1 import org.apache.tools.ant.filters.ReplaceTokens
2 import org.gradle.internal.os.OperatingSystem
3 import org.gradle.plugins.ide.eclipse.model.Output
4 import org.gradle.plugins.ide.eclipse.model.Library
5 import java.security.MessageDigest
6 import groovy.transform.ExternalizeMethods
7 import groovy.util.XmlParser
8 import groovy.xml.XmlUtil
17 classpath 'org.openclover:clover:4.4.1'
26 id 'com.github.johnrengelman.shadow' version '4.0.3'
27 id 'com.install4j.gradle' version '8.0.4'
28 id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
38 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
39 def string(Object o) {
40 return o == null ? "" : o.toString()
45 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
46 jalviewDirRelativePath = jalviewDir
48 // local build environment properties
49 // can be "projectDir/local.properties"
50 def localProps = "${projectDir}/local.properties"
52 if (file(localProps).exists()) {
53 propsFile = localProps
55 // or "../projectDir_local.properties"
56 def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
57 if (file(dirLocalProps).exists()) {
58 propsFile = dirLocalProps
60 if (propsFile != null) {
62 def p = new Properties()
63 def localPropsFIS = new FileInputStream(propsFile)
68 def oldval = findProperty(key)
71 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
73 println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
76 } catch (Exception e) {
77 System.out.println("Exception reading local.properties")
81 // this property set when running Eclipse headlessly
82 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
83 // this property set by Eclipse
84 eclipseApplicationProperty = string("eclipse.application")
85 // CHECK IF RUNNING FROM WITHIN ECLIPSE
86 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
87 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
88 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
89 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
90 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
94 println("WITHIN ECLIPSE IDE")
96 println("HEADLESS BUILD")
99 System.properties.sort { it.key }.each {
100 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
103 if (false && IN_ECLIPSE) {
104 jalviewDir = jalviewDirAbsolutePath
109 bareSourceDir = string(source_dir)
110 sourceDir = string("${jalviewDir}/${bareSourceDir}")
111 resourceDir = string("${jalviewDir}/${resource_dir}")
112 bareTestSourceDir = string(test_source_dir)
113 testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
116 cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
117 cloverDb = string("${buildDir}/clover/clover.db")
118 classesDir = string("${jalviewDir}/${classes_dir}")
119 if (clover.equals("true")) {
121 classesDir = string("${buildDir}/${cloverClassesDir}")
124 classesDir = string("${jalviewDir}/${classes_dir}")
129 getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
132 // the following values might be overridden by the CHANNEL switch
133 getdownChannelName = CHANNEL.toLowerCase()
134 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
135 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
136 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
137 getdownAppDistDir = getdown_app_dir_alt
138 buildProperties = string("${classesDir}/${build_properties_file}")
139 reportRsyncCommand = false
140 jvlChannelName = CHANNEL.toLowerCase()
141 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
142 install4jDSStore = "DS_Store-NON-RELEASE"
143 install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
144 install4jInstallerName = "${jalview_name} Non-Release Installer"
145 install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
146 install4jExtraScheme = "jalviewx"
150 // TODO: get bamboo build artifact URL for getdown artifacts
151 getdown_channel_base = bamboo_channelbase
152 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
153 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
154 jvlChannelName += "_${getdownChannelName}"
155 // automatically add the test group Not-bamboo for exclusion
156 if ("".equals(testngExcludedGroups)) {
157 testngExcludedGroups = "Not-bamboo"
159 install4jExtraScheme = "jalviewb"
163 getdownAppDistDir = getdown_app_dir_release
164 reportRsyncCommand = true
166 install4jDSStore = "DS_Store"
167 install4jDMGBackgroundImage = "jalview_dmg_background.png"
168 install4jInstallerName = "${jalview_name} Installer"
172 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
173 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
174 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
175 if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
176 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
178 packageDir = string("${ARCHIVEDIR}/${packageDir}")
179 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
182 reportRsyncCommand = true
183 install4jExtraScheme = "jalviewa"
187 getdownChannelName = string("archive/${JALVIEW_VERSION}")
188 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
