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
7 import groovy.transform.ExternalizeMethods
11 classpath 'org.openclover:clover:4.3.1'
19 id 'com.github.johnrengelman.shadow' version '4.0.3'
20 id 'com.install4j.gradle' version '7.0.9'
21 id 'com.dorongold.task-tree' version '1.4' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
34 compile 'org.apache.commons:commons-compress:1.18'
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) {
45 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
46 jalviewDirRelativePath = jalviewDir
48 // local build environment properties
49 def localProps = "${jalviewDirAbsolutePath}/local.properties"
50 if (file(localProps).exists()) {
52 def p = new Properties()
53 def localPropsFIS = new FileInputStream(localProps)
58 def over = getProperty(key) != null
61 println("Overriding property '${key}' with local.properties value '${val}'")
64 } catch (Exception e) {
65 System.out.println("Exception reading local.properties")
69 // this property set when running Eclipse headlessly
70 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
71 // this property set by Eclipse
72 eclipseApplicationProperty = string("eclipse.application")
73 // CHECK IF RUNNING FROM WITHIN ECLIPSE
74 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
75 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
76 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
77 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
78 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
82 println("WITHIN ECLIPSE IDE")
84 println("HEADLESS BUILD")
87 System.properties.sort { it.key }.each {
88 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
91 if (false && IN_ECLIPSE) {
92 jalviewDir = jalviewDirAbsolutePath
97 bareSourceDir = string(source_dir)
98 sourceDir = string("${jalviewDir}/${bareSourceDir}")
99 resourceDir = string("${jalviewDir}/${resource_dir}")
100 bareTestSourceDir = string(test_source_dir)
101 testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
104 cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
105 classesDir = string("${jalviewDir}/${classes_dir}")
106 if (clover.equals("true")) {
108 classesDir = string("${buildDir}/${cloverClassesDir}")
111 classesDir = string("${jalviewDir}/${classes_dir}")
116 getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
117 getdownDir = string("")
118 reportRsyncCmd = false
120 buildProperties = build_properties_file
121 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
125 // TODO: get bamboo build artifact URL for getdown artifacts
126 getdown_channel_base = bamboo_channelbase
127 getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}")
128 getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
129 getdown_app_dir = getdown_app_dir_alt
130 buildProperties = string("${classesDir}/${build_properties_file}")
134 getdown_channel_name = CHANNEL.toLowerCase()
135 getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
136 getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
137 getdown_app_dir = getdown_app_dir_release
138 buildProperties = string("${classesDir}/${build_properties_file}")
139 reportRsyncCommand = true
143 getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
144 getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
145 getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
146 getdown_app_dir = getdown_app_dir_alt
147 if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
148 print "Must provide an ARCHIVEDIR value to produce an archive distribution"
151 packageDir = string("${ARCHIVEDIR}/${packageDir}")
152 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
155 reportRsyncCommand = true
159 getdown_channel_name = string("archive/${JALVIEW_VERSION}")
160 getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
161 getdown_app_base = file(getdownWebsiteDir).toURI().toString()
162 getdown_app_dir = getdown_app_dir_alt
163 if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
164 print "Must provide an ARCHIVEDIR value to produce an archive distribution"
167 packageDir = string("${ARCHIVEDIR}/${packageDir}")
168 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
171 reportRsyncCommand = true
172 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
176 getdown_channel_name = CHANNEL.toLowerCase()
177 getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
178 getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
179 getdown_app_dir = getdown_app_dir_alt
180 buildProperties = string("${classesDir}/${build_properties_file}")
181 reportRsyncCommand = true
185 getdown_channel_name = CHANNEL.toLowerCase()
186 getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
187 getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
188 getdown_app_dir = getdown_app_dir_alt
189 buildProperties = string("${classesDir}/${build_properties_file}")
190 reportRsyncCommand = true
193 case ~/^SCRATCH(|-[-\w]*)$/:
194 getdown_channel_name = CHANNEL
195 getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
196 getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
197 getdown_app_dir = getdown_app_dir_alt
198 buildProperties = string("${classesDir}/${build_properties_file}")
199 reportRsyncCommand = true
203 getdown_app_base = file(getdownWebsiteDir).toURI().toString()
204 getdown_app_dir = getdown_app_dir_alt
205 buildProperties = string("${classesDir}/${build_properties_file}")
206 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
209 default: // something wrong specified
210 print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
216 getdownAppDir = string("${getdownWebsiteDir}/${getdown_app_dir}")
217 //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
218 getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
219 getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
220 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
221 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
222 /* compile without modules -- using classpath libraries
223 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
224 modules_runtimeClasspath = modules_compileClasspath
227 gitBranch = string("")
229 println("Using a ${CHANNEL} profile.")
