+/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
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 java.security.MessageDigest
-import groovy.transform.ExternalizeMethods
-buildscript {
- dependencies {
- 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'
- id 'com.dorongold.task-tree' version '1.4' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
-}
-
-repositories {
- jcenter()
- mavenCentral()
- mavenLocal()
- flatDir {
- dirs gradlePluginsDir
- }
}
-dependencies {
- compile 'org.apache.commons:commons-compress:1.18'
-}
// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
def string(Object o) {
- return o.toString()
+ return o == null ? "" : o.toString()
}
jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
jalviewDirRelativePath = jalviewDir
- // local build environment properties
- def localProps = "${jalviewDirAbsolutePath}/local.properties"
- if (file(localProps).exists()) {
- try {
- def p = new Properties()
- def localPropsFIS = new FileInputStream(localProps)
- p.load(localPropsFIS)
- localPropsFIS.close()
- p.each {
- key, val ->
- def over = getProperty(key) != null
- setProperty(key, val)
- if (over) {
- println("Overriding property '${key}' with local.properties value '${val}'")
- }
- }
- } catch (Exception e) {
- System.out.println("Exception reading local.properties")
- }
- }
- // this property set when running Eclipse headlessly
- j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
- // this property set by Eclipse
- eclipseApplicationProperty = string("eclipse.application")
- // CHECK IF RUNNING FROM WITHIN ECLIPSE
- def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
- IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
- // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
- if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
- println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
- IN_ECLIPSE = false
- }
- if (IN_ECLIPSE) {
- println("WITHIN ECLIPSE IDE")
- } else {
- println("HEADLESS BUILD")
- }
- /* *-/
- System.properties.sort { it.key }.each {
- key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+ // Expect jalview.version and target release branch in jalview.release
+ def releaseProps = new Properties();
+ def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+ def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+ try {
+ (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
+ releaseProps.load(it)
+ }
+ } catch (Exception fileLoadError) {
+ throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
}
- /-* *-/
- if (false && IN_ECLIPSE) {
- jalviewDir = jalviewDirAbsolutePath
+ ////
+ // Set JALVIEW_VERSION if it is not already set
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
}
- */
+
// essentials
bareSourceDir = string(source_dir)
sourceDir = string("${jalviewDir}/${bareSourceDir}")
resourceDir = string("${jalviewDir}/${resource_dir}")
bareTestSourceDir = string(test_source_dir)
- testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+ testDir = string("${jalviewDir}/${bareTestSourceDir}")
- // clover
- cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
classesDir = string("${jalviewDir}/${classes_dir}")
- if (clover.equals("true")) {
- use_clover = true
- classesDir = string("${buildDir}/${cloverClassesDir}")
- } else {
- use_clover = false
- classesDir = string("${jalviewDir}/${classes_dir}")
- }
- classes = classesDir
-
- getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
- getdownDir = string("")
- reportRsyncCmd = false
- buildDist = true
- buildProperties = build_properties_file
- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
- switch (CHANNEL) {
-
- case "BUILD":
- // TODO: get bamboo build artifact URL for getdown artifacts
- getdown_channel_base = bamboo_channelbase
- getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}")
- getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${classesDir}/${build_properties_file}")
- break
-
- case "RELEASE":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
- getdown_app_dir = getdown_app_dir_release
- buildProperties = string("${classesDir}/${build_properties_file}")
- reportRsyncCommand = true
- break
-
- case "ARCHIVE":
- getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
- getdown_app_dir = getdown_app_dir_alt
- if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
- print "Must provide an ARCHIVEDIR value to produce an archive distribution"
