1 /* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
2 * For properties set within build.gradle, use camelCaseNoSpace.
4 import org.apache.tools.ant.filters.ReplaceTokens
5 import org.gradle.internal.os.OperatingSystem
6 import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
7 import org.gradle.api.internal.PropertiesTransformer
8 import org.gradle.util.ConfigureUtil
9 import org.gradle.plugins.ide.eclipse.model.Output
10 import org.gradle.plugins.ide.eclipse.model.Library
11 import java.security.MessageDigest
12 import groovy.transform.ExternalizeMethods
13 import groovy.util.XmlParser
14 import groovy.xml.XmlUtil
15 import com.vladsch.flexmark.util.ast.Node
16 import com.vladsch.flexmark.html.HtmlRenderer
17 import com.vladsch.flexmark.parser.Parser
18 import com.vladsch.flexmark.util.data.MutableDataSet
19 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
20 import com.vladsch.flexmark.ext.tables.TablesExtension
21 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
22 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
23 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
24 import com.vladsch.flexmark.ext.toc.TocExtension
32 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
41 id "com.diffplug.gradle.spotless" version "3.28.0"
42 id 'com.github.johnrengelman.shadow' version '4.0.3'
43 id 'com.install4j.gradle' version '8.0.10'
44 id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
45 id 'com.palantir.git-version' version '0.12.3'
55 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
56 def string(Object o) {
57 return o == null ? "" : o.toString()
60 def overrideProperties(String propsFileName, boolean output = false) {
61 if (propsFileName == null) {
64 def propsFile = file(propsFileName)
65 if (propsFile != null && propsFile.exists()) {
66 println("Using properties from file '${propsFileName}'")
68 def p = new Properties()
69 def localPropsFIS = new FileInputStream(propsFile)
75 if (project.hasProperty(key)) {
76 oldval = project.findProperty(key)
77 project.setProperty(key, val)
79 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
82 ext.setProperty(key, val)
84 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
88 } catch (Exception e) {
89 println("Exception reading local.properties")
96 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
97 jalviewDirRelativePath = jalviewDir
99 getdownChannelName = CHANNEL.toLowerCase()
100 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
101 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
102 // Import channel_properties
103 channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
104 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
105 overrideProperties(channelGradleProperties, false)
106 // local build environment properties
107 // can be "projectDir/local.properties"
108 overrideProperties("${projectDir}/local.properties", true)
109 // or "../projectDir_local.properties"
110 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
113 // Import releaseProps from the RELEASE file
114 // or a file specified via JALVIEW_RELEASE_FILE if defined
115 // Expect jalview.version and target release branch in jalview.release
116 def releaseProps = new Properties();
117 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
118 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
120 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
121 releaseProps.load(it)
123 } catch (Exception fileLoadError) {
124 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
127 // Set JALVIEW_VERSION if it is not already set
128 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
129 JALVIEW_VERSION = releaseProps.get("jalview.version")
132 // this property set when running Eclipse headlessly
133 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
134 // this property set by Eclipse
135 eclipseApplicationProperty = string("eclipse.application")
136 // CHECK IF RUNNING FROM WITHIN ECLIPSE
137 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
138 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
139 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
140 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
141 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
145 println("WITHIN ECLIPSE IDE")
147 println("HEADLESS BUILD")
150 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
152 println("J2S ENABLED")
155 System.properties.sort { it.key }.each {
156 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
159 if (false && IN_ECLIPSE) {
160 jalviewDir = jalviewDirAbsolutePath
165 buildDate = new Date().format("yyyyMMdd")
168 bareSourceDir = string(source_dir)
169 sourceDir = string("${jalviewDir}/${bareSourceDir}")
170 resourceDir = string("${jalviewDir}/${resource_dir}")
171 bareTestSourceDir = string(test_source_dir)
172 testDir = string("${jalviewDir}/${bareTestSourceDir}")
174 classesDir = string("${jalviewDir}/${classes_dir}")
177 useClover = clover.equals("true")
178 cloverBuildDir = "${buildDir}/clover"
179 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
180 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
181 cloverReportDir = file("${buildDir}/reports/clover")
182 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
183 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
184 //cloverTestClassesDir = cloverClassesDir
185 cloverDb = string("${cloverBuildDir}/clover.db")
187 testSourceDir = useClover ? cloverTestInstrDir : testDir
188 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
190 getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
192 buildProperties = null
194 // the following values might be overridden by the CHANNEL switch
195 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
196 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
197 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
198 getdownAppDistDir = getdown_app_dir_alt
199 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
200 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
201 reportRsyncCommand = false
202 jvlChannelName = CHANNEL.toLowerCase()
203 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
204 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
205 install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
206 install4jInstallerName = "${jalview_name} Non-Release Installer"
207 install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
208 install4jExtraScheme = "jalviewx"
209 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
210 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
211 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
212 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
216 // TODO: get bamboo build artifact URL for getdown artifacts
217 getdown_channel_base = bamboo_channelbase
218 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
219 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
220 jvlChannelName += "_${getdownChannelName}"
221 // automatically add the test group Not-bamboo for exclusion
222 if ("".equals(testng_excluded_groups)) {
223 testng_excluded_groups = "Not-bamboo"
225 install4jExtraScheme = "jalviewb"
228 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
229 getdownAppDistDir = getdown_app_dir_release
230 reportRsyncCommand = true
232 install4jInstallerName = "${jalview_name} Installer"
236 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
237 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
238 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
239 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
240 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
242 package_dir = string("${ARCHIVEDIR}/${package_dir}")
243 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
246 reportRsyncCommand = true
247 install4jExtraScheme = "jalviewa"
251 getdownChannelName = string("archive/${JALVIEW_VERSION}")
252 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
253 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
254 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
255 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
257 package_dir = string("${ARCHIVEDIR}/${package_dir}")
258 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
261 reportRsyncCommand = true
262 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
263 install4jSuffix = "Archive"
264 install4jExtraScheme = "jalviewa"
268 reportRsyncCommand = true
269 getdownSetAppBaseProperty = true
270 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
271 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
273 install4jSuffix = "Develop"
274 install4jExtraScheme = "jalviewd"
275 install4jInstallerName = "${jalview_name} Develop Installer"
279 reportRsyncCommand = true
280 // Don't ignore transpile errors for release build
281 if (jalviewjs_ignore_transpile_errors.equals("true")) {
282 jalviewjs_ignore_transpile_errors = "false"
283 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
285 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
286 install4jSuffix = "Test"
287 install4jExtraScheme = "jalviewt"
288 install4jInstallerName = "${jalview_name} Test Installer"
291 case ~/^SCRATCH(|-[-\w]*)$/:
292 getdownChannelName = CHANNEL
293 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
295 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
296 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
297 reportRsyncCommand = true
298 install4jSuffix = "Scratch"
302 if (!file("${LOCALDIR}").exists()) {
303 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
305 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
306 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
308 JALVIEW_VERSION = "TEST"
309 install4jSuffix = "Test-Local"
310 install4jExtraScheme = "jalviewt"
311 install4jInstallerName = "${jalview_name} Test Installer"
314 case [ "LOCAL", "JALVIEWJS" ]:
315 JALVIEW_VERSION = "TEST"
316 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
317 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
318 install4jExtraScheme = "jalviewl"
321 default: // something wrong specified
322 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
326 // override getdownAppBase if requested
327 if (findProperty("getdown_appbase_override") != null) {
328 // revert to LOCAL if empty string
329 if (string(getdown_appbase_override) == "") {
330 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
331 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
332 } else if (string(getdown_appbase_override).startsWith("file://")) {
333 getdownAppBase = string(getdown_appbase_override)
334 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
336 getdownAppBase = string(getdown_appbase_override)
338 println("Overriding getdown appbase with '${getdownAppBase}'")
340 // sanitise file name for jalview launcher file for this channel
341 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
342 // install4j application and folder names
343 if (install4jSuffix == "") {
344 install4jApplicationName = "${jalview_name}"
345 install4jBundleId = "${install4j_bundle_id}"
346 install4jWinApplicationId = install4j_release_win_application_id
348 install4jApplicationName = "${jalview_name} ${install4jSuffix}"
349 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
350 // add int hash of install4jSuffix to the last part of the application_id
351 def id = install4j_release_win_application_id
352 def idsplitreverse = id.split("-").reverse()
353 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
354 install4jWinApplicationId = idsplitreverse.reverse().join("-")
356 // sanitise folder and id names
357 // install4jApplicationFolder = e.g. "Jalview Build"
358 install4jApplicationFolder = install4jApplicationName
359 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
360 .replaceAll("_+", "_") // collapse __
361 install4jInternalId = install4jApplicationName
363 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
364 .replaceAll("_+", "") // collapse __
365 //.replaceAll("_*-_*", "-") // collapse _-_
366 install4jUnixApplicationFolder = install4jApplicationName
368 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
369 .replaceAll("_+", "_") // collapse __
370 .replaceAll("_*-_*", "-") // collapse _-_
373 getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
374 //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
375 getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
376 getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
377 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
378 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
379 /* compile without modules -- using classpath libraries
380 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
381 modules_runtimeClasspath = modules_compileClasspath
383 def details = versionDetails()
384 gitHash = details.gitHash
385 gitBranch = details.branchName
387 println("Using a ${CHANNEL} profile.")
