import org.apache.tools.ant.filters.ReplaceTokens
+//import org.apache.tools.ant.filters.ReplaceRegexp
import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.eclipse.model.*
+
+
+import groovy.transform.ExternalizeMethods
buildscript {
dependencies {
ext {
// where the getdown channel will be built.
- // TODO: consider allowing this expression to be overrriden by -P arg
- getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + '/'
+ // TODO: consider allowing this expression to be overridden by -P arg
+ getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
- getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+ //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
getdownLauncher = jalviewDir + '/' + getdown_launcher
getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
- getdownLib1 = jalviewDir + '/' + getdown_lib1
- def getdownChannel = getdown_channel_name
- if (getdown_channel_name.equals("COMMIT")) {
- getdownChannel = getGitHash()
- }
- getdown_app_base = getdown_channel_base+"/"+getdownChannel+"/"+JAVA_VERSION+"/"
+ getdown_app_base = getdown_channel_base+"/"+getdown_channel_name+"/"+JAVA_VERSION+"/"
modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
+ gitHash = ""
+ gitBranch = ""
}
def JAVA_INTEGER_VERSION
def getdown_alt_java_min_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_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
compile_target_compatibility = 11
getdown_alt_java_min_version = getdown_alt_java11_min_version
getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+ eclipse_java_runtime_name = "JavaSE-11"
additional_compiler_args += [
'--module-path', ext.modules_compileClasspath.asPath,
'--add-modules', j11modules
resources {
srcDirs "$jalviewDir/$resourceDir"
- srcDirs "$jalviewDir/$libDistDir"
}
jar.destinationDir = file("$jalviewDir/$packageDir")
} else {
compileClasspath += files(sourceSets.main.java.outputDir)
}
- compileClasspath += sourceSets.main.compileClasspath
- compileClasspath += files( sourceSets.main.resources.srcDirs)
+
compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
removeThese += it
}
}
- containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
minusConfigurations += removeThese
plusConfigurations = [ ]
}
}
cp.entries.removeAll(removeTheseToo)
- }
-
- 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.appendNode('classpathentry', [kind:"output", path:"bin/main"])
- node.appendNode('classpathentry', [kind:"lib", path:helpParentDir])
- node.appendNode('classpathentry', [kind:"lib", path:resourceDir])
+
+ print ("CP="+cp.inspect())
+
+ cp.entries += new Output("bin/main")
+ cp.entries += new Library(fileReference(helpParentDir))
+ cp.entries += new Library(fileReference(resourceDir))
+
HashMap<String, Boolean> addedLibPath = new HashMap<>();
- def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath
- sourceSets.main.compileClasspath.each{
- //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+
+ // changing from sourcesets.main.classpath to specific Java version lib
+ //sourceSets.main.compileClasspath.each{
+ fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
+ //don't want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath
- //println("Not adding directory "+it)
return
}
def itPath = it.toString()
//println("Not adding duplicate entry "+itPath)
} else {
//println("Adding entry "+itPath)
- node.appendNode('classpathentry', [kind:"lib", path:itPath])
+ cp.entries += new Library(fileReference(itPath))
addedLibPath.put(itPath, true)
}
}
- sourceSets.test.compileClasspath.each{
+
+ // changing from sourcesets.main.classpath to specific Java version lib
+ //sourceSets.test.compileClasspath.each{
+ fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
//if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
//no longer want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath
- //println("Not adding directory "+it)
- return
+ return false // groovy "break" in .each loop
}
def itPath = it.toString()
if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
}
if (addedLibPath.get(itPath)) {
- //println("Not adding duplicate entry "+itPath)
+ // don't duplicate
} else {
- //println("Adding entry "+itPath)
- node.appendNode('classpathentry', [kind:"lib", path:itPath])
- .appendNode('attributes')
- .appendNode('attribute', [name:"test", value:"true"])
+ def lib = new Library(fileReference(itPath))
+ // this doesn't work... yet. Adding test=true attribute using withXml below
+ //def attrs = new Node(null, 'attributes', ["test":"true"])
+ //lib.appendNode(attrs) //
+ cp.entries += lib
addedLibPath.put(itPath, true)
}
}
- }
+ }
- }
- }
+ // 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 = 11
- targetCompatibility = 11
- javaRuntimeName = "JavaSE-11"
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ javaRuntimeName = eclipse_java_runtime_name
file {
withProperties { props ->
def jalview_prefs = new Properties()
- def ins = new FileInputStream(eclipse_extra_jdt_prefs_file)
+ def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
jalview_prefs.load(ins)
ins.close()
jalview_prefs.forEach { t, v ->
}
}
}
-
-}
+
+ //synchronizationTasks eclipseClasspath
+ //autoBuildTasks eclipseClasspath
+}
task cloverInstr() {
// only instrument source, we build test classes as normal
com.atlassian.clover.CloverInstr.mainImpl(args)
}
}
-
+
task cloverReport {
group = "Verification"
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/$buildPropertiesFile"
- /* taking time/date specific comment out to allow better incremental builds */
- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
- property "BUILD_DATE", getDate("dd MMMM yyyy")
+ // taking time specific comment out to allow better incremental builds
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
property "VERSION", JALVIEW_VERSION
- property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
+ property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
outputs.file(outputFile)
- outputs.dir("$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"
+ }
+
+ if (pandoc != null && file(pandoc).exists()) {
+ commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+ } else {
+ commandLine "true"
+ }
+
+ 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
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")
}
workingDir = jalviewDir
def help = "$classes/$helpDir"
args = [ "$classes/$helpDir", "-nointernet" ]
- //args = [ "$classesDir/$helpDir", "-nointernet" ]
doFirst {
helplinkscheckeroutputfile.createNewFile()
}
shadowJar {
+ group = "distribution"
dependsOn makeDist
from ("$jalviewDir/$libDistDir") {
include("*.jar")
props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+ if (getdown_local == "true") {
+ getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+ }
props.put("getdown_txt_appbase", getdown_app_base)
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_") && val != null) {
}
*/
- 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 = " + file(getdownLauncher).getName() + "\n"
getdownTextString += "class = " + mainClass + "\n"
def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
}
copy {
- from getdownLib1
- into project.ext.getdownFilesDir + '/' + packageDir
- }
-
- 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')
group = "distribution"
description = "Digest the getdown website folder"
dependsOn getdownWebsite
- classpath = files(jalviewDir + '/' + getdown_core)
- classpath file(jalviewDir + '/' + getdown_lib1)
+ classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher)
main = "com.threerings.getdown.tools.Digester"
args project.ext.getdownWebsiteDir
+ inputs.dir(project.ext.getdownWebsiteDir)
outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
}
}
installDir = file(install4jHomeDir)
mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
+ if (install4jFaster.equals("true")) {
+ faster = true
+ }
}
def install4jConf
include install4jTemplate
rename (install4jTemplate, install4jConfFile)
filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['JAVA_VERSION': JAVA_VERSION, 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, 'VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz])
+ 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
+ ]
+ )
if (OSX_KEYPASS=="") {
- println "Empty '"+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
- 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) {
git://source.jalview.org / jalview.git / blobdiff