id 'com.install4j.gradle' version '7.0.9'
}
+// local build environment properties
+def localProps = "${jalviewDir}/local.properties"
+if (file(localProps).exists()) {
+ try {
+ def p = new Properties()
+ def localPropsFIS = new FileInputStream(localProps)
+ p.load(localPropsFIS)
+ localPropsFIS.close()
+ p.each {
+ key, val ->
+ def over = getProperty(key) != null
+ setProperty(key, val)
+ if (over) {
+ println("Overriding property '${key}' with local.properties value '${val}'")
+ }
+ }
+ } catch (Exception e) {
+ System.out.println("Exception reading local.properties")
+ }
+}
+
repositories {
jcenter()
mavenCentral()
}
mainClassName = launcherClass
-def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
-def classes = "$jalviewDir/$classesDir"
+def cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
+def classes = "${jalviewDir}/${classesDir}"
if (clover.equals("true")) {
use_clover = true
- classes = "$buildDir/$cloverClassesDir"
+ classes = "${buildDir}/${cloverClassesDir}"
} else {
use_clover = false
- classes = "$jalviewDir/$classesDir"
+ classes = "${jalviewDir}/${classesDir}"
}
// configure classpath/args for j8/j11 compilation
def compile_target_compatibility
ext {
- getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
+ getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}"
getdownDir = ""
reportRsyncCmd = false
buildDist = true
- buildProperties = buildPropertiesFile
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher
+ buildProperties = build_properties_file
+ getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}"
switch (CHANNEL) {
case "BUILD":
// TODO: get bamboo build artifact URL for getdown artifacts
getdown_channel_base = bamboo_channelbase
- getdown_channel_name = bamboo_planKey + '/'+JAVA_VERSION
- getdown_app_base = bamboo_channelbase + '/'+ bamboo_planKey + bamboo_getdown_channel_suffix + '/'+JAVA_VERSION
+ getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}"
+ getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}"
getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ buildProperties = "${jalviewDir}/${classesDir}/${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 = "${getdown_channel_name}/${JAVA_VERSION}"
+ getdown_app_base = "${getdown_channel_base}/${getdownDir}"
getdown_app_dir = getdown_app_dir_release
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
reportRsyncCommand = true
break
case "ARCHIVE":
- getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_channel_name = CHANNEL.toLowerCase()+"/${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()) {
+ 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 = "${ARCHIVEDIR}/${packageDir}"
+ buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}"
buildDist = false
}
reportRsyncCommand = true
break
case "ARCHIVELOCAL":
- getdown_channel_name = "archive" + "/" + JALVIEW_VERSION
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_channel_name = "archive/${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()) {
+ 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 = "${ARCHIVEDIR}/${packageDir}"
+ buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}"
buildDist = false
}
reportRsyncCommand = true
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ getdownLauncher = "${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 = "${getdown_channel_name}/${JAVA_VERSION}"
+ getdown_app_base = "${getdown_channel_base}/${getdownDir}"
getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
reportRsyncCommand = true
break
case "TEST-RELEASE":
getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
+ getdown_app_base = "${getdown_channel_base}/${getdownDir}"
getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
reportRsyncCommand = true
break
case ~/^SCRATCH(|-[-\w]*)$/:
getdown_channel_name = CHANNEL
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
+ getdown_app_base = "${getdown_channel_base}/${getdownDir}"
getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ buildProperties = "${jalviewDir}/${classesDir}/${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 = "${jalviewDir}/${classesDir}/${build_properties_file}"
+ getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
break
default: // something wrong specified
}
- 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
+ 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}/${getdown_install_dir}"
/* compile without modules -- using classpath libraries
- modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
+ modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
*/
gitHash = ""
gitBranch = ""
- jalviewjsServer = ""
+ println("Using a ${CHANNEL} profile.")
