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 {
dependencies {
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 '1.4' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
}
repositories {
compile 'org.apache.commons:commons-compress:1.18'
}
-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"
+// 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.toString()
}
-// configure classpath/args for j8/j11 compilation
-
-def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
-def libDir
-def libDistDir
-def compile_source_compatibility
-def compile_target_compatibility
ext {
- getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}"
- getdownDir = ""
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+ // local build environment properties
+ def localProps = "${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 over = getProperty(key) != null
+ setProperty(key, val)
+ if (over) {
+ println("Overriding 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")
+ }
+
+ J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+ if (J2S_ENABLED) {
+ println("J2S ENABLED")
+ }
+
+ /* *-/
+ 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}/${JAVA_VERSION}")
+ getdownDir = string("")
reportRsyncCmd = false
buildDist = true
- buildProperties = buildPropertiesFile
- getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}"
+ buildProperties = build_properties_file
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
switch (CHANNEL) {
case "BUILD":
// TODO: get bamboo build artifact URL for getdown artifacts
getdown_channel_base = bamboo_channelbase
- getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}"
- getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}"
+ getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}")
+ getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+ buildProperties = string("${classesDir}/${build_properties_file}")
break
case "RELEASE":
getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
- getdown_app_base = "${getdown_channel_base}/${getdownDir}"
+ getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
+ getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_release
- buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
break
case "ARCHIVE":
getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
- getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
- getdown_app_base = "${getdown_channel_base}/${getdownDir}"
+ getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
+ getdown_app_base = string("${getdown_channel_base}/${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
} 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}/${JAVA_VERSION}"
+ getdown_channel_name = string("archive/${JALVIEW_VERSION}")
+ getdownDir = string("${getdown_channel_name}/${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
} 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}"
+ getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
+ getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
break
case "TEST-RELEASE":
getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
- getdown_app_base = "${getdown_channel_base}/${getdownDir}"
+ getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
+ getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
break
case ~/^SCRATCH(|-[-\w]*)$/:
getdown_channel_name = CHANNEL
- getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
- getdown_app_base = "${getdown_channel_base}/${getdownDir}"
+ getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
+ getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
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}"
+ buildProperties = string("${classesDir}/${build_properties_file}")
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
break
default: // something wrong specified
}
- getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}"
+ getdownAppDir = string("${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}"
+ 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 = ""
- gitBranch = ""
-
- println("Using a ${CHANNEL} profile. appbase=${getdown_app_base}")
-}
-
-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")
+ 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
+ getdown_alt_java_min_version = getdown_alt_java8_min_version
+ getdown_alt_java_max_version = getdown_alt_java8_max_version
+ // this property is assigned below and expanded to multiple lines in the getdown task
+ getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
+ // this property is for the Java library used in eclipse
+ eclipse_java_runtime_name = 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
+ 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 = 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
+ 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 = 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
+ macosJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre")
+ macosJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz")
+ windowsJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre")
+ windowsJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.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}")
compileClasspath = files(sourceSets.main.java.outputDir)
+ //compileClasspath += files(sourceSets.main.resources.srcDirs)
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
test {
java {
- srcDirs "${jalviewDir}/${testSourceDir}"
+ srcDirs testSourceDir
outputDir = file("${jalviewDir}/${testOutputDir}")
}
}
}
+
// clover bits
dependencies {
if (use_clover) {
}
}
+
configurations {
cloverRuntime
cloverRuntime.extendsFrom cloverCompile
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 == sourceDir || entry.path == testSourceDir)) {
+ if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
removeTheseToo += entry
} else {
alreadyAddedSrcPath.putAt(entry.path, true)
}
}
+
}
cp.entries.removeAll(removeTheseToo)
- if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
- cp.entries += new Output("${eclipse_bin_dir}/main")
- }
+ //cp.entries += new Output("${eclipse_bin_dir}/main")
if (file(helpParentDir).isDirectory()) {
cp.entries += new Library(fileReference(helpParentDir))
}
HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
- sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ 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
- return
+ // 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("${jalviewDirAbsolutePath}/")) {
}
}
- //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
- sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
