import org.apache.tools.ant.filters.ReplaceTokens
import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.eclipse.model.Output
+import org.gradle.plugins.ide.eclipse.model.Library
+
+import groovy.transform.ExternalizeMethods
buildscript {
dependencies {
- classpath 'org.openclover:clover:4.3.1'
- classpath 'org.apache.commons:commons-compress:1.18'
+ classpath 'org.openclover:clover:4.3.1'
}
}
plugins {
id 'java'
id 'application'
+ id 'eclipse'
id 'com.github.johnrengelman.shadow' version '4.0.3'
id 'com.install4j.gradle' version '7.0.9'
}
}
}
+dependencies {
+ 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"
// 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 = ""
+ reportRsyncCmd = false
+ buildDist = true
+ buildProperties = buildPropertiesFile
+ 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_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ break
+
+ case "RELEASE":
+ getdown_channel_name = CHANNEL.toLowerCase()
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_release
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case "ARCHIVE":
+ getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_alt
+ if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
+ print "Must provide an ARCHIVEDIR value to produce an archive distribution"
+ exit
+ } else {
+ packageDir = ARCHIVEDIR + "/" + packageDir
+ buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ buildDist = false
+ }
+ reportRsyncCommand = true
+ break
+
+ case "ARCHIVELOCAL":
+ getdown_channel_name = "archive" + "/" + JALVIEW_VERSION
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+ getdown_app_dir = getdown_app_dir_alt
+ if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
+ print "Must provide an ARCHIVEDIR value to produce an archive distribution"
+ exit
+ } else {
+ packageDir = ARCHIVEDIR + "/" + packageDir
+ buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ buildDist = false
+ }
+ reportRsyncCommand = true
+ 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
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case "TEST-RELEASE":
+ getdown_channel_name = CHANNEL.toLowerCase()
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case ~/^SCRATCH(|-[-\w]*)$/:
+ getdown_channel_name = CHANNEL
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case "LOCAL":
+ getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ break
+
+ default: // something wrong specified
+ print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
+ exit
+ break
+
+ }
+
+ println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base)
+ getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
+ //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+ getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
+ getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir
+ getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
+ getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir
+ /* compile without modules -- using classpath libraries
+ modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
+ modules_runtimeClasspath = modules_compileClasspath
+ */
+ gitHash = ""
+ gitBranch = ""
+
+ jalviewjsServer = ""
+}
+
+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', file("$jalviewDir/$j11modDir").getAbsolutePath(),
- '--add-modules', j11modules
+ '--module-path', ext.modules_compileClasspath.asPath,
+ '--add-modules', j11modules
]
+ */
} else {
throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
}
resources {
srcDirs "$jalviewDir/$resourceDir"
- srcDirs "$jalviewDir/$libDir"
}
jar.destinationDir = file("$jalviewDir/$packageDir")
runtimeClasspath = compileClasspath
}
-
+
clover {
java {
- srcDirs = [ cloverInstrDir ]
- outputDir = file("${buildDir}/${cloverClassesDir}")
+ srcDirs = [ cloverInstrDir ]
+ outputDir = file("${buildDir}/${cloverClassesDir}")
}
-
+
resources {
srcDirs = sourceSets.main.resources.srcDirs
}
compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
+ compileClasspath += files(sourceSets.main.java.outputDir)
+ compileClasspath += sourceSets.main.compileClasspath
compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
runtimeClasspath = compileClasspath
}
-
+
test {
java {
srcDirs "$jalviewDir/$testSourceDir"
srcDirs = sourceSets.main.resources.srcDirs
}
- compileClasspath = files( sourceSets.test.java.outputDir )
+ compileClasspath = files( sourceSets.test.java.outputDir )
+
if (use_clover) {
compileClasspath += sourceSets.clover.compileClasspath
} else {
- compileClasspath += sourceSets.main.compileClasspath
compileClasspath += files(sourceSets.main.java.outputDir)
}
- compileClasspath += files( sourceSets.main.resources.srcDirs)
- compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", 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
}
}
configurations {
- cloverRuntime
- cloverRuntime.extendsFrom cloverCompile
+ cloverRuntime
+ cloverRuntime.extendsFrom cloverCompile
}
-
+
+eclipse {
+ project {
+ name = eclipse_project_name
+
+ natures 'org.eclipse.jdt.core.javanature',
+ 'org.eclipse.jdt.groovy.core.groovyNature',
+ 'org.eclipse.buildship.core.gradleprojectnature'
+
+ buildCommand 'org.eclipse.jdt.core.javabuilder'
+ buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+ }
+
+ classpath {
+ //defaultOutputDir = sourceSets.main.java.outputDir
+ def removeThese = []
+ configurations.each{
+ if (it.isCanBeResolved()) {
+ removeThese += it
+ }
+ }
+
+ minusConfigurations += removeThese
+ plusConfigurations = [ ]
+ file {
+
+ whenMerged { cp ->
+ def removeTheseToo = []
+ HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
+ cp.entries.each { entry ->
+ if (entry.kind == 'src') {
+ if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+ 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(helpParentDir).isDirectory()) {
+ cp.entries += new Library(fileReference(helpParentDir))
+ }
+ if (file(resourceDir).isDirectory()) {
+ cp.entries += new Library(fileReference(resourceDir))
+ }
+
+ HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
+
+ sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ //don't want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath
+ return
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ // make relative path
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ //println("Not adding duplicate entry "+itPath)
+ } else {
+ //println("Adding entry "+itPath)
+ cp.entries += new Library(fileReference(itPath))
+ alreadyAddedLibPath.put(itPath, true)
+ }
+ }
+
+ //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
+ sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ //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
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ // don't duplicate
+ } else {
+ def lib = new Library(fileReference(itPath))
+ /* this doesn't work... yet. Adding test=true attribute using withXml below
+ def attrs = new Node(null, 'attributes')
+ attrs.appendNode('attribute', ["name":"test","value":"true"])
+ lib.appendNode(attrs)
+ /**/
+ cp.entries += lib
+ alreadyAddedLibPath.put(itPath, true)
+ }
+ }
+
+ } // whenMerged
+
+ // withXml changes ignored by buildship, these add the "test=true" attribute
+ withXml {
+ def node = it.asNode()
+
+ def srcTestAttributes
+ node.children().each{ cpe ->
+ def attributes = cpe.attributes()
+ if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
+ srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
+ return
+ }
+ }
+ def addTestAttribute = true
+ srcTestAttributes.each{a ->
+ if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
+ addTestAttribute = false
+ }
+ }
+ if (addTestAttribute) {
+ srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
+ }
+
+ node.children().each{ cpe ->
+ def attributes = cpe.attributes()
+ if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) {
+ cpe.appendNode('attributes')
+ .appendNode('attribute', [name:"test", value:"true"])
+ }
+ }
+ } // withXML
+
+
+ } // file
+
+ containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+
+ } // classpath
+
+ jdt {
+ // for the IDE, use java 11 compatibility
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ javaRuntimeName = eclipse_java_runtime_name
