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")
82 // Import releaseProps from the RELEASE file
83 // or a file specified via JALVIEW_RELEASE_FILE if defined
84 // Expect jalview.version and target release branch in jalview.release
85 def releaseProps = new Properties();
86 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
87 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
89 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
92 } catch (Exception fileLoadError) {
93 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
96 // Set JALVIEW_VERSION if it is not already set
97 if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
98 JALVIEW_VERSION = releaseProps.get("jalview.version")
101 // this property set when running Eclipse headlessly
102 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
103 // this property set by Eclipse
104 eclipseApplicationProperty = string("eclipse.application")
105 // CHECK IF RUNNING FROM WITHIN ECLIPSE
106 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
107 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
108 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
109 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
110 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
114 println("WITHIN ECLIPSE IDE")
116 println("HEADLESS BUILD")
119 System.properties.sort { it.key }.each {
120 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
123 if (false && IN_ECLIPSE) {
124 jalviewDir = jalviewDirAbsolutePath
129 bareSourceDir = string(source_dir)
130 sourceDir = string("${jalviewDir}/${bareSourceDir}")
131 resourceDir = string("${jalviewDir}/${resource_dir}")
132 bareTestSourceDir = string(test_source_dir)
133 testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
136 cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
137 cloverDb = string("${buildDir}/clover/clover.db")
138 classesDir = string("${jalviewDir}/${classes_dir}")
139 if (clover.equals("true")) {
141 classesDir = string("${buildDir}/${cloverClassesDir}")
144 classesDir = string("${jalviewDir}/${classes_dir}")
149 getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
152 // the following values might be overridden by the CHANNEL switch
153 getdownChannelName = CHANNEL.toLowerCase()
154 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
155 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
156 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
157 getdownAppDistDir = getdown_app_dir_alt
158 buildProperties = string("${classesDir}/${build_properties_file}")
159 reportRsyncCommand = false
160 jvlChannelName = CHANNEL.toLowerCase()
161 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
162 install4jDSStore = "DS_Store-NON-RELEASE"
163 install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
164 install4jInstallerName = "${jalview_name} Non-Release Installer"
165 install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
166 install4jExtraScheme = "jalviewx"
170 // TODO: get bamboo build artifact URL for getdown artifacts
171 getdown_channel_base = bamboo_channelbase
172 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
173 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
174 jvlChannelName += "_${getdownChannelName}"
175 // automatically add the test group Not-bamboo for exclusion
176 if ("".equals(testngExcludedGroups)) {
177 testngExcludedGroups = "Not-bamboo"
179 install4jExtraScheme = "jalviewb"
183 getdownAppDistDir = getdown_app_dir_release
184 reportRsyncCommand = true
186 install4jDSStore = "DS_Store"
187 install4jDMGBackgroundImage = "jalview_dmg_background.png"
188 install4jInstallerName = "${jalview_name} Installer"
192 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
193 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
194 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
195 if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
196 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
198 packageDir = string("${ARCHIVEDIR}/${packageDir}")
199 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
202 reportRsyncCommand = true
203 install4jExtraScheme = "jalviewa"
207 getdownChannelName = string("archive/${JALVIEW_VERSION}")
208 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
209 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
210 if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
211 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
213 packageDir = string("${ARCHIVEDIR}/${packageDir}")
214 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
217 reportRsyncCommand = true
218 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
219 install4jSuffix = "Archive"
220 install4jExtraScheme = "jalviewa"
224 reportRsyncCommand = true
226 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
227 JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
229 install4jSuffix = "Develop"
230 install4jDSStore = "DS_Store-DEVELOP"
231 install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
232 install4jExtraScheme = "jalviewd"
233 install4jInstallerName = "${jalview_name} Develop Installer"
237 reportRsyncCommand = true
239 // TEST-RELEASE is usually associated with a Jalview release series so set the version