//no longer want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath
- return false // groovy "break" in .each closure
+ return false // groovy "continue" in .any closure
}
+
def itPath = it.toString()
if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
} // 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) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+ inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
outputs.dir cloverInstrDir
doFirst {
com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
}
}
-
// end clover bits
}
+
compileTestJava {
if (use_clover) {
dependsOn compileCloverJava
classpath += configurations.cloverRuntime
}
+
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 {
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}/${docDir}/building.html"
+
task cleanBuildingHTML(type: Delete) {
doFirst {
delete buildingHTML
}
}
+
task convertBuildingMD(type: Exec) {
dependsOn cleanBuildingHTML
def buildingMD = "${jalviewDir}/${docDir}/building.md"
commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
} else {
println("Cannot find pandoc. Skipping convert building.md to HTML")
- throw new StopExecutionException()
+ throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
}
}
outputs.file(buildingHTML)
}
+
clean {
doFirst {
delete buildingHTML
}
}
+
task syncDocs(type: Sync) {
dependsOn convertBuildingMD
- def syncDir = "${classes}/${docDir}"
+ def syncDir = "${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}"
+ 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
}
+
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.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/TMAP")
}
+
task compileLinkCheck(type: JavaCompile) {
options.fork = true
classpath = files("${jalviewDir}/${utilsDir}")
outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
}
-def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch")
+
task linkCheck(type: JavaExec) {
dependsOn prepare, compileLinkCheck
+
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
classpath = files("${jalviewDir}/${utilsDir}")
main = "HelpLinksChecker"
workingDir = jalviewDir
- def help = "${classes}/${helpDir}"
- args = [ "${classes}/${helpDir}", "-nointernet" ]
+ args = [ "${classesDir}/${help_dir}", "-nointernet" ]
- doLast {
- helplinkscheckertouchfile.createNewFile()
- }
+ 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("${classes}/${helpDir}")
- outputs.file(helplinkscheckertouchfile)
+ inputs.dir("${classesDir}/${help_dir}")
+ outputs.file(helpLinksCheckerOutFile)
}
// import the pubhtmlhelp target
ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}"
+ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
ant.importBuild "${utilsDir}/publishHelp.xml"
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir("${classes}")
+ inputs.dir(classesDir)
outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
}
+
task copyJars(type: Copy) {
- from fileTree(dir: "${classes}", include: "**/*.jar").files
+ from fileTree(dir: classesDir, include: "**/*.jar").files
into "${jalviewDir}/${packageDir}"
}
+
// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
task syncJars(type: Sync) {
from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
}
}
+
task makeDist {
group = "build"
description = "Put all required libraries in dist"
outputs.dir("${jalviewDir}/${packageDir}")
}
+
task cleanDist {
dependsOn cleanPackageDir
dependsOn cleanTest
minimize()
}
+
task getdownWebsite() {
group = "distribution"
description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
def getdownWebsiteResourceFilenames = []
def getdownTextString = ""
- def getdownResourceDir = project.ext.getdownResourceDir
- def getdownAppDir = project.ext.getdownAppDir
+ def getdownResourceDir = getdownResourceDir
+ def getdownAppDir = getdownAppDir
def getdownResourceFilenames = []
doFirst {
// clean the getdown website and files dir before creating getdown folders
- delete project.ext.getdownWebsiteDir
- delete project.ext.getdownFilesDir
+ delete getdownWebsiteDir
+ delete getdownFilesDir
copy {
from buildProperties
- rename(buildPropertiesFile, getdown_build_properties)
- into project.ext.getdownAppDir
+ rename(build_properties_file, getdown_build_properties)
+ into getdownAppDir
}
getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
getdownResourceFilenames.each{ filename ->
copy {
from filename
- into project.ext.getdownResourceDir
+ into getdownResourceDir
}
}
getdownTextString += line
copy {
from f.getPath()
- into project.ext.getdownAppDir
+ into getdownAppDir
}
}
getdownTextString += line
copy {
from f.getPath()
- into project.ext.getdownJ11libDir
+ into getdownJ11libDir
}
}
}
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}/${getdown_launch_jvl}")
+ def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}")
launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
copy {
from getdownLauncher
rename(file(getdownLauncher).getName(), getdown_launcher_new)
- into project.ext.getdownWebsiteDir
+ into getdownWebsiteDir
}
copy {
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
- into project.ext.getdownWebsiteDir
+ into getdownWebsiteDir
}
if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
copy {
from getdownResourceDir
- into "${project.ext.getdownFilesDir}/${getdown_resource_dir}"
+ into "${getdownFilesDir}/${getdown_resource_dir}"
}
}
if (buildDist) {
inputs.dir("${jalviewDir}/${packageDir}")
}
- outputs.dir(project.ext.getdownWebsiteDir)
- outputs.dir(project.ext.getdownFilesDir)
+ outputs.dir(getdownWebsiteDir)
+ outputs.dir(getdownFilesDir)
}
+
task getdownDigest(type: JavaExec) {
group = "distribution"
description = "Digest the getdown website folder"
classpath = files("${getdownWebsiteDir}/${getdown_launcher}")
}
main = "com.threerings.getdown.tools.Digester"
- args project.ext.getdownWebsiteDir
- inputs.dir(project.ext.getdownWebsiteDir)
- outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt")
+ args getdownWebsiteDir
+ inputs.dir(getdownWebsiteDir)
+ outputs.file("${getdownWebsiteDir}/digest2.txt")
}
+
task getdown() {
group = "distribution"
description = "Create the minimal and full getdown app folder for installers and website and create digest file"
}
}
+
clean {
doFirst {
- delete project.ext.getdownWebsiteDir
- delete project.ext.getdownFilesDir
+ delete getdownWebsiteDir
+ delete getdownFilesDir
}
}
+
install4j {
- def install4jHomeDir = "/opt/install4j"
- def hostname = "hostname".execute().text.trim()
- if (hostname.equals("jv-bamboo")) {
+ if (file(install4jHomeDir).exists()) {
+ // good to go!
+ } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
- } else if (OperatingSystem.current().isMacOsX()) {
- install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app'
- if (! file(install4jHomeDir).exists()) {
- install4jHomeDir = System.getProperty("user.home")+install4jHomeDir
+ } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
+ install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
+ }
+ installDir(file(install4jHomeDir))
+
+ mediaTypes = Arrays.asList(install4j_media_types.split(","))
+}
+
+
+task copyInstall4jTemplate {
+ def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+ def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+ inputs.file(install4jTemplateFile)
+ inputs.file(install4jFileAssociationsFile)
+ outputs.file(install4jConfFile)
+
+ doLast {
+ def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
+
+ // turn off code signing if no OSX_KEYPASS
+ if (OSX_KEYPASS == "") {
+ install4jConfigXml.'**'.codeSigning.each { codeSigning ->
+ codeSigning.'@macEnabled' = "false"
+ }
+ install4jConfigXml.'**'.windows.each { windows ->
+ windows.'@runPostProcessor' = "false"
+ }
}
- } else if (OperatingSystem.current().isLinux()) {
- install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+
+ // put file association actions where placeholder action is
+ def install4jFileAssociationsText = install4jFileAssociationsFile.text
+ def fileAssociationActions = new XmlParser().parseText("<actions>${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)
}
- installDir = file(install4jHomeDir)
- mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
- if (install4jFaster.equals("true")) {
- faster = true
+}
+
+
+clean {
+ doFirst {
+ delete install4jConfFile
}
}
-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: [
+
+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${gitHash}"
+
+ variables = [
+ 'OSX_KEYSTORE': OSX_KEYSTORE,
+ 'JSIGN_SH': JSIGN_SH,
+ 'JRE_DIR': getdown_app_dir_java,
+ 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
+ 'JALVIEW_VERSION': JALVIEW_VERSION,
+ 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
+ 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
'JAVA_VERSION': JAVA_VERSION,
'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
'VERSION': JALVIEW_VERSION,
'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
- 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
- 'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
- 'MACOS_BUNDLE_ID': install4jMacOSBundleId,
+ 'COPYRIGHT_MESSAGE': install4j_copyright_message,
+ 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
'GETDOWN_DIST_DIR': getdown_app_dir,
'GETDOWN_ALT_DIR': getdown_app_dir_alt,
- 'GETDOWN_INSTALL_DIR': getdown_install_dir
- ]
- )
- if (OSX_KEYPASS=="") {
- filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
- filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
- }
- }
- into install4jDir
- outputs.files(install4jConf)
-
- doLast {
- // include file associations in installer
- def installerFileAssociationsXml = file("${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/$install4jDMGUninstallerAppFiles").text
- ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
- replace: installerDMGUninstallerXml,
- file: install4jConf
- )
- */
- }
-}
+ 'GETDOWN_INSTALL_DIR': getdown_install_dir,
+ 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
+ ]
-task installers(type: com.install4j.gradle.Install4jTask) {
- group = "distribution"
- description = "Create the install4j installers"
- dependsOn getdown
- dependsOn copyInstall4jTemplate
- projectFile = file(install4jConf)
- variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
- destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}"
+ destination = "${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}"
buildSelected = true
+ if (install4j_faster.equals("true") || CHANNEL.startsWith("DEVELOP") || CHANNEL.startsWith("LOCAL")) {
+ // this doesn't seem to work
+ faster = true
+ disableSigning = true
+ }
+
if (OSX_KEYPASS) {
- macKeystorePassword=OSX_KEYPASS
+ macKeystorePassword = OSX_KEYPASS
}
doFirst {
println("Using projectFile "+projectFile)
}
- inputs.dir(project.ext.getdownWebsiteDir)
- inputs.file(install4jConf)
+ inputs.dir(getdownWebsiteDir)
+ inputs.file(install4jConfFile)
+ inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
inputs.dir(macosJavaVMDir)
inputs.dir(windowsJavaVMDir)
- outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}")
+ outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
}
-clean {
- doFirst {
- delete install4jConf
- }
-}
-task sourceDist (type: Tar) {
+task sourceDist(type: Tar) {
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
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)
exclude (PROCESS_FILES)
- exclude ("appletlib")
- exclude ("**/*locales")
- exclude ("*locales/**")
- exclude ("utils/InstallAnywhere")
+ exclude ("appletlib")
+ exclude ("**/*locales")
+ exclude ("*locales/**")
+ exclude ("utils/InstallAnywhere")
exclude (getdown_files_dir)
- exclude (getdown_website_dir)
+ exclude (getdown_website_dir)
- // exluding these as not using jars as modules yet
- exclude ("${j11modDir}/**/*.jar")
-}
-// from (jalviewDir) {
-// // explicit includes for stuff that seemed to not get included
-// include(fileTree("test/**/*."))
-// exclude(EXCLUDE_FILES)
-// exclude(PROCESS_FILES)
-// }
+ // exluding these as not using jars as modules yet
+ exclude ("${j11modDir}/**/*.jar")
+ }
+ // from (jalviewDir) {
+ // // explicit includes for stuff that seemed to not get included
+ // include(fileTree("test/**/*."))
