import org.apache.tools.ant.filters.ReplaceTokens
- //import org.apache.tools.ant.filters.ReplaceRegexp
import org.gradle.internal.os.OperatingSystem
- import org.gradle.plugins.ide.eclipse.model.*
-
-
+ 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 {
dependencies {
classpath 'org.openclover:clover:4.4.1'
- classpath 'org.apache.commons:commons-compress:1.18'
}
}
id 'application'
id 'eclipse'
id 'com.github.johnrengelman.shadow' version '4.0.3'
- id 'com.install4j.gradle' version '7.0.9'
+ id 'com.install4j.gradle' version '8.0.2'
+ id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
}
repositories {
}
}
- 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"
+ dependencies {
}
- // configure classpath/args for j8/j11 compilation
- def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
- def libDir
- def libDistDir
- def compile_source_compatibility
- def compile_target_compatibility
+ // 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 {
- getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
- getdownDir = ""
- reportRsyncCmd = false
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+ // local build environment properties
+ def localProps = "${jalviewDirAbsolutePath}/local.properties"
+ if (file(localProps).exists()) {
+ try {
+ def p = new Properties()
+ def localPropsFIS = new FileInputStream(localProps)
+ p.load(localPropsFIS)
+ localPropsFIS.close()
+ p.each {
+ key, val ->
+ def oldval = findProperty(key)
+ setProperty(key, val)
+ if (oldval != null) {
+ println("Overriding property '${key}' ('${oldval}') with local.properties value '${val}'")
+ } else {
+ println("Setting unknown property '${key}' with local.properties value '${val}'")
+ }
+ }
+ } catch (Exception e) {
+ System.out.println("Exception reading local.properties")
+ }
+ }
+
+ // 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)
+ sourceDir = string("${jalviewDir}/${bareSourceDir}")
+ resourceDir = string("${jalviewDir}/${resource_dir}")
+ bareTestSourceDir = string(test_source_dir)
+ testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+ // clover
+ cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
+ classesDir = string("${jalviewDir}/${classes_dir}")
+ if (clover.equals("true")) {
+ use_clover = true
+ classesDir = string("${buildDir}/${cloverClassesDir}")
+ } else {
+ use_clover = false
+ classesDir = string("${jalviewDir}/${classes_dir}")
+ }
+
+ classes = classesDir
+
+ getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
buildDist = true
- buildProperties = buildPropertiesFile
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher
+
+ // the following values might be overridden by the CHANNEL switch
+ getdownChannelName = CHANNEL.toLowerCase()
+ getdownDir = string("${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}")
+ reportRsyncCmd = false
+ jvlChannelName = CHANNEL.toLowerCase()
switch (CHANNEL) {
case "BUILD":
// TODO: get bamboo build artifact URL for getdown artifacts
getdown_channel_base = bamboo_channelbase
- getdown_channel_name = bamboo_planKey + '/'+JAVA_VERSION
- getdown_app_base = bamboo_channelbase + '/'+ bamboo_planKey + bamboo_getdown_channel_suffix + '/'+JAVA_VERSION
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
+ getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
+ jvlChannelName += "_${getdownChannelName}"
break
case "RELEASE":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
- getdown_app_dir = getdown_app_dir_release
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdownAppDistDir = getdown_app_dir_release
reportRsyncCommand = true
break
case "ARCHIVE":
- getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
- getdown_app_dir = getdown_app_dir_alt
- if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
- print "Must provide an ARCHIVEDIR value to produce an archive distribution"
- exit
+ getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+ if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = ARCHIVEDIR + "/" + packageDir
- buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ packageDir = string("${ARCHIVEDIR}/${packageDir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
break
case "ARCHIVELOCAL":
- getdown_channel_name = "archive" + "/" + JALVIEW_VERSION
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = file(getdownWebsiteDir).toURI().toString()
- getdown_app_dir = getdown_app_dir_alt
- if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
- print "Must provide an ARCHIVEDIR value to produce an archive distribution"
- exit
+ getdownChannelName = string("archive/${JALVIEW_VERSION}")