+
+ // add in jalview project specific properties/preferences into eclipse core preferences
+ file {
+ withProperties { props ->
+ def jalview_prefs = new Properties()
+ def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
+ jalview_prefs.load(ins)
+ ins.close()
+ jalview_prefs.forEach { t, v ->
+ if (props.getAt(t) == null) {
+ props.putAt(t, v)
+ }
+ }
+ }
+ }
+
+ } // jdt
+
+}
+
task cloverInstr() {
// only instrument source, we build test classes as normal
- inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
- outputs.dir cloverInstrDir
+ inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+ outputs.dir cloverInstrDir
- doFirst {
- delete cloverInstrDir
- def argsList = ["--initstring", "${buildDir}/clover/clover.db",
- "-d", "${buildDir}/${cloverSourcesInstrDir}"]
- argsList.addAll(inputs.files.files.collect({ file ->
- file.absolutePath
- }))
- String[] args = argsList.toArray()
- println("About to instrument "+args.length +" files")
- com.atlassian.clover.CloverInstr.mainImpl(args)
- }
+ doFirst {
+ delete cloverInstrDir
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-d", "${buildDir}/${cloverSourcesInstrDir}"]
+ argsList.addAll(inputs.files.files.collect({ file ->
+ file.absolutePath
+ }))
+ String[] args = argsList.toArray()
+ println("About to instrument "+args.length +" files")
+ com.atlassian.clover.CloverInstr.mainImpl(args)
+ }
}
-
+
task cloverReport {
+ group = "Verification"
+ description = "Createst the Clover report"
inputs.dir "${buildDir}/clover"
outputs.dir "${reportsDir}/clover"
onlyIf {
- file("${buildDir}/clover/clover.db").exists()
- }
- doFirst {
- def argsList = ["--initstring", "${buildDir}/clover/clover.db",
- "-o", "${reportsDir}/clover"]
- String[] args = argsList.toArray()
- com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
-
- // and generate ${reportsDir}/clover/clover.xml
- args = ["--initstring", "${buildDir}/clover/clover.db",
- "-o", "${reportsDir}/clover/clover.xml"].toArray()
- com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+ file("${buildDir}/clover/clover.db").exists()
}
+ doFirst {
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover"]
+ String[] args = argsList.toArray()
+ com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+ // and generate ${reportsDir}/clover/clover.xml
+ args = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover/clover.xml"].toArray()
+ com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+ }
}
// end clover bits
}
compileTestJava {
-
if (use_clover) {
dependsOn compileCloverJava
classpath += configurations.cloverRuntime
delete cloverInstrDir
}
+// format is a string like date.format("dd MMMM yyyy")
def getDate(format) {
def date = new Date()
- //return date.format("dd MMMM yyyy")
return date.format(format)
}
-def getGitHash() {
- def stdout = new ByteArrayOutputStream()
+task setGitVals {
+ def hashStdOut = new ByteArrayOutputStream()
exec {
commandLine "git", "rev-parse", "--short", "HEAD"
- standardOutput = stdout
- workingDir = jalviewDir
+ standardOutput = hashStdOut
+ ignoreExitValue true
}
- return stdout.toString().trim()
-}
-def getGitBranch() {
- def stdout = new ByteArrayOutputStream()
+ def branchStdOut = new ByteArrayOutputStream()
exec {
commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
- standardOutput = stdout
- workingDir = jalviewDir
+ standardOutput = branchStdOut
+ ignoreExitValue true
}
- return stdout.toString().trim()
+
+ project.ext.gitHash = hashStdOut.toString().trim()
+ project.ext.gitBranch = branchStdOut.toString().trim()
+
+ outputs.upToDateWhen { false }
}
task createBuildProperties(type: WriteProperties) {
+ dependsOn setGitVals
inputs.dir("$jalviewDir/$sourceDir")
+ inputs.dir("$classes")
inputs.dir("$jalviewDir/$resourceDir")
- outputFile "$classes/$buildPropertiesFile"
- /* taking time/date specific comment out to allow better incremental builds */
- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
- property "BUILD_DATE", getDate("dd MMMM yyyy")
+ 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:"+getGitHash()+" ["+getGitBranch()+"]"
