+/* 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.internal.generator.PropertiesPersistableConfigurationObject
+import org.gradle.api.internal.PropertiesTransformer
+import org.gradle.util.ConfigureUtil
import org.gradle.plugins.ide.eclipse.model.Output
import org.gradle.plugins.ide.eclipse.model.Library
import java.security.MessageDigest
-
import groovy.transform.ExternalizeMethods
+import groovy.util.XmlParser
+import groovy.xml.XmlUtil
+
buildscript {
- dependencies {
- classpath 'org.openclover:clover:4.3.1'
+ repositories {
+ mavenCentral()
+ mavenLocal()
}
}
+
plugins {
id 'java'
id 'application'
id 'eclipse'
+ id "com.diffplug.gradle.spotless" version "3.28.0"
id 'com.github.johnrengelman.shadow' version '4.0.3'
- id 'com.install4j.gradle' version '8.0.2'
- id 'com.dorongold.task-tree' version '1.4' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+ id 'com.install4j.gradle' version '8.0.4'
+ id 'com.dorongold.task-tree' version '1.5' // 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()
}
jalviewDirRelativePath = jalviewDir
// local build environment properties
- def localProps = "${jalviewDirAbsolutePath}/local.properties"
+ // can be "projectDir/local.properties"
+ def localProps = "${projectDir}/local.properties"
+ def propsFile = null;
if (file(localProps).exists()) {
+ propsFile = localProps
+ }
+ // or "../projectDir_local.properties"
+ def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
+ if (file(dirLocalProps).exists()) {
+ propsFile = dirLocalProps
+ }
+ if (propsFile != null) {
try {
def p = new Properties()
- def localPropsFIS = new FileInputStream(localProps)
+ def localPropsFIS = new FileInputStream(propsFile)
p.load(localPropsFIS)
localPropsFIS.close()
p.each {
key, val ->
- def over = getProperty(key) != null
+ def oldval = findProperty(key)
setProperty(key, val)
- if (over) {
- println("Overriding property '${key}' with local.properties value '${val}'")
+ if (oldval != null) {
+ println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ } else {
+ println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
}
}
} catch (Exception e) {
}
}
+ ////
+ // 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);
+ }
+ ////
+ // Set JALVIEW_VERSION if it is not already set
+ if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+
// this property set when running Eclipse headlessly
j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
// this property set by Eclipse
} else {
println("HEADLESS BUILD")
}
+
+ J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+ if (J2S_ENABLED) {
+ println("J2S ENABLED")
+ }
/* *-/
System.properties.sort { it.key }.each {
key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
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
+ // clover
+ useClover = clover.equals("true")
+ cloverBuildDir = "${buildDir}/clover"
+ cloverInstrDir = file("${cloverBuildDir}/clover-instr")
+ cloverClassesDir = file("${cloverBuildDir}/clover-classes")
+ cloverReportDir = file("${buildDir}/reports/clover")
+ cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
+ cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
+ //cloverTestClassesDir = cloverClassesDir
+ cloverDb = string("${cloverBuildDir}/clover.db")
+
+ resourceClassesDir = useClover ? cloverClassesDir : classesDir
+
+ testSourceDir = useClover ? cloverTestInstrDir : testDir
+ testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
- getdownDir = string("")
- reportRsyncCmd = false
buildDist = true
- buildProperties = build_properties_file
+
+ // the following values might be overridden by the CHANNEL switch
+ getdownChannelName = CHANNEL.toLowerCase()
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
+ getdownAppDistDir = getdown_app_dir_alt
+ buildProperties = string("${resourceDir}/${build_properties_file}")
+ reportRsyncCommand = false
+ jvlChannelName = CHANNEL.toLowerCase()
+ install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
+ install4jDSStore = "DS_Store-NON-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
+ install4jInstallerName = "${jalview_name} Non-Release Installer"
+ install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+ install4jExtraScheme = "jalviewx"
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}")
+ getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
+ getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
+ jvlChannelName += "_${getdownChannelName}"
+ // automatically add the test group Not-bamboo for exclusion
+ if ("".equals(testng_excluded_groups)) {
+ testng_excluded_groups = "Not-bamboo"
+ }
+ install4jExtraScheme = "jalviewb"
break
case "RELEASE":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
- getdown_app_dir = getdown_app_dir_release
- buildProperties = string("${classesDir}/${build_properties_file}")
+ getdownAppDistDir = getdown_app_dir_release
reportRsyncCommand = true
+ install4jSuffix = ""
+ install4jDSStore = "DS_Store"
+ install4jDMGBackgroundImage = "jalview_dmg_background.png"
+ install4jInstallerName = "${jalview_name} Installer"
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}/${packageDir}").exists()) {
- print "Must provide an ARCHIVEDIR value to produce an archive distribution"
- exit
+ getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = string("${ARCHIVEDIR}/${packageDir}")
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
+ install4jExtraScheme = "jalviewa"
break
case "ARCHIVELOCAL":
- getdown_channel_name = string("archive/${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
+ getdownChannelName = string("archive/${JALVIEW_VERSION}")
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = string("${ARCHIVEDIR}/${packageDir}")
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jSuffix = "Archive"
+ install4jExtraScheme = "jalviewa"
break
case "DEVELOP":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
- getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
+
+ // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+ JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
+
+ install4jSuffix = "Develop"
+ install4jDSStore = "DS_Store-DEVELOP"
+ install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
+ install4jExtraScheme = "jalviewd"
+ install4jInstallerName = "${jalview_name} Develop Installer"
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
+ // Don't ignore transpile errors for release build
+ if (jalviewjs_ignore_transpile_errors.equals("true")) {
+ jalviewjs_ignore_transpile_errors = "false"
+ println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+ }
+ JALVIEW_VERSION = JALVIEW_VERSION+"-test"
+ install4jSuffix = "Test"
+ install4jDSStore = "DS_Store-TEST-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
break
case ~/^SCRATCH(|-[-\w]*)$/:
- 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}")
+ getdownChannelName = CHANNEL
+ JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
+
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
reportRsyncCommand = true
+ install4jSuffix = "Scratch"
+ break
+
+ case "TEST-LOCAL":
+ if (!file("${LOCALDIR}").exists()) {
+ throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
+ } else {
+ getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ }
+ JALVIEW_VERSION = "TEST"
+ install4jSuffix = "Test-Local"
+ install4jDSStore = "DS_Store-TEST-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
break
case "LOCAL":
- getdown_app_base = file(getdownWebsiteDir).toURI().toString()
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${classesDir}/${build_properties_file}")
+ JALVIEW_VERSION = "TEST"
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jExtraScheme = "jalviewl"
break
default: // something wrong specified
- print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
- exit
+ throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
break
}
-
- getdownAppDir = string("${getdownWebsiteDir}/${getdown_app_dir}")
+ // override getdownAppBase if requested
+ if (findProperty("getdown_appbase_override") != null) {
+ getdownAppBase = string(getProperty("getdown_appbase_override"))
+ println("Overriding getdown appbase with '${getdownAppBase}'")
+ }
+ // sanitise file name for jalview launcher file for this channel
+ jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
+ // install4j application and folder names
+ if (install4jSuffix == "") {
+ install4jApplicationName = "${jalview_name}"
+ install4jBundleId = "${install4j_bundle_id}"
+ install4jWinApplicationId = install4j_release_win_application_id
+ } else {
+ install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+ install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
+ // add int hash of install4jSuffix to the last part of the application_id
+ def id = install4j_release_win_application_id
+ def idsplitreverse = id.split("-").reverse()
+ idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
+ install4jWinApplicationId = idsplitreverse.reverse().join("-")
+ }
+ // sanitise folder and id names
+ // install4jApplicationFolder = e.g. "Jalview Build"
+ install4jApplicationFolder = install4jApplicationName
+ .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
+ .replaceAll("_+", "_") // collapse __
+ install4jInternalId = install4jApplicationName
+ .replaceAll(" ","_")
+ .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+ .replaceAll("_+", "") // collapse __
+ //.replaceAll("_*-_*", "-") // collapse _-_
+ install4jUnixApplicationFolder = install4jApplicationName
+ .replaceAll(" ","_")
+ .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+ .replaceAll("_+", "_") // collapse __
+ .replaceAll("_*-_*", "-") // collapse _-_
+ .toLowerCase()
+
+ getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
//getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
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
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("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
+ getdownAltMultiJavaLocation = string(findProperty("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")
+ eclipseJavaRuntimeName = 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")
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+ eclipseJavaRuntimeName = string("JavaSE-11")
/* compile without modules -- using classpath libraries
additional_compiler_args += [
'--module-path', modules_compileClasspath.asPath,
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")
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+ eclipseJavaRuntimeName = string("JavaSE-11")
/* compile without modules -- using classpath libraries
additional_compiler_args += [
'--module-path', modules_compileClasspath.asPath,
// for install4j
JAVA_MIN_VERSION = JAVA_VERSION
JAVA_MAX_VERSION = JAVA_VERSION
- macosJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre")
- macosJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz")
- windowsJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre")
- windowsJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz")
+ def jreInstallsDir = string(jre_installs_dir)
+ if (jreInstallsDir.startsWith("~/")) {
+ jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
+ }
+ macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
+ macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
+ windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
+ windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
+ linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
+ linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
- install4jConfFileName = string("jalview-installers-java${JAVA_VERSION}.install4j")
- install4jConfFile = string("${install4jDir}/${install4jConfFileName}")
+ install4jConfFileName = string("jalview-install4j-conf.install4j")
+ install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
install4jHomeDir = install4j_home_dir
if (install4jHomeDir.startsWith("~/")) {
install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
- buildingHTML = string("${jalviewDir}/${docDir}/building.html")
- helpFile = string("${classesDir}/${help_dir}/help.jhm")
+ buildingHTML = string("${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())
jalviewjsJalviewTemplateName = string(jalviewjs_name)
jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
jalviewjsJ2sProps = null
+ jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
eclipseWorkspace = null
eclipseBinary = string("")
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"])
clover {
java {
- srcDirs = [ cloverInstrDir ]
- outputDir = file("${buildDir}/${cloverClassesDir}")
+ srcDirs cloverInstrDir
+ outputDir = 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 = files( sourceSets.clover.java.outputDir )
+ //compileClasspath += files( testClassesDir )
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
}
test {
java {
srcDirs testSourceDir
- outputDir = file("${jalviewDir}/${testOutputDir}")
+ outputDir = file(testClassesDir)
}
resources {
- srcDirs = sourceSets.main.resources.srcDirs
+ srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
}
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 += useClover ? sourceSets.clover.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 and settings files creation, also used by buildship
eclipse {
project {
name = eclipse_project_name
cp.entries.removeAll(removeTheseToo)
//cp.entries += new Output("${eclipse_bin_dir}/main")
- if (file(helpSourceDir).isDirectory()) {
- cp.entries += new Library(fileReference(helpSourceDir))
+ if (file(helpParentDir).isDirectory()) {
+ cp.entries += new Library(fileReference(helpParentDir))
}
if (file(resourceDir).isDirectory()) {
cp.entries += new Library(fileReference(resourceDir))
HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
- sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
//don't want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath, especially if they don't exist
}
}
- //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
//no longer want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// for the IDE, use java 11 compatibility
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
- javaRuntimeName = eclipse_java_runtime_name
+ javaRuntimeName = eclipseJavaRuntimeName
// add in jalview project specific properties/preferences into eclipse core preferences
file {
props.putAt(t, v)
}
}
+ // codestyle file -- overrides previous formatter prefs
+ def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
+ if (csFile.exists()) {
+ XmlParser parser = new XmlParser()
+ def profiles = parser.parse(csFile)
+ def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
+ if (profile != null) {
+ profile.'setting'.each { s ->
+ def id = s.'@id'
+ def value = s.'@value'
+ if (id != null && value != null) {
+ props.putAt(id, value)
+ }
+ }
+ }
+ }
}
}
if (IN_ECLIPSE) {
// Don't want these to be activated if in headless build
synchronizationTasks "eclipseSynchronizationTask"
- autoBuildTasks "eclipseAutoBuildTask"
+ //autoBuildTasks "eclipseAutoBuildTask"
+
+ }
+}
+
+
+/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
+// Class to allow updating arbitrary properties files
+class PropertiesFile extends PropertiesPersistableConfigurationObject {
+ public PropertiesFile(PropertiesTransformer t) { super(t); }
+ @Override protected void load(Properties properties) { }
+ @Override protected void store(Properties properties) { }
+ @Override protected String getDefaultResourceName() { return ""; }
+ // This is necessary, because PropertiesPersistableConfigurationObject fails
+ // if no default properties file exists.