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = ARCHIVEDIR + "/" + packageDir
- buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ packageDir = string("${ARCHIVEDIR}/${packageDir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
break
case "DEVELOP":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
reportRsyncCommand = true
break
case "TEST-RELEASE":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
reportRsyncCommand = true
break
case ~/^SCRATCH(|-[-\w]*)$/:
- getdown_channel_name = CHANNEL
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdownChannelName = CHANNEL
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
reportRsyncCommand = true
break
+ case "TEST-LOCAL":
+ if (!file("${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}")
+ }
+ break
+
case "LOCAL":
- getdown_app_base = file(getdownWebsiteDir).toURI().toString()
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
break
default: // something wrong specified
- print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
- exit
+ throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
break
}
-
- println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base)
- getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
- //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
- getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
- getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir
- getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
- getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir
+ // override getdownAppBase if requested
+ if (findProperty("getdown_appbase_override") != null) {
+ getdownAppBase = string(getProperty("getdown_appbase_override"))
+ println("Overriding getdown appbase with '${getdownAppBase}'")
+ }
+ // sanitise file name for jalview launcher file for this channel
+ jvlChannelName = jvlChannelName.replaceAll(/[^\w\-]/,"_")
+
+ 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/$j11modDir", include: ["*.jar"])
+ modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
*/
- gitHash = ""
- gitBranch = ""
- }
+ 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
+ // these are getdown.txt properties defined dependent on the JAVA_VERSION
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
+ // this property is assigned below and expanded to multiple lines in the getdown task
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
+ // this property is for the Java library used in eclipse
+ eclipseJavaRuntimeName = string("JavaSE-1.8")
+ } else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = string("11")
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+ eclipseJavaRuntimeName = string("JavaSE-11")
+ /* compile without modules -- using classpath libraries
+ additional_compiler_args += [
+ '--module-path', modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ */
+ } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+ JAVA_INTEGER_VERSION = JAVA_VERSION
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = JAVA_VERSION
+ compile_target_compatibility = JAVA_VERSION
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+ eclipseJavaRuntimeName = string("JavaSE-11")
+ /* compile without modules -- using classpath libraries
+ additional_compiler_args += [
+ '--module-path', modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ */
+ } else {
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
+ }
- 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
- def getdown_alt_java_max_version
- // this property is assigned below and expanded to multiple lines in the getdown task
- def getdown_alt_multi_java_location
- // this property is for the Java library used in eclipse
- def eclipse_java_runtime_name
- if (JAVA_VERSION.equals("1.8")) {
- JAVA_INTEGER_VERSION = "8"
- //libDir = j8libDir
- 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_java_max_version = getdown_alt_java8_max_version
- getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
- eclipse_java_runtime_name = "JavaSE-1.8"
- } 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_java_max_version = getdown_alt_java11_max_version
- getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
- eclipse_java_runtime_name = "JavaSE-11"
- /* compile without modules -- using classpath libraries
- additional_compiler_args += [
- '--module-path', ext.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
- getdown_alt_java_min_version = getdown_alt_java11_min_version
- getdown_alt_java_max_version = getdown_alt_java11_max_version
- getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
- eclipse_java_runtime_name = "JavaSE-11"
- /* compile without modules -- using classpath libraries
- additional_compiler_args += [
- '--module-path', ext.modules_compileClasspath.asPath,
- '--add-modules', j11modules
- ]
- */
- } else {
- throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
+
+ // for install4j
+ JAVA_MIN_VERSION = JAVA_VERSION
+ JAVA_MAX_VERSION = JAVA_VERSION
+ def jreInstallsDir = string(jre_installs_dir)
+ if (jreInstallsDir.startsWith("~/")) {
+ jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
+ }
+ macosJavaVMDir = string("${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}/${docDir}/building.html")
+ helpFile = string("${classesDir}/${help_dir}/help.jhm")
+ helpParentDir = string("${jalviewDir}/${help_parent_dir}")
+ helpSourceDir = string("${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
}
- sourceSets {
+ sourceSets {
main {
java {
- srcDirs "$jalviewDir/$sourceDir"
- outputDir = file("$classes")
+ srcDirs sourceDir
+ outputDir = file(classesDir)
}
resources {
- srcDirs "$jalviewDir/$resourceDir"
+ srcDirs resourceDir
+ srcDirs += helpParentDir
}
- jar.destinationDir = file("$jalviewDir/$packageDir")
+ jar.destinationDir = file("${jalviewDir}/${packageDir}")
compileClasspath = files(sourceSets.main.java.outputDir)
- compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ //compileClasspath += files(sourceSets.main.resources.srcDirs)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
}
+
clover {
java {
srcDirs = [ cloverInstrDir ]
compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
compileClasspath += files(sourceSets.main.java.outputDir)
compileClasspath += sourceSets.main.compileClasspath
- compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
- compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
}
test {
java {
- srcDirs "$jalviewDir/$testSourceDir"
- outputDir = file("$jalviewDir/$testOutputDir")
+ srcDirs testSourceDir
+ outputDir = file("${jalviewDir}/${testOutputDir}")
}
resources {
compileClasspath += files(sourceSets.main.java.outputDir)
}
- compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
- compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
}
}
+
// clover bits
dependencies {
if (use_clover) {
}
}
+
configurations {
cloverRuntime
cloverRuntime.extendsFrom cloverCompile
eclipse {
project {
- name = "Jalview with gradle build"
+ name = eclipse_project_name
natures 'org.eclipse.jdt.core.javanature',
'org.eclipse.jdt.groovy.core.groovyNature',
classpath {
//defaultOutputDir = sourceSets.main.java.outputDir
def removeThese = []
- configurations.each{ if (it.isCanBeResolved()) {
- removeThese += it
+ configurations.each{
+ if (it.isCanBeResolved()) {
+ removeThese += it
+ }
}
- }
- minusConfigurations += removeThese
- plusConfigurations = [ ]
- file {
+ 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)
+ 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)
-
- print ("CP="+cp.inspect())
-
- cp.entries += new Output("bin/main")
- cp.entries += new Library(fileReference(helpParentDir))
- cp.entries += new Library(fileReference(resourceDir))
- HashMap<String, Boolean> addedLibPath = new HashMap<>();
-
- // changing from sourcesets.main.classpath to specific Java version lib
- //sourceSets.main.compileClasspath.each{
- fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
- //don't want to add outputDir as eclipse is using its own output dir in bin/main
- if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return
- }
- def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
- }
- if (addedLibPath.get(itPath)) {
- //println("Not adding duplicate entry "+itPath)
- } else {
- //println("Adding entry "+itPath)
- cp.entries += new Library(fileReference(itPath))
- addedLibPath.put(itPath, true)
}
- }
+ cp.entries.removeAll(removeTheseToo)
- // changing from sourcesets.main.classpath to specific Java version lib
- //sourceSets.test.compileClasspath.each{
- fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
- //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
- if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return false // groovy "break" in .each loop
- }
- def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
- }
- if (addedLibPath.get(itPath)) {
- // don't duplicate
- } else {
- def lib = new Library(fileReference(itPath))
- // this doesn't work... yet. Adding test=true attribute using withXml below
- //def attrs = new Node(null, 'attributes', ["test":"true"])
- //lib.appendNode(attrs) //