+ property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
outputs.file(outputFile)
- outputs.dir("$classes")
+}
+
+def buildingHTML = "$jalviewDir/$docDir/building.html"
+task deleteBuildingHTML(type: Delete) {
+ delete buildingHTML
+}
+
+task convertBuildingMD(type: Exec) {
+ dependsOn deleteBuildingHTML
+ def buildingMD = "$jalviewDir/$docDir/building.md"
+ def css = "$jalviewDir/$docDir/github.css"
+
+ def pandoc = null
+ pandoc_exec.split(",").each {
+ if (file(it.trim()).exists()) {
+ pandoc = it.trim()
+ return true
+ }
+ }
+
+ def hostname = "hostname".execute().text.trim()
+ if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
+ pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+ }
+
+ doFirst {
+ if (pandoc != null && file(pandoc).exists()) {
+ commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+ } else {
+ println("Cannot find pandoc. Skipping convert building.md to HTML")
+ throw new StopExecutionException()
+ }
+ }
+
+ ignoreExitValue true
+
+ inputs.file(buildingMD)
+ inputs.file(css)
+ outputs.file(buildingHTML)
+}
+clean {
+ delete buildingHTML
}
task syncDocs(type: Sync) {
+ dependsOn convertBuildingMD
def syncDir = "$classes/$docDir"
from fileTree("$jalviewDir/$docDir")
into syncDir
}
def helpFile = "$classes/$helpDir/help.jhm"
-task syncHelp(type: Sync) {
- inputs.files("$jalviewDir/$helpDir")
- outputs.files(helpFile)
-
- def syncDir = "$classes/$helpDir"
- from fileTree("$jalviewDir/$helpDir")
- into syncDir
-}
task copyHelp(type: Copy) {
- def inputDir = "$jalviewDir/$helpDir"
+ def inputDir = "$jalviewDir/$helpParentDir/$helpDir"
def outputDir = "$classes/$helpDir"
- from inputDir
+ from(inputDir) {
+ exclude '**/*.gif'
+ exclude '**/*.jpg'
+ exclude '**/*.png'
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+ }
+ from(inputDir) {
+ include '**/*.gif'
+ include '**/*.jpg'
+ include '**/*.png'
+ }
into outputDir
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"])
+
inputs.dir(inputDir)
outputs.files(helpFile)
outputs.dir(outputDir)
}
task syncLib(type: Sync) {
- def syncDir = "$classes/$libDir"
- from fileTree("$jalviewDir/$libDir")
+ def syncDir = "$classes/$libDistDir"
+ from fileTree("$jalviewDir/$libDistDir")
into syncDir
}
if (use_clover) {
dependsOn cloverInstr
}
- print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
-
+
+ if (use_clover) {
+ print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+ }
+
useTestNG() {
includeGroups testngGroups
preserveOrder true
useDefaultListeners=true
}
-
+
workingDir = jalviewDir
//systemProperties 'clover.jar' System.properties.clover.jar
sourceCompatibility = compile_source_compatibility
destinationDir = file("$jalviewDir/$utilsDir")
source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+ inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
+ inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
}
+def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch")
task linkCheck(type: JavaExec) {
dependsOn prepare, compileLinkCheck
classpath = files("$jalviewDir/$utilsDir")
workingDir = jalviewDir
def help = "$classes/$helpDir"
args = [ "$classes/$helpDir", "-nointernet" ]
- //args = [ "$classesDir/$helpDir", "-nointernet" ]
- doFirst {
- standardOutput new FileOutputStream("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+ doLast {
+ helplinkscheckertouchfile.createNewFile()
}
- outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+ inputs.dir("$classes/$helpDir")
+ outputs.file(helplinkscheckertouchfile)
}
+// import the pubhtmlhelp target
+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")
}
// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
task syncJars(type: Sync) {
- from fileTree("$jalviewDir/$libDir").include("**/*.jar").include("*.jar").files
+ from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files
into "$jalviewDir/$packageDir"
preserve {
include jar.archiveName
}
task makeDist {
+ group = "build"
+ description = "Put all required libraries in dist"
// order of "cleanPackageDir", "copyJars", "jar" important!