+ // exclude(EXCLUDE_FILES)
+ // exclude(PROCESS_FILES)
+ // }
}
-task helppages {
+
+task helppages {
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("${classes}/${helpDir}")
- outputs.dir("${helpOutputDir}")
-}
-
-def jalviewjsBuildDir
-def jalviewjsSiteDir
-def jalviewjsTransferSiteDir
-task jalviewjsSitePath {
- def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
- jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
- if (jalviewjs_site_dir.startsWith('/')) {
- jalviewjsSiteDir = jalviewjs_site_dir
- } else {
- jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
+ inputs.dir("${classesDir}/${help_dir}")
+ outputs.dir("${buildDir}/distributions/${help_dir}")
+}
+
+
+
+
+// JALVIEWJS STUFF HERE
+
+task j2sSetHeadlessBuild {
+ doFirst {
+ IN_ECLIPSE = false
}
- jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site"
}
-def eclipseWorkspace
+
task jalviewjsSetEclipseWorkspace {
def propKey = "jalviewjs_eclipse_workspace"
def propVal = null
if (project.hasProperty(propKey)) {
propVal = project.getProperty(propKey)
+ if (propVal.startsWith("~/")) {
+ propVal = System.getProperty("user.home") + propVal.substring(1)
+ }
}
- def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+ def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+ def propsFile = file(propsFileName)
def eclipseWsDir = propVal
def props = new Properties()
- if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) {
- def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}")
+ def writeProps = true
+ if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+ def ins = new FileInputStream(propsFileName)
props.load(ins)
ins.close()
if (props.getProperty(propKey, null) != null) {
eclipseWsDir = props.getProperty(propKey)
+ writeProps = false
}
}
if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
def tempDir = File.createTempDir()
eclipseWsDir = tempDir.getAbsolutePath()
- props.setProperty(propKey, eclipseWsDir)
- def propsFile = file(propsFileName)
- propsFile.parentFile.mkdirs()
- propsFile.createNewFile() // doesn't affect existing file
- def outs = new FileOutputStream(propsFile, false)
- props.store(outs, null)
- outs.close()
+ writeProps = true
}
-
eclipseWorkspace = file(eclipseWsDir)
doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+
+ if (writeProps) {
+ props.setProperty(propKey, eclipseWsDir)
+ propsFile.parentFile.mkdirs()
+ def bytes = new ByteArrayOutputStream()
+ props.store(bytes, null)
+ def propertiesString = bytes.toString()
+ propsFile.text = propertiesString
+ print("NEW ")
+ } else {
+ print("EXISTING ")
+ }
+
println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
}
- inputs.property(propKey, eclipseWsDir)
+
+ //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
outputs.file(propsFileName)
+ outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
}
-def eclipseDropinsDir
-def utilsDropinsDir
-def eclipseBinary
-def eclipseVersion
-def eclipseDebug = false
-def eclipseVersionSuffix = ""
task jalviewjsEclipsePaths {
def eclipseProduct
def eclipseRoot = jalviewjs_eclipse_root
- if (eclipseRoot.startsWith("~")) {
+ if (eclipseRoot.startsWith("~/")) {
eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
}
if (OperatingSystem.current().isMacOsX()) {
eclipseRoot += "/Eclipse.app"
- eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins"
eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
} else if (OperatingSystem.current().isWindows()) { // check these paths!!
if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
- eclipseRoot += "/eclipse"
+ eclipseRoot += "/eclipse.exe"
}
- eclipseDropinsDir = "${eclipseRoot}/dropins"
eclipseBinary = "${eclipseRoot}/eclipse"
eclipseProduct = "${eclipseRoot}/.eclipseproduct"
} else { // linux or unix
if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
eclipseRoot += "/eclipse"
}
- eclipseDropinsDir = "${eclipseRoot}/dropins"
eclipseBinary = "${eclipseRoot}/eclipse"
eclipseProduct = "${eclipseRoot}/.eclipseproduct"
}
- eclipseVersion = "4.12" // default
+ eclipseVersion = "4.13" // default
def assumedVersion = true
if (file(eclipseProduct).exists()) {
def fis = new FileInputStream(eclipseProduct)
fis.close()
assumedVersion = false
}
- String[] v = eclipseVersion.split("\\.")
- def v0 = Integer.valueOf(v[0])
- def v1 = Integer.valueOf(v[1])
- if (v0 < 4 || ( v0 == 4 && v1 < 13 )) {
- eclipseVersionSuffix = "_4.12"
- } else {
- eclipseVersionSuffix = "_4.13"
- }
-
- utilsDropinsDir = "${jalviewjs_utils_dir}/${jalviewjs_eclipse_dropins_dir}${eclipseVersionSuffix}"
+
def propKey = "eclipse_debug"
eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+
if (!assumedVersion) {
- println("ECLIPSE_VERSION=${eclipseVersion}")
+ println("ECLIPSE VERSION=${eclipseVersion}")
}
}
}
-task jalviewjsEclipseCopyDropins {
+
+task eclipseSetup {
+ dependsOn eclipseProject
+ dependsOn eclipseClasspath
+ dependsOn eclipseJdt
+}
+
+
+// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
+task jalviewjsEclipseCopyDropins(type: Copy) {
dependsOn jalviewjsEclipsePaths
- def inputFiles = fileTree(dir: utilsDropinsDir, include: "*.jar")
- def outputDir = eclipseDropinsDir
- inputs.files inputFiles
- inputFiles.each { file ->
- outputs.file("${outputDir}/${file.name}")
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+ inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
+ def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+
+ from inputFiles
+ into outputDir
+}
+
+
+// this eclipse -clean doesn't actually work
+task jalviewjsCleanEclipse(type: Exec) {
+ dependsOn eclipseSetup
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseCopyDropins
+
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