- cp.entries += lib
- addedLibPath.put(itPath, true)
+ //cp.entries += new Output("${eclipse_bin_dir}/main")
+ if (file(helpParentDir).isDirectory()) {
+ cp.entries += new Library(fileReference(helpParentDir))
}
+ if (file(resourceDir).isDirectory()) {
+ cp.entries += new Library(fileReference(resourceDir))
}
- }
- // withXml changes ignored by buildship, these add the "test=true" attribute
- withXml {
- def node = it.asNode()
+ HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
- 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
+ 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 addTestAttribute = true
- srcTestAttributes.each{a ->
- if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
- addTestAttribute = false
+ def itPath = it.toString()
+ if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
+ // make relative path
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ //println("Not adding duplicate entry "+itPath)
+ } else {
+ //println("Adding entry "+itPath)
+ cp.entries += new Library(fileReference(itPath))
+ alreadyAddedLibPath.put(itPath, true)
}
- }
- if (addTestAttribute) {
- srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
}
- node.children().each{ cpe ->
- def attributes = cpe.attributes()
- if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) {
- cpe.appendNode('attributes')
- .appendNode('attribute', [name:"test", value:"true"])
+ sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+ //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath
+ return false // groovy "continue" in .any closure
+ }
+
+ def itPath = it.toString()
+ if (itPath.startsWith("${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)
}
}
- } // withXML
+
+ } // 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 = eclipse_java_runtime_name
+ 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)
+ def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
jalview_prefs.load(ins)
ins.close()
jalview_prefs.forEach { t, v ->
}
}
}
- }
- //synchronizationTasks eclipseClasspath
- //autoBuildTasks eclipseClasspath
+ } // jdt
+
+ if (IN_ECLIPSE) {
+ // Don't want these to be activated if in headless build
+ synchronizationTasks "eclipseSynchronizationTask"
+ autoBuildTasks "eclipseAutoBuildTask"
+
+ }
}
+
task cloverInstr() {
// only instrument source, we build test classes as normal
inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
}
+task cloverReportHTML (type: JavaExec) {
+ inputs.dir "${buildDir}/clover"
+ outputs.dir "${reportsDir}/clover"
+
+ classpath configurations.cloverRuntime
+ maxHeapSize "${cloverReportJVMHeap}"
+ jvmArgs += "${cloverReportJVMArgs}"
+ main = "com.atlassian.clover.reporters.html.HtmlReporter"
+ args "--initstring", "${buildDir}/clover/clover.db", "-o", "${reportsDir}/clover"
+ "${cloverReportHTMLOptions}".split(",").each {
+ args+= it.trim()
+ }
+}
+
+task cloverReportXML (type: JavaExec) {
+ inputs.dir "${buildDir}/clover"
+ outputs.dir "${reportsDir}/clover"
+ maxHeapSize "${cloverReportJVMHeap}"
+ jvmArgs "${cloverReportJVMArgs}"
+ classpath configurations.cloverRuntime
+ main = "com.atlassian.clover.reporters.xml.XMLReporter"
+ args "--initstring", "${buildDir}/clover/clover.db", "-o", "${reportsDir}/clover/clover.xml"
+
+ "${cloverReportXMLOptions}".split(",").each {
+ args+= it.trim()
+ }
+}
task cloverReport {
group = "Verification"
- description = "Createst the Clover report"
+ description = "Creates 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", "${reportsDir}/clover/clover.xml"].toArray()
- com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
- }
+ dependsOn cloverReportXML
+ dependsOn cloverReportHTML
}
-
// end clover bits
}
+
compileTestJava {
if (use_clover) {
dependsOn compileCloverJava
classpath += configurations.cloverRuntime
}
+
clean {
- delete sourceSets.main.java.outputDir
+ doFirst {
+ delete sourceSets.main.java.outputDir
+ }
}
+
cleanTest {
- delete sourceSets.test.java.outputDir
- delete cloverInstrDir
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ delete cloverInstrDir
+ }
}
+
// format is a string like date.format("dd MMMM yyyy")
def getDate(format) {
def date = new Date()
return date.format(format)
}
+
task setGitVals {
def hashStdOut = new ByteArrayOutputStream()
exec {
ignoreExitValue true
}
- project.ext.gitHash = hashStdOut.toString().trim()
- project.ext.gitBranch = branchStdOut.toString().trim()
+ gitHash = hashStdOut.toString().trim()
+ gitBranch = branchStdOut.toString().trim()
outputs.upToDateWhen { false }
}
+
task createBuildProperties(type: WriteProperties) {