240 JALVIEW_VERSION=JALVIEW_VERSION+"-test"
242 install4jSuffix = "Test"
243 install4jDSStore = "DS_Store-TEST-RELEASE"
244 install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
245 install4jExtraScheme = "jalviewt"
246 install4jInstallerName = "${jalview_name} Test Installer"
249 case ~/^SCRATCH(|-[-\w]*)$/:
250 getdownChannelName = CHANNEL
251 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
252 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
253 reportRsyncCommand = true
254 install4jSuffix = "Scratch"
258 if (!file("${LOCALDIR}").exists()) {
259 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
261 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
262 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
264 JALVIEW_VERSION = "TEST"
265 install4jSuffix = "Test-Local"
266 install4jDSStore = "DS_Store-TEST-RELEASE"
267 install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
268 install4jExtraScheme = "jalviewt"
269 install4jInstallerName = "${jalview_name} Test Installer"
273 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
274 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
275 install4jExtraScheme = "jalviewl"
278 default: // something wrong specified
279 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
283 // override getdownAppBase if requested
284 if (findProperty("getdown_appbase_override") != null) {
285 getdownAppBase = string(getProperty("getdown_appbase_override"))
286 println("Overriding getdown appbase with '${getdownAppBase}'")
288 // sanitise file name for jalview launcher file for this channel
289 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
290 // install4j application and folder names
291 if (install4jSuffix == "") {
292 install4jApplicationName = "${jalview_name}"
293 install4jBundleId = "${install4j_bundle_id}"
294 install4jWinApplicationId = install4j_release_win_application_id
296 install4jApplicationName = "${jalview_name} ${install4jSuffix}"
297 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
298 // add int hash of install4jSuffix to the last part of the application_id
299 def id = install4j_release_win_application_id
300 def idsplitreverse = id.split("-").reverse()
301 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
302 install4jWinApplicationId = idsplitreverse.reverse().join("-")
304 // sanitise folder and id names
305 // install4jApplicationFolder = e.g. "Jalview Build"
306 install4jApplicationFolder = install4jApplicationName
307 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
308 .replaceAll("_+", "_") // collapse __
309 install4jInternalId = install4jApplicationName
311 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
312 .replaceAll("_+", "") // collapse __
313 //.replaceAll("_*-_*", "-") // collapse _-_
314 install4jUnixApplicationFolder = install4jApplicationName
316 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
317 .replaceAll("_+", "_") // collapse __
318 .replaceAll("_*-_*", "-") // collapse _-_
321 getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
322 //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
323 getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
324 getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
325 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
326 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
327 /* compile without modules -- using classpath libraries
328 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
329 modules_runtimeClasspath = modules_compileClasspath
332 gitBranch = string("")
334 println("Using a ${CHANNEL} profile.")
336 additional_compiler_args = []
337 // configure classpath/args for j8/j11 compilation
338 if (JAVA_VERSION.equals("1.8")) {
339 JAVA_INTEGER_VERSION = string("8")
342 libDistDir = j8libDir
343 compile_source_compatibility = 1.8
344 compile_target_compatibility = 1.8
345 // these are getdown.txt properties defined dependent on the JAVA_VERSION
346 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
347 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
348 // this property is assigned below and expanded to multiple lines in the getdown task
349 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
350 // this property is for the Java library used in eclipse
351 eclipseJavaRuntimeName = string("JavaSE-1.8")
352 } else if (JAVA_VERSION.equals("11")) {
353 JAVA_INTEGER_VERSION = string("11")
355 libDistDir = j11libDir
356 compile_source_compatibility = 11
357 compile_target_compatibility = 11
358 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
359 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
360 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
361 eclipseJavaRuntimeName = string("JavaSE-11")
362 /* compile without modules -- using classpath libraries
363 additional_compiler_args += [
364 '--module-path', modules_compileClasspath.asPath,
365 '--add-modules', j11modules
368 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
369 JAVA_INTEGER_VERSION = JAVA_VERSION
371 libDistDir = j11libDir
372 compile_source_compatibility = JAVA_VERSION
373 compile_target_compatibility = JAVA_VERSION
374 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