231 additional_compiler_args = []
232 // configure classpath/args for j8/j11 compilation
233 if (JAVA_VERSION.equals("1.8")) {
234 JAVA_INTEGER_VERSION = string("8")
237 libDistDir = j8libDir
238 compile_source_compatibility = 1.8
239 compile_target_compatibility = 1.8
240 // these are getdown.txt properties defined dependent on the JAVA_VERSION
241 getdown_alt_java_min_version = getdown_alt_java8_min_version
242 getdown_alt_java_max_version = getdown_alt_java8_max_version
243 // this property is assigned below and expanded to multiple lines in the getdown task
244 getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
245 // this property is for the Java library used in eclipse
246 eclipse_java_runtime_name = string("JavaSE-1.8")
247 } else if (JAVA_VERSION.equals("11")) {
248 JAVA_INTEGER_VERSION = string("11")
250 libDistDir = j11libDir
251 compile_source_compatibility = 11
252 compile_target_compatibility = 11
253 getdown_alt_java_min_version = getdown_alt_java11_min_version
254 getdown_alt_java_max_version = getdown_alt_java11_max_version
255 getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
256 eclipse_java_runtime_name = string("JavaSE-11")
257 /* compile without modules -- using classpath libraries
258 additional_compiler_args += [
259 '--module-path', modules_compileClasspath.asPath,
260 '--add-modules', j11modules
263 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
264 JAVA_INTEGER_VERSION = JAVA_VERSION
266 libDistDir = j11libDir
267 compile_source_compatibility = JAVA_VERSION
268 compile_target_compatibility = JAVA_VERSION
269 getdown_alt_java_min_version = getdown_alt_java11_min_version
270 getdown_alt_java_max_version = getdown_alt_java11_max_version
271 getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
272 eclipse_java_runtime_name = string("JavaSE-11")
273 /* compile without modules -- using classpath libraries
274 additional_compiler_args += [
275 '--module-path', modules_compileClasspath.asPath,
276 '--add-modules', j11modules
280 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
285 macosJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre")
286 macosJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz")
287 windowsJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre")
288 windowsJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz")
289 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
290 install4jConfFileName = string("jalview-installers-java${JAVA_VERSION}.install4j")
291 install4jConfFile = string("${install4jDir}/${install4jConfFileName}")
292 install4jHomeDir = install4j_home_dir
293 if (install4jHomeDir.startsWith("~/")) {
294 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
299 buildingHTML = string("${jalviewDir}/${docDir}/building.html")
300 helpFile = string("${classesDir}/${help_dir}/help.jhm")
301 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
302 helpDir = string("${help_dir}")
303 helpSourceDir = string("${helpParentDir}/${helpDir}")
306 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
307 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
308 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
310 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
312 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
314 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
315 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
316 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
317 jalviewjsJalviewCoreHtmlFile = string("")
318 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
319 jalviewjsCoreClasslists = []
320 jalviewjsJalviewTemplateName = string(jalviewjs_name)
321 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
322 jalviewjsJ2sProps = null
324 eclipseWorkspace = null
325 eclipseBinary = string("")
326 eclipseVersion = string("")
336 outputDir = file(classesDir)
343 jar.destinationDir = file("${jalviewDir}/${packageDir}")
345 compileClasspath = files(sourceSets.main.java.outputDir)
346 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
348 runtimeClasspath = compileClasspath
353 srcDirs = [ cloverInstrDir ]
354 outputDir = file("${buildDir}/${cloverClassesDir}")
358 srcDirs = sourceSets.main.resources.srcDirs
360 compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
361 compileClasspath += files(sourceSets.main.java.outputDir)
362 compileClasspath += sourceSets.main.compileClasspath