dependsOn setGitVals
- inputs.dir("$jalviewDir/$sourceDir")
- inputs.dir("$classes")
- inputs.dir("$jalviewDir/$resourceDir")
+ 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:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
+ property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
outputs.file(outputFile)
}
- def buildingHTML = "$jalviewDir/$docDir/building.html"
- task deleteBuildingHTML(type: Delete) {
- delete buildingHTML
+
+ task cleanBuildingHTML(type: Delete) {
+ doFirst {
+ delete buildingHTML
+ }
}
+
task convertBuildingMD(type: Exec) {
- dependsOn deleteBuildingHTML
- def buildingMD = "$jalviewDir/$docDir/building.md"
- def css = "$jalviewDir/$docDir/github.css"
+ dependsOn cleanBuildingHTML
+ def buildingMD = "${jalviewDir}/${docDir}/building.md"
+ def css = "${jalviewDir}/${docDir}/github.css"
def pandoc = null
pandoc_exec.split(",").each {
}
def hostname = "hostname".execute().text.trim()
- if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
+ 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"
}
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()
+ throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
}
}
inputs.file(css)
outputs.file(buildingHTML)
}
+
+
clean {
- delete buildingHTML
+ doFirst {
+ delete buildingHTML
+ }
}
+
task syncDocs(type: Sync) {
dependsOn convertBuildingMD
- def syncDir = "$classes/$docDir"
- from fileTree("$jalviewDir/$docDir")
+ def syncDir = "${classesDir}/${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/$helpDir"
+ def inputDir = helpSourceDir
+ def outputDir = "${classesDir}/${help_dir}"
from(inputDir) {
exclude '**/*.gif'
- exclude '**/*.jpg'
- exclude '**/*.png'
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+ 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'
+ include '**/*.jpg'
+ include '**/*.png'
}
into outputDir
outputs.dir(outputDir)
}
+
task syncLib(type: Sync) {
- def syncDir = "$classes/$libDistDir"
- from fileTree("$jalviewDir/$libDistDir")
+ def syncDir = "${classesDir}/${libDistDir}"
+ from fileTree("${jalviewDir}/${libDistDir}")
into syncDir
}
+
task syncResources(type: Sync) {
- from "$jalviewDir/$resourceDir"
+ from resourceDir
include "**/*.*"
- exclude "install4j"
- into "$classes"
+ into "${classesDir}"
preserve {
include "**"
}
}
+
task prepare {
dependsOn syncResources
dependsOn syncDocs
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"
+ workingDir = "${classesDir}/${help_dir}"
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")
+ 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("$jalviewDir/$utilsDir")
- destinationDir = file("$jalviewDir/$utilsDir")
- source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
-
- inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
- inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
- outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
- outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
+ classpath = files("${jalviewDir}/${utilsDir}")
+ destinationDir = file("${jalviewDir}/${utilsDir}")
+ source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+ inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
+ inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
+ outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
+ outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
}
- def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch")
+
task linkCheck(type: JavaExec) {
dependsOn prepare, compileLinkCheck
- classpath = files("$jalviewDir/$utilsDir")
+
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
+ classpath = files("${jalviewDir}/${utilsDir}")
main = "HelpLinksChecker"
workingDir = jalviewDir
- def help = "$classes/$helpDir"
- args = [ "$classes/$helpDir", "-nointernet" ]
-
- doLast {
- helplinkscheckertouchfile.createNewFile()
- }
-
- inputs.dir("$classes/$helpDir")
- outputs.file(helplinkscheckertouchfile)
+ 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/$helpDir"
- ant.importBuild "$utilsDir/publishHelp.xml"
+ ant.properties.basedir = "${jalviewDir}"
+ ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
+ ant.importBuild "${utilsDir}/publishHelp.xml"
task cleanPackageDir(type: Delete) {
- delete fileTree("$jalviewDir/$packageDir").include("*.jar")
+ doFirst {
+ delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
+ }
}
jar {
"Codebase": application_codebase
}
- destinationDir = file("$jalviewDir/$packageDir")
+ destinationDir = file("${jalviewDir}/${packageDir}")
archiveName = rootProject.name+".jar"
exclude "cache*/**"