189 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
190 if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
191 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
193 packageDir = string("${ARCHIVEDIR}/${packageDir}")
194 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
197 reportRsyncCommand = true
198 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
199 install4jSuffix = "Archive"
200 install4jExtraScheme = "jalviewa"
204 reportRsyncCommand = true
205 install4jExtraScheme = "jalviewd"
209 reportRsyncCommand = true
210 JALVIEW_VERSION = "TEST"
211 install4jSuffix = "Test"
212 install4jDSStore = "DS_Store-TEST-RELEASE"
213 install4jDMGBackgroundImage = "jalview_dmg_background.png"
214 install4jExtraScheme = "jalviewt"
215 install4jInstallerName = "${jalview_name} Test Installer"
218 case ~/^SCRATCH(|-[-\w]*)$/:
219 getdownChannelName = CHANNEL
220 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
221 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
222 reportRsyncCommand = true
223 install4jSuffix = "Scratch"
227 if (!file("${LOCALDIR}").exists()) {
228 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
230 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
231 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
233 JALVIEW_VERSION = "TEST"
234 install4jSuffix = "Test-Local"
235 install4jDSStore = "DS_Store-TEST-RELEASE"
236 install4jDMGBackgroundImage = "jalview_dmg_background.png"
237 install4jExtraScheme = "jalviewt"
238 install4jInstallerName = "${jalview_name} Test Installer"
242 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
243 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
244 install4jExtraScheme = "jalviewl"
247 default: // something wrong specified
248 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
252 // override getdownAppBase if requested
253 if (findProperty("getdown_appbase_override") != null) {
254 getdownAppBase = string(getProperty("getdown_appbase_override"))
255 println("Overriding getdown appbase with '${getdownAppBase}'")
257 // sanitise file name for jalview launcher file for this channel
258 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
259 // install4j application and folder names
260 if (install4jSuffix == "") {
261 install4jApplicationName = "${jalview_name}"
263 install4jApplicationName = "${jalview_name} ${install4jSuffix}"
265 // sanitise folder names
266 install4jApplicationFolder = install4jApplicationName
267 .replaceAll("[\"'~:\\\\]+", "_") // replace all awkward filename chars
268 install4jUnixApplicationFolder = install4jApplicationFolder
271 .replaceAll("[^\\w\\-\\.]+", "_") // replace other non [alphanumeric,_,-,.]
272 .replaceAll("_+", "_")
273 .replaceAll("_*-_*", "-")
275 getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
276 //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
277 getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
278 getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
279 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
280 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
281 /* compile without modules -- using classpath libraries
282 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
283 modules_runtimeClasspath = modules_compileClasspath
286 gitBranch = string("")
288 println("Using a ${CHANNEL} profile.")
290 additional_compiler_args = []
291 // configure classpath/args for j8/j11 compilation
292 if (JAVA_VERSION.equals("1.8")) {
293 JAVA_INTEGER_VERSION = string("8")
296 libDistDir = j8libDir
297 compile_source_compatibility = 1.8
298 compile_target_compatibility = 1.8
299 // these are getdown.txt properties defined dependent on the JAVA_VERSION
300 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
301 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
302 // this property is assigned below and expanded to multiple lines in the getdown task
303 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
304 // this property is for the Java library used in eclipse
305 eclipseJavaRuntimeName = string("JavaSE-1.8")
306 } else if (JAVA_VERSION.equals("11")) {
307 JAVA_INTEGER_VERSION = string("11")
309 libDistDir = j11libDir
310 compile_source_compatibility = 11
311 compile_target_compatibility = 11
312 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
313 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
314 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
315 eclipseJavaRuntimeName = string("JavaSE-11")
316 /* compile without modules -- using classpath libraries
317 additional_compiler_args += [
318 '--module-path', modules_compileClasspath.asPath,
319 '--add-modules', j11modules
322 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
323 JAVA_INTEGER_VERSION = JAVA_VERSION
325 libDistDir = j11libDir
326 compile_source_compatibility = JAVA_VERSION
327 compile_target_compatibility = JAVA_VERSION
328 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
329 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
330 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