375 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
376 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
377 eclipseJavaRuntimeName = string("JavaSE-11")
378 /* compile without modules -- using classpath libraries
379 additional_compiler_args += [
380 '--module-path', modules_compileClasspath.asPath,
381 '--add-modules', j11modules
385 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
390 JAVA_MIN_VERSION = JAVA_VERSION
391 JAVA_MAX_VERSION = JAVA_VERSION
392 def jreInstallsDir = string(jre_installs_dir)
393 if (jreInstallsDir.startsWith("~/")) {
394 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
396 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
397 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
398 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
399 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
400 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
401 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
402 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
403 install4jConfFileName = string("jalview-install4j-conf.install4j")
404 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
405 install4jHomeDir = install4j_home_dir
406 if (install4jHomeDir.startsWith("~/")) {
407 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
412 buildingHTML = string("${jalviewDir}/${docDir}/building.html")
413 helpFile = string("${classesDir}/${help_dir}/help.jhm")
414 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
415 helpSourceDir = string("${helpParentDir}/${help_dir}")
418 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
419 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
420 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
422 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
424 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
426 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
427 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
428 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
429 jalviewjsJalviewCoreHtmlFile = string("")
430 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
431 jalviewjsCoreClasslists = []
432 jalviewjsJalviewTemplateName = string(jalviewjs_name)
433 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
434 jalviewjsJ2sProps = null
436 eclipseWorkspace = null
437 eclipseBinary = string("")
438 eclipseVersion = string("")
448 outputDir = file(classesDir)
453 srcDirs += helpParentDir
456 jar.destinationDir = file("${jalviewDir}/${packageDir}")
458 compileClasspath = files(sourceSets.main.java.outputDir)
459 //compileClasspath += files(sourceSets.main.resources.srcDirs)
460 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
462 runtimeClasspath = compileClasspath
467 srcDirs = [ cloverInstrDir ]
468 outputDir = file("${buildDir}/${cloverClassesDir}")
472 srcDirs = sourceSets.main.resources.srcDirs
474 compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
475 compileClasspath += files(sourceSets.main.java.outputDir)
476 compileClasspath += sourceSets.main.compileClasspath
477 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
478 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
480 runtimeClasspath = compileClasspath
485 srcDirs testSourceDir
486 outputDir = file("${jalviewDir}/${testOutputDir}")
490 srcDirs = sourceSets.main.resources.srcDirs
493 compileClasspath = files( sourceSets.test.java.outputDir )
496 compileClasspath = sourceSets.clover.compileClasspath
498 compileClasspath += files(sourceSets.main.java.outputDir)
501 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
502 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
503 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
505 runtimeClasspath = compileClasspath
513 cloverCompile 'org.openclover:clover:4.4.1'
514 testCompile 'org.openclover:clover:4.4.1'
520 cloverRuntime.extendsFrom cloverCompile
524 // eclipse project and settings files creation, also used by buildship
527 name = eclipse_project_name
529 natures 'org.eclipse.jdt.core.javanature',
530 'org.eclipse.jdt.groovy.core.groovyNature',
531 'org.eclipse.buildship.core.gradleprojectnature'
533 buildCommand 'org.eclipse.jdt.core.javabuilder'
534 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
538 //defaultOutputDir = sourceSets.main.java.outputDir
541 if (it.isCanBeResolved()) {
546 minusConfigurations += removeThese
547 plusConfigurations = [ ]
551 def removeTheseToo = []
552 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
553 cp.entries.each { entry ->
554 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
555 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
556 // we add the resources and help/help dirs in as libs afterwards (see below)
557 if (entry.kind == 'src') {
558 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
559 removeTheseToo += entry
561 alreadyAddedSrcPath.putAt(entry.path, true)
566 cp.entries.removeAll(removeTheseToo)
568 //cp.entries += new Output("${eclipse_bin_dir}/main")
569 if (file(helpParentDir).isDirectory()) {
570 cp.entries += new Library(fileReference(helpParentDir))
572 if (file(resourceDir).isDirectory()) {
573 cp.entries += new Library(fileReference(resourceDir))