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir("$classes")
- outputs.file("$jalviewDir/$packageDir/$archiveName")
+ inputs.dir(classesDir)
+ outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
}
+
task copyJars(type: Copy) {
- from fileTree("$classes").include("**/*.jar").include("*.jar").files
- into "$jalviewDir/$packageDir"
+ from fileTree(dir: classesDir, include: "**/*.jar").files
+ into "${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/$packageDir"
+ from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
+ into "${jalviewDir}/${packageDir}"
preserve {
include jar.archiveName
}
}
+
task makeDist {
group = "build"
description = "Put all required libraries in dist"
dependsOn cleanPackageDir
dependsOn syncJars
dependsOn jar
- outputs.dir("$jalviewDir/$packageDir")
+ outputs.dir("${jalviewDir}/${packageDir}")
}
+
task cleanDist {
dependsOn cleanPackageDir
dependsOn cleanTest
if (buildDist) {
dependsOn makeDist
}
- from ("$jalviewDir/$libDistDir") {
+ from ("${jalviewDir}/${libDistDir}") {
include("*.jar")
}
manifest {
minimize()
}
+
task getdownWebsite() {
group = "distribution"
description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
dependsOn makeDist
}
- // clean the getdown website and files dir before creating getdown folders
- delete project.ext.getdownWebsiteDir
- delete project.ext.getdownFilesDir
-
def getdownWebsiteResourceFilenames = []
def getdownTextString = ""
- def getdownResourceDir = project.ext.getdownResourceDir
- def getdownAppDir = project.ext.getdownAppDir
+ def getdownResourceDir = getdownResourceDir
def getdownResourceFilenames = []
doFirst {
+ // clean the getdown website and files dir before creating getdown folders
+ delete getdownWebsiteDir
+ delete getdownFilesDir
+
copy {
from buildProperties
- rename(buildPropertiesFile, getdown_build_properties)
- into project.ext.getdownAppDir
+ rename(build_properties_file, getdown_build_properties)
+ into getdownAppDir
}
- getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties
+ getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
// go through properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
- if (getdown_alt_java_min_version.length() > 0) {
- props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
- }
- if (getdown_alt_java_max_version.length() > 0) {
- props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
- }
- props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
-
- props.put("getdown_txt_appbase", getdown_app_base)
+ if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
+ props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
+ }
+ if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
+ props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
+ }
+ if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
+ props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
+ }
+
+ props.put("getdown_txt_appbase", getdownAppBase)
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_") && val != null) {
if (prop.startsWith("getdown_txt_multi_")) {
def key = prop.substring(18)
val.split(",").each{ v ->
- def line = key + " = " + v + "\n"
+ def line = "${key} = ${v}\n"
getdownTextString += line
}
} else {
r = file(val)
} else if (val.indexOf('/') > 0) {
// relative path (relative to jalviewDir)
- r = file( jalviewDir + '/' + val )
+ r = file( "${jalviewDir}/${val}" )
}
if (r.exists()) {
- val = getdown_resource_dir + '/' + r.getName()
+ val = "${getdown_resource_dir}/" + r.getName()
getdownWebsiteResourceFilenames += val
getdownResourceFilenames += r.getPath()
}
}
if (! prop.startsWith("getdown_txt_resource")) {
- def line = prop.substring(12) + " = " + val + "\n"
+ def line = prop.substring(12) + " = ${val}\n"
getdownTextString += line
}
}
}
getdownWebsiteResourceFilenames.each{ filename ->
- getdownTextString += "resource = "+filename+"\n"
+ getdownTextString += "resource = ${filename}\n"
}
getdownResourceFilenames.each{ filename ->
copy {
from filename
- into project.ext.getdownResourceDir
+ into getdownResourceDir
}
}
}
}
codeFiles.sort().each{f ->
- def line = "code = " + getdown_app_dir + '/' + f.getName() + "\n"
+ def name = f.getName()
+ def line = "code = ${getdownAppDistDir}/${name}\n"
getdownTextString += line
copy {
from f.getPath()
- into project.ext.getdownAppDir
+ 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()
+ def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
j11libFiles.sort().each{f ->
- def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+ def name = f.getName()
+ def line = "code = ${getdown_j11lib_dir}/${name}\n"