jar.mustRunAfter cleanPackageDir
syncJars.mustRunAfter cleanPackageDir
}
shadowJar {
- dependsOn makeDist
- if (JAVA_VERSION.equals("11")) {
- from ("$jalviewDir/$j11libDir") {
- include("*.jar")
- }
+ group = "distribution"
+ if (buildDist) {
+ dependsOn makeDist
+ }
+ from ("$jalviewDir/$libDistDir") {
+ include("*.jar")
+ }
+ manifest {
+ attributes 'Implementation-Version': JALVIEW_VERSION
}
mainClassName = shadowJarMainClass
mergeServiceFiles()
- classifier = "all"
+ classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
}
-ext {
- getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir
- getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
- getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
- getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
- getdownLauncher = jalviewDir + '/' + getdown_launcher
- getdownFilesDir = jalviewDir + '/' + getdown_files_dir
- getdownLib1 = jalviewDir + '/' + getdown_lib1
- def getdownChannel = getdown_channel_name
- if (getdown_channel_name.equals("COMMIT")) {
- getdownChannel = getGitHash()
+task getdownWebsite() {
+ group = "distribution"
+ description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+ if (buildDist) {
+ dependsOn makeDist
}
- getdown_app_base = getdown_channel_base+"/"+JAVA_VERSION+"/"+getdownChannel+"/"
-}
-task getdownWebsite() {
- dependsOn makeDist
+ // clean the getdown website and files dir before creating getdown folders
+ delete project.ext.getdownWebsiteDir
+ delete project.ext.getdownFilesDir
+
def getdownWebsiteResourceFilenames = []
def getdownTextString = ""
def getdownResourceDir = project.ext.getdownResourceDir
def getdownAppDir = project.ext.getdownAppDir
def getdownResourceFilenames = []
+
doFirst {
+ copy {
+ from buildProperties
+ rename(buildPropertiesFile, getdown_build_properties)
+ into project.ext.getdownAppDir
+ }
+ getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties
+
// go through properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
- props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+ 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_") && val != null) {
}
} else {
// file values rationalised
- if (val.indexOf('/') > -1) {
+ if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
def r = null
if (val.indexOf('/') == 0) {
// absolute path
getdownResourceFilenames += r.getPath()
}
}
- def line = prop.substring(12) + " = " + val + "\n"
- getdownTextString += line
+ if (! prop.startsWith("getdown_txt_resource")) {
+ def line = prop.substring(12) + " = " + val + "\n"
+ getdownTextString += line
+ }
}
}
}
}
def codeFiles = []
- makeDist.outputs.files.each{ f ->
+ fileTree(file(packageDir)).each{ f ->
if (f.isDirectory()) {
def files = fileTree(dir: f, include: ["*"]).getFiles()
codeFiles += files
}
}
+ // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+ /*
if (JAVA_VERSION.equals("11")) {
- def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
- j11libFiles.sort().each{f ->
- def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
- getdownTextString += line
- copy {
- from f.getPath()
- into project.ext.getdownJ11libDir
- }
- }
+ def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
+ j11libFiles.sort().each{f ->
+ def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into project.ext.getdownJ11libDir
+ }
}
+ }
+ */
- getdownTextString += "code = " + file(getdownLauncher).getName() + "\n"
+ // 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"
def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
getdown_txt.write(getdownTextString)
- copy {
- from getdown_txt
- into project.ext.getdownFilesDir
- }
+ def launch_jvl = file(project.ext.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
}
copy {
from getdownLauncher
- into project.ext.getdownFilesDir
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into project.ext.getdownWebsiteDir
}
- copy {
- from getdownLib1
- into project.ext.getdownFilesDir
+ if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
+ copy {
+ from getdown_txt
+ from getdownLauncher
+ from getdownWebsiteDir+"/"+getdown_build_properties
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownInstallDir
+ }
+
+ copy {
+ from getdownInstallDir
+ into getdownFilesInstallDir
+ }
}
copy {
- from getdownLib1
- into project.ext.getdownWebsiteDir
+ from getdown_txt
+ from launch_jvl
+ from getdownLauncher
+ from getdownWebsiteDir+"/"+getdown_build_properties