363 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
364 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
366 runtimeClasspath = compileClasspath
371 srcDirs testSourceDir
372 outputDir = file("${jalviewDir}/${testOutputDir}")
376 srcDirs = sourceSets.main.resources.srcDirs
379 compileClasspath = files( sourceSets.test.java.outputDir )
382 compileClasspath += sourceSets.clover.compileClasspath
384 compileClasspath += files(sourceSets.main.java.outputDir)
387 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
388 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
389 compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
391 runtimeClasspath = compileClasspath
399 cloverCompile 'org.openclover:clover:4.3.1'
400 testCompile 'org.openclover:clover:4.3.1'
407 cloverRuntime.extendsFrom cloverCompile
412 name = eclipse_project_name
414 natures 'org.eclipse.jdt.core.javanature',
415 'org.eclipse.jdt.groovy.core.groovyNature',
416 'org.eclipse.buildship.core.gradleprojectnature'
418 buildCommand 'org.eclipse.jdt.core.javabuilder'
419 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
423 //defaultOutputDir = sourceSets.main.java.outputDir
426 if (it.isCanBeResolved()) {
431 minusConfigurations += removeThese
432 plusConfigurations = [ ]
436 def removeTheseToo = []
437 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
438 cp.entries.each { entry ->
439 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
440 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
441 // we add the resources and help/help dirs in as libs afterwards (see below)
442 if (entry.kind == 'src') {
443 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
444 removeTheseToo += entry
446 alreadyAddedSrcPath.putAt(entry.path, true)
451 cp.entries.removeAll(removeTheseToo)
453 //cp.entries += new Output("${eclipse_bin_dir}/main")
454 if (file(helpSourceDir).isDirectory()) {
455 cp.entries += new Library(fileReference(helpSourceDir))
457 if (file(resourceDir).isDirectory()) {
458 cp.entries += new Library(fileReference(resourceDir))
461 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
463 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
464 //don't want to add outputDir as eclipse is using its own output dir in bin/main
465 if (it.isDirectory() || ! it.exists()) {
466 // don't add dirs to classpath, especially if they don't exist
467 return false // groovy "continue" in .any closure
469 def itPath = it.toString()
470 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
471 // make relative path
472 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
474 if (alreadyAddedLibPath.get(itPath)) {
475 //println("Not adding duplicate entry "+itPath)
477 //println("Adding entry "+itPath)
478 cp.entries += new Library(fileReference(itPath))
479 alreadyAddedLibPath.put(itPath, true)
483 //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
484 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
485 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
486 if (it.isDirectory() || ! it.exists()) {
487 // don't add dirs to classpath
488 return false // groovy "continue" in .any closure
491 def itPath = it.toString()
492 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
493 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
495 if (alreadyAddedLibPath.get(itPath)) {
498 def lib = new Library(fileReference(itPath))
499 lib.entryAttributes["test"] = "true"
501 alreadyAddedLibPath.put(itPath, true)
509 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
514 // for the IDE, use java 11 compatibility
515 sourceCompatibility = compile_source_compatibility
516 targetCompatibility = compile_target_compatibility
517 javaRuntimeName = eclipse_java_runtime_name
519 // add in jalview project specific properties/preferences into eclipse core preferences
521 withProperties { props ->
522 def jalview_prefs = new Properties()
523 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
524 jalview_prefs.load(ins)
526 jalview_prefs.forEach { t, v ->
527 if (props.getAt(t) == null) {
537 // Don't want these to be activated if in headless build
538 synchronizationTasks "eclipseSynchronizationTask"
539 autoBuildTasks "eclipseAutoBuildTask"
546 // only instrument source, we build test classes as normal
547 inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
548 outputs.dir cloverInstrDir
551 delete cloverInstrDir
552 def argsList = ["--initstring", "${buildDir}/clover/clover.db",