- exit
- } else {
- packageDir = string("${ARCHIVEDIR}/${packageDir}")
- buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
- buildDist = false
- }
- reportRsyncCommand = true
- break
-
- case "ARCHIVELOCAL":
- getdown_channel_name = string("archive/${JALVIEW_VERSION}")
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = file(getdownWebsiteDir).toURI().toString()
- getdown_app_dir = getdown_app_dir_alt
- if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
- print "Must provide an ARCHIVEDIR value to produce an archive distribution"
- exit
- } else {
- packageDir = string("${ARCHIVEDIR}/${packageDir}")
- buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
- buildDist = false
- }
- reportRsyncCommand = true
- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
- break
-
- case "DEVELOP":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${classesDir}/${build_properties_file}")
- reportRsyncCommand = true
- break
-
- case "TEST-RELEASE":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${classesDir}/${build_properties_file}")
- reportRsyncCommand = true
- break
-
- case ~/^SCRATCH(|-[-\w]*)$/:
- getdown_channel_name = CHANNEL
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${classesDir}/${build_properties_file}")
- reportRsyncCommand = true
- break
-
- case "LOCAL":
- getdown_app_base = file(getdownWebsiteDir).toURI().toString()
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${classesDir}/${build_properties_file}")
- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
- break
-
- default: // something wrong specified
- print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
- exit
- break
- }
+ resourceClassesDir = classesDir
+
+ testSourceDir = testDir
+ testClassesDir = "${jalviewDir}/${test_output_dir}"
- getdownAppDir = string("${getdownWebsiteDir}/${getdown_app_dir}")
- //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
- getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
- getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
- getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
- getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
- /* compile without modules -- using classpath libraries
- modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
- modules_runtimeClasspath = modules_compileClasspath
- */
+ buildProperties = string("${classesDir}/${build_properties_file}")
gitHash = string("")
gitBranch = string("")
libDistDir = j8libDir
compile_source_compatibility = 1.8
compile_target_compatibility = 1.8
- // these are getdown.txt properties defined dependent on the JAVA_VERSION
- getdown_alt_java_min_version = getdown_alt_java8_min_version
- getdown_alt_java_max_version = getdown_alt_java8_max_version
- // this property is assigned below and expanded to multiple lines in the getdown task
- getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
- // this property is for the Java library used in eclipse
- eclipse_java_runtime_name = string("JavaSE-1.8")
} else if (JAVA_VERSION.equals("11")) {
JAVA_INTEGER_VERSION = string("11")
libDir = j11libDir
libDistDir = j11libDir
compile_source_compatibility = 11
compile_target_compatibility = 11
- getdown_alt_java_min_version = getdown_alt_java11_min_version
- getdown_alt_java_max_version = getdown_alt_java11_max_version
- getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
- eclipse_java_runtime_name = string("JavaSE-11")
- /* compile without modules -- using classpath libraries
- additional_compiler_args += [
- '--module-path', modules_compileClasspath.asPath,
- '--add-modules', j11modules
- ]
- */
} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
JAVA_INTEGER_VERSION = JAVA_VERSION
libDir = j11libDir
libDistDir = j11libDir
compile_source_compatibility = JAVA_VERSION
compile_target_compatibility = JAVA_VERSION
- getdown_alt_java_min_version = getdown_alt_java11_min_version
- getdown_alt_java_max_version = getdown_alt_java11_max_version
- getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
- eclipse_java_runtime_name = string("JavaSE-11")
- /* compile without modules -- using classpath libraries
- additional_compiler_args += [
- '--module-path', modules_compileClasspath.asPath,
- '--add-modules', j11modules
- ]
- */
} else {
throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
}
- // for install4j
- macosJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre")
- macosJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz")
- windowsJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre")
- windowsJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz")
- install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
- install4jConfFileName = string("jalview-installers-java${JAVA_VERSION}.install4j")
- install4jConfFile = string("${install4jDir}/${install4jConfFileName}")
- install4jHomeDir = install4j_home_dir
- if (install4jHomeDir.startsWith("~/")) {
- install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
- }
-
- buildingHTML = string("${jalviewDir}/${docDir}/building.html")
- helpFile = string("${classesDir}/${help_dir}/help.jhm")
+ buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
+ helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm")
helpParentDir = string("${jalviewDir}/${help_parent_dir}")
- helpDir = string("${help_dir}")
- helpSourceDir = string("${helpParentDir}/${helpDir}")
+ helpSourceDir = string("${helpParentDir}/${help_dir}")
- relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
- jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
- jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
- if (IN_ECLIPSE) {
- jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
- } else {
- jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
- }
- jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
- jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
- jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
- jalviewjsJalviewCoreHtmlFile = string("")
- jalviewjsJalviewCoreName = string(jalviewjs_core_name)
- jalviewjsCoreClasslists = []
- jalviewjsJalviewTemplateName = string(jalviewjs_name)
- jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
- jalviewjsJ2sProps = null
-
- eclipseWorkspace = null
- eclipseBinary = string("")
- eclipseVersion = string("")
- eclipseDebug = false
// ENDEXT
}
resources {
srcDirs resourceDir
+ srcDirs += helpParentDir
}
- jar.destinationDir = file("${jalviewDir}/${packageDir}")
+ jar.destinationDir = file("${jalviewDir}/${package_dir}")
compileClasspath = files(sourceSets.main.java.outputDir)
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
}
- clover {
- java {
- srcDirs = [ cloverInstrDir ]
- outputDir = file("${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}/${libDir}", include: ["*.jar"])
-
- runtimeClasspath = compileClasspath
- }
-
test {
java {
srcDirs testSourceDir
- outputDir = file("${jalviewDir}/${testOutputDir}")
+ outputDir = file(testClassesDir)
}
resources {
}
compileClasspath = files( sourceSets.test.java.outputDir )
-
- if (use_clover) {
- compileClasspath += sourceSets.clover.compileClasspath
- } else {
- compileClasspath += files(sourceSets.main.java.outputDir)
- }
-
- compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
- compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
- compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
}
-}
-
-
-// clover bits
-dependencies {
- if (use_clover) {
- cloverCompile 'org.openclover:clover:4.3.1'
- testCompile 'org.openclover:clover:4.3.1'
- }
-}
-
-
-configurations {
- cloverRuntime
- cloverRuntime.extendsFrom cloverCompile
-}
-
-eclipse {
- project {
- name = eclipse_project_name
-
- natures 'org.eclipse.jdt.core.javanature',
- 'org.eclipse.jdt.groovy.core.groovyNature',
- 'org.eclipse.buildship.core.gradleprojectnature'
-
- buildCommand 'org.eclipse.jdt.core.javabuilder'
- buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
- }
-
- classpath {
- //defaultOutputDir = sourceSets.main.java.outputDir
- def removeThese = []
- configurations.each{
- if (it.isCanBeResolved()) {
- removeThese += it
- }
- }
-
- minusConfigurations += removeThese
- plusConfigurations = [ ]
- file {
-
- whenMerged { cp ->
- def removeTheseToo = []
- HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
- cp.entries.each { entry ->
- // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
- // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
- // we add the resources and help/help dirs in as libs afterwards (see below)
- if (entry.kind == 'src') {
- if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
- removeTheseToo += entry
- } else {
- alreadyAddedSrcPath.putAt(entry.path, true)
- }
- }
-
- }
- cp.entries.removeAll(removeTheseToo)
-
- //cp.entries += new Output("${eclipse_bin_dir}/main")
- if (file(helpSourceDir).isDirectory()) {