getdownTextString += line
copy {
from f.getPath()
- into project.ext.getdownJ11libDir
+ 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 = " + mainClass + "\n"
+ getdownTextString += "resource = ${getdown_launcher_new}\n"
+ getdownTextString += "class = ${mainClass}\n"
- def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
+ def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
getdown_txt.write(getdownTextString)
- def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl)
- launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
+ def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+ def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+ launchJvl.write("appbase="+props.get("getdown_txt_appbase"))
copy {
from getdownLauncher
rename(file(getdownLauncher).getName(), getdown_launcher_new)
- into project.ext.getdownWebsiteDir
+ into getdownWebsiteDir
}
copy {
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
- into project.ext.getdownWebsiteDir
+ into getdownWebsiteDir
}
if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
copy {
from getdown_txt
from getdownLauncher
- from getdownWebsiteDir+"/"+getdown_build_properties
+ from "${getdownWebsiteDir}/${getdown_build_properties}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
copy {
from getdown_txt
- from launch_jvl
+ from launchJvl
from getdownLauncher
- from getdownWebsiteDir+"/"+getdown_build_properties
+ from "${getdownWebsiteDir}/${getdown_build_properties}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
}
copy {
- from getdownResourceDir
- into project.ext.getdownFilesDir + '/' + getdown_resource_dir
+ from getdownResourceDir
+ into "${getdownFilesDir}/${getdown_resource_dir}"
}
}
if (buildDist) {
- inputs.dir(jalviewDir + '/' + packageDir)
+ inputs.dir("${jalviewDir}/${packageDir}")
+ }
+ outputs.dir(getdownWebsiteDir)
+ outputs.dir(getdownFilesDir)
+ }
+
+
+ // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
+ task getdownDigestDir(type: JavaExec) {
+ def digestDirPropertyName = "DIGESTDIR"
+ description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown"
+ 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
}
- outputs.dir(project.ext.getdownWebsiteDir)
- outputs.dir(project.ext.getdownFilesDir)
+ main = "com.threerings.getdown.tools.Digester"
}
+
task getdownDigest(type: JavaExec) {
group = "distribution"
description = "Digest the getdown website folder"
dependsOn getdownWebsite
doFirst {
- classpath = files(getdownWebsiteDir + '/' + getdown_launcher)
+ classpath = files(getdownLauncher)
}
main = "com.threerings.getdown.tools.Digester"
- args project.ext.getdownWebsiteDir
- inputs.dir(project.ext.getdownWebsiteDir)
- outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
+ args getdownWebsiteDir
+ inputs.dir(getdownWebsiteDir)
+ outputs.file("${getdownWebsiteDir}/digest2.txt")
}
+
task getdown() {
group = "distribution"
description = "Create the minimal and full getdown app folder for installers and website and create digest file"
dependsOn getdownDigest
doLast {
if (reportRsyncCommand) {
- def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/")
- def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/")
+ def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+ def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
println "LIKELY RSYNC COMMAND:"
println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
if (RUNRSYNC == "true") {
}
}
+
clean {
- delete project.ext.getdownWebsiteDir
- delete project.ext.getdownFilesDir
+ doFirst {
+ delete getdownWebsiteDir
+ delete getdownFilesDir
+ }
}
+
install4j {
- def install4jHomeDir = "/opt/install4j"
- def hostname = "hostname".execute().text.trim()
- if (hostname.equals("jv-bamboo")) {
+ 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 (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
+ } 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(","))
}
- 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,
- 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
- 'GETDOWN_DIST_DIR': getdown_app_dir,
- 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
- 'GETDOWN_INSTALL_DIR': getdown_install_dir
- ]
- )
- 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'])
+
+ task copyInstall4jTemplate {
+ def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+ def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+ inputs.file(install4jTemplateFile)
+ inputs.file(install4jFileAssociationsFile)
+ 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>${install4jFileAssociationsText}</actions>")