+ @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
+}
+
+// Task to update arbitrary properties files (set outputFile)
+class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
+ private final PropertiesFileContentMerger file;
+ public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
+ protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
+ protected void configure(PropertiesFile props) {
+ file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
+ }
+ public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
+}
+
+task eclipseUIPreferences(type: PropertiesFileTask) {
+ description = "Generate Eclipse additional settings"
+ def filename = "org.eclipse.jdt.ui.prefs"
+ outputFile = "$projectDir/.settings/${filename}" as File
+ file {
+ withProperties {
+ it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
+ }
+ }
+}
+
+task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
+ description = "Generate Eclipse additional settings"
+ def filename = "org.eclipse.jdt.groovy.core.prefs"
+ outputFile = "$projectDir/.settings/${filename}" as File
+ file {
+ withProperties {
+ it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
+ }
+ }
+}
+
+task eclipseAllPreferences {
+ dependsOn eclipseJdt
+ dependsOn eclipseUIPreferences
+ dependsOn eclipseGroovyCorePreferences
+}
+
+eclipseUIPreferences.mustRunAfter eclipseJdt
+eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
+
+/* end of eclipse preferences hack */
+
+
+// clover bits
+
+task cleanClover {
+ doFirst {
+ delete cloverBuildDir
+ delete cloverReportDir
}
}
-task cloverInstr() {
- // only instrument source, we build test classes as normal
- inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
- outputs.dir cloverInstrDir
+task cloverInstrJava(type: JavaExec) {
+ group = "Verification"
+ description = "Create clover instrumented source java files"
+
+ dependsOn cleanClover
+
+ inputs.files(sourceSets.main.allJava)
+ outputs.dir(cloverInstrDir)
+
+ //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+ classpath = sourceSets.clover.compileClasspath
+ main = "com.atlassian.clover.CloverInstr"
+
+ def argsList = [
+ "--encoding",
+ "UTF-8",
+ "--initstring",
+ cloverDb,
+ "--destdir",
+ cloverInstrDir.getPath(),
+ ]
+ def srcFiles = sourceSets.main.allJava.files
+ argsList.addAll(
+ srcFiles.collect(
+ { file -> file.absolutePath }
+ )
+ )
+ args argsList.toArray()
doFirst {
delete cloverInstrDir
- def argsList = ["--initstring", "${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)
+ println("Clover: About to instrument "+srcFiles.size() +" files")
}
}
-task cloverReport {
+task cloverInstrTests(type: JavaExec) {
group = "Verification"
- description = "Createst the Clover report"
- inputs.dir "${buildDir}/clover"
- outputs.dir "${reportsDir}/clover"
- onlyIf {
- file("${buildDir}/clover/clover.db").exists()
- }
+ description = "Create clover instrumented source test files"
+
+ dependsOn cleanClover
+
+ inputs.files(testDir)
+ outputs.dir(cloverTestInstrDir)
+
+ classpath = sourceSets.clover.compileClasspath
+ main = "com.atlassian.clover.CloverInstr"
+
+ def argsList = [
+ "--encoding",
+ "UTF-8",
+ "--initstring",
+ cloverDb,
+ "--srcdir",
+ testDir,
+ "--destdir",
+ cloverTestInstrDir.getPath(),
+ ]
+ args argsList.toArray()
+
doFirst {
- def argsList = ["--initstring", "${buildDir}/clover/clover.db",
- "-o", "${reportsDir}/clover"]
- String[] args = argsList.toArray()
- com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+ delete cloverTestInstrDir
+ println("Clover: About to instrument test files")
+ }
+}
+
+
+task cloverInstr {
+ group = "Verification"
+ description = "Create clover instrumented all source files"
+
+ dependsOn cloverInstrJava
+ dependsOn cloverInstrTests
+}
+
+
+cloverClasses.dependsOn cloverInstr
+
+
+task cloverConsoleReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover console report"
+
+ onlyIf {
+ file(cloverDb).exists()
+ }
- // 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)
+ inputs.dir cloverClassesDir
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.console.ConsoleReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
}
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+ }
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--unittests"
+ ]
+
+ args argsList.toArray()
}
-// end clover bits
-compileJava {
+task cloverHtmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover HTML report"
- doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs = additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
+ onlyIf {
+ file(cloverDb).exists()
+ }
+
+ def cloverHtmlDir = cloverReportDir
+ inputs.dir cloverClassesDir
+ outputs.dir cloverHtmlDir
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+ }
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--outputdir",
+ cloverHtmlDir
+ ]
+
+ if (cloverreport_html_options.length() > 0) {
+ argsList += cloverreport_html_options.split(" ")
}
+ args argsList.toArray()
}
-compileTestJava {
- if (use_clover) {
- dependsOn compileCloverJava
- classpath += configurations.cloverRuntime
- } else {
- classpath += sourceSets.main.runtimeClasspath
+task cloverXmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover XML report"
+
+ onlyIf {
+ file(cloverDb).exists()
}
- doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs = additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
+
+ def cloverXmlFile = "${cloverReportDir}/clover.xml"
+ inputs.dir cloverClassesDir
+ outputs.file cloverXmlFile
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.xml.XMLReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+ }
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--outfile",
+ cloverXmlFile
+ ]
+
+ if (cloverreport_xml_options.length() > 0) {
+ argsList += cloverreport_xml_options.split(" ")
}
+
+ args argsList.toArray()
+}
+
+
+task cloverReport {
+ group = "Verification"
+ description = "Creates clover reports"
+
+ dependsOn cloverXmlReport
+ dependsOn cloverHtmlReport
}
options.compilerArgs += additional_compiler_args
print ("Setting target compatibility to "+targetCompatibility+"\n")
}
- classpath += configurations.cloverRuntime
+ //classpath += configurations.cloverRuntime
+}
+// end clover bits
+
+
+compileJava {
+ // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ options.encoding = "UTF-8"
+ doFirst {
+ print ("Setting target compatibility to "+compile_target_compatibility+"\n")
+ }
+
+}
+
+
+compileTestJava {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ doFirst {
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
}
cleanTest {
+ dependsOn cleanClover
doFirst {
delete sourceSets.test.java.outputDir
- delete cloverInstrDir
}
}
task createBuildProperties(type: WriteProperties) {
+ group = "build"
+ description = "Create the ${buildProperties} file"
+
dependsOn setGitVals
inputs.dir(sourceDir)
inputs.dir(resourceDir)
}
+clean {
+ doFirst {
+ delete buildProperties
+ }
+}
+
+
task cleanBuildingHTML(type: Delete) {
doFirst {
delete buildingHTML
task convertBuildingMD(type: Exec) {
dependsOn cleanBuildingHTML
- def buildingMD = "${jalviewDir}/${docDir}/building.md"
- def css = "${jalviewDir}/${docDir}/github.css"
+ def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
+ def css = "${jalviewDir}/${doc_dir}/github.css"
def pandoc = null
pandoc_exec.split(",").each {
}
}
- def hostname = "hostname".execute().text.trim()
- if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
+ def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+ if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
}
}
-clean {
- doFirst {
- delete buildingHTML
- }
-}
-
-
task syncDocs(type: Sync) {
dependsOn convertBuildingMD
- def syncDir = "${classesDir}/${docDir}"
- from fileTree("${jalviewDir}/${docDir}")
+ def syncDir = "${classesDir}/${doc_dir}"
+ from fileTree("${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}/${libDistDir}"
+ def syncDir = "${resourceClassesDir}/${libDistDir}"
from fileTree("${jalviewDir}/${libDistDir}")
into syncDir
}
task syncResources(type: Sync) {
+ dependsOn createBuildProperties
from resourceDir
include "**/*.*"
- into "${classesDir}"
+ into "${resourceClassesDir}"
preserve {
include "**"
}
//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
test {
dependsOn prepare
- dependsOn compileJava
- if (use_clover) {
- dependsOn cloverInstr
- }
+ //dependsOn compileJava ////? DELETE
- if (use_clover) {
- print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+ if (useClover) {
+ dependsOn cloverClasses
+ } else { //?
+ dependsOn compileJava //?
