
+ file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
+ def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
+ if (filesMd5.length() >= 8) {
+ filesMd5 = filesMd5.substring(0,8)
+ }
+ def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
+ // make install4jBuildDir relative to jalviewDir
+ def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
+
+ variables = [
+ 'JALVIEW_NAME': jalview_name,
+ 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
+ 'JALVIEW_DIR': "../..",
+ 'OSX_KEYSTORE': OSX_KEYSTORE,
+ 'JSIGN_SH': JSIGN_SH,
+ 'JRE_DIR': getdown_app_dir_java,
+ 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
+ 'JALVIEW_VERSION': JALVIEW_VERSION,
+ 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
+ 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
+ 'JAVA_VERSION': JAVA_VERSION,
+ 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+ 'VERSION': JALVIEW_VERSION,
+ 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+ 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+ 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
+ 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+ 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+ 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
+ 'COPYRIGHT_MESSAGE': install4j_copyright_message,
+ 'BUNDLE_ID': install4jBundleId,
+ 'INTERNAL_ID': install4jInternalId,
+ 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
+ 'MACOS_DS_STORE': install4jDSStore,
+ 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+ 'INSTALLER_NAME': install4jInstallerName,
+ 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
+ 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+ 'GETDOWN_FILES_DIR': getdown_files_dir,
+ 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+ 'GETDOWN_DIST_DIR': getdownAppDistDir,
+ 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+ 'GETDOWN_INSTALL_DIR': getdown_install_dir,
+ 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
+ 'BUILD_DIR': install4jBuildDir,
+ 'APPLICATION_CATEGORIES': install4j_application_categories,
+ 'APPLICATION_FOLDER': install4jApplicationFolder,
+ 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
+ 'EXECUTABLE_NAME': install4jExecutableName,
+ 'EXTRA_SCHEME': install4jExtraScheme,
+ ]
+
+ //println("INSTALL4J VARIABLES:")
+ //variables.each{k,v->println("${k}=${v}")}
+
+ destination = "${jalviewDir}/${install4jBuildDir}"
+ buildSelected = true
+
+ if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
+ faster = true
+ disableSigning = true
+ }
+
+ if (OSX_KEYPASS) {
+ macKeystorePassword = OSX_KEYPASS
+ }
+
+ doFirst {
+ println("Using projectFile "+projectFile)
+ }
+
+ inputs.dir(getdownWebsiteDir)
+ inputs.file(install4jConfFile)
+ inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
+ inputs.dir(macosJavaVMDir)
+ inputs.dir(windowsJavaVMDir)
+ outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
+}
+
+
+task sourceDist(type: Tar) {
+
+ def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+ def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
+ // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
+ try {
+ archiveFileName = outputFileName
+ } catch (Exception e) {
+ archiveName = outputFileName
+ }
+
+ compression Compression.GZIP
+
+ into project.name
+
+ def EXCLUDE_FILES=[
+ "build/*",
+ "bin/*",
+ "test-output/",
+ "test-reports",
+ "tests",
+ "clover*/*",
+ ".*",
+ "benchmarking/*",
+ "**/.*",
+ "*.class",
+ "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
+ "*locales/**",
+ "utils/InstallAnywhere",
+ "**/*.log",
+ ]
+ def PROCESS_FILES=[
+ "AUTHORS",
+ "CITATION",
+ "FEATURETODO",
+ "JAVA-11-README",
+ "FEATURETODO",
+ "LICENSE",
+ "**/README",
+ "RELEASE",
+ "THIRDPARTYLIBS",
+ "TESTNG",
+ "build.gradle",
+ "gradle.properties",
+ "**/*.java",
+ "**/*.html",
+ "**/*.xml",
+ "**/*.gradle",
+ "**/*.groovy",
+ "**/*.properties",
+ "**/*.perl",
+ "**/*.sh",
+ ]
+ def INCLUDE_FILES=[
+ ".settings/org.eclipse.jdt.core.jalview.prefs",
+ ]
+
+ from(jalviewDir) {
+ exclude (EXCLUDE_FILES)
+ include (PROCESS_FILES)
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(jalviewDir) {
+ exclude (EXCLUDE_FILES)
+ exclude (PROCESS_FILES)
+ exclude ("appletlib")
+ exclude ("**/*locales")
+ exclude ("*locales/**")
+ exclude ("utils/InstallAnywhere")
+
+ exclude (getdown_files_dir)
+ exclude (getdown_website_dir)
+
+ // exluding these as not using jars as modules yet
+ exclude ("$j11modDir/**/*.jar")
+ }
+ from(jalviewDir) {
+ include(INCLUDE_FILES)
+ }
+// from (jalviewDir) {
+// // explicit includes for stuff that seemed to not get included
+// include(fileTree("test/**/*."))