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownFilesDir
}
copy {
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon')
- into project.ext.getdownFilesDir + '/' + getdown_resource_dir
+ from getdownResourceDir
+ into project.ext.getdownFilesDir + '/' + getdown_resource_dir
}
}
- inputs.dir(jalviewDir + '/' + packageDir)
+ if (buildDist) {
+ inputs.dir(jalviewDir + '/' + packageDir)
+ }
outputs.dir(project.ext.getdownWebsiteDir)
outputs.dir(project.ext.getdownFilesDir)
}
task getdownDigest(type: JavaExec) {
+ group = "distribution"
+ description = "Digest the getdown website folder"
dependsOn getdownWebsite
- classpath = files(jalviewDir + '/' + getdown_core)
- classpath file(jalviewDir + '/' + getdown_lib1)
+ doFirst {
+ 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")
}
task getdown() {
+ group = "distribution"
+ description = "Create the minimal and full getdown app folder for installers and website and create digest file"
dependsOn getdownDigest
+ doLast {
+ if (reportRsyncCommand) {
+ def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/")
+ def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/")
+ println "LIKELY RSYNC COMMAND:"
+ println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
+ if (RUNRSYNC == "true") {
+ exec {
+ commandLine "mkdir", "-p", toDir
+ }
+ exec {
+ commandLine "rsync", "-avh", "--delete", fromDir, toDir
+ }
+ }
+ }
+ }
}
clean {
}
installDir = file(install4jHomeDir)
mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
+ if (install4jFaster.equals("true")) {
+ faster = true
+ }
}
def install4jConf
def macosJavaVMDir
+def macosJavaVMTgz
def windowsJavaVMDir
+def windowsJavaVMTgz
+def install4jDir = "$jalviewDir/$install4jResourceDir"
+def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
+install4jConf = "$install4jDir/$install4jConfFile"
+
task copyInstall4jTemplate(type: Copy) {
- def install4jDir = "$jalviewDir/$install4jResourceDir"
- def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
- macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/macos-jre"+JAVA_VERSION+"/java_vm"
- windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/windows-jre"+JAVA_VERSION+"/java_vm"
+ 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: ['VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir])
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
+ tokens: [
+ 'JAVA_VERSION': JAVA_VERSION,
+ 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+ 'VERSION': JALVIEW_VERSION,
+ 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+ 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+ 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+ 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+ 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
+ 'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
+ 'MACOS_BUNDLE_ID': install4jMacOSBundleId,
+ 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+ 'GETDOWN_DIST_DIR': getdown_app_dir,
+ 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+ 'GETDOWN_INSTALL_DIR': getdown_install_dir
+ ]
+ )
+ if (OSX_KEYPASS=="") {
+ filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
+ filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
+ }
}
into install4jDir
- install4jConf = "$install4jDir/$install4jConfFile"
- inputs.files("$install4jDir/$install4jTemplate")
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
+ )
+ */
+ }
}
task installers(type: com.install4j.gradle.Install4jTask) {
+ group = "distribution"
+ description = "Create the install4j installers"
dependsOn getdown
dependsOn copyInstall4jTemplate
- projectFile = install4jConf
- variables = [majorVersion: version.substring(2, 11), build: 001]
- destination = "$jalviewDir/$install4jBuildDir"
+ projectFile = file(install4jConf)
+ println("Using projectFile "+projectFile)
+ variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
+ destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
buildSelected = true
+
+ if (OSX_KEYPASS) {
+ macKeystorePassword=OSX_KEYPASS
+
+ }
+
inputs.dir(project.ext.getdownWebsiteDir)
inputs.file(install4jConf)
inputs.dir(macosJavaVMDir)
inputs.dir(windowsJavaVMDir)
- outputs.dir("$jalviewDir/$install4jBuildDir")
+ outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
+
}
clean {
delete install4jConf
}
+
+task sourceDist (type: Tar) {
+
+ def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+ def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