}
useTestNG() {
- includeGroups testngGroups
+ includeGroups testng_groups
+ excludeGroups testng_excluded_groups
preserveOrder true
useDefaultListeners=true
}
+ maxHeapSize = "1024m"
+
workingDir = jalviewDir
//systemProperties 'clover.jar' System.properties.clover.jar
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
jvmArgs += additional_compiler_args
+ doFirst {
+ if (useClover) {
+ println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+ }
+ }
}
dependsOn copyHelp
classpath = sourceSets.main.compileClasspath
main = "com.sun.java.help.search.Indexer"
- workingDir = "${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")
}
}
+
jar {
dependsOn linkCheck
dependsOn buildIndices
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}/${archiveName}")
+ outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
}
task copyJars(type: Copy) {
from fileTree(dir: classesDir, include: "**/*.jar").files
- into "${jalviewDir}/${packageDir}"
+ into "${jalviewDir}/${package_dir}"
}
// 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}"
+ into "${jalviewDir}/${package_dir}"
preserve {
include jar.archiveName
}
dependsOn cleanPackageDir
dependsOn syncJars
dependsOn jar
- outputs.dir("${jalviewDir}/${packageDir}")
+ outputs.dir("${jalviewDir}/${package_dir}")
}
manifest {
attributes 'Implementation-Version': JALVIEW_VERSION
}
- mainClassName = shadowJarMainClass
+ mainClassName = shadow_jar_main_class
mergeServiceFiles()
classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
def getdownWebsiteResourceFilenames = []
def getdownTextString = ""
def getdownResourceDir = getdownResourceDir
- def getdownAppDir = getdownAppDir
def getdownResourceFilenames = []
doFirst {
rename(build_properties_file, getdown_build_properties)
into getdownAppDir
}
- getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
+ getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
- // go through properties looking for getdown_txt_...
+ // set some getdown_txt_ properties then go through all 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 (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
+ props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
}
- if (getdown_alt_java_max_version.length() > 0) {
- props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
+ if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
+ props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
}
- props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+ if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
+ props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
+ }
+
+ props.put("getdown_txt_title", jalview_name)
+ props.put("getdown_txt_ui.name", install4jApplicationName)
- props.put("getdown_txt_appbase", getdown_app_base)
+ // start with appbase
+ getdownTextString += "appbase = ${getdownAppBase}\n"
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_") && val != null) {
if (prop.startsWith("getdown_txt_multi_")) {
}
def codeFiles = []
- fileTree(file(packageDir)).each{ f ->
+ fileTree(file(package_dir)).each{ f ->
if (f.isDirectory()) {
def files = fileTree(dir: f, include: ["*"]).getFiles()
codeFiles += files
}
codeFiles.sort().each{f ->
def name = f.getName()
- def line = "code = ${getdown_app_dir}/${name}\n"
+ def line = "code = ${getdownAppDistDir}/${name}\n"
getdownTextString += line
copy {
from f.getPath()
// getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
//getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
getdownTextString += "resource = ${getdown_launcher_new}\n"
- getdownTextString += "class = ${mainClass}\n"
+ getdownTextString += "class = ${main_class}\n"
def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
getdown_txt.write(getdownTextString)
- def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}")
- launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
+ def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+ def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+ launchJvl.write("appbase=${getdownAppBase}")
copy {
from getdownLauncher
copy {
from getdown_txt
- from launch_jvl
+ from launchJvl
from getdownLauncher
from "${getdownWebsiteDir}/${getdown_build_properties}"
if (file(getdownLauncher).getName() != getdown_launcher) {
}
if (buildDist) {
- inputs.dir("${jalviewDir}/${packageDir}")
+ inputs.dir("${jalviewDir}/${package_dir}")
}
outputs.dir(getdownWebsiteDir)
outputs.dir(getdownFilesDir)
}
+// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
+task getdownDigestDir(type: JavaExec) {
+ group "Help"
+ description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
+
+ def digestDirPropertyName = "DIGESTDIR"
+ doFirst {
+ classpath = files(getdownLauncher)
+ def digestDir = findProperty(digestDirPropertyName)
+ if (digestDir == null) {
+ throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
+ }
+ args digestDir
+ }
+ main = "com.threerings.getdown.tools.Digester"
+}
+
+
task getdownDigest(type: JavaExec) {
group = "distribution"
description = "Digest the getdown website folder"
dependsOn getdownWebsite
doFirst {
- classpath = files("${getdownWebsiteDir}/${getdown_launcher}")
+ classpath = files(getdownLauncher)
}
main = "com.threerings.getdown.tools.Digester"
args getdownWebsiteDir
}
+tasks.withType(JavaCompile) {
+ options.encoding = 'UTF-8'
+}
+
+
clean {
doFirst {
delete getdownWebsiteDir
}
-task copyInstall4jTemplate(type: Copy) {
- dependsOn setGitVals
-
- def install4jTemplateMd5 = ""
- def digest = MessageDigest.getInstance("MD5")
- digest.update(
- (file("${install4jDir}/${install4j_template}").text +
- file("${install4jDir}/${install4j_info_plist_file_associations}").text +
- file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
- def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
- if (filesMd5.length() >= 8) {
- filesMd5 = filesMd5.substring(0,8)
- }
- install4jTemplateMd5 += filesMd5
- install4jTemplateMd5 += "_${gitHash}"
+task copyInstall4jTemplate {
+ def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+ def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+ inputs.file(install4jTemplateFile)
+ inputs.file(install4jFileAssociationsFile)
+ inputs.property("CHANNEL", { CHANNEL })
+ outputs.file(install4jConfFile)
- inputs.file("${install4jDir}/${install4j_template}")
- inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
- inputs.file("${install4jDir}/${install4j_installer_file_associations}")
- outputs.files(install4jConfFile)
+ doLast {
+ def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
- from (install4jDir) {
- include install4j_template
- rename (install4j_template, install4jConfFileName)
- // TODO change these ReplaceTokens to something better. Possibly ${compiler:variables} but also the ant.replaceregexp below, or perhaps a proper xmldom parse
+ // turn off code signing if no OSX_KEYPASS
if (OSX_KEYPASS == "") {
- filter(ReplaceTokens,
- beginToken: 'codeSigning macEnabled="',
- endToken: '"',
- tokens: [
- 'true': 'codeSigning macEnabled="false"'
- ]
- )
- filter(ReplaceTokens,
- beginToken: 'runPostProcessor="true" ',
- endToken: 'Processor',
- tokens: [
- 'post': 'runPostProcessor="false" postProcessor'
- ]
- )
- }
- }
- into install4jDir
+ install4jConfigXml.'**'.codeSigning.each { codeSigning ->
+ codeSigning.'@macEnabled' = "false"
+ }
+ install4jConfigXml.'**'.windows.each { windows ->
+ windows.'@runPostProcessor' = "false"
+ }
+ }
- doLast {
- // include file associations in installer
- def installerFileAssociationsXml = file("${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/$install4j_DMG_uninstaller_app_files").text
- ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
- replace: installerDMGUninstallerXml,
- file: install4jConfFile
- )
- */
+ // turn off checksum creation for LOCAL channel
+ def e = install4jConfigXml.application[0]
+ if (CHANNEL == "LOCAL") {
+ e.'@createChecksums' = "false"
+ } else {
+ e.'@createChecksums' = "true"
+ }
+
+ // put file association actions where placeholder action is
+ def install4jFileAssociationsText = install4jFileAssociationsFile.text
+ def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
+ install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
+ if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
+ def parent = a.parent()
+ parent.remove(a)
+ fileAssociationActions.each { faa ->
+ parent.append(faa)
+ }
+ // don't need to continue in .any loop once replacements have been made
+ return true
+ }
+ }
+
+ // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
+ // NB we're deleting the /other/ one!