576 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
578 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
579 //don't want to add outputDir as eclipse is using its own output dir in bin/main
580 if (it.isDirectory() || ! it.exists()) {
581 // don't add dirs to classpath, especially if they don't exist
582 return false // groovy "continue" in .any closure
584 def itPath = it.toString()
585 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
586 // make relative path
587 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
589 if (alreadyAddedLibPath.get(itPath)) {
590 //println("Not adding duplicate entry "+itPath)
592 //println("Adding entry "+itPath)
593 cp.entries += new Library(fileReference(itPath))
594 alreadyAddedLibPath.put(itPath, true)
598 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
599 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
600 if (it.isDirectory() || ! it.exists()) {
601 // don't add dirs to classpath
602 return false // groovy "continue" in .any closure
605 def itPath = it.toString()
606 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
607 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
609 if (alreadyAddedLibPath.get(itPath)) {
612 def lib = new Library(fileReference(itPath))
613 lib.entryAttributes["test"] = "true"
615 alreadyAddedLibPath.put(itPath, true)
623 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
628 // for the IDE, use java 11 compatibility
629 sourceCompatibility = compile_source_compatibility
630 targetCompatibility = compile_target_compatibility
631 javaRuntimeName = eclipseJavaRuntimeName
633 // add in jalview project specific properties/preferences into eclipse core preferences
635 withProperties { props ->
636 def jalview_prefs = new Properties()
637 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
638 jalview_prefs.load(ins)
640 jalview_prefs.forEach { t, v ->
641 if (props.getAt(t) == null) {
651 // Don't want these to be activated if in headless build
652 synchronizationTasks "eclipseSynchronizationTask"
653 autoBuildTasks "eclipseAutoBuildTask"
660 // only instrument source, we build test classes as normal
661 inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
662 outputs.dir cloverInstrDir
665 delete cloverInstrDir
670 cloverInstrDir.getPath(),
673 inputs.files.files.collect(
674 { file -> file.absolutePath }
677 String[] args = argsList.toArray()
678 println("About to instrument "+args.length +" files")
679 com.atlassian.clover.CloverInstr.mainImpl(args)
684 cloverClasses.dependsOn cloverInstr
688 group = "Verification"
689 description = "Creates the Clover report"
690 inputs.dir "${buildDir}/clover"
691 outputs.dir "${reportsDir}/clover"
693 file(cloverDb).exists()
700 "${reportsDir}/clover"
702 String[] args = argsList.toArray()
703 com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
705 // and generate ${reportsDir}/clover/clover.xml
710 "${reportsDir}/clover/clover.xml"
712 com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
720 sourceCompatibility = compile_source_compatibility
721 targetCompatibility = compile_target_compatibility
722 options.compilerArgs += additional_compiler_args
723 print ("Setting target compatibility to "+targetCompatibility+"\n")
725 classpath += configurations.cloverRuntime
731 delete cloverInstrDir
741 sourceCompatibility = compile_source_compatibility
742 targetCompatibility = compile_target_compatibility
743 options.compilerArgs = additional_compiler_args
744 print ("Setting target compatibility to "+targetCompatibility+"\n")
752 dependsOn compileCloverJava
753 classpath += configurations.cloverRuntime
755 classpath += sourceSets.main.runtimeClasspath
758 sourceCompatibility = compile_source_compatibility
759 targetCompatibility = compile_target_compatibility
760 options.compilerArgs = additional_compiler_args
761 print ("Setting target compatibility to "+targetCompatibility+"\n")
768 delete sourceSets.main.java.outputDir
774 dependsOn cleanClover
776 delete sourceSets.test.java.outputDir
781 // format is a string like date.format("dd MMMM yyyy")
782 def getDate(format) {
783 def date = new Date()
784 return date.format(format)
789 def hashStdOut = new ByteArrayOutputStream()
791 commandLine "git", "rev-parse", "--short", "HEAD"
792 standardOutput = hashStdOut
796 def branchStdOut = new ByteArrayOutputStream()
798 commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
799 standardOutput = branchStdOut
803 gitHash = hashStdOut.toString().trim()
804 gitBranch = branchStdOut.toString().trim()
806 outputs.upToDateWhen { false }
810 task createBuildProperties(type: WriteProperties) {
812 inputs.dir(sourceDir)
813 inputs.dir(resourceDir)
814 file(buildProperties).getParentFile().mkdirs()
815 outputFile (buildProperties)
816 // taking time specific comment out to allow better incremental builds
817 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
818 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
819 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
820 property "VERSION", JALVIEW_VERSION
821 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
822 outputs.file(outputFile)
826 task cleanBuildingHTML(type: Delete) {
833 task convertBuildingMD(type: Exec) {