389 additional_compiler_args = []
390 // configure classpath/args for j8/j11 compilation
391 if (JAVA_VERSION.equals("1.8")) {
392 JAVA_INTEGER_VERSION = string("8")
395 libDistDir = j8libDir
396 compile_source_compatibility = 1.8
397 compile_target_compatibility = 1.8
398 // these are getdown.txt properties defined dependent on the JAVA_VERSION
399 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
400 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
401 // this property is assigned below and expanded to multiple lines in the getdown task
402 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
403 // this property is for the Java library used in eclipse
404 eclipseJavaRuntimeName = string("JavaSE-1.8")
405 } else if (JAVA_VERSION.equals("11")) {
406 JAVA_INTEGER_VERSION = string("11")
408 libDistDir = j11libDir
409 compile_source_compatibility = 11
410 compile_target_compatibility = 11
411 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
412 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
413 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
414 eclipseJavaRuntimeName = string("JavaSE-11")
415 /* compile without modules -- using classpath libraries
416 additional_compiler_args += [
417 '--module-path', modules_compileClasspath.asPath,
418 '--add-modules', j11modules
421 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
422 JAVA_INTEGER_VERSION = JAVA_VERSION
424 libDistDir = j11libDir
425 compile_source_compatibility = JAVA_VERSION
426 compile_target_compatibility = JAVA_VERSION
427 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
428 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
429 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
430 eclipseJavaRuntimeName = string("JavaSE-11")
431 /* compile without modules -- using classpath libraries
432 additional_compiler_args += [
433 '--module-path', modules_compileClasspath.asPath,
434 '--add-modules', j11modules
438 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
443 JAVA_MIN_VERSION = JAVA_VERSION
444 JAVA_MAX_VERSION = JAVA_VERSION
445 def jreInstallsDir = string(jre_installs_dir)
446 if (jreInstallsDir.startsWith("~/")) {
447 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
449 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
450 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
451 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
452 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
453 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
454 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
455 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
456 install4jConfFileName = string("jalview-install4j-conf.install4j")
457 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
458 install4jHomeDir = install4j_home_dir
459 if (install4jHomeDir.startsWith("~/")) {
460 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
463 resourceBuildDir = string("${buildDir}/resources")
464 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
465 helpBuildDir = string("${resourceBuildDir}/help_build")
466 docBuildDir = string("${resourceBuildDir}/doc_build")
468 if (buildProperties == null) {
469 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
471 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
472 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
473 helpSourceDir = string("${helpParentDir}/${help_dir}")
474 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
477 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
478 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
479 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
481 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
483 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
485 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
486 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
487 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
488 jalviewjsJalviewCoreHtmlFile = string("")
489 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
490 jalviewjsCoreClasslists = []
491 jalviewjsJalviewTemplateName = string(jalviewjs_name)
492 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
493 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
494 jalviewjsJ2sProps = null
495 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
497 eclipseWorkspace = null
498 eclipseBinary = string("")
499 eclipseVersion = string("")
509 outputDir = file(classesDir)
513 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
516 compileClasspath = files(sourceSets.main.java.outputDir)
517 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
519 runtimeClasspath = compileClasspath
520 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
525 srcDirs cloverInstrDir
526 outputDir = cloverClassesDir
530 srcDirs = sourceSets.main.resources.srcDirs
533 compileClasspath = files( sourceSets.clover.java.outputDir )
534 //compileClasspath += files( testClassesDir )
535 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
536 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
537 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
539 runtimeClasspath = compileClasspath
544 srcDirs testSourceDir
545 outputDir = file(testClassesDir)
549 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
552 compileClasspath = files( sourceSets.test.java.outputDir )
553 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
554 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
556 runtimeClasspath = compileClasspath
557 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
563 // eclipse project and settings files creation, also used by buildship
566 name = eclipse_project_name
568 natures 'org.eclipse.jdt.core.javanature',
569 'org.eclipse.jdt.groovy.core.groovyNature',
570 'org.eclipse.buildship.core.gradleprojectnature'
572 buildCommand 'org.eclipse.jdt.core.javabuilder'
573 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
577 //defaultOutputDir = sourceSets.main.java.outputDir
578 configurations.each{ c->
579 if (c.isCanBeResolved()) {
580 minusConfigurations += [c]
584 plusConfigurations = [ ]
588 def removeTheseToo = []
589 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
590 cp.entries.each { entry ->
591 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
592 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
593 // we add the resources and help/help dirs in as libs afterwards (see below)
594 if (entry.kind == 'src') {
595 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
596 removeTheseToo += entry
598 alreadyAddedSrcPath.putAt(entry.path, true)
603 cp.entries.removeAll(removeTheseToo)
605 //cp.entries += new Output("${eclipse_bin_dir}/main")
606 if (file(helpParentDir).isDirectory()) {
607 cp.entries += new Library(fileReference(helpParentDir))
609 if (file(resourceDir).isDirectory()) {
610 cp.entries += new Library(fileReference(resourceDir))
613 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
615 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
616 //don't want to add outputDir as eclipse is using its own output dir in bin/main
617 if (it.isDirectory() || ! it.exists()) {
618 // don't add dirs to classpath, especially if they don't exist
619 return false // groovy "continue" in .any closure
621 def itPath = it.toString()
622 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
623 // make relative path
624 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
626 if (alreadyAddedLibPath.get(itPath)) {
627 //println("Not adding duplicate entry "+itPath)
629 //println("Adding entry "+itPath)
630 cp.entries += new Library(fileReference(itPath))
631 alreadyAddedLibPath.put(itPath, true)
635 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
636 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
637 if (it.isDirectory() || ! it.exists()) {
638 // don't add dirs to classpath
639 return false // groovy "continue" in .any closure
642 def itPath = it.toString()
643 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
644 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
646 if (alreadyAddedLibPath.get(itPath)) {
649 def lib = new Library(fileReference(itPath))
650 lib.entryAttributes["test"] = "true"
652 alreadyAddedLibPath.put(itPath, true)
660 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
665 // for the IDE, use java 11 compatibility
666 sourceCompatibility = compile_source_compatibility
667 targetCompatibility = compile_target_compatibility
668 javaRuntimeName = eclipseJavaRuntimeName
670 // add in jalview project specific properties/preferences into eclipse core preferences
672 withProperties { props ->
673 def jalview_prefs = new Properties()
674 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
675 jalview_prefs.load(ins)
677 jalview_prefs.forEach { t, v ->
678 if (props.getAt(t) == null) {
682 // codestyle file -- overrides previous formatter prefs
683 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
684 if (csFile.exists()) {
685 XmlParser parser = new XmlParser()
686 def profiles = parser.parse(csFile)
687 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
688 if (profile != null) {
689 profile.'setting'.each { s ->
691 def value = s.'@value'
692 if (id != null && value != null) {
693 props.putAt(id, value)
704 // Don't want these to be activated if in headless build
705 synchronizationTasks "eclipseSynchronizationTask"
706 //autoBuildTasks "eclipseAutoBuildTask"
712 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
713 // Class to allow updating arbitrary properties files
714 class PropertiesFile extends PropertiesPersistableConfigurationObject {
715 public PropertiesFile(PropertiesTransformer t) { super(t); }
716 @Override protected void load(Properties properties) { }
717 @Override protected void store(Properties properties) { }
718 @Override protected String getDefaultResourceName() { return ""; }
719 // This is necessary, because PropertiesPersistableConfigurationObject fails
720 // if no default properties file exists.
721 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
724 // Task to update arbitrary properties files (set outputFile)
725 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
726 private final PropertiesFileContentMerger file;
727 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
728 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
729 protected void configure(PropertiesFile props) {
730 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
732 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
735 task eclipseUIPreferences(type: PropertiesFileTask) {
736 description = "Generate Eclipse additional settings"
737 def filename = "org.eclipse.jdt.ui.prefs"
738 outputFile = "$projectDir/.settings/${filename}" as File
741 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
746 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
747 description = "Generate Eclipse additional settings"
748 def filename = "org.eclipse.jdt.groovy.core.prefs"
749 outputFile = "$projectDir/.settings/${filename}" as File
752 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
757 task eclipseAllPreferences {
759 dependsOn eclipseUIPreferences
760 dependsOn eclipseGroovyCorePreferences
763 eclipseUIPreferences.mustRunAfter eclipseJdt
764 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
766 /* end of eclipse preferences hack */
774 delete cloverBuildDir
775 delete cloverReportDir
780 task cloverInstrJava(type: JavaExec) {
781 group = "Verification"
782 description = "Create clover instrumented source java files"
784 dependsOn cleanClover
786 inputs.files(sourceSets.main.allJava)
787 outputs.dir(cloverInstrDir)
789 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
790 classpath = sourceSets.clover.compileClasspath
791 main = "com.atlassian.clover.CloverInstr"
799 cloverInstrDir.getPath(),
801 def srcFiles = sourceSets.main.allJava.files
804 { file -> file.absolutePath }
807 args argsList.toArray()
810 delete cloverInstrDir
811 println("Clover: About to instrument "+srcFiles.size() +" files")
816 task cloverInstrTests(type: JavaExec) {
817 group = "Verification"
818 description = "Create clover instrumented source test files"
820 dependsOn cleanClover
822 inputs.files(testDir)
823 outputs.dir(cloverTestInstrDir)
825 classpath = sourceSets.clover.compileClasspath
826 main = "com.atlassian.clover.CloverInstr"
836 cloverTestInstrDir.getPath(),
838 args argsList.toArray()
841 delete cloverTestInstrDir
842 println("Clover: About to instrument test files")
848 group = "Verification"
849 description = "Create clover instrumented all source files"
851 dependsOn cloverInstrJava
852 dependsOn cloverInstrTests
856 cloverClasses.dependsOn cloverInstr
859 task cloverConsoleReport(type: JavaExec) {
860 group = "Verification"
861 description = "Creates clover console report"
864 file(cloverDb).exists()
867 inputs.dir cloverClassesDir
869 classpath = sourceSets.clover.runtimeClasspath
870 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
872 if (cloverreport_mem.length() > 0) {
873 maxHeapSize = cloverreport_mem
875 if (cloverreport_jvmargs.length() > 0) {
876 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
886 args argsList.toArray()
890 task cloverHtmlReport(type: JavaExec) {
891 group = "Verification"
892 description = "Creates clover HTML report"
895 file(cloverDb).exists()
898 def cloverHtmlDir = cloverReportDir
899 inputs.dir cloverClassesDir
900 outputs.dir cloverHtmlDir
902 classpath = sourceSets.clover.runtimeClasspath
903 main = "com.atlassian.clover.reporters.html.HtmlReporter"
905 if (cloverreport_mem.length() > 0) {
906 maxHeapSize = cloverreport_mem
908 if (cloverreport_jvmargs.length() > 0) {
909 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
920 if (cloverreport_html_options.length() > 0) {
921 argsList += cloverreport_html_options.split(" ")
924 args argsList.toArray()
928 task cloverXmlReport(type: JavaExec) {
929 group = "Verification"
930 description = "Creates clover XML report"
933 file(cloverDb).exists()
936 def cloverXmlFile = "${cloverReportDir}/clover.xml"
937 inputs.dir cloverClassesDir
938 outputs.file cloverXmlFile
940 classpath = sourceSets.clover.runtimeClasspath
941 main = "com.atlassian.clover.reporters.xml.XMLReporter"
943 if (cloverreport_mem.length() > 0) {
944 maxHeapSize = cloverreport_mem
946 if (cloverreport_jvmargs.length() > 0) {
947 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
958 if (cloverreport_xml_options.length() > 0) {
959 argsList += cloverreport_xml_options.split(" ")
962 args argsList.toArray()
967 group = "Verification"
968 description = "Creates clover reports"
970 dependsOn cloverXmlReport
971 dependsOn cloverHtmlReport
978 sourceCompatibility = compile_source_compatibility
979 targetCompatibility = compile_target_compatibility
980 options.compilerArgs += additional_compiler_args
981 print ("Setting target compatibility to "+targetCompatibility+"\n")
983 //classpath += configurations.cloverRuntime
989 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
990 sourceCompatibility = compile_source_compatibility
991 targetCompatibility = compile_target_compatibility
992 options.compilerArgs = additional_compiler_args
993 options.encoding = "UTF-8"
995 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1002 sourceCompatibility = compile_source_compatibility
1003 targetCompatibility = compile_target_compatibility
1004 options.compilerArgs = additional_compiler_args
1006 print ("Setting target compatibility to "+targetCompatibility+"\n")
1013 delete sourceSets.main.java.outputDir
1019 dependsOn cleanClover
1021 delete sourceSets.test.java.outputDir
1026 // format is a string like date.format("dd MMMM yyyy")
1027 def getDate(format) {
1028 def date = new Date()
1029 return date.format(format)
1033 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1034 MutableDataSet options = new MutableDataSet()
1036 def extensions = new ArrayList<>()
1037 extensions.add(AnchorLinkExtension.create())
1038 extensions.add(AutolinkExtension.create())
1039 extensions.add(StrikethroughExtension.create())
1040 extensions.add(TaskListExtension.create())
1041 extensions.add(TablesExtension.create())
1042 extensions.add(TocExtension.create())
1044 options.set(Parser.EXTENSIONS, extensions)
1046 // set GFM table parsing options
1047 options.set(TablesExtension.WITH_CAPTION, false)
1048 options.set(TablesExtension.COLUMN_SPANS, false)
1049 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1050 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1051 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1052 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1053 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1055 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1056 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1057 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1058 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1060 Parser parser = Parser.builder(options).build()
1061 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1063 mdFiles.each { mdFile ->
1064 // add table of contents
1065 def mdText = "[TOC]\n"+mdFile.text
1067 // grab the first top-level title
1069 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1070 def matcher = mdText =~ titleRegex
1071 if (matcher.size() > 0) {
1072 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1073 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1075 // or use the filename if none found
1076 if (title == null) {
1077 title = mdFile.getName()
1080 Node document = parser.parse(mdText)
1081 String htmlBody = renderer.render(document)
1082 def htmlText = '''<html>
1083 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1084 <html xmlns="http://www.w3.org/1999/xhtml">
1086 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1087 <meta http-equiv="Content-Style-Type" content="text/css" />
1088 <meta name="generator" content="flexmark" />
1090 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1092 <style type="text/css">code{white-space: pre;}</style>
1094 htmlText += ((cssFile != null) ? cssFile.text : '')
1095 htmlText += '''</head>
1098 htmlText += htmlBody
1104 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1105 def htmlFile = file(htmlFilePath)
1106 println("Creating ${htmlFilePath}")
1107 htmlFile.text = htmlText
1112 task copyDocs(type: Copy) {
1113 def inputDir = "${jalviewDir}/${doc_dir}"
1114 def outputDir = "${docBuildDir}/${doc_dir}"
1118 include('**/*.html')
1120 filter(ReplaceTokens,
1124 'Version-Rel': JALVIEW_VERSION,
1125 'Year-Rel': getDate("yyyy")
1132 exclude('**/*.html')
1137 inputs.dir(inputDir)
1138 outputs.dir(outputDir)
1142 task convertMdFiles {
1144 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1145 def cssFile = file("${jalviewDir}/${flexmark_css}")
1148 convertMdToHtml(mdFiles, cssFile)
1151 inputs.files(mdFiles)
1152 inputs.file(cssFile)
1155 mdFiles.each { mdFile ->
1156 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1157 htmlFiles.add(file(htmlFilePath))
1159 outputs.files(htmlFiles)
1163 task copyHelp(type: Copy) {
1164 def inputDir = helpSourceDir
1165 def outputDir = "${helpBuildDir}/${help_dir}"
1169 include('**/*.html')
1173 filter(ReplaceTokens,
1177 'Version-Rel': JALVIEW_VERSION,
1178 'Year-Rel': getDate("yyyy")
1185 exclude('**/*.html')
1192 inputs.dir(inputDir)
1193 outputs.files(helpFile)
1194 outputs.dir(outputDir)
1198 task copyResources(type: Copy) {
1200 description = "Copy (and make text substitutions in) the resources dir to the build area"
1202 def inputDir = resourceDir
1203 def outputDir = resourcesBuildDir
1207 include('**/*.html')
1209 filter(ReplaceTokens,
1213 'Version-Rel': JALVIEW_VERSION,
1214 'Year-Rel': getDate("yyyy")
1221 exclude('**/*.html')
1226 inputs.dir(inputDir)
1227 outputs.dir(outputDir)
1230 task copyChannelResources(type: Copy) {
1231 dependsOn copyResources
1233 description = "Copy the channel resources dir to the build resources area"
1235 def inputDir = "${channelDir}/${resource_dir}"
1236 def outputDir = resourcesBuildDir
1240 inputs.dir(inputDir)
1241 outputs.dir(outputDir)
1244 task createBuildProperties(type: WriteProperties) {
1245 dependsOn copyResources
1247 description = "Create the ${buildProperties} file"
1249 inputs.dir(sourceDir)
1250 inputs.dir(resourcesBuildDir)
1251 outputFile (buildProperties)
1252 // taking time specific comment out to allow better incremental builds
1253 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1254 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1255 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1256 property "VERSION", JALVIEW_VERSION
1257 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1258 if (getdownSetAppBaseProperty) {
1259 property "GETDOWNAPPBASE", getdownAppBase
1260 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1262 outputs.file(outputFile)
1266 task buildIndices(type: JavaExec) {
1268 classpath = sourceSets.main.compileClasspath
1269 main = "com.sun.java.help.search.Indexer"
1270 workingDir = "${helpBuildDir}/${help_dir}"
1273 inputs.dir("${workingDir}/${argDir}")
1275 outputs.dir("${classesDir}/doc")
1276 outputs.dir("${classesDir}/help")
1277 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1278 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1279 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1280 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1281 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1282 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1285 task buildResources {
1286 dependsOn copyResources
1287 dependsOn copyChannelResources
1288 dependsOn createBuildProperties
1292 dependsOn buildResources
1295 dependsOn convertMdFiles
1296 dependsOn buildIndices
1300 compileJava.dependsOn prepare
1301 run.dependsOn compileJava
1302 //run.dependsOn prepare
1305 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1310 dependsOn cloverClasses
1312 dependsOn compileJava //?
1316 includeGroups testng_groups
1317 excludeGroups testng_excluded_groups
1319 useDefaultListeners=true
1322 maxHeapSize = "1024m"
1324 workingDir = jalviewDir
1325 def testLaf = project.findProperty("test_laf")
1326 if (testLaf != null) {
1327 println("Setting Test LaF to '${testLaf}'")
1328 systemProperty "laf", testLaf
1330 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1331 if (testHiDPIScale != null) {
1332 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1333 systemProperty "sun.java2d.uiScale", testHiDPIScale
1335 sourceCompatibility = compile_source_compatibility
1336 targetCompatibility = compile_target_compatibility
1337 jvmArgs += additional_compiler_args
1341 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1347 task compileLinkCheck(type: JavaCompile) {
1349 classpath = files("${jalviewDir}/${utils_dir}")
1350 destinationDir = file("${jalviewDir}/${utils_dir}")
1351 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1353 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1354 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1355 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1356 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1360 task linkCheck(type: JavaExec) {
1362 dependsOn compileLinkCheck
1364 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1365 classpath = files("${jalviewDir}/${utils_dir}")
1366 main = "HelpLinksChecker"
1367 workingDir = jalviewDir
1368 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1370 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1372 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1375 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1379 inputs.dir(helpBuildDir)
1380 outputs.file(helpLinksCheckerOutFile)
1384 // import the pubhtmlhelp target
1385 ant.properties.basedir = "${jalviewDir}"
1386 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1387 ant.importBuild "${utils_dir}/publishHelp.xml"
1390 task cleanPackageDir(type: Delete) {
1392 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1402 attributes "Main-Class": main_class,
1403 "Permissions": "all-permissions",
1404 "Application-Name": install4jApplicationName,
1405 "Codebase": application_codebase,
1406 "Implementation-Version": JALVIEW_VERSION
1409 def outputDir = "${jalviewDir}/${package_dir}"
1410 destinationDirectory = file(outputDir)
1411 archiveFileName = rootProject.name+".jar"
1417 exclude "**/*.jar.*"
1419 inputs.dir(sourceSets.main.java.outputDir)
1420 sourceSets.main.resources.srcDirs.each{ dir ->
1423 outputs.file("${outputDir}/${archiveFileName}")
1427 task copyJars(type: Copy) {
1428 from fileTree(dir: classesDir, include: "**/*.jar").files
1429 into "${jalviewDir}/${package_dir}"
1433 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1434 task syncJars(type: Sync) {
1436 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1437 into "${jalviewDir}/${package_dir}"
1439 include jar.archiveFileName.getOrNull()
1446 description = "Put all required libraries in dist"
1447 // order of "cleanPackageDir", "copyJars", "jar" important!
1448 jar.mustRunAfter cleanPackageDir
1449 syncJars.mustRunAfter cleanPackageDir
1450 dependsOn cleanPackageDir
1453 outputs.dir("${jalviewDir}/${package_dir}")
1458 dependsOn cleanPackageDir
1465 group = "distribution"
1466 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1470 from ("${jalviewDir}/${libDistDir}") {
1474 attributes "Implementation-Version": JALVIEW_VERSION,
1475 "Application-Name": install4jApplicationName
1477 mainClassName = shadow_jar_main_class
1479 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1484 task getdownWebsite() {
1485 group = "distribution"
1486 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1491 def getdownWebsiteResourceFilenames = []
1492 def getdownTextString = ""
1493 def getdownResourceDir = getdownResourceDir
1494 def getdownResourceFilenames = []
1497 // clean the getdown website and files dir before creating getdown folders
1498 delete getdownWebsiteDir
1499 delete getdownFilesDir
1502 from buildProperties
1503 rename(file(buildProperties).getName(), getdown_build_properties)
1506 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1508 // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
1509 def props = project.properties.sort { it.key }
1510 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1511 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1513 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1514 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1516 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1517 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1519 if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
1520 props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
1521 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
1522 props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
1523 props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
1524 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
1525 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
1528 props.put("getdown_txt_title", jalview_name)
1529 props.put("getdown_txt_ui.name", install4jApplicationName)
1531 // start with appbase
1532 getdownTextString += "appbase = ${getdownAppBase}\n"
1533 props.each{ prop, val ->
1534 if (prop.startsWith("getdown_txt_") && val != null) {
1535 if (prop.startsWith("getdown_txt_multi_")) {
1536 def key = prop.substring(18)
1537 val.split(",").each{ v ->
1538 def line = "${key} = ${v}\n"
1539 getdownTextString += line
1542 // file values rationalised
1543 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1545 if (val.indexOf('/') == 0) {
1548 } else if (val.indexOf('/') > 0) {
1549 // relative path (relative to jalviewDir)
1550 r = file( "${jalviewDir}/${val}" )
1553 val = "${getdown_resource_dir}/" + r.getName()
1554 getdownWebsiteResourceFilenames += val
1555 getdownResourceFilenames += r.getPath()
1558 if (! prop.startsWith("getdown_txt_resource")) {
1559 def line = prop.substring(12) + " = ${val}\n"
1560 getdownTextString += line
1566 getdownWebsiteResourceFilenames.each{ filename ->
1567 getdownTextString += "resource = ${filename}\n"
1569 getdownResourceFilenames.each{ filename ->
1572 into getdownResourceDir
1577 fileTree(file(package_dir)).each{ f ->
1578 if (f.isDirectory()) {
1579 def files = fileTree(dir: f, include: ["*"]).getFiles()
1581 } else if (f.exists()) {
1585 codeFiles.sort().each{f ->
1586 def name = f.getName()
1587 def line = "code = ${getdownAppDistDir}/${name}\n"
1588 getdownTextString += line
1595 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1597 if (JAVA_VERSION.equals("11")) {
1598 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1599 j11libFiles.sort().each{f ->
1600 def name = f.getName()
1601 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1602 getdownTextString += line
1605 into getdownJ11libDir
1611 // 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.
1612 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1613 getdownTextString += "resource = ${getdown_launcher_new}\n"
1614 getdownTextString += "class = ${main_class}\n"
1615 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
1616 if (getdownSetAppBaseProperty) {
1617 getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
1618 getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
1621 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1622 getdown_txt.write(getdownTextString)
1624 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1625 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1626 launchJvl.write("appbase=${getdownAppBase}")
1628 // files going into the getdown website dir: getdown-launcher.jar
1630 from getdownLauncher
1631 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1632 into getdownWebsiteDir
1635 // files going into the getdown website dir: getdown-launcher(-local).jar
1637 from getdownLauncher
1638 if (file(getdownLauncher).getName() != getdown_launcher) {
1639 rename(file(getdownLauncher).getName(), getdown_launcher)
1641 into getdownWebsiteDir
1644 // files going into the getdown website dir: ./install dir and files
1645 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1648 from getdownLauncher
1649 from "${getdownAppDir}/${getdown_build_properties}"
1650 if (file(getdownLauncher).getName() != getdown_launcher) {
1651 rename(file(getdownLauncher).getName(), getdown_launcher)
1653 into getdownInstallDir
1656 // and make a copy in the getdown files dir (these are not downloaded by getdown)
1658 from getdownInstallDir
1659 into getdownFilesInstallDir
1663 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
1667 from getdownLauncher
1668 from "${getdownWebsiteDir}/${getdown_build_properties}"
1669 if (file(getdownLauncher).getName() != getdown_launcher) {
1670 rename(file(getdownLauncher).getName(), getdown_launcher)
1672 into getdownFilesDir
1675 // and ./resources (not all downloaded by getdown)
1677 from getdownResourceDir
1678 into "${getdownFilesDir}/${getdown_resource_dir}"
1683 inputs.dir("${jalviewDir}/${package_dir}")
1685 outputs.dir(getdownWebsiteDir)
1686 outputs.dir(getdownFilesDir)
1690 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1691 task getdownDigestDir(type: JavaExec) {
1693 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1695 def digestDirPropertyName = "DIGESTDIR"
1697 classpath = files(getdownLauncher)
1698 def digestDir = findProperty(digestDirPropertyName)
1699 if (digestDir == null) {
1700 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1704 main = "com.threerings.getdown.tools.Digester"
1708 task getdownDigest(type: JavaExec) {
1709 group = "distribution"
1710 description = "Digest the getdown website folder"
1711 dependsOn getdownWebsite
1713 classpath = files(getdownLauncher)
1715 main = "com.threerings.getdown.tools.Digester"
1716 args getdownWebsiteDir
1717 inputs.dir(getdownWebsiteDir)
1718 outputs.file("${getdownWebsiteDir}/digest2.txt")
1723 group = "distribution"
1724 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1725 dependsOn getdownDigest
1727 if (reportRsyncCommand) {
1728 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1729 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1730 println "LIKELY RSYNC COMMAND:"
1731 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1732 if (RUNRSYNC == "true") {
1734 commandLine "mkdir", "-p", toDir
1737 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1745 tasks.withType(JavaCompile) {
1746 options.encoding = 'UTF-8'
1752 delete getdownWebsiteDir
1753 delete getdownFilesDir
1759 if (file(install4jHomeDir).exists()) {
1761 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1762 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1763 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1764 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1766 installDir(file(install4jHomeDir))
1768 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1772 task copyInstall4jTemplate {
1773 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1774 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1775 inputs.file(install4jTemplateFile)
1776 inputs.file(install4jFileAssociationsFile)
1777 inputs.property("CHANNEL", { CHANNEL })
1778 outputs.file(install4jConfFile)
1781 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1783 // turn off code signing if no OSX_KEYPASS
1784 if (OSX_KEYPASS == "") {
1785 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1786 codeSigning.'@macEnabled' = "false"
1788 install4jConfigXml.'**'.windows.each { windows ->
1789 windows.'@runPostProcessor' = "false"
1793 // turn off checksum creation for LOCAL channel
1794 def e = install4jConfigXml.application[0]
1795 if (CHANNEL == "LOCAL") {
1796 e.'@createChecksums' = "false"
1798 e.'@createChecksums' = "true"
1801 // put file association actions where placeholder action is
1802 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1803 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1804 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1805 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1806 def parent = a.parent()
1808 fileAssociationActions.each { faa ->
1811 // don't need to continue in .any loop once replacements have been made
1816 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1817 // NB we're deleting the /other/ one!
1818 // Also remove the examples subdir from non-release versions
1819 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1820 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1821 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1822 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1824 // remove the examples subdir from Full File Set
1825 def files = install4jConfigXml.files[0]
1826 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1827 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1828 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1829 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1830 dirEntry.parent().remove(dirEntry)
1832 install4jConfigXml.'**'.action.any { a ->
1833 if (a.'@customizedId' == customizedIdToDelete) {
1834 def parent = a.parent()
1840 // write install4j file
1841 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1848 delete install4jConfFile
1853 task installers(type: com.install4j.gradle.Install4jTask) {
1854 group = "distribution"
1855 description = "Create the install4j installers"
1857 dependsOn copyInstall4jTemplate
1859 projectFile = install4jConfFile
1861 // create an md5 for the input files to use as version for install4j conf file
1862 def digest = MessageDigest.getInstance("MD5")
1864 (file("${install4jDir}/${install4j_template}").text +
1865 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1866 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1867 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1868 if (filesMd5.length() >= 8) {
1869 filesMd5 = filesMd5.substring(0,8)
1871 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1872 // make install4jBuildDir relative to jalviewDir
1873 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1876 'JALVIEW_NAME': jalview_name,
1877 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1878 'JALVIEW_DIR': "../..",
1879 'OSX_KEYSTORE': OSX_KEYSTORE,
1880 'OSX_APPLEID': OSX_APPLEID,
1881 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
1882 'JSIGN_SH': JSIGN_SH,
1883 'JRE_DIR': getdown_app_dir_java,
1884 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1885 'JALVIEW_VERSION': JALVIEW_VERSION,
1886 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1887 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1888 'JAVA_VERSION': JAVA_VERSION,
1889 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1890 'VERSION': JALVIEW_VERSION,
1891 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1892 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1893 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1894 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1895 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1896 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1897 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1898 'BUNDLE_ID': install4jBundleId,
1899 'INTERNAL_ID': install4jInternalId,
1900 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1901 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
1902 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1903 'MACOS_DMG_WRAPPER_SCRIPT': install4j_dmg_wrapper_script,
1904 'INSTALLER_NAME': install4jInstallerName,
1905 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1906 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1907 'GETDOWN_FILES_DIR': getdown_files_dir,
1908 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1909 'GETDOWN_DIST_DIR': getdownAppDistDir,
1910 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1911 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1912 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1913 'BUILD_DIR': install4jBuildDir,
1914 'APPLICATION_CATEGORIES': install4j_application_categories,
1915 'APPLICATION_FOLDER': install4jApplicationFolder,
1916 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1917 'EXECUTABLE_NAME': install4jExecutableName,
1918 'EXTRA_SCHEME': install4jExtraScheme,
1919 'MAC_ICONS_FILE': install4jMacIconsFile,
1920 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
1921 'PNG_ICON_FILE': install4jPngIconFile,
1922 'BACKGROUND': install4jBackground,
1926 //println("INSTALL4J VARIABLES:")
1927 //variables.each{k,v->println("${k}=${v}")}
1929 destination = "${jalviewDir}/${install4jBuildDir}"
1930 buildSelected = true
1932 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1934 disableSigning = true
1935 disableNotarization = true
1939 macKeystorePassword = OSX_KEYPASS
1942 if (OSX_ALTOOLPASS) {
1943 appleIdPassword = OSX_ALTOOLPASS
1944 disableNotarization = false
1946 disableNotarization = true
1950 println("Using projectFile "+projectFile)
1951 if (!disableNotarization) { println("Will notarize OSX App DMG") }
1955 inputs.dir(getdownWebsiteDir)
1956 inputs.file(install4jConfFile)
1957 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1958 inputs.dir(macosJavaVMDir)
1959 inputs.dir(windowsJavaVMDir)
1960 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
1966 eclipse().configFile(eclipse_codestyle_file)
1971 task sourceDist(type: Tar) {
1972 group "distribution"
1973 description "Create a source .tar.gz file for distribution"
1975 dependsOn createBuildProperties
1976 dependsOn convertMdFiles
1978 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1979 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1980 archiveFileName = outputFileName
1982 compression Compression.GZIP
1997 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
1999 "utils/InstallAnywhere",
2014 "gradle.properties",
2025 ".settings/org.eclipse.jdt.core.jalview.prefs",
2029 exclude (EXCLUDE_FILES)
2030 include (PROCESS_FILES)
2031 filter(ReplaceTokens,
2035 'Version-Rel': JALVIEW_VERSION,
2036 'Year-Rel': getDate("yyyy")
2041 exclude (EXCLUDE_FILES)
2042 exclude (PROCESS_FILES)
2043 exclude ("appletlib")
2044 exclude ("**/*locales")
2045 exclude ("*locales/**")
2046 exclude ("utils/InstallAnywhere")
2048 exclude (getdown_files_dir)
2049 exclude (getdown_website_dir)
2051 // exluding these as not using jars as modules yet
2052 exclude ("${j11modDir}/**/*.jar")
2055 include(INCLUDE_FILES)
2057 // from (jalviewDir) {
2058 // // explicit includes for stuff that seemed to not get included
2059 // include(fileTree("test/**/*."))
2060 // exclude(EXCLUDE_FILES)
2061 // exclude(PROCESS_FILES)
2064 from(file(buildProperties).getParent()) {
2065 include(file(buildProperties).getName())
2066 rename(file(buildProperties).getName(), "build_properties")
2068 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2077 dependsOn pubhtmlhelp
2079 inputs.dir("${helpBuildDir}/${help_dir}")
2080 outputs.dir("${buildDir}/distributions/${help_dir}")
2084 task j2sSetHeadlessBuild {
2091 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2093 description "Enable the alternative J2S Config file for headless build"
2095 outputFile = jalviewjsJ2sSettingsFileName
2096 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2097 def j2sProps = new Properties()
2098 if (j2sPropsFile.exists()) {
2100 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2101 j2sProps.load(j2sPropsFileFIS)
2102 j2sPropsFileFIS.close()
2104 j2sProps.each { prop, val ->
2107 } catch (Exception e) {
2108 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2112 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2113 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2118 task jalviewjsSetEclipseWorkspace {
2119 def propKey = "jalviewjs_eclipse_workspace"
2121 if (project.hasProperty(propKey)) {
2122 propVal = project.getProperty(propKey)
2123 if (propVal.startsWith("~/")) {
2124 propVal = System.getProperty("user.home") + propVal.substring(1)
2127 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2128 def propsFile = file(propsFileName)
2129 def eclipseWsDir = propVal
2130 def props = new Properties()
2132 def writeProps = true
2133 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2134 def ins = new FileInputStream(propsFileName)
2137 if (props.getProperty(propKey, null) != null) {
2138 eclipseWsDir = props.getProperty(propKey)
2143 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2144 def tempDir = File.createTempDir()
2145 eclipseWsDir = tempDir.getAbsolutePath()
2148 eclipseWorkspace = file(eclipseWsDir)
2151 // do not run a headless transpile when we claim to be in Eclipse
2153 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2154 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2156 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2160 props.setProperty(propKey, eclipseWsDir)
2161 propsFile.parentFile.mkdirs()
2162 def bytes = new ByteArrayOutputStream()
2163 props.store(bytes, null)
2164 def propertiesString = bytes.toString()
2165 propsFile.text = propertiesString
2171 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2174 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2175 outputs.file(propsFileName)
2176 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2180 task jalviewjsEclipsePaths {
2183 def eclipseRoot = jalviewjs_eclipse_root
2184 if (eclipseRoot.startsWith("~/")) {
2185 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2187 if (OperatingSystem.current().isMacOsX()) {
2188 eclipseRoot += "/Eclipse.app"
2189 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2190 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2191 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2192 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2193 eclipseRoot += "/eclipse"
2195 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2196 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2197 } else { // linux or unix
2198 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2199 eclipseRoot += "/eclipse"
2200 println("eclipseDir exists")
2202 eclipseBinary = "${eclipseRoot}/eclipse"
2203 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2206 eclipseVersion = "4.13" // default
2207 def assumedVersion = true
2208 if (file(eclipseProduct).exists()) {
2209 def fis = new FileInputStream(eclipseProduct)
2210 def props = new Properties()
2212 eclipseVersion = props.getProperty("version")
2214 assumedVersion = false
2217 def propKey = "eclipse_debug"
2218 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2221 // do not run a headless transpile when we claim to be in Eclipse
2223 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2224 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2226 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2229 if (!assumedVersion) {
2230 println("ECLIPSE VERSION=${eclipseVersion}")
2236 task printProperties {
2238 description "Output to console all System.properties"
2240 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2246 dependsOn eclipseProject
2247 dependsOn eclipseClasspath
2248 dependsOn eclipseJdt
2252 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2253 task jalviewjsEclipseCopyDropins(type: Copy) {
2254 dependsOn jalviewjsEclipsePaths
2256 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2257 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2258 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2265 // this eclipse -clean doesn't actually work
2266 task jalviewjsCleanEclipse(type: Exec) {
2267 dependsOn eclipseSetup
2268 dependsOn jalviewjsEclipsePaths
2269 dependsOn jalviewjsEclipseCopyDropins
2271 executable(eclipseBinary)
2272 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2278 def inputString = """exit
2281 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2282 standardInput = inputByteStream
2285 /* not really working yet
2286 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2290 task jalviewjsTransferUnzipSwingJs {
2291 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2295 from zipTree(file_zip)
2296 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2300 inputs.file file_zip
2301 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2305 task jalviewjsTransferUnzipLib {
2306 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2309 zipFiles.each { file_zip ->
2311 from zipTree(file_zip)
2312 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2317 inputs.files zipFiles
2318 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2322 task jalviewjsTransferUnzipAllLibs {
2323 dependsOn jalviewjsTransferUnzipSwingJs
2324 dependsOn jalviewjsTransferUnzipLib
2328 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2330 description "Create the alternative j2s file from the j2s.* properties"
2332 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2333 def siteDirProperty = "j2s.site.directory"
2334 def setSiteDir = false
2335 jalviewjsJ2sProps.each { prop, val ->
2337 if (prop == siteDirProperty) {
2338 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2339 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2345 if (!setSiteDir) { // default site location, don't override specifically set property
2346 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2349 outputFile = jalviewjsJ2sAltSettingsFileName
2352 inputs.properties(jalviewjsJ2sProps)
2353 outputs.file(jalviewjsJ2sAltSettingsFileName)
2358 task jalviewjsEclipseSetup {
2359 dependsOn jalviewjsEclipseCopyDropins
2360 dependsOn jalviewjsSetEclipseWorkspace
2361 dependsOn jalviewjsCreateJ2sSettings
2365 task jalviewjsSyncAllLibs (type: Sync) {
2366 dependsOn jalviewjsTransferUnzipAllLibs
2367 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2368 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2369 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2373 def outputFiles = []
2374 rename { filename ->
2375 outputFiles += "${outputDir}/${filename}"
2381 outputs.files outputFiles
2382 inputs.files inputFiles
2386 task jalviewjsSyncResources (type: Sync) {
2387 dependsOn buildResources
2389 def inputFiles = fileTree(dir: resourcesBuildDir)
2390 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2394 def outputFiles = []
2395 rename { filename ->
2396 outputFiles += "${outputDir}/${filename}"
2402 outputs.files outputFiles
2403 inputs.files inputFiles
2407 task jalviewjsSyncSiteResources (type: Sync) {
2408 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2409 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2413 def outputFiles = []
2414 rename { filename ->
2415 outputFiles += "${outputDir}/${filename}"
2421 outputs.files outputFiles
2422 inputs.files inputFiles
2426 task jalviewjsSyncBuildProperties (type: Sync) {
2427 dependsOn createBuildProperties
2428 def inputFiles = [file(buildProperties)]
2429 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2433 def outputFiles = []
2434 rename { filename ->
2435 outputFiles += "${outputDir}/${filename}"
2441 outputs.files outputFiles
2442 inputs.files inputFiles
2446 task jalviewjsProjectImport(type: Exec) {
2447 dependsOn eclipseSetup
2448 dependsOn jalviewjsEclipsePaths
2449 dependsOn jalviewjsEclipseSetup
2452 // do not run a headless import when we claim to be in Eclipse
2454 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2455 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2457 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2461 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2462 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2463 executable(eclipseBinary)
2464 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2468 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2470 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2471 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2474 inputs.file("${jalviewDir}/.project")
2475 outputs.upToDateWhen {
2476 file(projdir).exists()
2481 task jalviewjsTranspile(type: Exec) {
2482 dependsOn jalviewjsEclipseSetup
2483 dependsOn jalviewjsProjectImport
2484 dependsOn jalviewjsEclipsePaths
2486 dependsOn jalviewjsEnableAltFileProperty
2490 // do not run a headless transpile when we claim to be in Eclipse
2492 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2493 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2495 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2499 executable(eclipseBinary)
2500 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2504 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2506 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2507 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2513 stdout = new ByteArrayOutputStream()
2514 stderr = new ByteArrayOutputStream()
2516 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2517 def logOutFile = file(logOutFileName)
2518 logOutFile.createNewFile()
2519 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2520 BINARY: ${eclipseBinary}
2521 VERSION: ${eclipseVersion}
2522 WORKSPACE: ${eclipseWorkspace}
2523 DEBUG: ${eclipseDebug}
2526 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2527 // combine stdout and stderr
2528 def logErrFOS = logOutFOS
2530 if (jalviewjs_j2s_to_console.equals("true")) {
2531 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2532 new org.apache.tools.ant.util.TeeOutputStream(
2536 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2537 new org.apache.tools.ant.util.TeeOutputStream(
2542 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2545 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2552 if (stdout.toString().contains("Error processing ")) {
2553 // j2s did not complete transpile
2554 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2555 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2556 println("IGNORING TRANSPILE ERRORS")
2557 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2559 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2564 inputs.dir("${jalviewDir}/${sourceDir}")
2565 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2566 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2570 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2572 def stdout = new ByteArrayOutputStream()
2573 def stderr = new ByteArrayOutputStream()
2575 def coreFile = file(jsfile)
2577 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2579 logOutFile.createNewFile()
2580 logOutFile.append(msg+"\n")
2582 def coreTop = file(prefixFile)
2583 def coreBottom = file(suffixFile)
2584 coreFile.getParentFile().mkdirs()
2585 coreFile.createNewFile()
2586 coreFile.write( coreTop.getText("UTF-8") )
2590 def t = f.getText("UTF-8")
2591 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2592 coreFile.append( t )
2594 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2596 logOutFile.append(msg+"\n")
2599 coreFile.append( coreBottom.getText("UTF-8") )
2601 msg = "Generating ${zjsfile}"
2603 logOutFile.append(msg+"\n")
2604 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2605 def logErrFOS = logOutFOS
2608 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2609 main = "com.google.javascript.jscomp.CommandLineRunner"
2610 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2611 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2614 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2616 logOutFile.append(msg+"\n")
2618 if (logOutConsole) {
2619 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2620 new org.apache.tools.ant.util.TeeOutputStream(
2624 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2625 new org.apache.tools.ant.util.TeeOutputStream(
2630 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2633 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2640 logOutFile.append(msg+"\n")
2644 task jalviewjsBuildAllCores {
2646 description "Build the core js lib closures listed in the classlists dir"
2647 dependsOn jalviewjsTranspile
2648 dependsOn jalviewjsTransferUnzipSwingJs
2650 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2651 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2652 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2653 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2654 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2655 def prefixFile = "${jsDir}/core/coretop2.js"
2656 def suffixFile = "${jsDir}/core/corebottom2.js"
2658 inputs.file prefixFile
2659 inputs.file suffixFile
2661 def classlistFiles = []
2662 // add the classlists found int the jalviewjs_classlists_dir
2663 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2665 def name = file.getName() - ".txt"
2672 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2673 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2674 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2676 jalviewjsCoreClasslists = []
2678 classlistFiles.each {
2681 def file = hash['file']
2682 if (! file.exists()) {
2683 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2684 return false // this is a "continue" in groovy .each closure
2686 def name = hash['name']
2688 name = file.getName() - ".txt"
2696 def list = fileTree(dir: j2sDir, includes: filelist)
2698 def jsfile = "${outputDir}/core${name}.js"
2699 def zjsfile = "${outputDir}/core${name}.z.js"
2701 jalviewjsCoreClasslists += [
2710 outputs.file(jsfile)
2711 outputs.file(zjsfile)
2714 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2715 def stevesoftClasslistName = "_stevesoft"
2716 def stevesoftClasslist = [
2717 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2718 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2719 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2720 'name': stevesoftClasslistName
2722 jalviewjsCoreClasslists += stevesoftClasslist
2723 inputs.files(stevesoftClasslist['list'])
2724 outputs.file(stevesoftClasslist['jsfile'])
2725 outputs.file(stevesoftClasslist['zjsfile'])
2728 def allClasslistName = "_all"