+ try {
+ archiveFileName = outputFileName
+ } catch (Exception e) {
+ archiveName = outputFileName
+ }
+
+ compression Compression.GZIP
+
+ into project.name
+
+ def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
+ ,".*"
+ ,"benchmarking/*"
+ ,"**/.*"
+ ,"*.class"
+ ,"**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales"
+ ,"*locales/**",
+ ,"utils/InstallAnywhere"]
+ def PROCESS_FILES=[ "AUTHORS",
+ "CITATION",
+ "FEATURETODO",
+ "JAVA-11-README",
+ "FEATURETODO",
+ "LICENSE",
+ "**/README",
+ "RELEASE",
+ "THIRDPARTYLIBS","TESTNG",
+ "build.gradle",
+ "gradle.properties",
+ "**/*.java",
+ "**/*.html",
+ "**/*.xml",
+ "**/*.gradle",
+ "**/*.groovy",
+ "**/*.properties",
+ "**/*.perl",
+ "**/*.sh"]
+
+ from(jalviewDir) {
+ exclude (EXCLUDE_FILES)
+ include (PROCESS_FILES)
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+ }
+ from(jalviewDir) {
+ exclude (EXCLUDE_FILES)
+ exclude (PROCESS_FILES)
+ exclude ("appletlib")
+ exclude ("**/*locales")
+ exclude ("*locales/**")
+ exclude ("utils/InstallAnywhere")
+
+ exclude (getdown_files_dir)
+ exclude (getdown_website_dir)
+
+ // exluding these as not using jars as modules yet
+ exclude ("$j11modDir/**/*.jar")
+}
+// from (jalviewDir) {
+// // explicit includes for stuff that seemed to not get included
+// include(fileTree("test/**/*."))
+// exclude(EXCLUDE_FILES)
+// exclude(PROCESS_FILES)
+// }
+}
+
+task helppages {
+ dependsOn copyHelp
+ dependsOn pubhtmlhelp
+
+ inputs.dir("$classes/$helpDir")
+ outputs.dir("$helpOutputDir")
+}
+
+def jalviewjsBuildDir
+def jalviewjsSiteDir
+def jalviewjsTransferSiteDir
+task jalviewjsSitePath {
+ if (jalviewjs_site_dir.startsWith("/")) {
+ jalviewjsSiteDir = jalviewjs_site_dir
+ } else {
+ def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+ jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
+ jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir
+ }
+ jalviewjsTransferSiteDir = jalviewjsBuildDir + "/tmp/site"
+}
+
+def eclipseWorkspace
+task jalviewjsSetEclipseWorkspace {
+ def propKey = "jalviewjs_eclipse_workspace"
+ def propsFileName = "${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 (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) {
+ def ins = new FileInputStream(propsFileName)
+ props.load(ins)
+ ins.close()
+ if (props.getProperty(propKey, null) != null) {
+ eclipseWsDir = props.getProperty(propKey)
+ }
+ }
+
+ 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()
+ }
+
+ 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
+ }
+ }
+ }
+
+ inputs.files zipFiles
+ outputs.dir jalviewjsSiteDir
+}
+
+def eclipseDropinsDir
+def eclipseBinary
+def eclipseVersion
+def fromDropinsDir
+task jalviewjsEclipsePaths {
+ def eclipseRoot
+ def eclipseProduct
+ 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"
+ } else if (OperatingSystem.current().isWindows()) { // check these paths!!
+ if (file(eclipseRoot+"/eclipse").isDirectory() && file(eclipseRoot+"/eclipse/.eclipseproduct").exists()) {
+ eclipseRoot += "/eclipse"
+ }
+ 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"
+ }
+
+ 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"
+ }
+}
+
+task jalviewjsEclipseCopyDropins {
+ 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)
+ }
+
+ doLast {
+ def outputFiles = []
+ inputFiles.each { file ->
+ copy {
+ from file
+ into outputDir
+ }
+ }
+ }
+}
+
+task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+ dependsOn jalviewjsSitePath
+ outputFile (jalviewDir+"/"+jalviewjs_j2s_settings)
+ def props = project.properties.sort { it.key }
+ def siteDirProperty = "j2s.site.directory"
+ def setSiteDir = false
+ props.each { prop, val ->
+ if (prop.startsWith("j2s.") && val != null) {
+ if (prop == siteDirProperty) {
+ if (!(val.startsWith("/") || val.startsWith("file://") )) {
+ val = jalviewjsTransferSiteDir+"/"+val
+ }
+ setSiteDir = true
+ }
+ property(prop,val)
+ }
+ if (!setSiteDir) {
+ property(siteDirProperty,jalviewjsTransferSiteDir)
+ }
+ }
+ outputs.file(outputFile)
+}
+
+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
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += outputDir+"/"+filename
+ null
+ }
+ 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
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += outputDir+"/"+filename
+ null
+ }
+ 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 jalviewjsProjectImport(type: Exec) {
+ // work out how to do this!