+ if (eclipseDebug) {
+ args += "-debug"
}
+ args += "-l"
+
+ def inputString = """exit
+y
+"""
+ def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
+ standardInput = inputByteStream
+}
+
+/* not really working yet
+jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
+*/
+
+
+task jalviewjsTransferUnzipSwingJs {
+ def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
doLast {
- inputFiles.each { file ->
- copy {
- from file
- into outputDir
- }
+ copy {
+ from zipTree(file_zip)
+ into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
}
}
-}
-// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
-task NEWjalviewjsEclipseCopyDropins(type: Copy) {
- dependsOn jalviewjsEclipsePaths
- from utilsDropinsDir
- into eclipseDropinsDir
+ inputs.file file_zip
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
}
-task jalviewjsUnzipFiles {
- dependsOn jalviewjsSitePath
- def zipFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_libjs_dir}", include: "*.zip")
- zipFiles += "${jalviewjs_utils_dir}/${jalviewjs_swingjs_zip}${eclipseVersionSuffix}"
+task jalviewjsTransferUnzipLib {
+ def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
doLast {
zipFiles.each { file_zip ->
copy {
from zipTree(file_zip)
- into jalviewjsSiteDir
+ into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
}
}
}
inputs.files zipFiles
- outputs.dir jalviewjsSiteDir
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+}
+
+
+task jalviewjsTransferUnzipAllLibs {
+ dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTransferUnzipLib
}
+
task jalviewjsCreateJ2sSettings(type: WriteProperties) {
- dependsOn jalviewjsSitePath
- outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
- def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+ group "JalviewJS"
+ description "Create the .j2s file from the j2s.* properties"
+
+ jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
def siteDirProperty = "j2s.site.directory"
def setSiteDir = false
- j2s_props.each { prop, val ->
+ jalviewjsJ2sProps.each { prop, val ->
if (val != null) {
if (prop == siteDirProperty) {
if (!(val.startsWith('/') || val.startsWith("file://") )) {
- val = "${jalviewjsTransferSiteDir}/${val}"
+ val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
}
setSiteDir = true
}
property(prop,val)
}
if (!setSiteDir) { // default site location, don't override specifically set property
- property(siteDirProperty,jalviewjsTransferSiteDir)
+ property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
}
}
- inputs.properties(j2s_props)
- outputs.file(outputFile)
+ outputFile = jalviewjsJ2sSettingsFileName
+
+ if (! IN_ECLIPSE) {
+ inputs.properties(jalviewjsJ2sProps)
+ outputs.file(jalviewjsJ2sSettingsFileName)
+ }
}
+
task jalviewjsEclipseSetup {
dependsOn jalviewjsEclipseCopyDropins
dependsOn jalviewjsSetEclipseWorkspace
dependsOn jalviewjsCreateJ2sSettings
}
-task jalviewjsCopyResources (type: Copy) {
- dependsOn jalviewjsSitePath
- def inputFiles = fileTree(dir: jalviewjs_resource_dir)
- def outputDir = "${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+task jalviewjsSyncAllLibs (type: Sync) {
+ dependsOn jalviewjsTransferUnzipAllLibs
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+ inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsSyncResources (type: Sync) {
+ def inputFiles = fileTree(dir: resourceDir)
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
into outputDir
outputFiles += "${outputDir}/${filename}"
null
}
+ preserve {
+ include "**"
+ }
outputs.files outputFiles
inputs.files inputFiles
}
-task jalviewjsCopySiteResources (type: Copy) {
- dependsOn jalviewjsSitePath
- def inputFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_site_resource_dir}")
- def outputDir = jalviewjsSiteDir
+
+task jalviewjsSyncSiteResources (type: Sync) {
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
into outputDir
outputFiles += "${outputDir}/${filename}"
null
}
+ preserve {
+ include "**"
+ }
outputs.files outputFiles
inputs.files inputFiles
}
+
+task jalviewjsSyncBuildProperties (type: Sync) {
+ dependsOn createBuildProperties
+ def inputFiles = [file(buildProperties)]
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
task jalviewjsProjectImport(type: Exec) {
- dependsOn eclipseProject
- dependsOn eclipseClasspath
- dependsOn eclipseJdt
+ dependsOn eclipseSetup
dependsOn jalviewjsEclipsePaths
dependsOn jalviewjsEclipseSetup
- def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+ doFirst {
+ // do not run a headless import when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+ }
+
+ //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+ def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
executable(eclipseBinary)
args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
if (eclipseDebug) {
args += "-debug"
}
-
- doFirst {
- println("IMPORT ECLIPSE_DEBUG=${eclipseDebug}")
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+ if (!IN_ECLIPSE) {
+ args += [ "-D${j2sHeadlessBuildProperty}=true" ]
}
inputs.file("${jalviewDir}/.project")
- outputs.dir(projdir)
- outputs.upToDateWhen { file(projdir).exists() }
+ outputs.upToDateWhen {
+ file(projdir).exists()
+ }
}
+
task jalviewjsTranspile(type: Exec) {
dependsOn jalviewjsEclipseSetup
dependsOn jalviewjsProjectImport
dependsOn jalviewjsEclipsePaths
+ doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+ }
+
executable(eclipseBinary)
- args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipseBuildArg}", eclipse_project_name ])
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
if (eclipseDebug) {
args += "-debug"
}
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+ if (!IN_ECLIPSE) {
+ args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+ }