553 "-d", "${buildDir}/${cloverSourcesInstrDir}"]
554 argsList.addAll(inputs.files.files.collect({ file ->
557 String[] args = argsList.toArray()
558 println("About to instrument "+args.length +" files")
559 com.atlassian.clover.CloverInstr.mainImpl(args)
565 group = "Verification"
566 description = "Createst the Clover report"
567 inputs.dir "${buildDir}/clover"
568 outputs.dir "${reportsDir}/clover"
570 file("${buildDir}/clover/clover.db").exists()
573 def argsList = ["--initstring", "${buildDir}/clover/clover.db",
574 "-o", "${reportsDir}/clover"]
575 String[] args = argsList.toArray()
576 com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
578 // and generate ${reportsDir}/clover/clover.xml
579 args = ["--initstring", "${buildDir}/clover/clover.db",
580 "-o", "${reportsDir}/clover/clover.xml"].toArray()
581 com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
590 sourceCompatibility = compile_source_compatibility
591 targetCompatibility = compile_target_compatibility
592 options.compilerArgs = additional_compiler_args
593 print ("Setting target compatibility to "+targetCompatibility+"\n")
601 dependsOn compileCloverJava
602 classpath += configurations.cloverRuntime
604 classpath += sourceSets.main.runtimeClasspath
607 sourceCompatibility = compile_source_compatibility
608 targetCompatibility = compile_target_compatibility
609 options.compilerArgs = additional_compiler_args
610 print ("Setting target compatibility to "+targetCompatibility+"\n")
618 sourceCompatibility = compile_source_compatibility
619 targetCompatibility = compile_target_compatibility
620 options.compilerArgs += additional_compiler_args
621 print ("Setting target compatibility to "+targetCompatibility+"\n")
623 classpath += configurations.cloverRuntime
629 delete sourceSets.main.java.outputDir
636 delete sourceSets.test.java.outputDir
637 delete cloverInstrDir
642 // format is a string like date.format("dd MMMM yyyy")
643 def getDate(format) {
644 def date = new Date()
645 return date.format(format)
650 def hashStdOut = new ByteArrayOutputStream()
652 commandLine "git", "rev-parse", "--short", "HEAD"
653 standardOutput = hashStdOut
657 def branchStdOut = new ByteArrayOutputStream()
659 commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
660 standardOutput = branchStdOut
664 gitHash = hashStdOut.toString().trim()
665 gitBranch = branchStdOut.toString().trim()
667 outputs.upToDateWhen { false }
671 task createBuildProperties(type: WriteProperties) {
673 inputs.dir(sourceDir)
674 inputs.dir(resourceDir)
675 file(buildProperties).getParentFile().mkdirs()
676 outputFile (buildProperties)
677 // taking time specific comment out to allow better incremental builds
678 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
679 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
680 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
681 property "VERSION", JALVIEW_VERSION
682 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
683 outputs.file(outputFile)
687 task cleanBuildingHTML(type: Delete) {
694 task convertBuildingMD(type: Exec) {
695 dependsOn cleanBuildingHTML
696 def buildingMD = "${jalviewDir}/${docDir}/building.md"
697 def css = "${jalviewDir}/${docDir}/github.css"
700 pandoc_exec.split(",").each {
701 if (file(it.trim()).exists()) {
707 def hostname = "hostname".execute().text.trim()
708 if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
709 pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
713 if (pandoc != null && file(pandoc).exists()) {
714 commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
716 println("Cannot find pandoc. Skipping convert building.md to HTML")
717 throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
723 inputs.file(buildingMD)
725 outputs.file(buildingHTML)
736 task syncDocs(type: Sync) {
737 dependsOn convertBuildingMD
738 def syncDir = "${classesDir}/${docDir}"
739 from fileTree("${jalviewDir}/${docDir}")
745 task copyHelp(type: Copy) {
746 def inputDir = helpSourceDir
747 def outputDir = "${classesDir}/${helpDir}"
752 filter(ReplaceTokens,
756 'Version-Rel': JALVIEW_VERSION,
757 'Year-Rel': getDate("yyyy")
769 outputs.files(helpFile)
770 outputs.dir(outputDir)
774 task syncLib(type: Sync) {
775 def syncDir = "${classesDir}/${libDistDir}"
776 from fileTree("${jalviewDir}/${libDistDir}")
781 task syncResources(type: Sync) {
792 dependsOn syncResources