- cp.entries += new Library(fileReference(helpSourceDir))
- }
- 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, especially if they don't exist
- return false // groovy "continue" in .any closure
- }
- 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/$utilsDir", include: ["test*/*.jar"]).each {
- sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
- if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return false // groovy "continue" in .any closure
- }
-
- def itPath = it.toString()
- if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
- }
- if (alreadyAddedLibPath.get(itPath)) {
- // don't duplicate
- } else {
- def lib = new Library(fileReference(itPath))
- lib.entryAttributes["test"] = "true"
- cp.entries += lib
- alreadyAddedLibPath.put(itPath, true)
- }
- }
-
- } // whenMerged
-
- } // file
-
- containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
-
- } // classpath
-
- jdt {
- // for the IDE, use java 11 compatibility
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- javaRuntimeName = eclipse_java_runtime_name
-
- // 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
-
- if (IN_ECLIPSE) {
- // Don't want these to be activated if in headless build
- synchronizationTasks "eclipseSynchronizationTask"
- autoBuildTasks "eclipseAutoBuildTask"
-
- }
-}
-
-task cloverInstr() {
- // only instrument source, we build test classes as normal
- inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
- outputs.dir cloverInstrDir
-
- doFirst {
- delete cloverInstrDir
- def argsList = ["--initstring", "${buildDir}/clover/clover.db",
- "-d", "${buildDir}/${cloverSourcesInstrDir}"]
- argsList.addAll(inputs.files.files.collect({ file ->
- file.absolutePath
- }))
- String[] args = argsList.toArray()
- println("About to instrument "+args.length +" files")
- com.atlassian.clover.CloverInstr.mainImpl(args)
- }
}
-task cloverReport {
- group = "Verification"
- description = "Createst the Clover report"
- inputs.dir "${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", "${reportsDir}/clover/clover.xml"].toArray()
- com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
- }
-}
-// end clover bits
compileJava {
compileTestJava {
- if (use_clover) {
- dependsOn compileCloverJava
- classpath += configurations.cloverRuntime
- } else {
- classpath += sourceSets.main.runtimeClasspath
- }
doFirst {
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
}
-compileCloverJava {
-
- doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs += additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
- }
- classpath += configurations.cloverRuntime
-}
-
-
clean {
doFirst {
delete sourceSets.main.java.outputDir
cleanTest {
doFirst {
delete sourceSets.test.java.outputDir
- delete cloverInstrDir
}
}
task convertBuildingMD(type: Exec) {
dependsOn cleanBuildingHTML
- def buildingMD = "${jalviewDir}/${docDir}/building.md"
- def css = "${jalviewDir}/${docDir}/github.css"
+ def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
+ def css = "${jalviewDir}/${doc_dir}/github.css"
def pandoc = null
pandoc_exec.split(",").each {
}
def hostname = "hostname".execute().text.trim()
- if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
+ def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+ if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
}
task syncDocs(type: Sync) {
dependsOn convertBuildingMD
- def syncDir = "${classesDir}/${docDir}"
- from fileTree("${jalviewDir}/${docDir}")
+ def syncDir = "${resourceClassesDir}/${doc_dir}"
+ from fileTree("${jalviewDir}/${doc_dir}")
into syncDir
}
task copyHelp(type: Copy) {
def inputDir = helpSourceDir
- def outputDir = "${classesDir}/${helpDir}"
+ def outputDir = "${resourceClassesDir}/${help_dir}"
from(inputDir) {
exclude '**/*.gif'
exclude '**/*.jpg'
}
-task syncLib(type: Sync) {
- def syncDir = "${classesDir}/${libDistDir}"
- from fileTree("${jalviewDir}/${libDistDir}")
- into syncDir
-}
-
-
task syncResources(type: Sync) {
from resourceDir
include "**/*.*"
- into "${classesDir}"
+ into "${resourceClassesDir}"
preserve {
include "**"
}
//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
test {
dependsOn prepare
- dependsOn compileJava
- if (use_clover) {
- dependsOn cloverInstr
- }
+ //dependsOn compileJava ////? DELETE
- if (use_clover) {
- print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
- }
+ dependsOn compileJava //?
useTestNG() {
- includeGroups testngGroups
+ includeGroups testng_groups
+ excludeGroups testng_excluded_groups
preserveOrder true
useDefaultListeners=true
}
+ maxHeapSize = "1024m"
+
workingDir = jalviewDir
//systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+ systemProperty "laf", testLaf
+ }
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
jvmArgs += additional_compiler_args
+ doFirst {
+ }
}
dependsOn copyHelp
classpath = sourceSets.main.compileClasspath
main = "com.sun.java.help.search.Indexer"
- workingDir = "${classesDir}/${helpDir}"
+ workingDir = "${classesDir}/${help_dir}"
def argDir = "html"
args = [ argDir ]
inputs.dir("${workingDir}/${argDir}")
task compileLinkCheck(type: JavaCompile) {
options.fork = true
- classpath = files("${jalviewDir}/${utilsDir}")
- destinationDir = file("${jalviewDir}/${utilsDir}")
- source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
-
- inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
- inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
- outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
- outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
+ classpath = files("${jalviewDir}/${utils_dir}")
+ destinationDir = file("${jalviewDir}/${utils_dir}")
+ source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+ outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
}
task linkCheck(type: JavaExec) {
dependsOn prepare, compileLinkCheck
- def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
- classpath = files("${jalviewDir}/${utilsDir}")
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+ classpath = files("${jalviewDir}/${utils_dir}")
main = "HelpLinksChecker"
workingDir = jalviewDir
- def help = "${classesDir}/${helpDir}"
- args = [ "${classesDir}/${helpDir}", "-nointernet" ]
+ args = [ "${classesDir}/${help_dir}", "-nointernet" ]
def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
def errFOS = outFOS
outFOS,
errorOutput)
- inputs.dir("${classesDir}/${helpDir}")
+ inputs.dir("${classesDir}/${help_dir}")
outputs.file(helpLinksCheckerOutFile)
}
// import the pubhtmlhelp target
ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}"
-ant.importBuild "${utilsDir}/publishHelp.xml"
+ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
+ant.importBuild "${utils_dir}/publishHelp.xml"
task cleanPackageDir(type: Delete) {
doFirst {
- delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
+ delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
}
}
dependsOn createBuildProperties
manifest {
- attributes "Main-Class": mainClass,
+ attributes "Main-Class": main_class,
"Permissions": "all-permissions",
"Application-Name": "Jalview Desktop",
"Codebase": application_codebase
}
- destinationDir = file("${jalviewDir}/${packageDir}")
+ destinationDir = file("${jalviewDir}/${package_dir}")
archiveName = rootProject.name+".jar"
exclude "cache*/**"
exclude "**/*.jar.*"
inputs.dir(classesDir)
- outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
-}
-
-
-task copyJars(type: Copy) {
- from fileTree(dir: classesDir, include: "**/*.jar").files
- into "${jalviewDir}/${packageDir}"
-}
-
-
-// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
-task syncJars(type: Sync) {
- from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
- into "${jalviewDir}/${packageDir}"
- preserve {
- include jar.archiveName
- }
-}
-
-
-task makeDist {
- group = "build"
- description = "Put all required libraries in dist"
- // order of "cleanPackageDir", "copyJars", "jar" important!
- jar.mustRunAfter cleanPackageDir
- syncJars.mustRunAfter cleanPackageDir
- dependsOn cleanPackageDir
- dependsOn syncJars
- dependsOn jar
- outputs.dir("${jalviewDir}/${packageDir}")
-}
-
-
-task cleanDist {
- dependsOn cleanPackageDir
- dependsOn cleanTest
- dependsOn clean
-}
-
-shadowJar {
- group = "distribution"
- if (buildDist) {
- dependsOn makeDist
- }
- from ("${jalviewDir}/${libDistDir}") {
- include("*.jar")
- }
- manifest {
- attributes 'Implementation-Version': JALVIEW_VERSION
- }
- mainClassName = shadowJarMainClass
- mergeServiceFiles()
- classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
- minimize()
-}
-
-
-task getdownWebsite() {
- group = "distribution"
- description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
- if (buildDist) {
- dependsOn makeDist
- }
-
- def getdownWebsiteResourceFilenames = []
- def getdownTextString = ""
- def getdownResourceDir = getdownResourceDir
- def getdownAppDir = getdownAppDir
- def getdownResourceFilenames = []
-
- doFirst {
- // clean the getdown website and files dir before creating getdown folders
- delete getdownWebsiteDir
- delete getdownFilesDir
-
- copy {
- from buildProperties
- rename(build_properties_file, getdown_build_properties)
- into getdownAppDir
- }
- getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
-
- // go through properties looking for getdown_txt_...