+// exclude(EXCLUDE_FILES)
+// exclude(PROCESS_FILES)
+// }
+}
+
+
+task helppages {
+ dependsOn copyHelp
+ dependsOn pubhtmlhelp
+
+ inputs.dir("${classesDir}/${help_dir}")
+ outputs.dir("${buildDir}/distributions/${help_dir}")
+}
+
+// LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
+task eclipseAutoBuildTask {}
+task eclipseSynchronizationTask {}
--- /dev/null
+/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
+import org.apache.tools.ant.filters.ReplaceTokens
+
+
+
+
+plugins {
+ id 'java'
+}
+
+
+
+// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
+def string(Object o) {
+ return o == null ? "" : o.toString()
+}
+
+
+ext {
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+ // Expect jalview.version and target release branch in jalview.release
+ def releaseProps = new Properties();
+ def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+ def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+ try {
+ (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
+ releaseProps.load(it)
+ }
+ } catch (Exception fileLoadError) {
+ throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+ }
+ ////
+ // Set JALVIEW_VERSION if it is not already set
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+
+
+ // essentials
+ bareSourceDir = string(source_dir)
+ sourceDir = string("${jalviewDir}/${bareSourceDir}")
+ resourceDir = string("${jalviewDir}/${resource_dir}")
+ bareTestSourceDir = string(test_source_dir)
+ testDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+ classesDir = string("${jalviewDir}/${classes_dir}")
+
+
+ resourceClassesDir = classesDir
+
+ testSourceDir = testDir
+ testClassesDir = "${jalviewDir}/${test_output_dir}"
+
+ buildProperties = string("${classesDir}/${build_properties_file}")
+ gitHash = string("")
+ gitBranch = string("")
+
+ println("Using a ${CHANNEL} profile.")
+
+ additional_compiler_args = []
+ // configure classpath/args for j8/j11 compilation
+ if (JAVA_VERSION.equals("1.8")) {
+ JAVA_INTEGER_VERSION = string("8")
+ //libDir = j8libDir
+ libDir = j11libDir
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+ } else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = string("11")
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+ } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+ JAVA_INTEGER_VERSION = JAVA_VERSION
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = JAVA_VERSION
+ compile_target_compatibility = JAVA_VERSION
+ } else {
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
+ }
+
+
+
+
+ buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
+ helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm")
+ helpParentDir = string("${jalviewDir}/${help_parent_dir}")
+ helpSourceDir = string("${helpParentDir}/${help_dir}")
+
+
+ // ENDEXT
+}
+
+
+sourceSets {
+ main {
+ java {
+ srcDirs sourceDir
+ outputDir = file(classesDir)
+ }
+
+ resources {
+ srcDirs resourceDir
+ srcDirs += helpParentDir
+ }
+
+ jar.destinationDir = file("${jalviewDir}/${package_dir}")
+
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+
+ test {
+ java {
+ srcDirs testSourceDir
+ outputDir = file(testClassesDir)
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+
+ compileClasspath = files( sourceSets.test.java.outputDir )
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+
+}
+
+
+
+
+compileJava {
+
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+
+}
+
+
+compileTestJava {
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+}
+
+
+clean {
+ doFirst {
+ delete sourceSets.main.java.outputDir
+ }
+}
+
+
+cleanTest {
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ }
+}
+
+
+// format is a string like date.format("dd MMMM yyyy")
+def getDate(format) {
+ def date = new Date()
+ return date.format(format)
+}
+
+
+task setGitVals {
+ def hashStdOut = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--short", "HEAD"
+ standardOutput = hashStdOut
+ ignoreExitValue true
+ }
+
+ def branchStdOut = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
+ standardOutput = branchStdOut
+ ignoreExitValue true
+ }
+
+ gitHash = hashStdOut.toString().trim()
+ gitBranch = branchStdOut.toString().trim()
+
+ outputs.upToDateWhen { false }
+}
+
+
+task createBuildProperties(type: WriteProperties) {
+ dependsOn setGitVals
+ inputs.dir(sourceDir)
+ inputs.dir(resourceDir)
+ file(buildProperties).getParentFile().mkdirs()
+ outputFile (buildProperties)
+ // taking time specific comment out to allow better incremental builds
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+ property "VERSION", JALVIEW_VERSION
+ property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+ outputs.file(outputFile)
+}
+
+
+task cleanBuildingHTML(type: Delete) {
+ doFirst {
+ delete buildingHTML
+ }
+}
+
+
+task convertBuildingMD(type: Exec) {
+ dependsOn cleanBuildingHTML
+ def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
+ def css = "${jalviewDir}/${doc_dir}/github.css"
+
+ def pandoc = null
+ pandoc_exec.split(",").each {
+ if (file(it.trim()).exists()) {
+ pandoc = it.trim()
+ return true
+ }
+ }
+
+ def hostname = "hostname".execute().text.trim()
+ def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+ if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
+ pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+ }
+
+ doFirst {
+ if (pandoc != null && file(pandoc).exists()) {
+ commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+ } else {
+ println("Cannot find pandoc. Skipping convert building.md to HTML")
+ throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
+ }
+ }
+
+ ignoreExitValue true
+
+ inputs.file(buildingMD)
+ inputs.file(css)
+ outputs.file(buildingHTML)
+}
+
+
+clean {
+ doFirst {
+ delete buildingHTML
+ }
+}
+
+
+task syncDocs(type: Sync) {
+ dependsOn convertBuildingMD
+ def syncDir = "${resourceClassesDir}/${doc_dir}"
+ from fileTree("${jalviewDir}/${doc_dir}")
+ into syncDir
+
+}
+
+
+task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${resourceClassesDir}/${help_dir}"
+ from(inputDir) {
+ exclude '**/*.gif'
+ exclude '**/*.jpg'
+ exclude '**/*.png'
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ include '**/*.gif'
+ include '**/*.jpg'
+ include '**/*.png'
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.files(helpFile)
+ outputs.dir(outputDir)
+}
+
+
+task syncResources(type: Sync) {
+ from resourceDir
+ include "**/*.*"
+ into "${resourceClassesDir}"
+ preserve {
+ include "**"
+ }
+}
+
+
+task prepare {
+ dependsOn syncResources
+ dependsOn syncDocs
+ dependsOn copyHelp
+}
+
+
+//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+test {
+ dependsOn prepare
+ //dependsOn compileJava ////? DELETE
+
+ dependsOn compileJava //?
+
+ useTestNG() {
+ includeGroups testng_groups
+ excludeGroups testng_excluded_groups
+ preserveOrder true
+ useDefaultListeners=true
+ }
+
+ maxHeapSize = "1024m"
+
+ workingDir = jalviewDir
+ //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+ systemProperty "laf", testLaf
+ }
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ jvmArgs += additional_compiler_args
+
+ doFirst {
+ }
+}
+
+
+task buildIndices(type: JavaExec) {
+ dependsOn copyHelp
+ classpath = sourceSets.main.compileClasspath
+ main = "com.sun.java.help.search.Indexer"
+ workingDir = "${classesDir}/${help_dir}"
+ def argDir = "html"
+ args = [ argDir ]
+ inputs.dir("${workingDir}/${argDir}")
+
+ outputs.dir("${classesDir}/doc")
+ outputs.dir("${classesDir}/help")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+ outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+ outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+ outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+ outputs.file("${workingDir}/JavaHelpSearch/TMAP")
+}
+
+
+task compileLinkCheck(type: JavaCompile) {
+ options.fork = true
+ classpath = files("${jalviewDir}/${utils_dir}")
+ destinationDir = file("${jalviewDir}/${utils_dir}")
+ source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+ outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
+}
+
+
+task linkCheck(type: JavaExec) {
+ dependsOn prepare, compileLinkCheck
+
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+ classpath = files("${jalviewDir}/${utils_dir}")
+ main = "HelpLinksChecker"
+ workingDir = jalviewDir
+ args = [ "${classesDir}/${help_dir}", "-nointernet" ]
+
+ def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
+ def errFOS = outFOS
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ errorOutput)
+
+ inputs.dir("${classesDir}/${help_dir}")
+ outputs.file(helpLinksCheckerOutFile)
+}
+
+// import the pubhtmlhelp target
+ant.properties.basedir = "${jalviewDir}"
+ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
+ant.importBuild "${utils_dir}/publishHelp.xml"
+
+
+task cleanPackageDir(type: Delete) {
+ doFirst {
+ delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
+ }
+}
+
+jar {
+ dependsOn linkCheck
+ dependsOn buildIndices
+ dependsOn createBuildProperties
+
+ manifest {
+ attributes "Main-Class": main_class,
+ "Permissions": "all-permissions",
+ "Application-Name": "Jalview Desktop",
+ "Codebase": application_codebase
+ }
+
+ destinationDir = file("${jalviewDir}/${package_dir}")
+ archiveName = rootProject.name+".jar"
+
+ exclude "cache*/**"
+ exclude "*.jar"
+ exclude "*.jar.*"
+ exclude "**/*.jar"
+ exclude "**/*.jar.*"
+
+ inputs.dir(classesDir)
+ outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
+}
git://source.jalview.org / jalview.git / commitdiff