+ dependsOn eclipseProject
+ dependsOn eclipseClasspath
+ dependsOn eclipseJdt
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseSetup
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+
+ 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() }
+}
+
+task jalviewjsTranspile(type: Exec) {
+ dependsOn jalviewjsEclipseSetup
+ dependsOn jalviewjsProjectImport
+ dependsOn jalviewjsEclipsePaths
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ])
+
+ def stdout
+ def stderr
+ doFirst {
+ stdout = new ByteArrayOutputStream()
+ stderr = new ByteArrayOutputStream()
+
+ def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
+ def logOutFile = file(logOutFileName)
+ logOutFile.createNewFile()
+ def logOutFOS = new FileOutputStream(logOutFile, false)
+ //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
+ //def logErrFile = file(logFileName)
+ //logErrFile.createNewFile()
+ //def logErrFOS = new FileErrputStream(logErrFile, false)
+ // combine stdout and stderr
+ def logErrFOS = logOutFOS
+ if (jalviewjs_j2s_to_console.equals("true")) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr),
+ errorOutput)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr)
+ }
+ }
+ doLast {
+ if (stdout.toString().contains("Error processing ")) {
+ // j2s did not complete transpile
+ throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
+ }
+ }
+
+ inputs.dir(sourceDir)
+ outputs.dir(eclipse_bin_dir+"/main")
+ outputs.dir(jalviewjsTransferSiteDir)
+
+}
+
+task jalviewjsCopyTransferSite(type: Copy) {
+ dependsOn jalviewjsTranspile
+ from jalviewjsTransferSiteDir
+ into jalviewjsSiteDir
+}
+
+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
+}
+
+task jalviewjsBuildSite {
+ group "JalviewJS"
+ description "Builds the whole website including transpiled code"
+ dependsOn jalviewjsCopyTransferSite
+ dependsOn jalviewjsPrepareSite
+}
+
+task jalviewjsSiteTar(type: Tar) {
+ group "JalviewJS"
+ description "Creates a tar.gz file for the website"
+ dependsOn jalviewjsBuildSite
+ def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
+ try {
+ archiveFileName = outputFilename
+ } catch (Exception e) {
+ archiveName = outputFilename
+ }
+
+ compression Compression.GZIP
+
+ from jalviewjsSiteDir
+ into jalviewjs_site_dir // this is inside the tar file
+
+ inputs.dir(jalviewjsSiteDir)
+}
+
+task jalviewjsServer {
+ group "JalviewJS"
+ description "Starts a webserver on localhost to test the website"
+ dependsOn jalviewjsSitePath
+ doLast {
+
+ SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+ def port = Integer.valueOf(jalviewjs_server_port)
+ def start = port
+ def running = false
+ while(port < start+1000 && !running) {
+ try {
+ def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir)
+ jalviewjsServer = factory.start(doc_root, port)
+ running = true
+ println("SERVER STARTED with document root ${doc_root}.")
+ println("Go to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run gradle --stop to stop (kills all gradle daemons).")
+ println("For debug: "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+"?j2sdebug")
+ } catch (Exception e) {
+ port++;
+ }
+ }
+
+ }
+
+}
+
+task jalviewjs {
+ group "JalviewJS"
+ description "Build the site"
+ dependsOn jalviewjsBuildSite
+}
+
+
git://source.jalview.org / jalview.git / blobdiff