- def props = project.properties.sort { it.key }
- if (getdown_alt_java_min_version.length() > 0) {
- props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
- }
- if (getdown_alt_java_max_version.length() > 0) {
- props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
- }
- props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
-
- props.put("getdown_txt_appbase", getdown_app_base)
- props.each{ prop, val ->
- if (prop.startsWith("getdown_txt_") && val != null) {
- if (prop.startsWith("getdown_txt_multi_")) {
- def key = prop.substring(18)
- val.split(",").each{ v ->
- def line = "${key} = ${v}\n"
- getdownTextString += line
- }
- } else {
- // file values rationalised
- if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
- def r = null
- if (val.indexOf('/') == 0) {
- // absolute path
- r = file(val)
- } else if (val.indexOf('/') > 0) {
- // relative path (relative to jalviewDir)
- r = file( "${jalviewDir}/${val}" )
- }
- if (r.exists()) {
- val = "${getdown_resource_dir}/" + r.getName()
- getdownWebsiteResourceFilenames += val
- getdownResourceFilenames += r.getPath()
- }
- }
- if (! prop.startsWith("getdown_txt_resource")) {
- def line = prop.substring(12) + " = ${val}\n"
- getdownTextString += line
- }
- }
- }
- }
-
- getdownWebsiteResourceFilenames.each{ filename ->
- getdownTextString += "resource = ${filename}\n"
- }
- getdownResourceFilenames.each{ filename ->
- copy {
- from filename
- into getdownResourceDir
- }
- }
-
- def codeFiles = []
- fileTree(file(packageDir)).each{ f ->
- if (f.isDirectory()) {
- def files = fileTree(dir: f, include: ["*"]).getFiles()
- codeFiles += files
- } else if (f.exists()) {
- codeFiles += f
- }
- }
- codeFiles.sort().each{f ->
- def name = f.getName()
- def line = "code = ${getdown_app_dir}/${name}\n"
- getdownTextString += line
- copy {
- from f.getPath()
- into getdownAppDir
- }
- }
-
- // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
- /*
- if (JAVA_VERSION.equals("11")) {
- def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
- j11libFiles.sort().each{f ->
- def name = f.getName()
- def line = "code = ${getdown_j11lib_dir}/${name}\n"
- getdownTextString += line
- copy {
- from f.getPath()
- into getdownJ11libDir
- }
- }
- }
- */
-
- // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
- //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
- getdownTextString += "resource = ${getdown_launcher_new}\n"
- getdownTextString += "class = ${mainClass}\n"
-
- def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
- getdown_txt.write(getdownTextString)
-
- def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}")
- launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
-
- copy {
- from getdownLauncher
- rename(file(getdownLauncher).getName(), getdown_launcher_new)
- into getdownWebsiteDir
- }
-
- copy {
- from getdownLauncher
- if (file(getdownLauncher).getName() != getdown_launcher) {
- rename(file(getdownLauncher).getName(), getdown_launcher)
- }
- into getdownWebsiteDir
- }
-
- 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 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 getdownResourceDir
- into "${getdownFilesDir}/${getdown_resource_dir}"
- }
- }
-
- if (buildDist) {
- inputs.dir("${jalviewDir}/${packageDir}")
- }
- outputs.dir(getdownWebsiteDir)
- outputs.dir(getdownFilesDir)
-}
-
-
-task getdownDigest(type: JavaExec) {
- group = "distribution"
- description = "Digest the getdown website folder"
- dependsOn getdownWebsite
- doFirst {
- classpath = files("${getdownWebsiteDir}/${getdown_launcher}")
- }
- main = "com.threerings.getdown.tools.Digester"
- args getdownWebsiteDir
- inputs.dir(getdownWebsiteDir)
- outputs.file("${getdownWebsiteDir}/digest2.txt")
-}
-
-
-task getdown() {
- group = "distribution"
- description = "Create the minimal and full getdown app folder for installers and website and create digest file"
- dependsOn getdownDigest
- doLast {
- if (reportRsyncCommand) {
- def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
- def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
- println "LIKELY RSYNC COMMAND:"
- println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
- if (RUNRSYNC == "true") {
- exec {
- commandLine "mkdir", "-p", toDir
- }
- exec {
- commandLine "rsync", "-avh", "--delete", fromDir, toDir
- }
- }
- }
- }
-}
-
-
-clean {
- doFirst {
- delete getdownWebsiteDir
- delete getdownFilesDir
- }
-}
-
-
-install4j {
- if (file(install4jHomeDir).exists()) {
- // good to go!
- } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
- install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
- } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
- install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
- }
- installDir(file(install4jHomeDir))
-
- mediaTypes = Arrays.asList(install4j_media_types.split(","))
- if (install4j_faster.equals("true")) {
- faster = true
- }
-}
-
-
-task copyInstall4jTemplate(type: Copy) {
- from (install4jDir) {
- include install4j_template
- rename (install4j_template, install4jConfFileName)
- filter(ReplaceTokens,
- beginToken: '',
- endToken: '',
- tokens: [
- '9999999999': JAVA_VERSION
- ]
- )
- filter(ReplaceTokens,
- beginToken: '$$',
- endToken: '$$',
- tokens: [
- 'JAVA_VERSION': JAVA_VERSION,
- 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
- 'VERSION': JALVIEW_VERSION,
- 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
- 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
- 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
- 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
- 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4j_info_plist_file_associations,
- 'COPYRIGHT_MESSAGE': install4j_copyright_message,
- 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
- 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
- 'GETDOWN_DIST_DIR': getdown_app_dir,
- 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
- 'GETDOWN_INSTALL_DIR': getdown_install_dir
- ]
- )
- if (OSX_KEYPASS == "") {
- filter(ReplaceTokens,
- beginToken: 'codeSigning macEnabled="',
- endToken: '"',
- tokens: [
- 'true': 'codeSigning macEnabled="false"'
- ]
- )
- filter(ReplaceTokens,
- beginToken: 'runPostProcessor="true" ',
- endToken: 'Processor',
- tokens: [
- 'post': 'runPostProcessor="false" postProcessor'
- ]
- )
- }
- }
- into install4jDir
- inputs.file("${install4jDir}/${install4j_template}")
- inputs.file("${install4jDir}/${install4j_installer_file_associations}")
- inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
- outputs.files(install4jConfFile)
-
- doLast {
- // include file associations in installer
- def installerFileAssociationsXml = file("${install4jDir}/${install4j_installer_file_associations}").text
- ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
- replace: installerFileAssociationsXml,
- file: install4jConfFile
- )
- /*
- // include uninstaller applescript app files in dmg
- def installerDMGUninstallerXml = file("$install4jDir/$install4j_DMG_uninstaller_app_files").text
- ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
- replace: installerDMGUninstallerXml,
- file: install4jConfFile
- )
- */
- }
+ outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
}
-
-
-clean {
- doFirst {
- delete install4jConfFile
- }
-}
-
-
-task installers(type: com.install4j.gradle.Install4jTask) {
- group = "distribution"
- description = "Create the install4j installers"
- dependsOn getdown
- dependsOn copyInstall4jTemplate
- projectFile = file(install4jConfFile)
- variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
- destination = "${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}"
- buildSelected = true
-
- if (OSX_KEYPASS) {
- macKeystorePassword=OSX_KEYPASS
- }
-
- doFirst {
- println("Using projectFile "+projectFile)
- }
-
- inputs.dir(getdownWebsiteDir)
- inputs.file(install4jConfFile)
- inputs.dir(macosJavaVMDir)
- inputs.dir(windowsJavaVMDir)
- outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
-}
-
-
-task sourceDist (type: Tar) {
-
- def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
- def outputFileName = "${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 ("${j11modDir}/**/*.jar")
- }
- // from (jalviewDir) {
- // // explicit includes for stuff that seemed to not get included
- // include(fileTree("test/**/*."))
- // exclude(EXCLUDE_FILES)
- // exclude(PROCESS_FILES)
- // }
-}
-
-
-task helppages {
- dependsOn copyHelp
- dependsOn pubhtmlhelp
-
- inputs.dir("${classesDir}/${helpDir}")
- outputs.dir("${buildDir}/distributions/${helpDir}")
-}
-
-// LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
git://source.jalview.org / jalview.git / blobdiff