834 dependsOn cleanBuildingHTML
835 def buildingMD = "${jalviewDir}/${docDir}/building.md"
836 def css = "${jalviewDir}/${docDir}/github.css"
839 pandoc_exec.split(",").each {
840 if (file(it.trim()).exists()) {
846 def hostname = "hostname".execute().text.trim()
847 def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
848 if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
849 pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
853 if (pandoc != null && file(pandoc).exists()) {
854 commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
856 println("Cannot find pandoc. Skipping convert building.md to HTML")
857 throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
863 inputs.file(buildingMD)
865 outputs.file(buildingHTML)
876 task syncDocs(type: Sync) {
877 dependsOn convertBuildingMD
878 def syncDir = "${classesDir}/${docDir}"
879 from fileTree("${jalviewDir}/${docDir}")
885 task copyHelp(type: Copy) {
886 def inputDir = helpSourceDir
887 def outputDir = "${classesDir}/${help_dir}"
892 filter(ReplaceTokens,
896 'Version-Rel': JALVIEW_VERSION,
897 'Year-Rel': getDate("yyyy")
909 outputs.files(helpFile)
910 outputs.dir(outputDir)
914 task syncLib(type: Sync) {
915 def syncDir = "${classesDir}/${libDistDir}"
916 from fileTree("${jalviewDir}/${libDistDir}")
921 task syncResources(type: Sync) {
932 dependsOn syncResources
938 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
941 dependsOn compileJava
943 dependsOn cloverInstr
947 print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
951 includeGroups testngGroups
952 excludeGroups testngExcludedGroups
954 useDefaultListeners=true
957 maxHeapSize = "1024m"
959 workingDir = jalviewDir
960 //systemProperties 'clover.jar' System.properties.clover.jar
961 def testLaf = project.findProperty("test_laf")
962 if (testLaf != null) {
963 println("Setting Test LaF to '${testLaf}'")
964 systemProperty "laf", testLaf
966 def testHiDPIScale = project.findProperty("test_HiDPIScale")
967 if (testHiDPIScale != null) {
968 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
969 systemProperty "sun.java2d.uiScale", testHiDPIScale
971 sourceCompatibility = compile_source_compatibility
972 targetCompatibility = compile_target_compatibility
973 jvmArgs += additional_compiler_args
978 task buildIndices(type: JavaExec) {
980 classpath = sourceSets.main.compileClasspath
981 main = "com.sun.java.help.search.Indexer"
982 workingDir = "${classesDir}/${help_dir}"
985 inputs.dir("${workingDir}/${argDir}")
987 outputs.dir("${classesDir}/doc")
988 outputs.dir("${classesDir}/help")
989 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
990 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
991 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
992 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
993 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
994 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
998 task compileLinkCheck(type: JavaCompile) {
1000 classpath = files("${jalviewDir}/${utilsDir}")
1001 destinationDir = file("${jalviewDir}/${utilsDir}")
1002 source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1004 inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
1005 inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
1006 outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
1007 outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
1011 task linkCheck(type: JavaExec) {
1012 dependsOn prepare, compileLinkCheck
1014 def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
1015 classpath = files("${jalviewDir}/${utilsDir}")
1016 main = "HelpLinksChecker"
1017 workingDir = jalviewDir
1018 args = [ "${classesDir}/${help_dir}", "-nointernet" ]
1020 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1022 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1025 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1029 inputs.dir("${classesDir}/${help_dir}")
1030 outputs.file(helpLinksCheckerOutFile)
1033 // import the pubhtmlhelp target
1034 ant.properties.basedir = "${jalviewDir}"
1035 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
1036 ant.importBuild "${utilsDir}/publishHelp.xml"
1039 task cleanPackageDir(type: Delete) {
1041 delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
1047 dependsOn buildIndices
1048 dependsOn createBuildProperties
1051 attributes "Main-Class": mainClass,
1052 "Permissions": "all-permissions",
1053 "Application-Name": "Jalview Desktop",
1054 "Codebase": application_codebase
1057 destinationDir = file("${jalviewDir}/${packageDir}")
1058 archiveName = rootProject.name+".jar"
1064 exclude "**/*.jar.*"
1066 inputs.dir(classesDir)
1067 outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
1071 task copyJars(type: Copy) {
1072 from fileTree(dir: classesDir, include: "**/*.jar").files
1073 into "${jalviewDir}/${packageDir}"
1077 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1078 task syncJars(type: Sync) {
1079 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1080 into "${jalviewDir}/${packageDir}"
1082 include jar.archiveName
1089 description = "Put all required libraries in dist"
1090 // order of "cleanPackageDir", "copyJars", "jar" important!
1091 jar.mustRunAfter cleanPackageDir
1092 syncJars.mustRunAfter cleanPackageDir
1093 dependsOn cleanPackageDir
1096 outputs.dir("${jalviewDir}/${packageDir}")
1101 dependsOn cleanPackageDir
1107 group = "distribution"
1111 from ("${jalviewDir}/${libDistDir}") {
1115 attributes 'Implementation-Version': JALVIEW_VERSION
1117 mainClassName = shadowJarMainClass
1119 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1124 task getdownWebsite() {
1125 group = "distribution"
1126 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1131 def getdownWebsiteResourceFilenames = []
1132 def getdownTextString = ""
1133 def getdownResourceDir = getdownResourceDir
1134 def getdownResourceFilenames = []
1137 // clean the getdown website and files dir before creating getdown folders
1138 delete getdownWebsiteDir
1139 delete getdownFilesDir
1142 from buildProperties
1143 rename(build_properties_file, getdown_build_properties)
1146 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1148 // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
1149 def props = project.properties.sort { it.key }
1150 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1151 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1153 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1154 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1156 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1157 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1160 props.put("getdown_txt_title", jalview_name)
1161 props.put("getdown_txt_ui.name", install4jApplicationName)
1163 // start with appbase
1164 getdownTextString += "appbase = ${getdownAppBase}\n"
1165 props.each{ prop, val ->
1166 if (prop.startsWith("getdown_txt_") && val != null) {
1167 if (prop.startsWith("getdown_txt_multi_")) {
1168 def key = prop.substring(18)
1169 val.split(",").each{ v ->
1170 def line = "${key} = ${v}\n"
1171 getdownTextString += line
1174 // file values rationalised
1175 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1177 if (val.indexOf('/') == 0) {
1180 } else if (val.indexOf('/') > 0) {
1181 // relative path (relative to jalviewDir)
1182 r = file( "${jalviewDir}/${val}" )
1185 val = "${getdown_resource_dir}/" + r.getName()
1186 getdownWebsiteResourceFilenames += val
1187 getdownResourceFilenames += r.getPath()
1190 if (! prop.startsWith("getdown_txt_resource")) {
1191 def line = prop.substring(12) + " = ${val}\n"
1192 getdownTextString += line
1198 getdownWebsiteResourceFilenames.each{ filename ->
1199 getdownTextString += "resource = ${filename}\n"
1201 getdownResourceFilenames.each{ filename ->
1204 into getdownResourceDir
1209 fileTree(file(packageDir)).each{ f ->
1210 if (f.isDirectory()) {
1211 def files = fileTree(dir: f, include: ["*"]).getFiles()
1213 } else if (f.exists()) {
1217 codeFiles.sort().each{f ->
1218 def name = f.getName()
1219 def line = "code = ${getdownAppDistDir}/${name}\n"
1220 getdownTextString += line
1227 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1229 if (JAVA_VERSION.equals("11")) {
1230 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1231 j11libFiles.sort().each{f ->
1232 def name = f.getName()
1233 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1234 getdownTextString += line
1237 into getdownJ11libDir
1243 // 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.
1244 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1245 getdownTextString += "resource = ${getdown_launcher_new}\n"
1246 getdownTextString += "class = ${mainClass}\n"
1248 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1249 getdown_txt.write(getdownTextString)
1251 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1252 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1253 launchJvl.write("appbase=${getdownAppBase}")
1256 from getdownLauncher
1257 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1258 into getdownWebsiteDir
1262 from getdownLauncher
1263 if (file(getdownLauncher).getName() != getdown_launcher) {
1264 rename(file(getdownLauncher).getName(), getdown_launcher)
1266 into getdownWebsiteDir
1269 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1272 from getdownLauncher
1273 from "${getdownWebsiteDir}/${getdown_build_properties}"
1274 if (file(getdownLauncher).getName() != getdown_launcher) {
1275 rename(file(getdownLauncher).getName(), getdown_launcher)
1277 into getdownInstallDir
1281 from getdownInstallDir
1282 into getdownFilesInstallDir
1289 from getdownLauncher
1290 from "${getdownWebsiteDir}/${getdown_build_properties}"
1291 if (file(getdownLauncher).getName() != getdown_launcher) {
1292 rename(file(getdownLauncher).getName(), getdown_launcher)
1294 into getdownFilesDir
1298 from getdownResourceDir
1299 into "${getdownFilesDir}/${getdown_resource_dir}"
1304 inputs.dir("${jalviewDir}/${packageDir}")
1306 outputs.dir(getdownWebsiteDir)
1307 outputs.dir(getdownFilesDir)
1311 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1312 task getdownDigestDir(type: JavaExec) {
1314 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1316 def digestDirPropertyName = "DIGESTDIR"
1318 classpath = files(getdownLauncher)
1319 def digestDir = findProperty(digestDirPropertyName)
1320 if (digestDir == null) {
1321 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1325 main = "com.threerings.getdown.tools.Digester"
1329 task getdownDigest(type: JavaExec) {
1330 group = "distribution"
1331 description = "Digest the getdown website folder"
1332 dependsOn getdownWebsite
1334 classpath = files(getdownLauncher)
1336 main = "com.threerings.getdown.tools.Digester"
1337 args getdownWebsiteDir
1338 inputs.dir(getdownWebsiteDir)
1339 outputs.file("${getdownWebsiteDir}/digest2.txt")
1344 group = "distribution"
1345 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1346 dependsOn getdownDigest
1348 if (reportRsyncCommand) {
1349 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1350 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1351 println "LIKELY RSYNC COMMAND:"
1352 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1353 if (RUNRSYNC == "true") {
1355 commandLine "mkdir", "-p", toDir
1358 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1368 delete getdownWebsiteDir
1369 delete getdownFilesDir
1375 if (file(install4jHomeDir).exists()) {
1377 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1378 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1379 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1380 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1382 installDir(file(install4jHomeDir))
1384 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1388 task copyInstall4jTemplate {
1389 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1390 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1391 inputs.file(install4jTemplateFile)
1392 inputs.file(install4jFileAssociationsFile)
1393 inputs.property("CHANNEL", { CHANNEL })
1394 outputs.file(install4jConfFile)
1397 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1399 // turn off code signing if no OSX_KEYPASS
1400 if (OSX_KEYPASS == "") {
1401 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1402 codeSigning.'@macEnabled' = "false"
1404 install4jConfigXml.'**'.windows.each { windows ->
1405 windows.'@runPostProcessor' = "false"
1409 // turn off checksum creation for LOCAL channel
1410 def e = install4jConfigXml.application[0]
1411 if (CHANNEL == "LOCAL") {
1412 e.'@createChecksums' = "false"
1414 e.'@createChecksums' = "true"
1417 // put file association actions where placeholder action is
1418 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1419 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1420 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1421 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1422 def parent = a.parent()
1424 fileAssociationActions.each { faa ->
1427 // don't need to continue in .any loop once replacements have been made
1432 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1433 // NB we're deleting the /other/ one!