331 eclipseJavaRuntimeName = string("JavaSE-11")
332 /* compile without modules -- using classpath libraries
333 additional_compiler_args += [
334 '--module-path', modules_compileClasspath.asPath,
335 '--add-modules', j11modules
339 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
344 JAVA_MIN_VERSION = JAVA_VERSION
345 JAVA_MAX_VERSION = JAVA_VERSION
346 def jreInstallsDir = string(jre_installs_dir)
347 if (jreInstallsDir.startsWith("~/")) {
348 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
350 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
351 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
352 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
353 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
354 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
355 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
356 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
357 install4jConfFileName = string("jalview-install4j-conf.install4j")
358 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
359 install4jHomeDir = install4j_home_dir
360 if (install4jHomeDir.startsWith("~/")) {
361 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
366 buildingHTML = string("${jalviewDir}/${docDir}/building.html")
367 helpFile = string("${classesDir}/${help_dir}/help.jhm")
368 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
369 helpSourceDir = string("${helpParentDir}/${help_dir}")
372 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
373 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
374 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
376 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
378 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
380 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
381 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
382 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
383 jalviewjsJalviewCoreHtmlFile = string("")
384 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
385 jalviewjsCoreClasslists = []
386 jalviewjsJalviewTemplateName = string(jalviewjs_name)
387 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
388 jalviewjsJ2sProps = null
390 eclipseWorkspace = null
391 eclipseBinary = string("")
392 eclipseVersion = string("")
402 outputDir = file(classesDir)
407 srcDirs += helpParentDir
410 jar.destinationDir = file("${jalviewDir}/${packageDir}")
412 compileClasspath = files(sourceSets.main.java.outputDir)
413 //compileClasspath += files(sourceSets.main.resources.srcDirs)
414 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
416 runtimeClasspath = compileClasspath
421 srcDirs = [ cloverInstrDir ]
422 outputDir = file("${buildDir}/${cloverClassesDir}")
426 srcDirs = sourceSets.main.resources.srcDirs
428 compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
429 compileClasspath += files(sourceSets.main.java.outputDir)
430 compileClasspath += sourceSets.main.compileClasspath
431 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
432 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
434 runtimeClasspath = compileClasspath
439 srcDirs testSourceDir
440 outputDir = file("${jalviewDir}/${testOutputDir}")
444 srcDirs = sourceSets.main.resources.srcDirs
447 compileClasspath = files( sourceSets.test.java.outputDir )
450 compileClasspath = sourceSets.clover.compileClasspath
452 compileClasspath += files(sourceSets.main.java.outputDir)
455 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
456 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
457 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
459 runtimeClasspath = compileClasspath
467 cloverCompile 'org.openclover:clover:4.4.1'
468 testCompile 'org.openclover:clover:4.4.1'
474 cloverRuntime.extendsFrom cloverCompile
478 // eclipse project and settings files creation, also used by buildship
481 name = eclipse_project_name
483 natures 'org.eclipse.jdt.core.javanature',
484 'org.eclipse.jdt.groovy.core.groovyNature',
485 'org.eclipse.buildship.core.gradleprojectnature'
487 buildCommand 'org.eclipse.jdt.core.javabuilder'
488 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
492 //defaultOutputDir = sourceSets.main.java.outputDir
495 if (it.isCanBeResolved()) {
500 minusConfigurations += removeThese
501 plusConfigurations = [ ]
505 def removeTheseToo = []
506 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
507 cp.entries.each { entry ->
508 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
509 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
510 // we add the resources and help/help dirs in as libs afterwards (see below)
511 if (entry.kind == 'src') {
512 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
513 removeTheseToo += entry
515 alreadyAddedSrcPath.putAt(entry.path, true)
520 cp.entries.removeAll(removeTheseToo)
522 //cp.entries += new Output("${eclipse_bin_dir}/main")
523 if (file(helpParentDir).isDirectory()) {
524 cp.entries += new Library(fileReference(helpParentDir))
526 if (file(resourceDir).isDirectory()) {