}
def JAVA_INTEGER_VERSION
]
*/
} else {
- throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
}
+
sourceSets {
main {
java {
- srcDirs "$jalviewDir/$sourceDir"
- outputDir = file("$classes")
+ srcDirs "${jalviewDir}/${sourceDir}"
+ outputDir = file("${classes}")
}
resources {
- srcDirs "$jalviewDir/$resourceDir"
+ srcDirs "${jalviewDir}/${resourceDir}"
}
- jar.destinationDir = file("$jalviewDir/$packageDir")
+ jar.destinationDir = file("${jalviewDir}/${packageDir}")
compileClasspath = files(sourceSets.main.java.outputDir)
- compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
}
compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
compileClasspath += files(sourceSets.main.java.outputDir)
compileClasspath += sourceSets.main.compileClasspath
- compileClasspath += fileTree(dir: "$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/$testOutputDir")
+ srcDirs "${jalviewDir}/${testSourceDir}"
+ outputDir = file("${jalviewDir}/${testOutputDir}")
}
resources {
compileClasspath += files(sourceSets.main.java.outputDir)
}
- compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
- compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testnglibs", include: ["**/*.jar"])
- compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testlibs", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
}
}
+
// clover bits
dependencies {
if (use_clover) {
}
}
+
configurations {
cloverRuntime
cloverRuntime.extendsFrom cloverCompile
}
+
eclipse {
project {
name = eclipse_project_name
HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
cp.entries.each { entry ->
if (entry.kind == 'src') {
- if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+ if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) {
removeTheseToo += entry
} else {
alreadyAddedSrcPath.putAt(entry.path, true)
}
cp.entries.removeAll(removeTheseToo)
- if (file(eclipse_bin_dir+"/main").isDirectory()) {
- cp.entries += new Output(eclipse_bin_dir+"/main")
+ if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
+ cp.entries += new Output("${eclipse_bin_dir}/main")
}
if (file(helpParentDir).isDirectory()) {
cp.entries += new Library(fileReference(helpParentDir))
return
}
def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
// make relative path
itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
}
}
//fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
- sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
//no longer want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath
- return false // groovy "break" in .each closure
+ return false // groovy "continue" in .any closure
}
+
def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
}
if (alreadyAddedLibPath.get(itPath)) {
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 ->
}
} // jdt
+
+ 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"]))
com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
}
}
-
// 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 {
outputs.upToDateWhen { false }
}
+
task createBuildProperties(type: WriteProperties) {
dependsOn setGitVals
- inputs.dir("$jalviewDir/$sourceDir")
- inputs.dir("$classes")
- inputs.dir("$jalviewDir/$resourceDir")
+ inputs.dir("${jalviewDir}/${sourceDir}")
+ inputs.dir("${jalviewDir}/${resourceDir}")
+ file(buildProperties).getParentFile().mkdirs()
outputFile (buildProperties)
// taking time specific comment out to allow better incremental builds
comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
outputs.file(outputFile)
}
-def buildingHTML = "$jalviewDir/$docDir/building.html"
-task deleteBuildingHTML(type: Delete) {
- delete buildingHTML
+
+def buildingHTML = "${jalviewDir}/${docDir}/building.html"
+task cleanBuildingHTML(type: Delete) {
+ doFirst {
+ delete buildingHTML
+ }
}
+
task convertBuildingMD(type: Exec) {
- dependsOn deleteBuildingHTML
- def buildingMD = "$jalviewDir/$docDir/building.md"
- def css = "$jalviewDir/$docDir/github.css"
+ dependsOn cleanBuildingHTML
+ def buildingMD = "${jalviewDir}/${docDir}/building.md"
+ def css = "${jalviewDir}/${docDir}/github.css"
def pandoc = null
pandoc_exec.split(",").each {
inputs.file(css)
outputs.file(buildingHTML)
}
+
+
clean {
- delete buildingHTML
+ doFirst {
+ delete buildingHTML
+ }
}
+
task syncDocs(type: Sync) {
dependsOn convertBuildingMD
- def syncDir = "$classes/$docDir"
- from fileTree("$jalviewDir/$docDir")
+ def syncDir = "${classes}/${docDir}"
+ from fileTree("${jalviewDir}/${docDir}")
into syncDir
}
-def helpFile = "$classes/$helpDir/help.jhm"
+def helpFile = "${classes}/${helpDir}/help.jhm"
task copyHelp(type: Copy) {
- def inputDir = "$jalviewDir/$helpParentDir/$helpDir"
- def outputDir = "$classes/$helpDir"
+ def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