1434 // Also remove the examples subdir from non-release versions
1435 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1436 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1437 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1438 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1440 // remove the examples subdir from Full File Set
1441 def files = install4jConfigXml.files[0]
1442 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1443 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1444 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1445 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1446 dirEntry.parent().remove(dirEntry)
1448 install4jConfigXml.'**'.action.any { a ->
1449 if (a.'@customizedId' == customizedIdToDelete) {
1450 def parent = a.parent()
1456 // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
1457 if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
1458 def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
1459 symlink.parent().remove(symlink)
1462 // write install4j file
1463 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1470 delete install4jConfFile
1475 task installers(type: com.install4j.gradle.Install4jTask) {
1476 group = "distribution"
1477 description = "Create the install4j installers"
1478 dependsOn setGitVals
1480 dependsOn copyInstall4jTemplate
1482 projectFile = install4jConfFile
1484 // create an md5 for the input files to use as version for install4j conf file
1485 def digest = MessageDigest.getInstance("MD5")
1487 (file("${install4jDir}/${install4j_template}").text +
1488 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1489 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1490 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1491 if (filesMd5.length() >= 8) {
1492 filesMd5 = filesMd5.substring(0,8)
1494 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1495 // make install4jBuildDir relative to jalviewDir
1496 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1499 'JALVIEW_NAME': jalview_name,
1500 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1501 'JALVIEW_DIR': "../..",
1502 'OSX_KEYSTORE': OSX_KEYSTORE,
1503 'JSIGN_SH': JSIGN_SH,
1504 'JRE_DIR': getdown_app_dir_java,
1505 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1506 'JALVIEW_VERSION': JALVIEW_VERSION,
1507 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1508 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1509 'JAVA_VERSION': JAVA_VERSION,
1510 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1511 'VERSION': JALVIEW_VERSION,
1512 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1513 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1514 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1515 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1516 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1517 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1518 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1519 'BUNDLE_ID': install4jBundleId,
1520 'INTERNAL_ID': install4jInternalId,
1521 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1522 'MACOS_DS_STORE': install4jDSStore,
1523 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1524 'INSTALLER_NAME': install4jInstallerName,
1525 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1526 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1527 'GETDOWN_FILES_DIR': getdown_files_dir,
1528 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1529 'GETDOWN_DIST_DIR': getdownAppDistDir,
1530 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1531 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1532 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1533 'BUILD_DIR': install4jBuildDir,
1534 'APPLICATION_CATEGORIES': install4j_application_categories,
1535 'APPLICATION_FOLDER': install4jApplicationFolder,
1536 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1537 'EXECUTABLE_NAME': install4jExecutableName,
1538 'EXTRA_SCHEME': install4jExtraScheme,
1541 //println("INSTALL4J VARIABLES:")
1542 //variables.each{k,v->println("${k}=${v}")}
1544 destination = "${jalviewDir}/${install4jBuildDir}"
1545 buildSelected = true
1547 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1549 disableSigning = true
1553 macKeystorePassword = OSX_KEYPASS
1557 println("Using projectFile "+projectFile)
1560 inputs.dir(getdownWebsiteDir)
1561 inputs.file(install4jConfFile)
1562 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1563 inputs.dir(macosJavaVMDir)
1564 inputs.dir(windowsJavaVMDir)
1565 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
1569 task sourceDist(type: Tar) {
1571 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1572 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1573 // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
1575 archiveFileName = outputFileName
1576 } catch (Exception e) {
1577 archiveName = outputFileName
1580 compression Compression.GZIP
1595 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
1597 "utils/InstallAnywhere",
1612 "gradle.properties",
1623 ".settings/org.eclipse.jdt.core.jalview.prefs",
1627 exclude (EXCLUDE_FILES)
1628 include (PROCESS_FILES)
1629 filter(ReplaceTokens,
1633 'Version-Rel': JALVIEW_VERSION,
1634 'Year-Rel': getDate("yyyy")
1639 exclude (EXCLUDE_FILES)
1640 exclude (PROCESS_FILES)
1641 exclude ("appletlib")
1642 exclude ("**/*locales")
1643 exclude ("*locales/**")
1644 exclude ("utils/InstallAnywhere")
1646 exclude (getdown_files_dir)
1647 exclude (getdown_website_dir)
1649 // exluding these as not using jars as modules yet
1650 exclude ("$j11modDir/**/*.jar")
1653 include(INCLUDE_FILES)
1655 // from (jalviewDir) {
1656 // // explicit includes for stuff that seemed to not get included
1657 // include(fileTree("test/**/*."))
1658 // exclude(EXCLUDE_FILES)
1659 // exclude(PROCESS_FILES)
1666 dependsOn pubhtmlhelp
1668 inputs.dir("${classesDir}/${help_dir}")
1669 outputs.dir("${buildDir}/distributions/${help_dir}")
1672 // LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
1673 task eclipseAutoBuildTask {}
1674 task eclipseSynchronizationTask {}