527 cp.entries += new Library(fileReference(resourceDir))
530 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
532 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
533 //don't want to add outputDir as eclipse is using its own output dir in bin/main
534 if (it.isDirectory() || ! it.exists()) {
535 // don't add dirs to classpath, especially if they don't exist
536 return false // groovy "continue" in .any closure
538 def itPath = it.toString()
539 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
540 // make relative path
541 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
543 if (alreadyAddedLibPath.get(itPath)) {
544 //println("Not adding duplicate entry "+itPath)
546 //println("Adding entry "+itPath)
547 cp.entries += new Library(fileReference(itPath))
548 alreadyAddedLibPath.put(itPath, true)
552 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
553 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
554 if (it.isDirectory() || ! it.exists()) {
555 // don't add dirs to classpath
556 return false // groovy "continue" in .any closure
559 def itPath = it.toString()
560 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
561 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
563 if (alreadyAddedLibPath.get(itPath)) {
566 def lib = new Library(fileReference(itPath))
567 lib.entryAttributes["test"] = "true"
569 alreadyAddedLibPath.put(itPath, true)
577 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
582 // for the IDE, use java 11 compatibility
583 sourceCompatibility = compile_source_compatibility
584 targetCompatibility = compile_target_compatibility
585 javaRuntimeName = eclipseJavaRuntimeName
587 // add in jalview project specific properties/preferences into eclipse core preferences
589 withProperties { props ->
590 def jalview_prefs = new Properties()
591 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
592 jalview_prefs.load(ins)
594 jalview_prefs.forEach { t, v ->
595 if (props.getAt(t) == null) {
605 // Don't want these to be activated if in headless build
606 synchronizationTasks "eclipseSynchronizationTask"
607 autoBuildTasks "eclipseAutoBuildTask"
614 // only instrument source, we build test classes as normal
615 inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
616 outputs.dir cloverInstrDir
619 delete cloverInstrDir
624 cloverInstrDir.getPath(),
627 inputs.files.files.collect(
628 { file -> file.absolutePath }
631 String[] args = argsList.toArray()
632 println("About to instrument "+args.length +" files")
633 com.atlassian.clover.CloverInstr.mainImpl(args)
638 cloverClasses.dependsOn cloverInstr
642 group = "Verification"
643 description = "Creates the Clover report"
644 inputs.dir "${buildDir}/clover"
645 outputs.dir "${reportsDir}/clover"
647 file(cloverDb).exists()
654 "${reportsDir}/clover"
656 String[] args = argsList.toArray()
657 com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
659 // and generate ${reportsDir}/clover/clover.xml
664 "${reportsDir}/clover/clover.xml"
666 com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
674 sourceCompatibility = compile_source_compatibility
675 targetCompatibility = compile_target_compatibility
676 options.compilerArgs += additional_compiler_args
677 print ("Setting target compatibility to "+targetCompatibility+"\n")
679 classpath += configurations.cloverRuntime
685 delete cloverInstrDir
695 sourceCompatibility = compile_source_compatibility
696 targetCompatibility = compile_target_compatibility
697 options.compilerArgs = additional_compiler_args
698 print ("Setting target compatibility to "+targetCompatibility+"\n")
706 dependsOn compileCloverJava
707 classpath += configurations.cloverRuntime
709 classpath += sourceSets.main.runtimeClasspath
712 sourceCompatibility = compile_source_compatibility
713 targetCompatibility = compile_target_compatibility
714 options.compilerArgs = additional_compiler_args
715 print ("Setting target compatibility to "+targetCompatibility+"\n")
722 delete sourceSets.main.java.outputDir
728 dependsOn cleanClover
730 delete sourceSets.test.java.outputDir
735 // format is a string like date.format("dd MMMM yyyy")
736 def getDate(format) {
737 def date = new Date()
738 return date.format(format)
743 def hashStdOut = new ByteArrayOutputStream()
745 commandLine "git", "rev-parse", "--short", "HEAD"
746 standardOutput = hashStdOut
750 def branchStdOut = new ByteArrayOutputStream()
752 commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
753 standardOutput = branchStdOut
757 gitHash = hashStdOut.toString().trim()
758 gitBranch = branchStdOut.toString().trim()
760 outputs.upToDateWhen { false }
764 task createBuildProperties(type: WriteProperties) {
766 inputs.dir(sourceDir)
767 inputs.dir(resourceDir)
768 file(buildProperties).getParentFile().mkdirs()
769 outputFile (buildProperties)
770 // taking time specific comment out to allow better incremental builds
771 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
772 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