798 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
801 dependsOn compileJava
803 dependsOn cloverInstr
807 print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
811 includeGroups testngGroups
813 useDefaultListeners=true
816 workingDir = jalviewDir
817 //systemProperties 'clover.jar' System.properties.clover.jar
818 sourceCompatibility = compile_source_compatibility
819 targetCompatibility = compile_target_compatibility
820 jvmArgs += additional_compiler_args
825 task buildIndices(type: JavaExec) {
827 classpath = sourceSets.main.compileClasspath
828 main = "com.sun.java.help.search.Indexer"
829 workingDir = "${classesDir}/${helpDir}"
832 inputs.dir("${workingDir}/${argDir}")
834 outputs.dir("${classesDir}/doc")
835 outputs.dir("${classesDir}/help")
836 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
837 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
838 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
839 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
840 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
841 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
845 task compileLinkCheck(type: JavaCompile) {
847 classpath = files("${jalviewDir}/${utilsDir}")
848 destinationDir = file("${jalviewDir}/${utilsDir}")
849 source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
851 inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
852 inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
853 outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
854 outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
858 task linkCheck(type: JavaExec) {
859 dependsOn prepare, compileLinkCheck
861 def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
862 classpath = files("${jalviewDir}/${utilsDir}")
863 main = "HelpLinksChecker"
864 workingDir = jalviewDir
865 def help = "${classesDir}/${helpDir}"
866 args = [ "${classesDir}/${helpDir}", "-nointernet" ]
868 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
870 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
873 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
877 inputs.dir("${classesDir}/${helpDir}")
878 outputs.file(helpLinksCheckerOutFile)
881 // import the pubhtmlhelp target
882 ant.properties.basedir = "${jalviewDir}"
883 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}"
884 ant.importBuild "${utilsDir}/publishHelp.xml"
887 task cleanPackageDir(type: Delete) {
889 delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
895 dependsOn buildIndices
896 dependsOn createBuildProperties
899 attributes "Main-Class": mainClass,
900 "Permissions": "all-permissions",
901 "Application-Name": "Jalview Desktop",
902 "Codebase": application_codebase
905 destinationDir = file("${jalviewDir}/${packageDir}")
906 archiveName = rootProject.name+".jar"
914 inputs.dir(classesDir)
915 outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
919 task copyJars(type: Copy) {
920 from fileTree(dir: classesDir, include: "**/*.jar").files
921 into "${jalviewDir}/${packageDir}"
925 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
926 task syncJars(type: Sync) {
927 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
928 into "${jalviewDir}/${packageDir}"
930 include jar.archiveName
937 description = "Put all required libraries in dist"
938 // order of "cleanPackageDir", "copyJars", "jar" important!
939 jar.mustRunAfter cleanPackageDir
940 syncJars.mustRunAfter cleanPackageDir
941 dependsOn cleanPackageDir
944 outputs.dir("${jalviewDir}/${packageDir}")
949 dependsOn cleanPackageDir
955 group = "distribution"
959 from ("${jalviewDir}/${libDistDir}") {
963 attributes 'Implementation-Version': JALVIEW_VERSION
965 mainClassName = shadowJarMainClass
967 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
972 task getdownWebsite() {
973 group = "distribution"
974 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
979 def getdownWebsiteResourceFilenames = []
980 def getdownTextString = ""
981 def getdownResourceDir = getdownResourceDir
982 def getdownAppDir = getdownAppDir
983 def getdownResourceFilenames = []
986 // clean the getdown website and files dir before creating getdown folders
987 delete getdownWebsiteDir
988 delete getdownFilesDir
992 rename(build_properties_file, getdown_build_properties)
995 getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
997 // go through properties looking for getdown_txt_...