def stdout
def stderr
- stdout = new ByteArrayOutputStream()
- stderr = new ByteArrayOutputStream()
+ doFirst {
+ stdout = new ByteArrayOutputStream()
+ stderr = new ByteArrayOutputStream()
- def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
- def logOutFile = file(logOutFileName)
- logOutFile.createNewFile()
- logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+ def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+ def logOutFile = file(logOutFileName)
+ logOutFile.createNewFile()
+ logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
BINARY: ${eclipseBinary}
VERSION: ${eclipseVersion}
WORKSPACE: ${eclipseWorkspace}
DEBUG: ${eclipseDebug}
----
"""
- def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
- //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
- //def logErrFile = file(logFileName)
- //logErrFile.createNewFile()
- //def logErrFOS = new FileErrputStream(logErrFile, false)
- // combine stdout and stderr
- def logErrFOS = logOutFOS
+ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+ // combine stdout and stderr
+ def logErrFOS = logOutFOS
- if (jalviewjs_j2s_to_console.equals("true")) {
- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
- new org.apache.tools.ant.util.TeeOutputStream(
- logOutFOS,
- stdout),
- standardOutput)
+ if (jalviewjs_j2s_to_console.equals("true")) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout),
+ standardOutput)
errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
new org.apache.tools.ant.util.TeeOutputStream(
logErrFOS,
stderr),
errorOutput)
- } else {
- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
- logOutFOS,
- stdout)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout)
errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
logErrFOS,
stderr)
+ }
}
doLast {
if (stdout.toString().contains("Error processing ")) {
// j2s did not complete transpile
- throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
+ //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+ throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+ }
+ }
+
+ inputs.dir("${jalviewDir}/${sourceDir}")
+ outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+ outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+}
+
+
+def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+
+ def stdout = new ByteArrayOutputStream()
+ def stderr = new ByteArrayOutputStream()
+
+ def coreFile = file(jsfile)
+ def msg = ""
+ msg = "Creating core for ${name}...\nGenerating ${jsfile}"
+ println(msg)
+ logOutFile.createNewFile()
+ logOutFile.append(msg+"\n")
+
+ def coreTop = file(prefixFile)
+ def coreBottom = file(suffixFile)
+ coreFile.getParentFile().mkdirs()
+ coreFile.createNewFile()
+ coreFile.write( coreTop.text )
+ list.each {
+ f ->
+ if (f.exists()) {
+ def t = f.text
+ t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
+ coreFile.append( t )
+ } else {
+ msg = "...file '"+f.getPath()+"' does not exist, skipping"
+ println(msg)
+ logOutFile.append(msg+"\n")
+ }
+ }
+ coreFile.append( coreBottom.text )
+
+ msg = "Generating ${zjsfile}"
+ println(msg)
+ logOutFile.append(msg+"\n")
+ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+ def logErrFOS = logOutFOS
+
+ javaexec {
+ classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
+ args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+ maxHeapSize = "2g"
+
+ msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+ println(msg)
+ logOutFile.append(msg+"\n")
+
+ if (logOutConsole) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr),
+ errorOutput)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr)
+ }
+ }
+ msg = "--"
+ println(msg)
+ logOutFile.append(msg+"\n")
+}
+
+
+task jalviewjsBuildAllCores {
+ group "JalviewJS"
+ description "Build the core js lib closures listed in the classlists dir"
+ dependsOn jalviewjsTranspile
+ dependsOn jalviewjsTransferUnzipSwingJs
+
+ def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+ def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+ def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
+ def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+ def prefixFile = "${jsDir}/core/coretop2.js"
+ def suffixFile = "${jsDir}/core/corebottom2.js"
+
+ inputs.file prefixFile
+ inputs.file suffixFile
+
+ def classlistFiles = []
+ // add the classlists found int the jalviewjs_classlists_dir
+ fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
+ file ->
+ def name = file.getName() - ".txt"
+ classlistFiles += [
+ 'file': file,
+ 'name': name
+ ]
+ }
+
+ // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+ //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+ classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
+
+ jalviewjsCoreClasslists = []
+
+ classlistFiles.each {
+ hash ->
+
+ def file = hash['file']
+ if (! file.exists()) {
+ //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+ return false // this is a "continue" in groovy .each closure
+ }
+ def name = hash['name']
+ if (name == null) {
+ name = file.getName() - ".txt"
+ }
+
+ def filelist = []
+ file.eachLine {
+ line ->
+ filelist += line
}
+ def list = fileTree(dir: j2sDir, includes: filelist)
+
+ def jsfile = "${outputDir}/core${name}.js"
+ def zjsfile = "${outputDir}/core${name}.z.js"
+
+ jalviewjsCoreClasslists += [
+ 'jsfile': jsfile,
+ 'zjsfile': zjsfile,
+ 'list': list,
+ 'name': name
+ ]
+
+ inputs.file(file)
+ inputs.files(list)
+ outputs.file(jsfile)
+ outputs.file(zjsfile)
}
+
+ // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+ def stevesoftClasslistName = "_stevesoft"
+ def stevesoftClasslist = [