+ install4jConfigXml.'**'.action.any { a ->
+ if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
+ def parent = a.parent()
+ parent.remove(a)
+ fileAssociationActions.each { faa ->
+ parent.append(faa)
+ }
+ // don't need to continue in .any loop once replacements have been made
+ return true
+ }
+ }
+
+ // write install4j file
+ install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
}
- into install4jDir
- outputs.files(install4jConf)
+ }
- doLast {
- // include file associations in installer
- def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
- ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
- replace: installerFileAssociationsXml,
- file: install4jConf
- )
- /*
- // include uninstaller applescript app files in dmg
- def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
- ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
- replace: installerDMGUninstallerXml,
- file: install4jConf
- )
- */
+
+ clean {
+ doFirst {
+ delete install4jConfFile
}
}
+
task installers(type: com.install4j.gradle.Install4jTask) {
group = "distribution"
description = "Create the install4j installers"
+ dependsOn setGitVals
dependsOn getdown
dependsOn copyInstall4jTemplate
- projectFile = file(install4jConf)
- println("Using projectFile "+projectFile)
- variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
- destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
+
+ 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}/${JAVA_VERSION}"
+
+ variables = [
+ 'JALVIEW_NAME': getdown_txt_title,
+ 'JALVIEW_DIR': "../..",
+ 'OSX_KEYSTORE': OSX_KEYSTORE,
+ 'JSIGN_SH': JSIGN_SH,
+ 'JRE_DIR': getdown_app_dir_java,
+ 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
+ 'JALVIEW_VERSION': JALVIEW_VERSION,
+ 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
+ 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
+ 'JAVA_VERSION': JAVA_VERSION,
+ 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+ 'VERSION': JALVIEW_VERSION,
+ 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+ 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+ 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
+ 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+ 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+ 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
+ 'COPYRIGHT_MESSAGE': install4j_copyright_message,
+ 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
+ 'INSTALLER_NAME': install4j_installer_name,
+ 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
+ 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+ 'GETDOWN_FILES_DIR': getdown_files_dir,
+ 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+ 'GETDOWN_DIST_DIR': getdownAppDistDir,
+ 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+ 'GETDOWN_INSTALL_DIR': getdown_install_dir,
+ 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
+ 'BUILD_DIR': install4jBuildDir,
+ ]
+
+ destination = "${jalviewDir}/${install4jBuildDir}"
buildSelected = true
+ if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
+ faster = true
+ disableSigning = true
+ }
+
if (OSX_KEYPASS) {
- macKeystorePassword=OSX_KEYPASS
+ macKeystorePassword = OSX_KEYPASS
+ }
+ doFirst {
+ println("Using projectFile "+projectFile)
}
- inputs.dir(project.ext.getdownWebsiteDir)
- inputs.file(install4jConf)
+ inputs.dir(getdownWebsiteDir)
+ inputs.file(install4jConfFile)
+ inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
inputs.dir(macosJavaVMDir)
inputs.dir(windowsJavaVMDir)
- outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
-
+ outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
}
- clean {
- delete install4jConf
- }
- task sourceDist (type: Tar) {
+ task sourceDist(type: Tar) {
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
- def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
// cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
try {
archiveFileName = outputFileName
from(jalviewDir) {
exclude (EXCLUDE_FILES)
include (PROCESS_FILES)
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
}
from(jalviewDir) {
exclude (EXCLUDE_FILES)
// }
}
- task helppages {
+
+ task helppages {
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("$classes/$helpDir")
- outputs.dir("$helpOutputDir")
+ inputs.dir("${classesDir}/${help_dir}")
+ outputs.dir("${buildDir}/distributions/${help_dir}")
}
+
+ // LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
+ task eclipseAutoBuildTask {}
+ task eclipseSynchronizationTask {}
git://source.jalview.org / jalview.git / commitdiff