998 def props = project.properties.sort { it.key }
999 if (getdown_alt_java_min_version.length() > 0) {
1000 props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
1002 if (getdown_alt_java_max_version.length() > 0) {
1003 props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
1005 props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
1007 props.put("getdown_txt_appbase", getdown_app_base)
1008 props.each{ prop, val ->
1009 if (prop.startsWith("getdown_txt_") && val != null) {
1010 if (prop.startsWith("getdown_txt_multi_")) {
1011 def key = prop.substring(18)
1012 val.split(",").each{ v ->
1013 def line = "${key} = ${v}\n"
1014 getdownTextString += line
1017 // file values rationalised
1018 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1020 if (val.indexOf('/') == 0) {
1023 } else if (val.indexOf('/') > 0) {
1024 // relative path (relative to jalviewDir)
1025 r = file( "${jalviewDir}/${val}" )
1028 val = "${getdown_resource_dir}/" + r.getName()
1029 getdownWebsiteResourceFilenames += val
1030 getdownResourceFilenames += r.getPath()
1033 if (! prop.startsWith("getdown_txt_resource")) {
1034 def line = prop.substring(12) + " = ${val}\n"
1035 getdownTextString += line
1041 getdownWebsiteResourceFilenames.each{ filename ->
1042 getdownTextString += "resource = ${filename}\n"
1044 getdownResourceFilenames.each{ filename ->
1047 into getdownResourceDir
1052 fileTree(file(packageDir)).each{ f ->
1053 if (f.isDirectory()) {
1054 def files = fileTree(dir: f, include: ["*"]).getFiles()
1056 } else if (f.exists()) {
1060 codeFiles.sort().each{f ->
1061 def name = f.getName()
1062 def line = "code = ${getdown_app_dir}/${name}\n"
1063 getdownTextString += line
1070 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1072 if (JAVA_VERSION.equals("11")) {
1073 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1074 j11libFiles.sort().each{f ->
1075 def name = f.getName()
1076 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1077 getdownTextString += line
1080 into getdownJ11libDir
1086 // 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.
1087 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1088 getdownTextString += "resource = ${getdown_launcher_new}\n"
1089 getdownTextString += "class = ${mainClass}\n"
1091 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1092 getdown_txt.write(getdownTextString)
1094 def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}")
1095 launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
1098 from getdownLauncher
1099 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1100 into getdownWebsiteDir
1104 from getdownLauncher
1105 if (file(getdownLauncher).getName() != getdown_launcher) {
1106 rename(file(getdownLauncher).getName(), getdown_launcher)
1108 into getdownWebsiteDir
1111 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1114 from getdownLauncher
1115 from "${getdownWebsiteDir}/${getdown_build_properties}"
1116 if (file(getdownLauncher).getName() != getdown_launcher) {
1117 rename(file(getdownLauncher).getName(), getdown_launcher)
1119 into getdownInstallDir
1123 from getdownInstallDir
1124 into getdownFilesInstallDir
1131 from getdownLauncher
1132 from "${getdownWebsiteDir}/${getdown_build_properties}"
1133 if (file(getdownLauncher).getName() != getdown_launcher) {
1134 rename(file(getdownLauncher).getName(), getdown_launcher)
1136 into getdownFilesDir
1140 from getdownResourceDir
1141 into "${getdownFilesDir}/${getdown_resource_dir}"
1146 inputs.dir("${jalviewDir}/${packageDir}")
1148 outputs.dir(getdownWebsiteDir)
1149 outputs.dir(getdownFilesDir)
1153 task getdownDigest(type: JavaExec) {
1154 group = "distribution"
1155 description = "Digest the getdown website folder"
1156 dependsOn getdownWebsite
1158 classpath = files("${getdownWebsiteDir}/${getdown_launcher}")
1160 main = "com.threerings.getdown.tools.Digester"
1161 args getdownWebsiteDir
1162 inputs.dir(getdownWebsiteDir)
1163 outputs.file("${getdownWebsiteDir}/digest2.txt")
1168 group = "distribution"
1169 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1170 dependsOn getdownDigest
1172 if (reportRsyncCommand) {
1173 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1174 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1175 println "LIKELY RSYNC COMMAND:"
1176 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1177 if (RUNRSYNC == "true") {
1179 commandLine "mkdir", "-p", toDir
1182 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1192 delete getdownWebsiteDir
1193 delete getdownFilesDir