2729 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2730 allJsFiles += fileTree(
2734 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2735 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2736 "**/org/jmol/export/JSExporter.js"
2739 allJsFiles += fileTree(
2743 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2744 "**/sun/misc/Unsafe.js",
2745 "**/swingjs/jquery/jquery-editable-select.js",
2746 "**/swingjs/jquery/j2sComboBox.js",
2747 "**/sun/misc/FloatingDecimal.js"
2750 def allClasslist = [
2751 'jsfile': "${outputDir}/core${allClasslistName}.js",
2752 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2754 'name': allClasslistName
2756 // not including this version of "all" core at the moment
2757 //jalviewjsCoreClasslists += allClasslist
2758 inputs.files(allClasslist['list'])
2759 outputs.file(allClasslist['jsfile'])
2760 outputs.file(allClasslist['zjsfile'])
2763 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2764 logOutFile.getParentFile().mkdirs()
2765 logOutFile.createNewFile()
2766 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2768 jalviewjsCoreClasslists.each {
2769 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2776 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2779 into file(outputFile).getParentFile()
2780 rename { filename ->
2781 if (filename.equals(inputFile.getName())) {
2782 return file(outputFile).getName()
2786 filter(ReplaceTokens,
2790 'MAIN': '"'+main_class+'"',
2792 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2793 'COREKEY': jalviewjs_core_key,
2794 'CORENAME': coreName
2801 task jalviewjsPublishCoreTemplates {
2802 dependsOn jalviewjsBuildAllCores
2803 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2804 def inputFile = file(inputFileName)
2805 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2807 def outputFiles = []
2808 jalviewjsCoreClasslists.each { cl ->
2809 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2810 cl['outputfile'] = outputFile
2811 outputFiles += outputFile
2815 jalviewjsCoreClasslists.each { cl ->
2816 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2819 inputs.file(inputFile)
2820 outputs.files(outputFiles)
2824 task jalviewjsSyncCore (type: Sync) {
2825 dependsOn jalviewjsBuildAllCores
2826 dependsOn jalviewjsPublishCoreTemplates
2827 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2828 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2832 def outputFiles = []
2833 rename { filename ->
2834 outputFiles += "${outputDir}/${filename}"
2840 outputs.files outputFiles
2841 inputs.files inputFiles
2845 // this Copy version of TransferSiteJs will delete anything else in the target dir
2846 task jalviewjsCopyTransferSiteJs(type: Copy) {
2847 dependsOn jalviewjsTranspile
2848 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2849 into "${jalviewDir}/${jalviewjsSiteDir}"
2853 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2854 task jalviewjsSyncTransferSiteJs(type: Sync) {
2855 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2857 into "${jalviewDir}/${jalviewjsSiteDir}"
2864 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2865 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2866 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2867 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2869 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2870 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2871 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2872 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2875 task jalviewjsPrepareSite {
2877 description "Prepares the website folder including unzipping files and copying resources"
2878 dependsOn jalviewjsSyncAllLibs
2879 dependsOn jalviewjsSyncResources
2880 dependsOn jalviewjsSyncSiteResources
2881 dependsOn jalviewjsSyncBuildProperties
2882 dependsOn jalviewjsSyncCore
2886 task jalviewjsBuildSite {
2888 description "Builds the whole website including transpiled code"
2889 dependsOn jalviewjsCopyTransferSiteJs
2890 dependsOn jalviewjsPrepareSite
2894 task cleanJalviewjsTransferSite {
2896 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2897 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2898 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2899 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2904 task cleanJalviewjsSite {
2905 dependsOn cleanJalviewjsTransferSite
2907 delete "${jalviewDir}/${jalviewjsSiteDir}"
2912 task jalviewjsSiteTar(type: Tar) {
2914 description "Creates a tar.gz file for the website"
2915 dependsOn jalviewjsBuildSite
2916 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2917 archiveFileName = outputFilename
2919 compression Compression.GZIP
2921 from "${jalviewDir}/${jalviewjsSiteDir}"
2922 into jalviewjs_site_dir // this is inside the tar file
2924 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
2928 task jalviewjsServer {
2930 def filename = "jalviewjsTest.html"
2931 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
2932 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
2935 SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
2936 def port = Integer.valueOf(jalviewjs_server_port)
2941 while(port < start+1000 && !running) {
2943 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
2944 jalviewjsServer = factory.start(doc_root, port)
2946 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
2947 println("SERVER STARTED with document root ${doc_root}.")
2948 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
2949 println("For debug: "+url+"?j2sdebug")
2950 println("For verbose: "+url+"?j2sverbose")
2951 } catch (Exception e) {
2956 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
2957 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
2958 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
2960 jalviewjsCoreClasslists.each { cl ->
2961 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
2963 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
2965 println("For core ${cl.name}: "+urlcore)
2968 file(htmlFile).text = htmlText
2971 outputs.file(htmlFile)
2972 outputs.upToDateWhen({false})
2976 task cleanJalviewjsAll {
2978 description "Delete all configuration and build artifacts to do with JalviewJS build"
2979 dependsOn cleanJalviewjsSite
2980 dependsOn jalviewjsEclipsePaths
2983 delete "${jalviewDir}/${jalviewjsBuildDir}"
2984 delete "${jalviewDir}/${eclipse_bin_dir}"
2985 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
2986 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
2988 delete jalviewjsJ2sAltSettingsFileName
2991 outputs.upToDateWhen( { false } )
2995 task jalviewjsIDE_checkJ2sPlugin {
2996 group "00 JalviewJS in Eclipse"
2997 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3000 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3001 def j2sPluginFile = file(j2sPlugin)
3002 def eclipseHome = System.properties["eclipse.home.location"]
3003 if (eclipseHome == null || ! IN_ECLIPSE) {
3004 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3006 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3007 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3008 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3009 eclipseJ2sPluginDirs += altPluginsDir
3011 def foundPlugin = false
3012 def j2sPluginFileName = j2sPluginFile.getName()
3013 def eclipseJ2sPlugin
3014 def eclipseJ2sPluginFile
3015 eclipseJ2sPluginDirs.any { dir ->
3016 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3017 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3018 if (eclipseJ2sPluginFile.exists()) {
3024 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3025 System.err.println(msg)
3026 throw new StopExecutionException(msg)
3029 def digest = MessageDigest.getInstance("MD5")
3031 digest.update(j2sPluginFile.text.bytes)
3032 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3034 digest.update(eclipseJ2sPluginFile.text.bytes)
3035 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3037 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3038 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3039 System.err.println(msg)
3040 throw new StopExecutionException(msg)
3042 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3048 task jalviewjsIDE_copyJ2sPlugin {
3049 group "00 JalviewJS in Eclipse"
3050 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3053 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3054 def j2sPluginFile = file(j2sPlugin)
3055 def eclipseHome = System.properties["eclipse.home.location"]
3056 if (eclipseHome == null || ! IN_ECLIPSE) {
3057 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3059 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3060 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3061 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3062 System.err.println(msg)
3065 eclipseJ2sPluginFile.getParentFile().mkdirs()
3066 into eclipseJ2sPluginFile.getParent()
3072 task jalviewjsIDE_j2sFile {
3073 group "00 JalviewJS in Eclipse"
3074 description "Creates the .j2s file"
3075 dependsOn jalviewjsCreateJ2sSettings
3079 task jalviewjsIDE_SyncCore {
3080 group "00 JalviewJS in Eclipse"
3081 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3082 dependsOn jalviewjsSyncCore
3086 task jalviewjsIDE_SyncSiteAll {
3087 dependsOn jalviewjsSyncAllLibs
3088 dependsOn jalviewjsSyncResources
3089 dependsOn jalviewjsSyncSiteResources
3090 dependsOn jalviewjsSyncBuildProperties
3094 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3097 task jalviewjsIDE_PrepareSite {
3098 group "00 JalviewJS in Eclipse"
3099 description "Sync libs and resources to site dir, but not closure cores"
3101 dependsOn jalviewjsIDE_SyncSiteAll
3102 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3106 task jalviewjsIDE_AssembleSite {
3107 group "00 JalviewJS in Eclipse"
3108 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3109 dependsOn jalviewjsPrepareSite
3113 task jalviewjsIDE_SiteClean {
3114 group "00 JalviewJS in Eclipse"
3115 description "Deletes the Eclipse transpiled site"
3116 dependsOn cleanJalviewjsSite
3120 task jalviewjsIDE_Server {
3121 group "00 JalviewJS in Eclipse"
3122 description "Starts a webserver on localhost to test the website"
3123 dependsOn jalviewjsServer
3127 // buildship runs this at import or gradle refresh
3128 task eclipseSynchronizationTask {
3129 //dependsOn eclipseSetup
3130 dependsOn createBuildProperties
3132 dependsOn jalviewjsIDE_j2sFile
3133 dependsOn jalviewjsIDE_checkJ2sPlugin
3134 dependsOn jalviewjsIDE_PrepareSite
3139 // buildship runs this at build time or project refresh
3140 task eclipseAutoBuildTask {
3141 //dependsOn jalviewjsIDE_checkJ2sPlugin
3142 //dependsOn jalviewjsIDE_PrepareSite
3148 description "Build the site"
3149 dependsOn jalviewjsBuildSite