+ // Also remove the examples subdir from non-release versions
+ def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
+ // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
+ if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
+ customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
+ } else {
+ // remove the examples subdir from Full File Set
+ def files = install4jConfigXml.files[0]
+ def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
+ def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
+ def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
+ def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
+ dirEntry.parent().remove(dirEntry)
+ }
+ install4jConfigXml.'**'.action.any { a ->
+ if (a.'@customizedId' == customizedIdToDelete) {
+ def parent = a.parent()
+ parent.remove(a)
+ return true
+ }
+ }
+
+ // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
+ if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
+ def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
+ symlink.parent().remove(symlink)
+ }
+
+ // write install4j file
+ install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
}
}
task installers(type: com.install4j.gradle.Install4jTask) {
group = "distribution"
description = "Create the install4j installers"
+ dependsOn setGitVals
dependsOn getdown
dependsOn copyInstall4jTemplate
- projectFile = file(install4jConfFile)
- def install4jTemplateMd5 = ""
+ projectFile = install4jConfFile
+
+ // create an md5 for the input files to use as version for install4j conf file
def digest = MessageDigest.getInstance("MD5")
digest.update(
(file("${install4jDir}/${install4j_template}").text +
if (filesMd5.length() >= 8) {
filesMd5 = filesMd5.substring(0,8)
}
- install4jTemplateMd5 += filesMd5
- install4jTemplateMd5 += "_${gitHash}"
- def install4jTemplateVersion = "${JALVIEW_VERSION}_${install4jTemplateMd5}"
+ def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
+ // make install4jBuildDir relative to jalviewDir
+ def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
variables = [
- 'OSX_KEYSTORE': OSX_KEYSTORE,
- 'JSIGN_SH': JSIGN_SH,
- 'JALVIEW_VERSION': JALVIEW_VERSION,
- 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
- 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
- 'JAVA_VERSION': JAVA_VERSION,
- 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
- 'VERSION': JALVIEW_VERSION,
- 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
- 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
- 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
- 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
- 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4j_info_plist_file_associations,
- 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
- '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
+ 'JALVIEW_NAME': jalview_name,
+ 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
+ 'JALVIEW_DIR': "../..",
+ 'OSX_KEYSTORE': OSX_KEYSTORE,
+ 'JSIGN_SH': JSIGN_SH,
+ 'JRE_DIR': getdown_app_dir_java,
+ 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
+ 'JALVIEW_VERSION': JALVIEW_VERSION,
+ 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
+ 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
+ 'JAVA_VERSION': JAVA_VERSION,
+ 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+ 'VERSION': JALVIEW_VERSION,
+ 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+ 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+ 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
+ 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+ 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+ 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
+ 'COPYRIGHT_MESSAGE': install4j_copyright_message,
+ 'BUNDLE_ID': install4jBundleId,
+ 'INTERNAL_ID': install4jInternalId,
+ 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
+ 'MACOS_DS_STORE': install4jDSStore,
+ 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+ 'INSTALLER_NAME': install4jInstallerName,
+ 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
+ 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+ 'GETDOWN_FILES_DIR': getdown_files_dir,
+ 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+ 'GETDOWN_DIST_DIR': getdownAppDistDir,
+ 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+ 'GETDOWN_INSTALL_DIR': getdown_install_dir,
+ 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
+ 'BUILD_DIR': install4jBuildDir,
+ 'APPLICATION_CATEGORIES': install4j_application_categories,
+ 'APPLICATION_FOLDER': install4jApplicationFolder,
+ 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
+ 'EXECUTABLE_NAME': install4jExecutableName,
+ 'EXTRA_SCHEME': install4jExtraScheme,
]
- destination = "${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}"
+
+ //println("INSTALL4J VARIABLES:")
+ //variables.each{k,v->println("${k}=${v}")}
+
+ destination = "${jalviewDir}/${install4jBuildDir}"
buildSelected = true
- if (install4j_faster.equals("true") || CHANNEL.startsWith("DEVELOP") || CHANNEL.startsWith("LOCAL")) {
- // this doesn't seem to work
+ if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
faster = true
disableSigning = true
}
if (OSX_KEYPASS) {
- macKeystorePassword=OSX_KEYPASS
+ macKeystorePassword = OSX_KEYPASS
}
doFirst {
inputs.dir(getdownWebsiteDir)
inputs.file(install4jConfFile)
+ inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
inputs.dir(macosJavaVMDir)
inputs.dir(windowsJavaVMDir)
outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
}
-task sourceDist (type: Tar) {
+spotless {
+ java {
+ eclipse().configFile(eclipse_codestyle_file)
+ }
+}
+
+
+task sourceDist(type: Tar) {
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
into project.name
- def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
- ,".*"
- ,"benchmarking/*"
- ,"**/.*"
- ,"*.class"
- ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
- ,"*locales/**",
- ,"utils/InstallAnywhere"]
- def PROCESS_FILES=[ "AUTHORS",
- "CITATION",
- "FEATURETODO",
- "JAVA-11-README",
- "FEATURETODO",
- "LICENSE",
- "**/README",
- "RELEASE",
- "THIRDPARTYLIBS","TESTNG",
- "build.gradle",
- "gradle.properties",
- "**/*.java",
- "**/*.html",
- "**/*.xml",
- "**/*.gradle",
- "**/*.groovy",
- "**/*.properties",
- "**/*.perl",
- "**/*.sh"]
+ def EXCLUDE_FILES=[
+ "build/*",
+ "bin/*",
+ "test-output/",
+ "test-reports",
+ "tests",
+ "clover*/*",
+ ".*",
+ "benchmarking/*",
+ "**/.*",
+ "*.class",
+ "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
+ "*locales/**",
+ "utils/InstallAnywhere",
+ "**/*.log",
+ ]
+ 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",
+ ]
+ def INCLUDE_FILES=[
+ ".settings/org.eclipse.jdt.core.jalview.prefs",
+ ]
from(jalviewDir) {
exclude (EXCLUDE_FILES)
// exluding these as not using jars as modules yet
exclude ("${j11modDir}/**/*.jar")
}
- // from (jalviewDir) {
- // // explicit includes for stuff that seemed to not get included
- // include(fileTree("test/**/*."))
- // exclude(EXCLUDE_FILES)
- // exclude(PROCESS_FILES)
- // }
+ from(jalviewDir) {
+ include(INCLUDE_FILES)
+ }
+// from (jalviewDir) {
+// // explicit includes for stuff that seemed to not get included
+// include(fileTree("test/**/*."))