+ def outputDir = "${classes}/${helpDir}"
from(inputDir) {
exclude '**/*.gif'
- exclude '**/*.jpg'
- exclude '**/*.png'
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'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 = "${classes}/${libDistDir}"
+ from fileTree("${jalviewDir}/${libDistDir}")
into syncDir
}
+
task syncResources(type: Sync) {
- from "$jalviewDir/$resourceDir"
+ from "${jalviewDir}/${resourceDir}"
include "**/*.*"
- exclude "install4j"
- into "$classes"
+ into "${classes}"
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 = "${classes}/${helpDir}"
def argDir = "html"
args = [ argDir ]
- inputs.dir("$workingDir/$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")
+ outputs.dir("${classes}/doc")
+ outputs.dir("${classes}/help")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+ outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+ outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+ outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+ outputs.file("${workingDir}/JavaHelpSearch/TMAP")
}
+
task compileLinkCheck(type: JavaCompile) {
options.fork = true
- classpath = files("$jalviewDir/$utilsDir")
- destinationDir = file("$jalviewDir/$utilsDir")
- source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+ 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")
+ 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" ]
+ def help = "${classes}/${helpDir}"
+ args = [ "${classes}/${helpDir}", "-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("${classes}/${helpDir}")
+ 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}/${classes}/${helpDir}"
+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/$archiveName")
+ inputs.dir("${classes}")
+ outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
}
+
task copyJars(type: Copy) {
- from fileTree("$classes").include("**/*.jar").include("*.jar").files
- into "$jalviewDir/$packageDir"
+ from fileTree(dir: "${classes}", include: "**/*.jar").files
+ into "${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}/${libDistDir}") {
include("*.jar")
}
manifest {
minimize()
}
+
task getdownWebsite() {
group = "distribution"
description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
dependsOn makeDist
}
- // clean the getdown website and files dir before creating getdown folders
- delete project.ext.getdownWebsiteDir
- delete project.ext.getdownFilesDir
-
def getdownWebsiteResourceFilenames = []
def getdownTextString = ""
def getdownResourceDir = project.ext.getdownResourceDir
def getdownResourceFilenames = []
doFirst {
+ // clean the getdown website and files dir before creating getdown folders
+ delete project.ext.getdownWebsiteDir
+ delete project.ext.getdownFilesDir
+
copy {
from buildProperties
- rename(buildPropertiesFile, getdown_build_properties)
+ rename(build_properties_file, getdown_build_properties)
into project.ext.getdownAppDir
}
- getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties
+ getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
// go through properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
- if (getdown_alt_java_min_version.length() > 0) {
- props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
- }
- if (getdown_alt_java_max_version.length() > 0) {
- props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
- }
- props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+ if (getdown_alt_java_min_version.length() > 0) {
+ props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+ }
+ if (getdown_alt_java_max_version.length() > 0) {
+ props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
+ }
+ props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
props.put("getdown_txt_appbase", getdown_app_base)
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_multi_")) {
def key = prop.substring(18)
val.split(",").each{ v ->
- def line = key + " = " + v + "\n"
+ def line = "${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 {
}
}
codeFiles.sort().each{f ->
- def line = "code = " + getdown_app_dir + '/' + f.getName() + "\n"
+ def name = f.getName()
+ def line = "code = ${getdown_app_dir}/${name}\n"
getdownTextString += line
copy {
from f.getPath()
// 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()
// 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 = ${mainClass}\n"
- def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
+ def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt")
getdown_txt.write(getdownTextString)
- def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl)
+ def launch_jvl = file("${project.ext.getdownWebsiteDir}/${getdown_launch_jvl}")
launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
copy {
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)
}
from getdown_txt
from launch_jvl
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 "${project.ext.getdownFilesDir}/${getdown_resource_dir}"
}
}
if (buildDist) {
- inputs.dir(jalviewDir + '/' + packageDir)
+ inputs.dir("${jalviewDir}/${packageDir}")
}
outputs.dir(project.ext.getdownWebsiteDir)
outputs.dir(project.ext.getdownFilesDir)
}
+
task getdownDigest(type: JavaExec) {
group = "distribution"
description = "Digest the getdown website folder"
dependsOn getdownWebsite
doFirst {
- classpath = files(getdownWebsiteDir + '/' + getdown_launcher)
+ 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")
+ outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt")
}
+
task getdown() {
group = "distribution"
description = "Create the minimal and full getdown app folder for installers and website and create digest file"
dependsOn getdownDigest
doLast {
if (reportRsyncCommand) {
- def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/")
- def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/")
+ def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+ def toDir = "${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 project.ext.getdownWebsiteDir
+ delete project.ext.getdownFilesDir
+ }
}
+
install4j {
def install4jHomeDir = "/opt/install4j"
def hostname = "hostname".execute().text.trim()
}
}
+
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"
+def install4jDir = "${jalviewDir}/${install4jResourceDir}"
+def install4jConfFile = "jalview-installers-java${JAVA_VERSION}.install4j"
+install4jConf = "${install4jDir}/${install4jConfFile}"
task copyInstall4jTemplate(type: Copy) {
- macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre"
- macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
- windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre"
- windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
+ macosJavaVMDir = "${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${JAVA_VERSION}.tar.gz"
from (install4jDir) {
include install4jTemplate
rename (install4jTemplate, install4jConfFile)
doLast {
// include file associations in installer
- def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
+ def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text
ant.replaceregexp(
byline: false,
flags: "s",
}
}
+
task installers(type: com.install4j.gradle.Install4jTask) {
group = "distribution"
description = "Create the install4j installers"
dependsOn getdown
dependsOn copyInstall4jTemplate
projectFile = file(install4jConf)
- println("Using projectFile "+projectFile)
variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
- destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
+ destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}"
buildSelected = true
if (OSX_KEYPASS) {
macKeystorePassword=OSX_KEYPASS
+ }
+ doFirst {
+ println("Using projectFile "+projectFile)
}
inputs.dir(project.ext.getdownWebsiteDir)
inputs.file(install4jConf)
inputs.dir(macosJavaVMDir)
inputs.dir(windowsJavaVMDir)
- outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
-
+ outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}")
}
+
clean {
- delete install4jConf
+ doFirst {
+ delete install4jConf
+ }
}
+
task sourceDist (type: Tar) {
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
- def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
// cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
try {
archiveFileName = outputFileName
,"benchmarking/*"
,"**/.*"
,"*.class"
- ,"**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales"
+ ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
,"*locales/**",
,"utils/InstallAnywhere"]
def PROCESS_FILES=[ "AUTHORS",
exclude (getdown_website_dir)
// exluding these as not using jars as modules yet
- exclude ("$j11modDir/**/*.jar")
+ exclude ("${j11modDir}/**/*.jar")
}
// from (jalviewDir) {
// // explicit includes for stuff that seemed to not get included
// }
}
+
task helppages {
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("$classes/$helpDir")
- outputs.dir("$helpOutputDir")
+ inputs.dir("${classes}/${helpDir}")
+ outputs.dir("${helpOutputDir}")
}
+
def jalviewjsBuildDir
def jalviewjsSiteDir
-def jalviewjsTransferSiteDir
+def jalviewjsTransferSiteJsDir
+def jalviewjsTransferSiteLibDir
+def jalviewjsTransferSiteSwingJsDir
+def jalviewjsTransferSiteCoreDir
task jalviewjsSitePath {
def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
- if (jalviewjs_site_dir.startsWith("/")) {
- jalviewjsSiteDir = jalviewjs_site_dir
- } else {
- jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir
- }
- jalviewjsTransferSiteDir = jalviewjsBuildDir + "/tmp/site"
+ jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
+ jalviewjsTransferSiteJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js"
+ jalviewjsTransferSiteLibDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib"
+ jalviewjsTransferSiteSwingJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs"
+ jalviewjsTransferSiteCoreDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core"
}
+
def eclipseWorkspace
task jalviewjsSetEclipseWorkspace {
def propKey = "jalviewjs_eclipse_workspace"
- def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
- def props = new Properties()
- def eclipseWsDir
def propVal = null
if (project.hasProperty(propKey)) {
propVal = project.getProperty(propKey)
- eclipseWsDir = propVal
+ if (propVal.startsWith("~/")) {
+ propVal = System.getProperty("user.home") + propVal.substring(1)
+ }
}
- if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) {
- def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}")
+ 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() ) && propsFile.exists()) {
+ def ins = new FileInputStream(propsFileName)
props.load(ins)
ins.close()
if (props.getProperty(propKey, null) != null) {
}
}
+ def 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)
-
- println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
-
- inputs.property(propKey, propVal)
- outputs.file(propsFileName)
-}
-
-task jalviewjsUnzipFiles {
- dependsOn jalviewjsSitePath
-
- def zipFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_libjs_dir).include("*.zip")
- zipFiles += jalviewjs_utils_dir+"/"+jalviewjs_swingjs_zip
-
- doLast {
- zipFiles.each { file_zip ->
- copy {
- from zipTree(file_zip)
- into jalviewjsSiteDir
- }
+ doFirst {
+ if (writeProps) {
+ props.setProperty(propKey, eclipseWsDir)
+ propsFile.parentFile.mkdirs()
+ def bytes = new ByteArrayOutputStream()
+ props.store(bytes, null)
+ def propertiesString = bytes.toString()
+ propsFile.text = propertiesString
}
+
+ println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
}
- inputs.files zipFiles
- outputs.dir jalviewjsSiteDir
+ //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() }
}
-def eclipseDropinsDir
+
def eclipseBinary
def eclipseVersion
-def fromDropinsDir
+def eclipseDebug = false
+def eclipseVersionSuffix = ""
task jalviewjsEclipsePaths {
- def eclipseRoot
def eclipseProduct
- eclipseRoot = jalviewjs_eclipse_root
- if (eclipseRoot.startsWith("~")) {
+
+ def eclipseRoot = jalviewjs_eclipse_root
+ if (eclipseRoot.startsWith("~/")) {
eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
}
if (OperatingSystem.current().isMacOsX()) {
eclipseRoot += "/Eclipse.app"
- eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins"
- eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse"
- eclipseProduct = eclipseRoot+"/Contents/Eclipse/.eclipseproduct"
+ eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
+ eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
} else if (OperatingSystem.current().isWindows()) { // check these paths!!
- if (file(eclipseRoot+"/eclipse").isDirectory() && file(eclipseRoot+"/eclipse/.eclipseproduct").exists()) {
- eclipseRoot += "/eclipse"
+ if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+ eclipseRoot += "/eclipse.exe"
}
- eclipseDropinsDir = eclipseRoot+"/dropins"
- eclipseBinary = eclipseRoot+"/eclipse"
- eclipseProduct = eclipseRoot+"/.eclipseproduct"
+ eclipseBinary = "${eclipseRoot}/eclipse"
+ eclipseProduct = "${eclipseRoot}/.eclipseproduct"
} else { // linux or unix
- if (file(eclipseRoot+"/eclipse").isDirectory() && file(eclipseRoot+"/eclipse/.eclipseproduct").exists()) {
+ if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
eclipseRoot += "/eclipse"
}
- eclipseDropinsDir = eclipseRoot+"/dropins"
- eclipseBinary = eclipseRoot+"/eclipse"
- eclipseProduct = eclipseRoot+"/.eclipseproduct"
+ eclipseBinary = "${eclipseRoot}/eclipse"
+ eclipseProduct = "${eclipseRoot}/.eclipseproduct"
}
- def fis = new FileInputStream(eclipseProduct)
- def props = new Properties()
- props.load(fis)
- eclipseVersion = props.getProperty("version")
- fis.close()
- println("ECLIPSE_VERSION=${eclipseVersion}")
- String[] v = eclipseVersion.split("\\.")
- def v0 = Integer.valueOf(v[0])
- def v1 = Integer.valueOf(v[1])
- if (v0 < 4 || ( v0 == 4 && v1 < 13 )) {
- fromDropinsDir = "eclipse/dropins_4.12"
- } else {
- fromDropinsDir = "eclipse/dropins_4.13"
- }
+ eclipseVersion = "4.13" // default
+ def assumedVersion = true
+ if (file(eclipseProduct).exists()) {
+ def fis = new FileInputStream(eclipseProduct)
+ def props = new Properties()
+ props.load(fis)
+ eclipseVersion = props.getProperty("version")
+ fis.close()
+ assumedVersion = false
+ }
+
+ def propKey = "eclipse_debug"
+ eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