+ 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+ 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+ 'name': stevesoftClasslistName
+ ]
+ jalviewjsCoreClasslists += stevesoftClasslist
+ inputs.files(stevesoftClasslist['list'])
+ outputs.file(stevesoftClasslist['jsfile'])
+ outputs.file(stevesoftClasslist['zjsfile'])
+
+ // _all core
+ def allClasslistName = "_all"
+ def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+ allJsFiles += fileTree(
+ dir: libJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+ "**/org/jmol/export/JSExporter.js"
+ ]
+ )
+ allJsFiles += fileTree(
+ dir: swingJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/sun/misc/Unsafe.js",
+ "**/swingjs/jquery/jquery-editable-select.js",
+ "**/swingjs/jquery/j2sComboBox.js",
+ "**/sun/misc/FloatingDecimal.js"
+ ]
+ )
+ def allClasslist = [
+ 'jsfile': "${outputDir}/core${allClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+ 'list': allJsFiles,
+ 'name': allClasslistName
+ ]
+ // not including this version of "all" core at the moment
+ //jalviewjsCoreClasslists += allClasslist
+ inputs.files(allClasslist['list'])
+ outputs.file(allClasslist['jsfile'])
+ outputs.file(allClasslist['zjsfile'])
doFirst {
- println("TRANSPILE ECLIPSE_DEBUG=${eclipseDebug}")
+ def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+ logOutFile.getParentFile().mkdirs()
+ logOutFile.createNewFile()
+ logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+
+ jalviewjsCoreClasslists.each {
+ jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+ }
}
- inputs.dir(sourceDir)
- outputs.dir("${eclipse_bin_dir}/main")
- outputs.dir(jalviewjsTransferSiteDir)
- outputs.upToDateWhen { file("${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
+}
+
+def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+ copy {
+ from inputFile
+ into file(outputFile).getParentFile()
+ rename { filename ->
+ if (filename.equals(inputFile.getName())) {
+ return file(outputFile).getName()
+ }
+ return null
+ }
+ filter(ReplaceTokens,
+ beginToken: '_',
+ endToken: '_',
+ tokens: [
+ 'MAIN': '"'+mainClass+'"',
+ 'CODE': "null",
+ 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+ 'COREKEY': jalviewjs_core_key,
+ 'CORENAME': coreName
+ ]
+ )
+ }
+}
+
+
+task jalviewjsPublishCoreTemplates {
+ dependsOn jalviewjsBuildAllCores
+ def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+ def inputFile = file(inputFileName)
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+
+ def outputFiles = []
+ jalviewjsCoreClasslists.each { cl ->
+ def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+ cl['outputfile'] = outputFile
+ outputFiles += outputFile
+ }
+
+ doFirst {
+ jalviewjsCoreClasslists.each { cl ->
+ jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+ }
+ }
+ inputs.file(inputFile)
+ outputs.files(outputFiles)
+}
+
+
+task jalviewjsSyncCore (type: Sync) {
+ dependsOn jalviewjsBuildAllCores
+ dependsOn jalviewjsPublishCoreTemplates
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
}
-task jalviewjsCopyTransferSite(type: Copy) {
+
+// this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteJs(type: Copy) {
dependsOn jalviewjsTranspile
- from jalviewjsTransferSiteDir
- into jalviewjsSiteDir
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+}
+
+
+// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+task jalviewjsSyncTransferSiteJs(type: Sync) {
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ include "**/*.*"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+ preserve {
+ include "**"
+ }
}
-jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+
task jalviewjsPrepareSite {
group "JalviewJS"
description "Prepares the website folder including unzipping files and copying resources"
- dependsOn jalviewjsSitePath
- dependsOn jalviewjsUnzipFiles
- dependsOn jalviewjsCopyResources
- dependsOn jalviewjsCopySiteResources
+ dependsOn jalviewjsSyncAllLibs
+ dependsOn jalviewjsSyncResources
+ dependsOn jalviewjsSyncSiteResources
+ dependsOn jalviewjsSyncBuildProperties
+ dependsOn jalviewjsSyncCore
}
+
task jalviewjsBuildSite {
group "JalviewJS"
description "Builds the whole website including transpiled code"
- dependsOn jalviewjsCopyTransferSite
+ dependsOn jalviewjsCopyTransferSiteJs
dependsOn jalviewjsPrepareSite
}
+
+task cleanJalviewjsTransferSite {
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+ }
+}
+
+
task cleanJalviewjsSite {
+ dependsOn cleanJalviewjsTransferSite
doFirst {
- delete jalviewjsTransferSiteDir
- delete jalviewjsSiteDir
+ delete "${jalviewDir}/${jalviewjsSiteDir}"
}
}
+
task jalviewjsSiteTar(type: Tar) {
group "JalviewJS"
description "Creates a tar.gz file for the website"
compression Compression.GZIP
- from jalviewjsSiteDir
+ from "${jalviewDir}/${jalviewjsSiteDir}"
into jalviewjs_site_dir // this is inside the tar file
- inputs.dir(jalviewjsSiteDir)
+ inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
}
+
task jalviewjsServer {
group "JalviewJS"
- description "Starts a webserver on localhost to test the website"
- dependsOn jalviewjsSitePath
- def htmlFile = "${jalviewDirAbsolutePath}/jalviewjsTest.html"
+ def filename = "jalviewjsTest.html"
+ description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
+ def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
doLast {
SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
def start = port
def running = false
def url
+ def jalviewjsServer
while(port < start+1000 && !running) {
try {
def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
- def jalviewjsServer = factory.start(doc_root, port)
+ jalviewjsServer = factory.start(doc_root, port)
running = true
url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
println("SERVER STARTED with document root ${doc_root}.")