+// exclude(EXCLUDE_FILES)
+// exclude(PROCESS_FILES)
+// }
}
-task helppages {
+task helppages {
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("${classesDir}/${helpDir}")
- outputs.dir("${buildDir}/distributions/${helpDir}")
+ inputs.dir("${classesDir}/${help_dir}")
+ outputs.dir("${buildDir}/distributions/${help_dir}")
}
-// LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
-task eclipseAutoBuildTask {}
-task eclipseSynchronizationTask {}
+
+task j2sSetHeadlessBuild {
+ doFirst {
+ IN_ECLIPSE = false
+ }
+}
+
+
+task jalviewjsSetEclipseWorkspace {
+ def propKey = "jalviewjs_eclipse_workspace"
+ def propVal = null
+ if (project.hasProperty(propKey)) {
+ propVal = project.getProperty(propKey)
+ if (propVal.startsWith("~/")) {
+ propVal = System.getProperty("user.home") + propVal.substring(1)
+ }
+ }
+ def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+ def propsFile = file(propsFileName)
+ def eclipseWsDir = propVal
+ def props = new Properties()
+
+ def writeProps = true
+ if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+ def ins = new FileInputStream(propsFileName)
+ props.load(ins)
+ ins.close()
+ if (props.getProperty(propKey, null) != null) {
+ eclipseWsDir = props.getProperty(propKey)
+ writeProps = false
+ }
+ }
+
+ if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
+ def tempDir = File.createTempDir()
+ eclipseWsDir = tempDir.getAbsolutePath()
+ writeProps = true
+ }
+ eclipseWorkspace = file(eclipseWsDir)
+
+ doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+
+ if (writeProps) {
+ props.setProperty(propKey, eclipseWsDir)
+ propsFile.parentFile.mkdirs()
+ def bytes = new ByteArrayOutputStream()
+ props.store(bytes, null)
+ def propertiesString = bytes.toString()
+ propsFile.text = propertiesString
+ print("NEW ")
+ } else {
+ print("EXISTING ")
+ }
+
+ println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+ }
+
+ //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
+ outputs.file(propsFileName)
+ outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
+}
+
+
+task jalviewjsEclipsePaths {
+ def eclipseProduct
+
+ def eclipseRoot = jalviewjs_eclipse_root
+ if (eclipseRoot.startsWith("~/")) {
+ eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+ }
+ if (OperatingSystem.current().isMacOsX()) {
+ eclipseRoot += "/Eclipse.app"
+ 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"
+ }
+ eclipseBinary = "${eclipseRoot}/eclipse.exe"
+ eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+ } else { // linux or unix
+ if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+ eclipseRoot += "/eclipse"
+println("eclipseDir exists")
+ }
+ eclipseBinary = "${eclipseRoot}/eclipse"
+ eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+ }
+
+ eclipseVersion = "4.13" // default
+ def assumedVersion = true
+ if (file(eclipseProduct).exists()) {
+ def fis = new FileInputStream(eclipseProduct)
+ def props = new Properties()
+ props.load(fis)
+ eclipseVersion = props.getProperty("version")
+ fis.close()
+ assumedVersion = false
+ }
+
+ def propKey = "eclipse_debug"
+ eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
+
+ doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+
+ if (!assumedVersion) {
+ println("ECLIPSE VERSION=${eclipseVersion}")
+ }
+ }
+}
+
+
+task printProperties {
+ group "Debug"
+ description "Output to console all System.properties"
+ doFirst {
+ System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
+ }
+}
+
+
+task eclipseSetup {
+ dependsOn eclipseProject
+ dependsOn eclipseClasspath
+ dependsOn eclipseJdt
+}
+
+
+// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
+task jalviewjsEclipseCopyDropins(type: Copy) {
+ dependsOn jalviewjsEclipsePaths
+
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+ inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
+ def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+
+ from inputFiles
+ into outputDir
+}
+
+
+// this eclipse -clean doesn't actually work
+task jalviewjsCleanEclipse(type: Exec) {
+ dependsOn eclipseSetup
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseCopyDropins
+
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += "-l"
+
+ def inputString = """exit
+y
+"""
+ def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
+ standardInput = inputByteStream
+}
+
+/* not really working yet
+jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
+*/
+
+
+task jalviewjsTransferUnzipSwingJs {
+ def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
+
+ doLast {
+ copy {
+ from zipTree(file_zip)
+ into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ }
+ }
+
+ inputs.file file_zip
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+}
+
+
+task jalviewjsTransferUnzipLib {
+ def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+
+ doLast {
+ zipFiles.each { file_zip ->
+ copy {
+ from zipTree(file_zip)
+ into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+ }
+ }
+ }
+
+ inputs.files zipFiles
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+}
+
+
+task jalviewjsTransferUnzipAllLibs {
+ dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTransferUnzipLib
+}
+
+
+task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+ group "JalviewJS"
+ description "Create the .j2s file from the j2s.* properties"
+
+ jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+ def siteDirProperty = "j2s.site.directory"
+ def setSiteDir = false
+ jalviewjsJ2sProps.each { prop, val ->
+ if (val != null) {
+ if (prop == siteDirProperty) {
+ if (!(val.startsWith('/') || val.startsWith("file://") )) {
+ val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
+ }
+ setSiteDir = true
+ }
+ property(prop,val)
+ }
+ if (!setSiteDir) { // default site location, don't override specifically set property
+ property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
+ }
+ }
+ outputFile = jalviewjsJ2sSettingsFileName
+
+ if (! IN_ECLIPSE) {
+ inputs.properties(jalviewjsJ2sProps)
+ outputs.file(jalviewjsJ2sSettingsFileName)
+ }
+}
+
+
+task jalviewjsEclipseSetup {
+ dependsOn jalviewjsEclipseCopyDropins
+ dependsOn jalviewjsSetEclipseWorkspace
+ dependsOn jalviewjsCreateJ2sSettings
+}
+
+
+task jalviewjsSyncAllLibs (type: Sync) {
+ dependsOn jalviewjsTransferUnzipAllLibs
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+ inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsSyncResources (type: Sync) {
+ def inputFiles = fileTree(dir: resourceDir)
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsSyncSiteResources (type: Sync) {
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsSyncBuildProperties (type: Sync) {
+ dependsOn createBuildProperties
+ def inputFiles = [file(buildProperties)]
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsProjectImport(type: Exec) {
+ dependsOn eclipseSetup
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseSetup
+
+ doFirst {
+ // do not run a headless import when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+ }
+
+ //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+ def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+ if (!IN_ECLIPSE) {
+ args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+ }
+
+ inputs.file("${jalviewDir}/.project")
+ outputs.upToDateWhen {
+ file(projdir).exists()
+ }
+}
+
+
+task jalviewjsTranspile(type: Exec) {
+ dependsOn jalviewjsEclipseSetup
+ dependsOn jalviewjsProjectImport
+ dependsOn jalviewjsEclipsePaths
+
+ doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+ }
+
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+ if (!IN_ECLIPSE) {
+ args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+ }
+
+ def stdout
+ def stderr
+ doFirst {
+ stdout = new ByteArrayOutputStream()
+ stderr = new ByteArrayOutputStream()
+
+ def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+ def logOutFile = file(logOutFileName)
+ logOutFile.createNewFile()
+ logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+BINARY: ${eclipseBinary}
+VERSION: ${eclipseVersion}
+WORKSPACE: ${eclipseWorkspace}
+DEBUG: ${eclipseDebug}
+----
+"""
+ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+ // combine stdout and stderr
+ def logErrFOS = logOutFOS
+
+ if (jalviewjs_j2s_to_console.equals("true")) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr),
+ errorOutput)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr)
+ }
+ }
+
+ doLast {
+ if (stdout.toString().contains("Error processing ")) {
+ // j2s did not complete transpile
+ //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+ if (jalviewjs_ignore_transpile_errors.equals("true")) {
+ println("IGNORING TRANSPILE ERRORS")
+ println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+ } else {
+ throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+ }
+ }
+ }
+
+ inputs.dir("${jalviewDir}/${sourceDir}")
+ outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+ outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+}
+
+
+def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+
+ def stdout = new ByteArrayOutputStream()
+ def stderr = new ByteArrayOutputStream()
+
+ def coreFile = file(jsfile)
+ def msg = ""
+ msg = "Creating core for ${name}...\nGenerating ${jsfile}"
+ println(msg)
+ logOutFile.createNewFile()
+ logOutFile.append(msg+"\n")
+
+ def coreTop = file(prefixFile)
+ def coreBottom = file(suffixFile)
+ coreFile.getParentFile().mkdirs()
+ coreFile.createNewFile()
+ coreFile.write( coreTop.getText("UTF-8") )
+ list.each {
+ f ->
+ if (f.exists()) {
+ def t = f.getText("UTF-8")
+ t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
+ coreFile.append( t )
+ } else {
+ msg = "...file '"+f.getPath()+"' does not exist, skipping"
+ println(msg)
+ logOutFile.append(msg+"\n")
+ }
+ }
+ coreFile.append( coreBottom.getText("UTF-8") )
+
+ msg = "Generating ${zjsfile}"
+ println(msg)
+ logOutFile.append(msg+"\n")
+ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+ def logErrFOS = logOutFOS
+
+ javaexec {
+ classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
+ main = "com.google.javascript.jscomp.CommandLineRunner"
+ jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+ args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+ maxHeapSize = "2g"
+
+ msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+ println(msg)
+ logOutFile.append(msg+"\n")
+
+ if (logOutConsole) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr),
+ errorOutput)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr)
+ }
+ }
+ msg = "--"
+ println(msg)
+ logOutFile.append(msg+"\n")
+}
+
+
+task jalviewjsBuildAllCores {
+ group "JalviewJS"
+ description "Build the core js lib closures listed in the classlists dir"
+ dependsOn jalviewjsTranspile
+ dependsOn jalviewjsTransferUnzipSwingJs
+
+ def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+ def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+ def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
+ def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+ def prefixFile = "${jsDir}/core/coretop2.js"
+ def suffixFile = "${jsDir}/core/corebottom2.js"
+
+ inputs.file prefixFile
+ inputs.file suffixFile
+
+ def classlistFiles = []
+ // add the classlists found int the jalviewjs_classlists_dir
+ fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
+ file ->
+ def name = file.getName() - ".txt"
+ classlistFiles += [
+ 'file': file,
+ 'name': name
+ ]
+ }
+
+ // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+ //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+ classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
+
+ jalviewjsCoreClasslists = []
+
+ classlistFiles.each {
+ hash ->
+
+ def file = hash['file']
+ if (! file.exists()) {
+ //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+ return false // this is a "continue" in groovy .each closure
+ }
+ def name = hash['name']
+ if (name == null) {
+ name = file.getName() - ".txt"
+ }
+
+ def filelist = []
+ file.eachLine {
+ line ->
+ filelist += line
+ }
+ def list = fileTree(dir: j2sDir, includes: filelist)
+
+ def jsfile = "${outputDir}/core${name}.js"
+ def zjsfile = "${outputDir}/core${name}.z.js"
+
+ jalviewjsCoreClasslists += [
+ 'jsfile': jsfile,
+ 'zjsfile': zjsfile,
+ 'list': list,
+ 'name': name
+ ]
+
+ inputs.file(file)
+ inputs.files(list)
+ outputs.file(jsfile)
+ outputs.file(zjsfile)
+ }
+
+ // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+ def stevesoftClasslistName = "_stevesoft"
+ def stevesoftClasslist = [
+ 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+ 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+ 'name': stevesoftClasslistName
+ ]
+ jalviewjsCoreClasslists += stevesoftClasslist
+ inputs.files(stevesoftClasslist['list'])
+ outputs.file(stevesoftClasslist['jsfile'])
+ outputs.file(stevesoftClasslist['zjsfile'])
+
+ // _all core
+ def allClasslistName = "_all"
+ def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+ allJsFiles += fileTree(
+ dir: libJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+ "**/org/jmol/export/JSExporter.js"
+ ]
+ )
+ allJsFiles += fileTree(
+ dir: swingJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/sun/misc/Unsafe.js",
+ "**/swingjs/jquery/jquery-editable-select.js",
+ "**/swingjs/jquery/j2sComboBox.js",
+ "**/sun/misc/FloatingDecimal.js"
+ ]
+ )
+ def allClasslist = [
+ 'jsfile': "${outputDir}/core${allClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+ 'list': allJsFiles,
+ 'name': allClasslistName
+ ]
+ // not including this version of "all" core at the moment
+ //jalviewjsCoreClasslists += allClasslist
+ inputs.files(allClasslist['list'])
+ outputs.file(allClasslist['jsfile'])
+ outputs.file(allClasslist['zjsfile'])
+
+ doFirst {
+ def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+ logOutFile.getParentFile().mkdirs()
+ logOutFile.createNewFile()
+ logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+
+ jalviewjsCoreClasslists.each {
+ jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+ }
+ }
+
+}
+
+
+def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+ copy {
+ from inputFile
+ into file(outputFile).getParentFile()
+ rename { filename ->
+ if (filename.equals(inputFile.getName())) {
+ return file(outputFile).getName()
+ }
+ return null
+ }
+ filter(ReplaceTokens,
+ beginToken: '_',
+ endToken: '_',
+ tokens: [
+ 'MAIN': '"'+main_class+'"',
+ 'CODE': "null",
+ 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+ 'COREKEY': jalviewjs_core_key,
+ 'CORENAME': coreName
+ ]
+ )
+ }
+}
+
+
+task jalviewjsPublishCoreTemplates {
+ dependsOn jalviewjsBuildAllCores
+ def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+ def inputFile = file(inputFileName)
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+
+ def outputFiles = []
+ jalviewjsCoreClasslists.each { cl ->
+ def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+ cl['outputfile'] = outputFile
+ outputFiles += outputFile
+ }
+
+ doFirst {
+ jalviewjsCoreClasslists.each { cl ->
+ jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+ }
+ }
+ inputs.file(inputFile)
+ outputs.files(outputFiles)
+}
+
+
+task jalviewjsSyncCore (type: Sync) {
+ dependsOn jalviewjsBuildAllCores
+ dependsOn jalviewjsPublishCoreTemplates
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+// this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteJs(type: Copy) {
+ dependsOn jalviewjsTranspile
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+}
+
+
+// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+task jalviewjsSyncTransferSiteJs(type: Sync) {
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ include "**/*.*"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+ preserve {
+ include "**"
+ }
+}
+
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+
+
+task jalviewjsPrepareSite {
+ group "JalviewJS"
+ description "Prepares the website folder including unzipping files and copying resources"
+ dependsOn jalviewjsSyncAllLibs
+ dependsOn jalviewjsSyncResources
+ dependsOn jalviewjsSyncSiteResources
+ dependsOn jalviewjsSyncBuildProperties
+ dependsOn jalviewjsSyncCore
+}
+
+
+task jalviewjsBuildSite {
+ group "JalviewJS"
+ description "Builds the whole website including transpiled code"
+ dependsOn jalviewjsCopyTransferSiteJs
+ dependsOn jalviewjsPrepareSite
+}
+
+
+task cleanJalviewjsTransferSite {
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+ }
+}
+
+
+task cleanJalviewjsSite {
+ dependsOn cleanJalviewjsTransferSite
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsSiteDir}"
+ }
+}
+
+
+task jalviewjsSiteTar(type: Tar) {
+ group "JalviewJS"
+ description "Creates a tar.gz file for the website"
+ dependsOn jalviewjsBuildSite
+ def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
+ try {
+ archiveFileName = outputFilename
+ } catch (Exception e) {
+ archiveName = outputFilename
+ }
+
+ compression Compression.GZIP
+
+ from "${jalviewDir}/${jalviewjsSiteDir}"
+ into jalviewjs_site_dir // this is inside the tar file
+
+ inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
+}
+
+
+task jalviewjsServer {
+ group "JalviewJS"
+ def filename = "jalviewjsTest.html"
+ description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
+ def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
+ doLast {
+
+ SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+ def port = Integer.valueOf(jalviewjs_server_port)
+ def start = port
+ def running = false
+ def url
+ def jalviewjsServer
+ while(port < start+1000 && !running) {
+ try {
+ def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
+ jalviewjsServer = factory.start(doc_root, port)
+ running = true
+ url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
+ println("SERVER STARTED with document root ${doc_root}.")
+ println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
+ println("For debug: "+url+"?j2sdebug")
+ println("For verbose: "+url+"?j2sverbose")
+ } catch (Exception e) {
+ port++;
+ }
+ }
+ def htmlText = """
+ <p><a href="${url}">JalviewJS Test. <${url}></a></p>
+ <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
+ <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
+ """
+ jalviewjsCoreClasslists.each { cl ->
+ def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+ htmlText += """
+ <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
+ """
+ println("For core ${cl.name}: "+urlcore)
+ }
+
+ file(htmlFile).text = htmlText
+ }
+
+ outputs.file(htmlFile)
+ outputs.upToDateWhen({false})
+}
+
+
+task cleanJalviewjsAll {
+ group "JalviewJS"
+ description "Delete all configuration and build artifacts to do with JalviewJS build"
+ dependsOn cleanJalviewjsSite
+ dependsOn jalviewjsEclipsePaths
+
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsBuildDir}"
+ delete "${jalviewDir}/${eclipse_bin_dir}"
+ if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
+ delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+ }
+ delete "${jalviewDir}/${jalviewjs_j2s_settings}"
+ }
+
+ outputs.upToDateWhen( { false } )
+}
+
+
+task jalviewjsIDE_checkJ2sPlugin {
+ group "00 JalviewJS in Eclipse"
+ description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+
+ doFirst {
+ def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+ def j2sPluginFile = file(j2sPlugin)
+ def eclipseHome = System.properties["eclipse.home.location"]
+ if (eclipseHome == null || ! IN_ECLIPSE) {
+ throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+ }
+ def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+ def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+ if (!eclipseJ2sPluginFile.exists()) {
+ def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin"
+ System.err.println(msg)
+ throw new StopExecutionException(msg)
+ }
+
+ def digest = MessageDigest.getInstance("MD5")
+
+ digest.update(j2sPluginFile.text.bytes)
+ def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ digest.update(eclipseJ2sPluginFile.text.bytes)
+ def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+ def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+ System.err.println(msg)
+ throw new StopExecutionException(msg)
+ } else {
+ def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+ println(msg)
+ }
+ }
+}
+
+task jalviewjsIDE_copyJ2sPlugin {
+ group "00 JalviewJS in Eclipse"
+ description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
+
+ doFirst {
+ def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+ def j2sPluginFile = file(j2sPlugin)
+ def eclipseHome = System.properties["eclipse.home.location"]
+ if (eclipseHome == null || ! IN_ECLIPSE) {
+ throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
+ }
+ def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+ def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+ def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
+ System.err.println(msg)
+ copy {
+ from j2sPlugin
+ eclipseJ2sPluginFile.getParentFile().mkdirs()
+ into eclipseJ2sPluginFile.getParent()
+ }
+ }
+}
+
+
+task jalviewjsIDE_j2sFile {
+ group "00 JalviewJS in Eclipse"
+ description "Creates the .j2s file"
+ dependsOn jalviewjsCreateJ2sSettings
+}
+
+
+task jalviewjsIDE_SyncCore {
+ group "00 JalviewJS in Eclipse"
+ description "Build the core js lib closures listed in the classlists dir and publish core html from template"
+ dependsOn jalviewjsSyncCore
+}
+
+
+task jalviewjsIDE_SyncSiteAll {
+ dependsOn jalviewjsSyncAllLibs
+ dependsOn jalviewjsSyncResources
+ dependsOn jalviewjsSyncSiteResources
+ dependsOn jalviewjsSyncBuildProperties
+}
+
+
+cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+
+
+task jalviewjsIDE_PrepareSite {
+ group "00 JalviewJS in Eclipse"
+ description "Sync libs and resources to site dir, but not closure cores"
+
+ dependsOn jalviewjsIDE_SyncSiteAll
+ //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
+}
+
+
+task jalviewjsIDE_AssembleSite {
+ group "00 JalviewJS in Eclipse"
+ description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
+ dependsOn jalviewjsPrepareSite
+}
+
+
+task jalviewjsIDE_SiteClean {
+ group "00 JalviewJS in Eclipse"
+ description "Deletes the Eclipse transpiled site"
+ dependsOn cleanJalviewjsSite
+}
+
+
+task jalviewjsIDE_Server {
+ group "00 JalviewJS in Eclipse"
+ description "Starts a webserver on localhost to test the website"
+ dependsOn jalviewjsServer
+}
+
+
+// buildship runs this at import or gradle refresh
+task eclipseSynchronizationTask {
+ //dependsOn eclipseSetup
+ dependsOn createBuildProperties
+ if (J2S_ENABLED) {
+ dependsOn jalviewjsIDE_j2sFile
+ dependsOn jalviewjsIDE_checkJ2sPlugin
+ dependsOn jalviewjsIDE_PrepareSite
+ }
+}
+
+
+// buildship runs this at build time or project refresh
+task eclipseAutoBuildTask {
+ //dependsOn jalviewjsIDE_checkJ2sPlugin
+ //dependsOn jalviewjsIDE_PrepareSite
+}
+
+
+task jalviewjs {
+ group "JalviewJS"
+ description "Build the site"
+ dependsOn jalviewjsBuildSite
+}