+
+ doFirst {
+ if (!assumedVersion) {
+ println("ECLIPSE VERSION=${eclipseVersion}")
+ }
+ }
+}
+
+
+task eclipseSetup {
+ dependsOn eclipseProject
+ dependsOn eclipseClasspath
+ dependsOn eclipseJdt
}
-task jalviewjsEclipseCopyDropins {
+
+// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
+task jalviewjsEclipseCopyDropins(type: Copy) {
dependsOn jalviewjsEclipsePaths
- def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+fromDropinsDir, include: "*.jar")
- def outputDir = eclipseDropinsDir
- inputs.files inputFiles
- inputFiles.each { file ->
- outputs.file(outputDir+"/"+file.name)
+ def inputFiles = fileTree(dir: "${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 {
+ dependsOn jalviewjsSitePath
+
+ def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
doLast {
- def outputFiles = []
- inputFiles.each { file ->
+ copy {
+ from zipTree(file_zip)
+ into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ }
+ }
+
+ inputs.file file_zip
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+}
+
+
+task jalviewjsTransferUnzipLib {
+ dependsOn jalviewjsSitePath
+
+ def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+
+ doLast {
+ zipFiles.each { file_zip ->
copy {
- from file
- into outputDir
+ from zipTree(file_zip)
+ into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
}
}
}
+
+ inputs.files zipFiles
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
}
+
+task jalviewjsTransferUnzipAllLibs {
+ dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTransferUnzipLib
+}
+
+
task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+ group "JalviewJS"
+ description "Create the .j2s file from the j2s.* properties"
+
dependsOn jalviewjsSitePath
- outputFile (jalviewDir+"/"+jalviewjs_j2s_settings)
- def props = project.properties.sort { it.key }
+
+ outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
+ def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
def siteDirProperty = "j2s.site.directory"
def setSiteDir = false
- props.each { prop, val ->
- if (prop.startsWith("j2s.") && val != null) {
+ j2s_props.each { prop, val ->
+ if (val != null) {
if (prop == siteDirProperty) {
- if (!(val.startsWith("/") || val.startsWith("file://") )) {
- val = jalviewjsTransferSiteDir+"/"+val
+ if (!(val.startsWith('/') || val.startsWith("file://") )) {
+ val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
}
setSiteDir = true
}
property(prop,val)
}
- if (!setSiteDir) {
- property(siteDirProperty,jalviewjsTransferSiteDir)
+ if (!setSiteDir) { // default site location, don't override specifically set property
+ property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}")
}
}
+ inputs.properties(j2s_props)
outputs.file(outputFile)
}
+
task jalviewjsEclipseSetup {
dependsOn jalviewjsEclipseCopyDropins
dependsOn jalviewjsSetEclipseWorkspace
dependsOn jalviewjsCreateJ2sSettings
}
-task jalviewjsCopyResources (type: Copy) {
+
+task jalviewjsSyncAllLibs (type: Sync) {
dependsOn jalviewjsSitePath
- def inputFiles = fileTree(dir: jalviewjs_resource_dir)
- def outputDir = jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir
+ dependsOn jalviewjsTransferUnzipAllLibs
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+ inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
into outputDir
def outputFiles = []
rename { filename ->
- outputFiles += outputDir+"/"+filename
+ outputFiles += "${outputDir}/${filename}"
null
}
+ preserve {
+ include "**"
+ }
outputs.files outputFiles
inputs.files inputFiles
}
-task jalviewjsCopySiteResources (type: Copy) {
+
+task jalviewjsSyncResources (type: Sync) {
dependsOn jalviewjsSitePath
- def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_site_resource_dir)
- def outputDir = jalviewjsSiteDir
+ def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
into outputDir
def outputFiles = []
rename { filename ->
- outputFiles += outputDir+"/"+filename
+ outputFiles += "${outputDir}/${filename}"
null
}
+ preserve {
+ include "**"
+ }
outputs.files outputFiles
inputs.files inputFiles
}
-task cleanJalviewjs {
- //delete jalviewjsBuildDir
- //delete jalviewDir+"/"+eclipse_bin_dir
- //delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
- //delete jalviewDir+"/"+jalviewjs_j2s_settings
+
+task jalviewjsSyncSiteResources (type: Sync) {
+ dependsOn jalviewjsSitePath
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+ 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 jalviewjsSyncBuildProperties (type: Sync) {
+ dependsOn jalviewjsSitePath
+ dependsOn createBuildProperties
+ def inputFiles = [file(buildProperties)]
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
task jalviewjsProjectImport(type: Exec) {
- // work out how to do this!
- dependsOn eclipseProject
- dependsOn eclipseClasspath
- dependsOn eclipseJdt
+ dependsOn eclipseSetup
dependsOn jalviewjsEclipsePaths
dependsOn jalviewjsEclipseSetup
+
+ doFirst {
+ // do not run a headless import when we claim to be in Eclipse
+ if (ECLIPSE_IDE_DEVELOPER.equals("true")) {
+ throw new StopExecutionException("Not running headless import whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'")
+ }
+ }
+
+ //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+ def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
executable(eclipseBinary)
args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
- def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
- inputs.file(jalviewDir+"/.project")
- outputs.dir(projdir)
- outputs.upToDateWhen { file(projdir).exists() }
+ inputs.file("${jalviewDir}/.project")
+ outputs.upToDateWhen {
+ file(projdir).exists()
+ }
}
+
task jalviewjsTranspile(type: Exec) {
dependsOn jalviewjsEclipseSetup
dependsOn jalviewjsProjectImport
dependsOn jalviewjsEclipsePaths
+
+ doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (ECLIPSE_IDE_DEVELOPER.equals("true")) {
+ throw new StopExecutionException("Not running headless transpile whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'")
+ }
+ }
+
executable(eclipseBinary)
- args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ])
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
def stdout
def stderr
stdout = new ByteArrayOutputStream()
stderr = new ByteArrayOutputStream()
- def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
+ def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
def logOutFile = file(logOutFileName)
logOutFile.createNewFile()
- def logOutFOS = new FileOutputStream(logOutFile, false)
- //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
+ logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+BINARY: ${eclipseBinary}
+VERSION: ${eclipseVersion}
+WORKSPACE: ${eclipseWorkspace}
+DEBUG: ${eclipseDebug}
+----
+"""
+ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+ //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
//def logErrFile = file(logFileName)
//logErrFile.createNewFile()
//def logErrFOS = new FileErrputStream(logErrFile, false)
// 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(
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}/${jalviewjs_j2s_transpile_stdout}'")
}
}
- inputs.dir(sourceDir)
- outputs.dir(eclipse_bin_dir+"/main")
- outputs.dir(jalviewjsTransferSiteDir)
+ inputs.dir("${jalviewDir}/${sourceDir}")
+ outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+ outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+}
+
+task jalviewjsNoTranspileSyncCore (type: Sync) {
+ dependsOn jalviewjsSitePath
+ dependsOn "jalviewjsNoTranspileBuildAllCores"
+ 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 jalviewjsSyncCore (type: Sync) {
+ dependsOn jalviewjsTranspile
+ dependsOn jalviewjsNoTranspileSyncCore
+ dependsOn "jalviewjsBuildAllCores"
}
-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 jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) {
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ include "**/*.*"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+ preserve {
+ include "**"
+ }
+}
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+
+
+task jalviewjsNoTranspilePrepareSite {
+ dependsOn jalviewjsSyncAllLibs
+ dependsOn jalviewjsSyncResources
+ dependsOn jalviewjsSyncSiteResources
+ dependsOn jalviewjsSyncBuildProperties
+ dependsOn jalviewjsNoTranspileSyncCore
}
-jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite
task jalviewjsPrepareSite {
group "JalviewJS"
description "Prepares the website folder including unzipping files and copying resources"
- dependsOn jalviewjsSitePath
- dependsOn jalviewjsUnzipFiles
- dependsOn jalviewjsCopyResources
- dependsOn jalviewjsCopySiteResources
+ 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 cleanJalviewjsSite {
- delete jalviewjsTransferSiteDir
- delete jalviewjsSiteDir
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+ 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"
+ def filename = "jalviewjsTest.html"
+ description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
dependsOn jalviewjsSitePath
- def htmlFile = "${jalviewDirAbsolutePath}/jalviewjsTest.html"
+ def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
doLast {
SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
def url
while(port < start+1000 && !running) {
try {
- def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir)
- jalviewjsServer = factory.start(doc_root, port)
+ def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
+ def jalviewjsServer = factory.start(doc_root, port)
running = true
url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
println("SERVER STARTED with document root ${doc_root}.")
}
outputs.file(htmlFile)
+ outputs.upToDateWhen({false})
+}
+
+
+task cleanJalviewjsAll {
+ group "JalviewJS"
+ description "Delete all configuration and build artifacts to do with JalviewJS build"
+ dependsOn cleanJalviewjsSite
+ dependsOn jalviewjsEclipsePaths
+
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsBuildDir}"
+ delete "${jalviewDir}/${eclipse_bin_dir}"
+ if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
+ delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+ }
+ delete "${jalviewDir}/${jalviewjs_j2s_settings}"
+ }
+
+ outputs.upToDateWhen( { false } )
}
+
task jalviewjs {
group "JalviewJS"
description "Build the site"
}
-task jalviewjsIDECopyTransferSite(type: Copy) {
- from jalviewjsTransferSiteDir
- into jalviewjsSiteDir
+
+task jalviewjsIDE_CopyTransferSiteJs(type: Copy) {
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
}
-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
- dependsOn jalviewjsPrepareSite
+
+task jalviewjsIDE_AssembleSite {
+ group "00 JalviewJS in Eclipse"
+ description "Assembles the Eclipse transpiled site and unzips supporting zipfiles"
+ dependsOn jalviewjsIDE_CopyTransferSiteJs
+ dependsOn jalviewjsNoTranspilePrepareSite
}
-task cleanJalviewjsIDESite {
- 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
+task eclipseSynchronizationTask {
+ dependsOn eclipseSetup
+ dependsOn jalviewjsIDE_j2sFile
+}
+
+
+// buildship runs this at build time
+task eclipseAutoBuildTask {
+ dependsOn jalviewjsNoTranspileSyncTransferSiteJs
+ dependsOn jalviewjsNoTranspilePrepareSite
+}
+
+
+
+
+
+
+
+
+// closure
+
+def jalviewjsCallCore(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 = "Generating ${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_")
+ t.replaceAll("Class__","Clazz._")
+ 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 ]
+
+ 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 jalviewjsNoTranspileBuildAllCores {
+ dependsOn jalviewjsSitePath
+ dependsOn jalviewjsTransferUnzipSwingJs
+
+ def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+ def jsDir = "${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}/${jalviewjs_classlist_jalview}"), 'name': "_jalview" ]
+
+ def classlists = []
+
+ classlistFiles.each {
+ hash ->
+
+ def file = hash['file']
+ if (! file.exists()) {
+ println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+ return false // this is a "continue" in groovy .each closure
+ }
+ def name = hash['name']
+ if (name == null) {
+ name = file.getName() - ".txt"
+ }
+
+ def filelist = []
+ file.eachLine {
+ line ->
+ filelist += line
+ }
+ def list = fileTree(dir: j2sDir, includes: filelist)
+
+ def jsfile = "${outputDir}/core${name}.js"
+ def zjsfile = "${outputDir}/core${name}.z.js"
+
+ classlists += [
+ 'jsfile': jsfile,
+ 'zjsfile': zjsfile,
+ 'list': list
+ ]
+
+ inputs.file(file)
+ inputs.files(list)
+ outputs.file(jsfile)
+ outputs.file(zjsfile)
+ }
+
+ // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+ def stevesoftClasslist = [
+ 'jsfile': "${outputDir}/core_stevesoft.js",
+ 'zjsfile': "${outputDir}/core_stevesoft.z.js",
+ 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js")
+ ]
+ classlists += stevesoftClasslist
+ inputs.files(stevesoftClasslist['list'])
+ outputs.file(stevesoftClasslist['jsfile'])
+ outputs.file(stevesoftClasslist['zjsfile'])
+
+ doFirst {
+ def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+ logOutFile.getParentFile().mkdirs()
+ logOutFile.createNewFile()
+ logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsNoTranspileBuildAllCores\n----\n")
+
+ classlists.each {
+ jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+ }
+ }
+
+}
+
+
+jalviewjsNoTranspileBuildAllCores.mustRunAfter jalviewjsTranspile
+
+
+task jalviewjsBuildAllCores {
+ group "JalviewJS"
+ description "Build the core js lib closures listed in the classlists dir"
+ dependsOn jalviewjsTranspile
+ dependsOn jalviewjsNoTranspileBuildAllCores
+}
+
+
+task jalviewjsIDE_BuildAllCores {
+ group "00 JalviewJS in Eclipse"
+ description "Build the core js lib closures listed in the classlists dir"
+ dependsOn jalviewjsNoTranspileBuildAllCores
+}
+
+
+task jalviewjsPublishCoreTemplate(type: Sync) {
+ dependsOn jalviewjsSitePath
+ dependsOn jalviewjsBuildAllCores
+
+// clean this up
+ def inputFile = file("${jalviewDir}/${j2s_template_html}")
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+
+// clean this up
+ def jalviewTemplateName = "JalviewJS"
+ def jalviewCoreName = "_jalview"
+
+ from inputFile
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ if (filename.equals(inputFile.getName())) {
+ return "${jalviewTemplateName}_${jalviewCoreName}.html"
+ }
+ return null
+ }
+ filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['NONE': jalviewCoreName])
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFile
+}