println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
println("For debug: "+url+"?j2sdebug")
-
- file(htmlFile).text = """
- <p><a href="${url}">Jalview JS Test. <${url}></a></p>
- <p><a href="${url}?j2sdebug">Jalview JS Test with debug. <${url}?j2sdebug<</a></p>
- """
-
+ println("For verbose: "+url+"?j2sverbose")
} catch (Exception e) {
port++;
}
}
+ def htmlText = """
+ <p><a href="${url}">JalviewJS Test. <${url}></a></p>
+ <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
+ <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
+ """
+ jalviewjsCoreClasslists.each { cl ->
+ def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+ htmlText += """
+ <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
+ """
+ println("For core ${cl.name}: "+urlcore)
+ }
+ file(htmlFile).text = htmlText
}
outputs.file(htmlFile)
+ outputs.upToDateWhen({false})
}
+
task cleanJalviewjsAll {
group "JalviewJS"
description "Delete all configuration and build artifacts to do with JalviewJS build"
dependsOn jalviewjsEclipsePaths
doFirst {
- delete jalviewjsBuildDir
+ delete "${jalviewDir}/${jalviewjsBuildDir}"
delete "${jalviewDir}/${eclipse_bin_dir}"
if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
}
delete "${jalviewDir}/${jalviewjs_j2s_settings}"
}
-}
-task jalviewjs {
- group "JalviewJS"
- description "Build the site"
- dependsOn jalviewjsBuildSite
+ outputs.upToDateWhen( { false } )
}
-task jalviewjsIDECopyTransferSite(type: Copy) {
- from jalviewjsTransferSiteDir
- into jalviewjsSiteDir
+task jalviewjsIDE_checkJ2sPlugin {
+ group "00 JalviewJS in Eclipse"
+ description "Compare the swingjs/net.sf.j2s.core.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+
+ doFirst {
+ def j2sPlugin = string("${jalviewDir}/${jalviewjs_j2s_plugin}")
+ def j2sPluginFile = file(j2sPlugin)
+ def copyPlugin = jalviewjs_eclipseIDE_auto_copy_j2s_plugin == "true"
+ def eclipseHome = System.properties["eclipse.home.location"]
+ def doCopy = false
+ if (eclipseHome == null || ! IN_ECLIPSE) {
+ throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+ }
+ def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+ def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+ if (!eclipseJ2sPluginFile.exists()) {
+ def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')"
+ System.err.println(msg)
+ if (! copyPlugin) {
+ throw new GradleException(msg)
+ }
+ doCopy = true
+ }
+
+ def digest = MessageDigest.getInstance("MD5")
+
+ digest.update(j2sPluginFile.text.bytes)
+ def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ digest.update(eclipseJ2sPluginFile.text.bytes)
+ def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+ def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+ System.err.println(msg)
+ if (! copyPlugin) {
+ throw new StopExecutionException(msg)
+ }
+ doCopy = true
+ }
+
+ if (doCopy) {
+ def msg = "WARNING! Auto-copying this commit's j2s plugin version '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n May require an Eclipse restart"
+ println(msg)
+ copy {
+ from j2sPlugin
+ eclipseJ2sPluginFile.getParentFile().mkdirs()
+ into eclipseJ2sPluginFile.getParent()
+ }
+ } else {
+ def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+ println(msg)
+ }
+ }
}
-task jalviewjsIDEj2s {
- group "JalviewJS in Eclipse"
+
+task jalviewjsIDE_j2sFile {
+ group "00 JalviewJS in Eclipse"
description "Creates the .j2s file"
dependsOn jalviewjsCreateJ2sSettings
}
-task jalviewjsIDEBuildSite {
- group "JalviewJS in Eclipse"
- description "Copies the Eclipse transpiled site and unzips supporting zipfiles"
- dependsOn jalviewjsIDECopyTransferSite
+
+task jalviewjsIDE_SyncCore {
+ group "00 JalviewJS in Eclipse"
+ description "Build the core js lib closures listed in the classlists dir and publish core html from template"
+ dependsOn jalviewjsSyncCore
+}
+
+
+task jalviewjsIDE_SyncSiteAll {
+ dependsOn jalviewjsSyncAllLibs
+ dependsOn jalviewjsSyncResources
+ dependsOn jalviewjsSyncSiteResources
+ dependsOn jalviewjsSyncBuildProperties
+}
+
+
+cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+
+
+task jalviewjsIDE_PrepareSite {
+ group "00 JalviewJS in Eclipse"
+ description "Sync libs and resources to site dir, but not closure cores"
+
+ dependsOn jalviewjsIDE_SyncSiteAll
+ dependsOn cleanJalviewjsTransferSite
+}
+
+
+task jalviewjsIDE_AssembleSite {
+ group "00 JalviewJS in Eclipse"
+ description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
dependsOn jalviewjsPrepareSite
}
-task jalviewjsIDESiteClean {
- group "JalviewJS in Eclipse"
+
+task jalviewjsIDE_SiteClean {
+ group "00 JalviewJS in Eclipse"
description "Deletes the Eclipse transpiled site"
dependsOn cleanJalviewjsSite
}
-task jalviewjsIDEServer {
- group "JalviewJS in Eclipse"
+
+task jalviewjsIDE_Server {
+ group "00 JalviewJS in Eclipse"
description "Starts a webserver on localhost to test the website"
dependsOn jalviewjsServer
}
+
+// buildship runs this at import or gradle refresh
+task eclipseSynchronizationTask {
+ //dependsOn eclipseSetup
+ dependsOn createBuildProperties
+ if (J2S_ENABLED) {
+ dependsOn jalviewjsIDE_j2sFile
+ dependsOn jalviewjsIDE_checkJ2sPlugin
+ dependsOn jalviewjsIDE_PrepareSite
+ }
+}
+
+
+// buildship runs this at build time or project refresh
+task eclipseAutoBuildTask {
+ //dependsOn jalviewjsIDE_checkJ2sPlugin
+ //dependsOn jalviewjsIDE_PrepareSite
+}
+
+
+
+
+
+
+
+
+task jalviewjs {
+ group "JalviewJS"
+ description "Build the site"
+ dependsOn jalviewjsBuildSite
+}
git://source.jalview.org / jalview.git / blobdiff