773 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
774 property "VERSION", JALVIEW_VERSION
775 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
776 outputs.file(outputFile)
780 task cleanBuildingHTML(type: Delete) {
787 task convertBuildingMD(type: Exec) {
788 dependsOn cleanBuildingHTML
789 def buildingMD = "${jalviewDir}/${docDir}/building.md"
790 def css = "${jalviewDir}/${docDir}/github.css"
793 pandoc_exec.split(",").each {
794 if (file(it.trim()).exists()) {
800 def hostname = "hostname".execute().text.trim()
801 def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
802 if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
803 pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
807 if (pandoc != null && file(pandoc).exists()) {
808 commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
810 println("Cannot find pandoc. Skipping convert building.md to HTML")
811 throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
817 inputs.file(buildingMD)
819 outputs.file(buildingHTML)
830 task syncDocs(type: Sync) {
831 dependsOn convertBuildingMD
832 def syncDir = "${classesDir}/${docDir}"
833 from fileTree("${jalviewDir}/${docDir}")
839 task copyHelp(type: Copy) {
840 def inputDir = helpSourceDir
841 def outputDir = "${classesDir}/${help_dir}"
846 filter(ReplaceTokens,
850 'Version-Rel': JALVIEW_VERSION,
851 'Year-Rel': getDate("yyyy")
863 outputs.files(helpFile)
864 outputs.dir(outputDir)
868 task syncLib(type: Sync) {
869 def syncDir = "${classesDir}/${libDistDir}"
870 from fileTree("${jalviewDir}/${libDistDir}")
875 task syncResources(type: Sync) {
886 dependsOn syncResources
892 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
895 dependsOn compileJava
897 dependsOn cloverInstr
901 print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
905 includeGroups testngGroups
906 excludeGroups testngExcludedGroups
908 useDefaultListeners=true
911 maxHeapSize = "1024m"
913 workingDir = jalviewDir
914 //systemProperties 'clover.jar' System.properties.clover.jar
915 sourceCompatibility = compile_source_compatibility
916 targetCompatibility = compile_target_compatibility
917 jvmArgs += additional_compiler_args
922 task buildIndices(type: JavaExec) {
924 classpath = sourceSets.main.compileClasspath
925 main = "com.sun.java.help.search.Indexer"
926 workingDir = "${classesDir}/${help_dir}"
929 inputs.dir("${workingDir}/${argDir}")
931 outputs.dir("${classesDir}/doc")
932 outputs.dir("${classesDir}/help")
933 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
934 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
935 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
936 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
937 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
938 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
942 task compileLinkCheck(type: JavaCompile) {
944 classpath = files("${jalviewDir}/${utilsDir}")
945 destinationDir = file("${jalviewDir}/${utilsDir}")
946 source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
948 inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
949 inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
950 outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
951 outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
955 task linkCheck(type: JavaExec) {
956 dependsOn prepare, compileLinkCheck
958 def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
959 classpath = files("${jalviewDir}/${utilsDir}")
960 main = "HelpLinksChecker"
961 workingDir = jalviewDir
962 args = [ "${classesDir}/${help_dir}", "-nointernet" ]
964 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
966 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
969 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
973 inputs.dir("${classesDir}/${help_dir}")
974 outputs.file(helpLinksCheckerOutFile)
977 // import the pubhtmlhelp target
978 ant.properties.basedir = "${jalviewDir}"
979 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
980 ant.importBuild "${utilsDir}/publishHelp.xml"
983 task cleanPackageDir(type: Delete) {
985 delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
991 dependsOn buildIndices
992 dependsOn createBuildProperties
995 attributes "Main-Class": mainClass,
996 "Permissions": "all-permissions",
997 "Application-Name": "Jalview Desktop",
998 "Codebase": application_codebase
1001 destinationDir = file("${jalviewDir}/${packageDir}")
1002 archiveName = rootProject.name+".jar"
1008 exclude "**/*.jar.*"
1010 inputs.dir(classesDir)
1011 outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
1015 task copyJars(type: Copy) {
1016 from fileTree(dir: classesDir, include: "**/*.jar").files
1017 into "${jalviewDir}/${packageDir}"
1021 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1022 task syncJars(type: Sync) {
1023 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1024 into "${jalviewDir}/${packageDir}"
1026 include jar.archiveName
1033 description = "Put all required libraries in dist"
1034 // order of "cleanPackageDir", "copyJars", "jar" important!
1035 jar.mustRunAfter cleanPackageDir
1036 syncJars.mustRunAfter cleanPackageDir
1037 dependsOn cleanPackageDir
1040 outputs.dir("${jalviewDir}/${packageDir}")
1045 dependsOn cleanPackageDir
1051 group = "distribution"
1055 from ("${jalviewDir}/${libDistDir}") {
1059 attributes 'Implementation-Version': JALVIEW_VERSION
1061 mainClassName = shadowJarMainClass
1063 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1068 task getdownWebsite() {
1069 group = "distribution"
1070 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1075 def getdownWebsiteResourceFilenames = []
1076 def getdownTextString = ""
1077 def getdownResourceDir = getdownResourceDir
1078 def getdownResourceFilenames = []
1081 // clean the getdown website and files dir before creating getdown folders
1082 delete getdownWebsiteDir
1083 delete getdownFilesDir
1086 from buildProperties
1087 rename(build_properties_file, getdown_build_properties)
1090 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1092 // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
1093 def props = project.properties.sort { it.key }
1094 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1095 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1097 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1098 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1100 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1101 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1104 props.put("getdown_txt_title", jalview_name)
1105 props.put("getdown_txt_ui.name", install4jApplicationName)
1107 // start with appbase
1108 getdownTextString += "appbase = ${getdownAppBase}\n"
1109 props.each{ prop, val ->
1110 if (prop.startsWith("getdown_txt_") && val != null) {
1111 if (prop.startsWith("getdown_txt_multi_")) {
1112 def key = prop.substring(18)
1113 val.split(",").each{ v ->
1114 def line = "${key} = ${v}\n"
1115 getdownTextString += line
1118 // file values rationalised
1119 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1121 if (val.indexOf('/') == 0) {
1124 } else if (val.indexOf('/') > 0) {
1125 // relative path (relative to jalviewDir)
1126 r = file( "${jalviewDir}/${val}" )
1129 val = "${getdown_resource_dir}/" + r.getName()
1130 getdownWebsiteResourceFilenames += val
1131 getdownResourceFilenames += r.getPath()
1134 if (! prop.startsWith("getdown_txt_resource")) {
1135 def line = prop.substring(12) + " = ${val}\n"
1136 getdownTextString += line
1142 getdownWebsiteResourceFilenames.each{ filename ->
1143 getdownTextString += "resource = ${filename}\n"
1145 getdownResourceFilenames.each{ filename ->
1148 into getdownResourceDir
1153 fileTree(file(packageDir)).each{ f ->
1154 if (f.isDirectory()) {
1155 def files = fileTree(dir: f, include: ["*"]).getFiles()
1157 } else if (f.exists()) {
1161 codeFiles.sort().each{f ->
1162 def name = f.getName()
1163 def line = "code = ${getdownAppDistDir}/${name}\n"
1164 getdownTextString += line
1171 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1173 if (JAVA_VERSION.equals("11")) {
1174 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1175 j11libFiles.sort().each{f ->
1176 def name = f.getName()
1177 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1178 getdownTextString += line
1181 into getdownJ11libDir
1187 // 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.
1188 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1189 getdownTextString += "resource = ${getdown_launcher_new}\n"
1190 getdownTextString += "class = ${mainClass}\n"
1192 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1193 getdown_txt.write(getdownTextString)
1195 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1196 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1197 launchJvl.write("appbase=${getdownAppBase}")
1200 from getdownLauncher
1201 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1202 into getdownWebsiteDir
1206 from getdownLauncher
1207 if (file(getdownLauncher).getName() != getdown_launcher) {
1208 rename(file(getdownLauncher).getName(), getdown_launcher)
1210 into getdownWebsiteDir
1213 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1216 from getdownLauncher
1217 from "${getdownWebsiteDir}/${getdown_build_properties}"
1218 if (file(getdownLauncher).getName() != getdown_launcher) {
1219 rename(file(getdownLauncher).getName(), getdown_launcher)
1221 into getdownInstallDir
1225 from getdownInstallDir
1226 into getdownFilesInstallDir
1233 from getdownLauncher
1234 from "${getdownWebsiteDir}/${getdown_build_properties}"
1235 if (file(getdownLauncher).getName() != getdown_launcher) {
1236 rename(file(getdownLauncher).getName(), getdown_launcher)
1238 into getdownFilesDir
1242 from getdownResourceDir
1243 into "${getdownFilesDir}/${getdown_resource_dir}"
1248 inputs.dir("${jalviewDir}/${packageDir}")
1250 outputs.dir(getdownWebsiteDir)
1251 outputs.dir(getdownFilesDir)
1255 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1256 task getdownDigestDir(type: JavaExec) {
1257 def digestDirPropertyName = "DIGESTDIR"
1258 description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown"
1260 classpath = files(getdownLauncher)
1261 def digestDir = findProperty(digestDirPropertyName)
1262 if (digestDir == null) {
1263 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1267 main = "com.threerings.getdown.tools.Digester"
1271 task getdownDigest(type: JavaExec) {
1272 group = "distribution"
1273 description = "Digest the getdown website folder"
1274 dependsOn getdownWebsite
1276 classpath = files(getdownLauncher)
1278 main = "com.threerings.getdown.tools.Digester"
1279 args getdownWebsiteDir
1280 inputs.dir(getdownWebsiteDir)
1281 outputs.file("${getdownWebsiteDir}/digest2.txt")
1286 group = "distribution"
1287 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1288 dependsOn getdownDigest
1290 if (reportRsyncCommand) {
1291 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1292 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1293 println "LIKELY RSYNC COMMAND:"
1294 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1295 if (RUNRSYNC == "true") {
1297 commandLine "mkdir", "-p", toDir
1300 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1310 delete getdownWebsiteDir
1311 delete getdownFilesDir
1317 if (file(install4jHomeDir).exists()) {
1319 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1320 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1321 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1322 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1324 installDir(file(install4jHomeDir))
1326 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1330 task copyInstall4jTemplate {
1331 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1332 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1333 inputs.file(install4jTemplateFile)
1334 inputs.file(install4jFileAssociationsFile)
1335 outputs.file(install4jConfFile)
1338 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1340 // turn off code signing if no OSX_KEYPASS
1341 if (OSX_KEYPASS == "") {
1342 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1343 codeSigning.'@macEnabled' = "false"
1345 install4jConfigXml.'**'.windows.each { windows ->
1346 windows.'@runPostProcessor' = "false"
1350 // turn off checksum creation for LOCAL channel
1351 def e = install4jConfigXml.application[0]
1352 if (CHANNEL == "LOCAL") {
1353 e.'@createChecksums' = "false"
1355 e.'@createChecksums' = "true"
1358 // put file association actions where placeholder action is
1359 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1360 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1361 install4jConfigXml.'**'.action.any { a ->
1362 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1363 def parent = a.parent()
1365 fileAssociationActions.each { faa ->
1368 // don't need to continue in .any loop once replacements have been made
1373 // write install4j file
1374 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1381 delete install4jConfFile
1386 task installers(type: com.install4j.gradle.Install4jTask) {
1387 group = "distribution"
1388 description = "Create the install4j installers"
1389 dependsOn setGitVals
1391 dependsOn copyInstall4jTemplate
1393 projectFile = install4jConfFile
1395 // create an md5 for the input files to use as version for install4j conf file
1396 def digest = MessageDigest.getInstance("MD5")
1398 (file("${install4jDir}/${install4j_template}").text +
1399 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1400 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1401 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1402 if (filesMd5.length() >= 8) {
1403 filesMd5 = filesMd5.substring(0,8)
1405 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1406 // make install4jBuildDir relative to jalviewDir
1407 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1410 'JALVIEW_NAME': install4jApplicationName,
1411 'JALVIEW_DIR': "../..",
1412 'OSX_KEYSTORE': OSX_KEYSTORE,
1413 'JSIGN_SH': JSIGN_SH,
1414 'JRE_DIR': getdown_app_dir_java,
1415 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1416 'JALVIEW_VERSION': JALVIEW_VERSION,
1417 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1418 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1419 'JAVA_VERSION': JAVA_VERSION,
1420 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1421 'VERSION': JALVIEW_VERSION,
1422 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1423 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1424 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1425 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1426 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1427 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1428 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1429 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
1430 'MACOS_DS_STORE': install4jDSStore,
1431 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1432 'INSTALLER_NAME': install4jInstallerName,
1433 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1434 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1435 'GETDOWN_FILES_DIR': getdown_files_dir,
1436 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1437 'GETDOWN_DIST_DIR': getdownAppDistDir,
1438 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1439 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1440 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1441 'BUILD_DIR': install4jBuildDir,
1442 'UNIX_DESKTOP_ADDITIONS': install4j_unix_desktop_additions,
1443 'APPLICATION_FOLDER': install4jApplicationFolder,
1444 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1445 'EXECUTABLE_NAME': install4jExecutableName,
1446 'EXTRA_SCHEME': install4jExtraScheme,
1449 destination = "${jalviewDir}/${install4jBuildDir}"
1450 buildSelected = true
1452 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1454 disableSigning = true
1458 macKeystorePassword = OSX_KEYPASS
1462 println("Using projectFile "+projectFile)
1465 inputs.dir(getdownWebsiteDir)
1466 inputs.file(install4jConfFile)
1467 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1468 inputs.dir(macosJavaVMDir)
1469 inputs.dir(windowsJavaVMDir)
1470 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
1474 task sourceDist(type: Tar) {
1476 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1477 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1478 // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
1480 archiveFileName = outputFileName
1481 } catch (Exception e) {
1482 archiveName = outputFileName
1485 compression Compression.GZIP
1500 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
1502 "utils/InstallAnywhere",
1517 "gradle.properties",
1528 ".settings/org.eclipse.jdt.core.jalview.prefs",
1532 exclude (EXCLUDE_FILES)
1533 include (PROCESS_FILES)
1534 filter(ReplaceTokens,
1538 'Version-Rel': JALVIEW_VERSION,
1539 'Year-Rel': getDate("yyyy")
1544 exclude (EXCLUDE_FILES)
1545 exclude (PROCESS_FILES)
1546 exclude ("appletlib")
1547 exclude ("**/*locales")
1548 exclude ("*locales/**")
1549 exclude ("utils/InstallAnywhere")
1551 exclude (getdown_files_dir)
1552 exclude (getdown_website_dir)
1554 // exluding these as not using jars as modules yet
1555 exclude ("$j11modDir/**/*.jar")
1558 include(INCLUDE_FILES)
1560 // from (jalviewDir) {
1561 // // explicit includes for stuff that seemed to not get included
1562 // include(fileTree("test/**/*."))
1563 // exclude(EXCLUDE_FILES)
1564 // exclude(PROCESS_FILES)
1571 dependsOn pubhtmlhelp
1573 inputs.dir("${classesDir}/${help_dir}")
1574 outputs.dir("${buildDir}/distributions/${help_dir}")
1577 // LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
1578 task eclipseAutoBuildTask {}
1579 task eclipseSynchronizationTask {}