1199 if (file(install4jHomeDir).exists()) {
1201 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1202 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1203 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1204 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1206 installDir(file(install4jHomeDir))
1208 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1209 if (install4j_faster.equals("true")) {
1215 task copyInstall4jTemplate(type: Copy) {
1216 from (install4jDir) {
1217 include install4j_template
1218 rename (install4j_template, install4jConfFileName)
1219 filter(ReplaceTokens,
1223 '9999999999': JAVA_VERSION
1226 filter(ReplaceTokens,
1230 'JAVA_VERSION': JAVA_VERSION,
1231 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1232 'VERSION': JALVIEW_VERSION,
1233 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1234 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1235 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1236 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1237 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4j_info_plist_file_associations,
1238 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1239 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
1240 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1241 'GETDOWN_DIST_DIR': getdown_app_dir,
1242 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1243 'GETDOWN_INSTALL_DIR': getdown_install_dir
1246 if (OSX_KEYPASS == "") {
1247 filter(ReplaceTokens,
1248 beginToken: 'codeSigning macEnabled="',
1251 'true': 'codeSigning macEnabled="false"'
1254 filter(ReplaceTokens,
1255 beginToken: 'runPostProcessor="true" ',
1256 endToken: 'Processor',
1258 'post': 'runPostProcessor="false" postProcessor'
1264 outputs.files(install4jConfFile)
1267 // include file associations in installer
1268 def installerFileAssociationsXml = file("${install4jDir}/${install4j_installer_file_associations}").text
1272 match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
1273 replace: installerFileAssociationsXml,
1274 file: install4jConfFile
1277 // include uninstaller applescript app files in dmg
1278 def installerDMGUninstallerXml = file("$install4jDir/$install4j_DMG_uninstaller_app_files").text
1282 match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
1283 replace: installerDMGUninstallerXml,
1284 file: install4jConfFile
1293 delete install4jConfFile
1298 task installers(type: com.install4j.gradle.Install4jTask) {
1299 group = "distribution"
1300 description = "Create the install4j installers"
1302 dependsOn copyInstall4jTemplate
1303 projectFile = file(install4jConfFile)
1304 variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
1305 destination = "${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}"
1306 buildSelected = true
1309 macKeystorePassword=OSX_KEYPASS
1313 println("Using projectFile "+projectFile)
1316 inputs.dir(getdownWebsiteDir)
1317 inputs.file(install4jConfFile)
1318 inputs.dir(macosJavaVMDir)
1319 inputs.dir(windowsJavaVMDir)
1320 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
1324 task sourceDist (type: Tar) {
1326 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1327 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1328 // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
1330 archiveFileName = outputFileName
1331 } catch (Exception e) {
1332 archiveName = outputFileName
1335 compression Compression.GZIP
1339 def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
1344 ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
1346 ,"utils/InstallAnywhere"]
1347 def PROCESS_FILES=[ "AUTHORS",
1355 "THIRDPARTYLIBS","TESTNG",
1357 "gradle.properties",
1368 exclude (EXCLUDE_FILES)
1369 include (PROCESS_FILES)
1370 filter(ReplaceTokens,
1374 'Version-Rel': JALVIEW_VERSION,
1375 'Year-Rel': getDate("yyyy")
1380 exclude (EXCLUDE_FILES)
1381 exclude (PROCESS_FILES)
1382 exclude ("appletlib")
1383 exclude ("**/*locales")
1384 exclude ("*locales/**")
1385 exclude ("utils/InstallAnywhere")
1387 exclude (getdown_files_dir)
1388 exclude (getdown_website_dir)
1390 // exluding these as not using jars as modules yet
1391 exclude ("${j11modDir}/**/*.jar")
1393 // from (jalviewDir) {
1394 // // explicit includes for stuff that seemed to not get included
1395 // include(fileTree("test/**/*."))
1396 // exclude(EXCLUDE_FILES)
1397 // exclude(PROCESS_FILES)
1404 dependsOn pubhtmlhelp
1406 inputs.dir("${classesDir}/${helpDir}")
1407 outputs.dir("${buildDir}/distributions/${helpDir}")
1410 // LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE