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 '8.0.4'
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()
62 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
63 jalviewDirRelativePath = jalviewDir
65 // local build environment properties
66 // can be "projectDir/local.properties"
67 def localProps = "${projectDir}/local.properties"
69 if (file(localProps).exists()) {
70 propsFile = localProps
72 // or "../projectDir_local.properties"
73 def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
74 if (file(dirLocalProps).exists()) {
75 propsFile = dirLocalProps
77 if (propsFile != null) {
79 def p = new Properties()
80 def localPropsFIS = new FileInputStream(propsFile)
85 def oldval = findProperty(key)
88 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
90 println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
93 } catch (Exception e) {
94 System.out.println("Exception reading local.properties")
99 // Import releaseProps from the RELEASE file
100 // or a file specified via JALVIEW_RELEASE_FILE if defined
101 // Expect jalview.version and target release branch in jalview.release
102 def releaseProps = new Properties();
103 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
104 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
106 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
107 releaseProps.load(it)
109 } catch (Exception fileLoadError) {
110 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
113 // Set JALVIEW_VERSION if it is not already set
114 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
115 JALVIEW_VERSION = releaseProps.get("jalview.version")
118 // this property set when running Eclipse headlessly
119 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
120 // this property set by Eclipse
121 eclipseApplicationProperty = string("eclipse.application")
122 // CHECK IF RUNNING FROM WITHIN ECLIPSE
123 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
124 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
125 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
126 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
127 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
131 println("WITHIN ECLIPSE IDE")
133 println("HEADLESS BUILD")
136 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
138 println("J2S ENABLED")
141 System.properties.sort { it.key }.each {
142 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
145 if (false && IN_ECLIPSE) {
146 jalviewDir = jalviewDirAbsolutePath
151 bareSourceDir = string(source_dir)
152 sourceDir = string("${jalviewDir}/${bareSourceDir}")
153 resourceDir = string("${jalviewDir}/${resource_dir}")
154 bareTestSourceDir = string(test_source_dir)
155 testDir = string("${jalviewDir}/${bareTestSourceDir}")
157 classesDir = string("${jalviewDir}/${classes_dir}")
160 useClover = clover.equals("true")
161 cloverBuildDir = "${buildDir}/clover"
162 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
163 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
164 cloverReportDir = file("${buildDir}/reports/clover")
165 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
166 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
167 //cloverTestClassesDir = cloverClassesDir
168 cloverDb = string("${cloverBuildDir}/clover.db")
170 testSourceDir = useClover ? cloverTestInstrDir : testDir
171 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
173 getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
176 // the following values might be overridden by the CHANNEL switch
177 getdownChannelName = CHANNEL.toLowerCase()
178 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
179 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
180 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
181 getdownAppDistDir = getdown_app_dir_alt
182 reportRsyncCommand = false
183 jvlChannelName = CHANNEL.toLowerCase()
184 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
185 install4jDSStore = "DS_Store-NON-RELEASE"
186 install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
187 install4jInstallerName = "${jalview_name} Non-Release Installer"
188 install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
189 install4jExtraScheme = "jalviewx"
193 // TODO: get bamboo build artifact URL for getdown artifacts
194 getdown_channel_base = bamboo_channelbase
195 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
196 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
197 jvlChannelName += "_${getdownChannelName}"
198 // automatically add the test group Not-bamboo for exclusion
199 if ("".equals(testng_excluded_groups)) {
200 testng_excluded_groups = "Not-bamboo"
202 install4jExtraScheme = "jalviewb"
206 getdownAppDistDir = getdown_app_dir_release
207 reportRsyncCommand = true
209 install4jDSStore = "DS_Store"
210 install4jDMGBackgroundImage = "jalview_dmg_background.png"
211 install4jInstallerName = "${jalview_name} Installer"
215 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
216 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
217 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
218 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
219 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
221 package_dir = string("${ARCHIVEDIR}/${package_dir}")
222 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
225 reportRsyncCommand = true
226 install4jExtraScheme = "jalviewa"
230 getdownChannelName = string("archive/${JALVIEW_VERSION}")
231 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
232 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
233 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
234 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
236 package_dir = string("${ARCHIVEDIR}/${package_dir}")
237 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
240 reportRsyncCommand = true
241 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
242 install4jSuffix = "Archive"
243 install4jExtraScheme = "jalviewa"
247 reportRsyncCommand = true
249 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
250 JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
252 channelPropertiesFile = string("${channel_properties_dir}/develop_properties")
253 getdownImagesDir = "${getdown_images_dir}/develop"
254 getdownBgColour = "000000"
255 getdownFgColour = "FFFFFF"
256 getdownLightFgColour = "CCCCFF"
257 install4jSuffix = "Develop"
258 install4jDSStore = "DS_Store-DEVELOP"
259 install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
260 install4jExtraScheme = "jalviewd"
261 install4jInstallerName = "${jalview_name} Develop Installer"
262 install4jMacIconsFile = string("${install4j_utils_dir}/develop/${install4j_mac_icons_file}")
263 install4jWindowsIconsFile = string("${install4j_utils_dir}/develop/${install4j_windows_icons_file}")
264 install4jPngIconFile = string("${install4j_utils_dir}/develop/${install4j_png_icon_file}")
268 reportRsyncCommand = true
269 // Don't ignore transpile errors for release build
270 if (jalviewjs_ignore_transpile_errors.equals("true")) {
271 jalviewjs_ignore_transpile_errors = "false"
272 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
274 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
275 install4jSuffix = "Test"
276 install4jDSStore = "DS_Store-TEST-RELEASE"
277 install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
278 install4jExtraScheme = "jalviewt"
279 install4jInstallerName = "${jalview_name} Test Installer"
282 case ~/^SCRATCH(|-[-\w]*)$/:
283 getdownChannelName = CHANNEL
284 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
286 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
287 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
288 reportRsyncCommand = true
289 install4jSuffix = "Scratch"
293 if (!file("${LOCALDIR}").exists()) {
294 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
296 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
299 JALVIEW_VERSION = "TEST"
300 install4jSuffix = "Test-Local"
301 install4jDSStore = "DS_Store-TEST-RELEASE"
302 install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
303 install4jExtraScheme = "jalviewt"
304 install4jInstallerName = "${jalview_name} Test Installer"
308 JALVIEW_VERSION = "TEST"
309 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
310 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
311 install4jExtraScheme = "jalviewl"
314 default: // something wrong specified
315 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
319 // override getdownAppBase if requested
320 if (findProperty("getdown_appbase_override") != null) {
321 getdownAppBase = string(getProperty("getdown_appbase_override"))
322 println("Overriding getdown appbase with '${getdownAppBase}'")
324 // sanitise file name for jalview launcher file for this channel
325 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
326 // install4j application and folder names
327 if (install4jSuffix == "") {
328 install4jApplicationName = "${jalview_name}"
329 install4jBundleId = "${install4j_bundle_id}"
330 install4jWinApplicationId = install4j_release_win_application_id
332 install4jApplicationName = "${jalview_name} ${install4jSuffix}"
333 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
334 // add int hash of install4jSuffix to the last part of the application_id
335 def id = install4j_release_win_application_id
336 def idsplitreverse = id.split("-").reverse()
337 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
338 install4jWinApplicationId = idsplitreverse.reverse().join("-")
340 // sanitise folder and id names
341 // install4jApplicationFolder = e.g. "Jalview Build"
342 install4jApplicationFolder = install4jApplicationName
343 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
344 .replaceAll("_+", "_") // collapse __
345 install4jInternalId = install4jApplicationName
347 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
348 .replaceAll("_+", "") // collapse __
349 //.replaceAll("_*-_*", "-") // collapse _-_
350 install4jUnixApplicationFolder = install4jApplicationName
352 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
353 .replaceAll("_+", "_") // collapse __
354 .replaceAll("_*-_*", "-") // collapse _-_
357 getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
358 //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
359 getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
360 getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
361 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
362 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
363 /* compile without modules -- using classpath libraries
364 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
365 modules_runtimeClasspath = modules_compileClasspath
367 def details = versionDetails()
368 gitHash = details.gitHash
369 gitBranch = details.branchName
371 println("Using a ${CHANNEL} profile.")
373 additional_compiler_args = []
374 // configure classpath/args for j8/j11 compilation
375 if (JAVA_VERSION.equals("1.8")) {
376 JAVA_INTEGER_VERSION = string("8")
379 libDistDir = j8libDir
380 compile_source_compatibility = 1.8
381 compile_target_compatibility = 1.8
382 // these are getdown.txt properties defined dependent on the JAVA_VERSION
383 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
384 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
385 // this property is assigned below and expanded to multiple lines in the getdown task
386 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
387 // this property is for the Java library used in eclipse
388 eclipseJavaRuntimeName = string("JavaSE-1.8")
389 } else if (JAVA_VERSION.equals("11")) {
390 JAVA_INTEGER_VERSION = string("11")
392 libDistDir = j11libDir
393 compile_source_compatibility = 11
394 compile_target_compatibility = 11
395 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
396 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
397 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
398 eclipseJavaRuntimeName = string("JavaSE-11")
399 /* compile without modules -- using classpath libraries
400 additional_compiler_args += [
401 '--module-path', modules_compileClasspath.asPath,
402 '--add-modules', j11modules
405 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
406 JAVA_INTEGER_VERSION = JAVA_VERSION
408 libDistDir = j11libDir
409 compile_source_compatibility = JAVA_VERSION
410 compile_target_compatibility = JAVA_VERSION
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
422 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
427 JAVA_MIN_VERSION = JAVA_VERSION
428 JAVA_MAX_VERSION = JAVA_VERSION
429 def jreInstallsDir = string(jre_installs_dir)
430 if (jreInstallsDir.startsWith("~/")) {
431 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
433 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
434 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
435 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
436 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
437 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
438 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
439 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
440 install4jConfFileName = string("jalview-install4j-conf.install4j")
441 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
442 install4jHomeDir = install4j_home_dir
443 if (install4jHomeDir.startsWith("~/")) {
444 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
447 resourceBuildDir = string("${buildDir}/resources")
448 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
449 helpBuildDir = string("${resourceBuildDir}/help_build")
450 docBuildDir = string("${resourceBuildDir}/doc_build")
452 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
453 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
454 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
455 helpSourceDir = string("${helpParentDir}/${help_dir}")
456 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
459 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
460 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
461 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
463 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
465 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
467 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
468 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
469 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
470 jalviewjsJalviewCoreHtmlFile = string("")
471 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
472 jalviewjsCoreClasslists = []
473 jalviewjsJalviewTemplateName = string(jalviewjs_name)
474 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
475 jalviewjsJ2sProps = null
476 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
478 eclipseWorkspace = null
479 eclipseBinary = string("")
480 eclipseVersion = string("")
490 outputDir = file(classesDir)
494 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
497 compileClasspath = files(sourceSets.main.java.outputDir)
498 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
500 runtimeClasspath = compileClasspath
501 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
506 srcDirs cloverInstrDir
507 outputDir = cloverClassesDir
511 srcDirs = sourceSets.main.resources.srcDirs
514 compileClasspath = files( sourceSets.clover.java.outputDir )
515 //compileClasspath += files( testClassesDir )
516 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
517 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
518 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
520 runtimeClasspath = compileClasspath
525 srcDirs testSourceDir
526 outputDir = file(testClassesDir)
530 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
533 compileClasspath = files( sourceSets.test.java.outputDir )
534 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
535 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
537 runtimeClasspath = compileClasspath
538 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
544 // eclipse project and settings files creation, also used by buildship
547 name = eclipse_project_name
549 natures 'org.eclipse.jdt.core.javanature',
550 'org.eclipse.jdt.groovy.core.groovyNature',
551 'org.eclipse.buildship.core.gradleprojectnature'
553 buildCommand 'org.eclipse.jdt.core.javabuilder'
554 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
558 //defaultOutputDir = sourceSets.main.java.outputDir
559 configurations.each{ c->
560 if (c.isCanBeResolved()) {
561 minusConfigurations += [c]
565 plusConfigurations = [ ]
569 def removeTheseToo = []
570 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
571 cp.entries.each { entry ->
572 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
573 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
574 // we add the resources and help/help dirs in as libs afterwards (see below)
575 if (entry.kind == 'src') {
576 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
577 removeTheseToo += entry
579 alreadyAddedSrcPath.putAt(entry.path, true)
584 cp.entries.removeAll(removeTheseToo)
586 //cp.entries += new Output("${eclipse_bin_dir}/main")
587 if (file(helpParentDir).isDirectory()) {
588 cp.entries += new Library(fileReference(helpParentDir))
590 if (file(resourceDir).isDirectory()) {
591 cp.entries += new Library(fileReference(resourceDir))
594 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
596 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
597 //don't want to add outputDir as eclipse is using its own output dir in bin/main
598 if (it.isDirectory() || ! it.exists()) {
599 // don't add dirs to classpath, especially if they don't exist
600 return false // groovy "continue" in .any closure
602 def itPath = it.toString()
603 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
604 // make relative path
605 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
607 if (alreadyAddedLibPath.get(itPath)) {
608 //println("Not adding duplicate entry "+itPath)
610 //println("Adding entry "+itPath)
611 cp.entries += new Library(fileReference(itPath))
612 alreadyAddedLibPath.put(itPath, true)
616 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
617 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
618 if (it.isDirectory() || ! it.exists()) {
619 // don't add dirs to classpath
620 return false // groovy "continue" in .any closure
623 def itPath = it.toString()
624 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
625 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
627 if (alreadyAddedLibPath.get(itPath)) {
630 def lib = new Library(fileReference(itPath))
631 lib.entryAttributes["test"] = "true"
633 alreadyAddedLibPath.put(itPath, true)
641 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
646 // for the IDE, use java 11 compatibility
647 sourceCompatibility = compile_source_compatibility
648 targetCompatibility = compile_target_compatibility
649 javaRuntimeName = eclipseJavaRuntimeName
651 // add in jalview project specific properties/preferences into eclipse core preferences
653 withProperties { props ->
654 def jalview_prefs = new Properties()
655 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
656 jalview_prefs.load(ins)
658 jalview_prefs.forEach { t, v ->
659 if (props.getAt(t) == null) {
663 // codestyle file -- overrides previous formatter prefs
664 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
665 if (csFile.exists()) {
666 XmlParser parser = new XmlParser()
667 def profiles = parser.parse(csFile)
668 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
669 if (profile != null) {
670 profile.'setting'.each { s ->
672 def value = s.'@value'
673 if (id != null && value != null) {
674 props.putAt(id, value)
685 // Don't want these to be activated if in headless build
686 synchronizationTasks "eclipseSynchronizationTask"
687 //autoBuildTasks "eclipseAutoBuildTask"
693 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
694 // Class to allow updating arbitrary properties files
695 class PropertiesFile extends PropertiesPersistableConfigurationObject {
696 public PropertiesFile(PropertiesTransformer t) { super(t); }
697 @Override protected void load(Properties properties) { }
698 @Override protected void store(Properties properties) { }
699 @Override protected String getDefaultResourceName() { return ""; }
700 // This is necessary, because PropertiesPersistableConfigurationObject fails
701 // if no default properties file exists.
702 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
705 // Task to update arbitrary properties files (set outputFile)
706 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
707 private final PropertiesFileContentMerger file;
708 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
709 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
710 protected void configure(PropertiesFile props) {
711 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
713 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
716 task eclipseUIPreferences(type: PropertiesFileTask) {
717 description = "Generate Eclipse additional settings"
718 def filename = "org.eclipse.jdt.ui.prefs"
719 outputFile = "$projectDir/.settings/${filename}" as File
722 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
727 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
728 description = "Generate Eclipse additional settings"
729 def filename = "org.eclipse.jdt.groovy.core.prefs"
730 outputFile = "$projectDir/.settings/${filename}" as File
733 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
738 task eclipseAllPreferences {
740 dependsOn eclipseUIPreferences
741 dependsOn eclipseGroovyCorePreferences
744 eclipseUIPreferences.mustRunAfter eclipseJdt
745 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
747 /* end of eclipse preferences hack */
755 delete cloverBuildDir
756 delete cloverReportDir
761 task cloverInstrJava(type: JavaExec) {
762 group = "Verification"
763 description = "Create clover instrumented source java files"
765 dependsOn cleanClover
767 inputs.files(sourceSets.main.allJava)
768 outputs.dir(cloverInstrDir)
770 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
771 classpath = sourceSets.clover.compileClasspath
772 main = "com.atlassian.clover.CloverInstr"
780 cloverInstrDir.getPath(),
782 def srcFiles = sourceSets.main.allJava.files
785 { file -> file.absolutePath }
788 args argsList.toArray()
791 delete cloverInstrDir
792 println("Clover: About to instrument "+srcFiles.size() +" files")
797 task cloverInstrTests(type: JavaExec) {
798 group = "Verification"
799 description = "Create clover instrumented source test files"
801 dependsOn cleanClover
803 inputs.files(testDir)
804 outputs.dir(cloverTestInstrDir)
806 classpath = sourceSets.clover.compileClasspath
807 main = "com.atlassian.clover.CloverInstr"
817 cloverTestInstrDir.getPath(),
819 args argsList.toArray()
822 delete cloverTestInstrDir
823 println("Clover: About to instrument test files")
829 group = "Verification"
830 description = "Create clover instrumented all source files"
832 dependsOn cloverInstrJava
833 dependsOn cloverInstrTests
837 cloverClasses.dependsOn cloverInstr
840 task cloverConsoleReport(type: JavaExec) {
841 group = "Verification"
842 description = "Creates clover console report"
845 file(cloverDb).exists()
848 inputs.dir cloverClassesDir
850 classpath = sourceSets.clover.runtimeClasspath
851 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
853 if (cloverreport_mem.length() > 0) {
854 maxHeapSize = cloverreport_mem
856 if (cloverreport_jvmargs.length() > 0) {
857 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
867 args argsList.toArray()
871 task cloverHtmlReport(type: JavaExec) {
872 group = "Verification"
873 description = "Creates clover HTML report"
876 file(cloverDb).exists()
879 def cloverHtmlDir = cloverReportDir
880 inputs.dir cloverClassesDir
881 outputs.dir cloverHtmlDir
883 classpath = sourceSets.clover.runtimeClasspath
884 main = "com.atlassian.clover.reporters.html.HtmlReporter"
886 if (cloverreport_mem.length() > 0) {
887 maxHeapSize = cloverreport_mem
889 if (cloverreport_jvmargs.length() > 0) {
890 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
901 if (cloverreport_html_options.length() > 0) {
902 argsList += cloverreport_html_options.split(" ")
905 args argsList.toArray()
909 task cloverXmlReport(type: JavaExec) {
910 group = "Verification"
911 description = "Creates clover XML report"
914 file(cloverDb).exists()
917 def cloverXmlFile = "${cloverReportDir}/clover.xml"
918 inputs.dir cloverClassesDir
919 outputs.file cloverXmlFile
921 classpath = sourceSets.clover.runtimeClasspath
922 main = "com.atlassian.clover.reporters.xml.XMLReporter"
924 if (cloverreport_mem.length() > 0) {
925 maxHeapSize = cloverreport_mem
927 if (cloverreport_jvmargs.length() > 0) {
928 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
939 if (cloverreport_xml_options.length() > 0) {
940 argsList += cloverreport_xml_options.split(" ")
943 args argsList.toArray()
948 group = "Verification"
949 description = "Creates clover reports"
951 dependsOn cloverXmlReport
952 dependsOn cloverHtmlReport
959 sourceCompatibility = compile_source_compatibility
960 targetCompatibility = compile_target_compatibility
961 options.compilerArgs += additional_compiler_args
962 print ("Setting target compatibility to "+targetCompatibility+"\n")
964 //classpath += configurations.cloverRuntime
970 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
971 sourceCompatibility = compile_source_compatibility
972 targetCompatibility = compile_target_compatibility
973 options.compilerArgs = additional_compiler_args
974 options.encoding = "UTF-8"
976 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
983 sourceCompatibility = compile_source_compatibility
984 targetCompatibility = compile_target_compatibility
985 options.compilerArgs = additional_compiler_args
987 print ("Setting target compatibility to "+targetCompatibility+"\n")
994 delete sourceSets.main.java.outputDir
1000 dependsOn cleanClover
1002 delete sourceSets.test.java.outputDir
1007 // format is a string like date.format("dd MMMM yyyy")
1008 def getDate(format) {
1009 def date = new Date()
1010 return date.format(format)
1014 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1015 MutableDataSet options = new MutableDataSet()
1017 def extensions = new ArrayList<>()
1018 extensions.add(AnchorLinkExtension.create())
1019 extensions.add(AutolinkExtension.create())
1020 extensions.add(StrikethroughExtension.create())
1021 extensions.add(TaskListExtension.create())
1022 extensions.add(TablesExtension.create())
1023 extensions.add(TocExtension.create())
1025 options.set(Parser.EXTENSIONS, extensions)
1027 // set GFM table parsing options
1028 options.set(TablesExtension.WITH_CAPTION, false)
1029 options.set(TablesExtension.COLUMN_SPANS, false)
1030 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1031 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1032 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1033 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1034 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1036 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1037 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1038 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1039 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1041 Parser parser = Parser.builder(options).build()
1042 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1044 mdFiles.each { mdFile ->
1045 // add table of contents
1046 def mdText = "[TOC]\n"+mdFile.text
1048 // grab the first top-level title
1050 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1051 def matcher = mdText =~ titleRegex
1052 if (matcher.size() > 0) {
1053 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1054 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1056 // or use the filename if none found
1057 if (title == null) {
1058 title = mdFile.getName()
1061 Node document = parser.parse(mdText)
1062 String htmlBody = renderer.render(document)
1063 def htmlText = '''<html>
1064 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1065 <html xmlns="http://www.w3.org/1999/xhtml">
1067 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1068 <meta http-equiv="Content-Style-Type" content="text/css" />
1069 <meta name="generator" content="flexmark" />
1071 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1073 <style type="text/css">code{white-space: pre;}</style>
1075 htmlText += ((cssFile != null) ? cssFile.text : '')
1076 htmlText += '''</head>
1079 htmlText += htmlBody
1085 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1086 def htmlFile = file(htmlFilePath)
1087 println("Creating ${htmlFilePath}")
1088 htmlFile.text = htmlText
1093 task copyDocs(type: Copy) {
1094 def inputDir = "${jalviewDir}/${doc_dir}"
1095 def outputDir = "${docBuildDir}/${doc_dir}"
1099 include('**/*.html')
1101 filter(ReplaceTokens,
1105 'Version-Rel': JALVIEW_VERSION,
1106 'Year-Rel': getDate("yyyy")
1113 exclude('**/*.html')
1118 inputs.dir(inputDir)
1119 outputs.dir(outputDir)
1123 task convertMdFiles {
1125 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1126 def cssFile = file("${jalviewDir}/${flexmark_css}")
1129 convertMdToHtml(mdFiles, cssFile)
1132 inputs.files(mdFiles)
1133 inputs.file(cssFile)
1136 mdFiles.each { mdFile ->
1137 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1138 htmlFiles.add(file(htmlFilePath))
1140 outputs.files(htmlFiles)
1144 task copyHelp(type: Copy) {
1145 def inputDir = helpSourceDir
1146 def outputDir = "${helpBuildDir}/${help_dir}"
1150 include('**/*.html')
1154 filter(ReplaceTokens,
1158 'Version-Rel': JALVIEW_VERSION,
1159 'Year-Rel': getDate("yyyy")
1166 exclude('**/*.html')
1173 inputs.dir(inputDir)
1174 outputs.files(helpFile)
1175 outputs.dir(outputDir)
1179 task copyResources(type: Copy) {
1180 def inputDir = resourceDir
1181 def outputDir = resourcesBuildDir
1185 include('**/*.html')
1187 filter(ReplaceTokens,
1191 'Version-Rel': JALVIEW_VERSION,
1192 'Year-Rel': getDate("yyyy")
1199 exclude('**/*.html')
1204 inputs.dir(inputDir)
1205 outputs.dir(outputDir)
1209 task createBuildProperties(type: WriteProperties) {
1210 dependsOn copyResources
1212 description = "Create the ${buildProperties} file"
1214 inputs.dir(sourceDir)
1215 inputs.dir(resourcesBuildDir)
1216 outputFile (buildProperties)
1217 // taking time specific comment out to allow better incremental builds
1218 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1219 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1220 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1221 property "VERSION", JALVIEW_VERSION
1222 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1223 outputs.file(outputFile)
1227 task buildIndices(type: JavaExec) {
1229 classpath = sourceSets.main.compileClasspath
1230 main = "com.sun.java.help.search.Indexer"
1231 workingDir = "${helpBuildDir}/${help_dir}"
1234 inputs.dir("${workingDir}/${argDir}")
1236 outputs.dir("${classesDir}/doc")
1237 outputs.dir("${classesDir}/help")
1238 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1239 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1240 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1241 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1242 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1243 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1248 dependsOn copyResources
1251 dependsOn createBuildProperties
1252 dependsOn convertMdFiles
1253 dependsOn buildIndices
1257 compileJava.dependsOn prepare
1258 run.dependsOn compileJava
1259 //run.dependsOn prepare
1262 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1267 dependsOn cloverClasses
1269 dependsOn compileJava //?
1273 includeGroups testng_groups
1274 excludeGroups testng_excluded_groups
1276 useDefaultListeners=true
1279 maxHeapSize = "1024m"
1281 workingDir = jalviewDir
1282 def testLaf = project.findProperty("test_laf")
1283 if (testLaf != null) {
1284 println("Setting Test LaF to '${testLaf}'")
1285 systemProperty "laf", testLaf
1287 sourceCompatibility = compile_source_compatibility
1288 targetCompatibility = compile_target_compatibility
1289 jvmArgs += additional_compiler_args
1293 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1299 task compileLinkCheck(type: JavaCompile) {
1301 classpath = files("${jalviewDir}/${utils_dir}")
1302 destinationDir = file("${jalviewDir}/${utils_dir}")
1303 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1305 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1306 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1307 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1308 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1312 task linkCheck(type: JavaExec) {
1314 dependsOn compileLinkCheck
1316 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1317 classpath = files("${jalviewDir}/${utils_dir}")
1318 main = "HelpLinksChecker"
1319 workingDir = jalviewDir
1320 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1322 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1324 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1327 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1331 inputs.dir(helpBuildDir)
1332 outputs.file(helpLinksCheckerOutFile)
1336 // import the pubhtmlhelp target
1337 ant.properties.basedir = "${jalviewDir}"
1338 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1339 ant.importBuild "${utils_dir}/publishHelp.xml"
1342 task cleanPackageDir(type: Delete) {
1344 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1354 attributes "Main-Class": main_class,
1355 "Permissions": "all-permissions",
1356 "Application-Name": install4jApplicationName,
1357 "Codebase": application_codebase,
1358 "Implementation-Version": JALVIEW_VERSION
1361 def outputDir = "${jalviewDir}/${package_dir}"
1362 destinationDirectory = file(outputDir)
1363 archiveFileName = rootProject.name+".jar"
1369 exclude "**/*.jar.*"
1371 inputs.dir(sourceSets.main.java.outputDir)
1372 sourceSets.main.resources.srcDirs.each{ dir ->
1375 outputs.file("${outputDir}/${archiveFileName}")
1379 task copyJars(type: Copy) {
1380 from fileTree(dir: classesDir, include: "**/*.jar").files
1381 into "${jalviewDir}/${package_dir}"
1385 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1386 task syncJars(type: Sync) {
1388 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1389 into "${jalviewDir}/${package_dir}"
1391 include jar.archiveFileName.getOrNull()
1398 description = "Put all required libraries in dist"
1399 // order of "cleanPackageDir", "copyJars", "jar" important!
1400 jar.mustRunAfter cleanPackageDir
1401 syncJars.mustRunAfter cleanPackageDir
1402 dependsOn cleanPackageDir
1405 outputs.dir("${jalviewDir}/${package_dir}")
1410 dependsOn cleanPackageDir
1417 group = "distribution"
1418 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1422 from ("${jalviewDir}/${libDistDir}") {
1426 attributes "Implementation-Version": JALVIEW_VERSION,
1427 "Application-Name": install4jApplicationName
1429 mainClassName = shadow_jar_main_class
1431 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1436 task getdownWebsite() {
1437 group = "distribution"
1438 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1443 def getdownWebsiteResourceFilenames = []
1444 def getdownTextString = ""
1445 def getdownResourceDir = getdownResourceDir
1446 def getdownResourceFilenames = []
1449 // clean the getdown website and files dir before creating getdown folders
1450 delete getdownWebsiteDir
1451 delete getdownFilesDir
1454 from buildProperties
1455 rename(build_properties_file, getdown_build_properties)
1458 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1460 // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
1461 def props = project.properties.sort { it.key }
1462 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1463 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1465 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1466 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1468 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1469 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1472 props.put("getdown_txt_title", jalview_name)
1473 props.put("getdown_txt_ui.name", install4jApplicationName)
1475 // start with appbase
1476 getdownTextString += "appbase = ${getdownAppBase}\n"
1477 props.each{ prop, val ->
1478 if (prop.startsWith("getdown_txt_") && val != null) {
1479 if (prop.startsWith("getdown_txt_multi_")) {
1480 def key = prop.substring(18)
1481 val.split(",").each{ v ->
1482 def line = "${key} = ${v}\n"
1483 getdownTextString += line
1486 // file values rationalised
1487 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1489 if (val.indexOf('/') == 0) {
1492 } else if (val.indexOf('/') > 0) {
1493 // relative path (relative to jalviewDir)
1494 r = file( "${jalviewDir}/${val}" )
1497 val = "${getdown_resource_dir}/" + r.getName()
1498 getdownWebsiteResourceFilenames += val
1499 getdownResourceFilenames += r.getPath()
1502 if (! prop.startsWith("getdown_txt_resource")) {
1503 def line = prop.substring(12) + " = ${val}\n"
1504 getdownTextString += line
1510 getdownWebsiteResourceFilenames.each{ filename ->
1511 getdownTextString += "resource = ${filename}\n"
1513 getdownResourceFilenames.each{ filename ->
1516 into getdownResourceDir
1521 fileTree(file(package_dir)).each{ f ->
1522 if (f.isDirectory()) {
1523 def files = fileTree(dir: f, include: ["*"]).getFiles()
1525 } else if (f.exists()) {
1529 codeFiles.sort().each{f ->
1530 def name = f.getName()
1531 def line = "code = ${getdownAppDistDir}/${name}\n"
1532 getdownTextString += line
1539 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1541 if (JAVA_VERSION.equals("11")) {
1542 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1543 j11libFiles.sort().each{f ->
1544 def name = f.getName()
1545 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1546 getdownTextString += line
1549 into getdownJ11libDir
1555 // 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.
1556 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1557 getdownTextString += "resource = ${getdown_launcher_new}\n"
1558 getdownTextString += "class = ${main_class}\n"
1560 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1561 getdown_txt.write(getdownTextString)
1563 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1564 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1565 launchJvl.write("appbase=${getdownAppBase}")
1568 from getdownLauncher
1569 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1570 into getdownWebsiteDir
1574 from getdownLauncher
1575 if (file(getdownLauncher).getName() != getdown_launcher) {
1576 rename(file(getdownLauncher).getName(), getdown_launcher)
1578 into getdownWebsiteDir
1581 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1584 from getdownLauncher
1585 from "${getdownWebsiteDir}/${getdown_build_properties}"
1586 if (file(getdownLauncher).getName() != getdown_launcher) {
1587 rename(file(getdownLauncher).getName(), getdown_launcher)
1589 into getdownInstallDir
1593 from getdownInstallDir
1594 into getdownFilesInstallDir
1601 from getdownLauncher
1602 from "${getdownWebsiteDir}/${getdown_build_properties}"
1603 if (file(getdownLauncher).getName() != getdown_launcher) {
1604 rename(file(getdownLauncher).getName(), getdown_launcher)
1606 into getdownFilesDir
1610 from getdownResourceDir
1611 into "${getdownFilesDir}/${getdown_resource_dir}"
1616 inputs.dir("${jalviewDir}/${package_dir}")
1618 outputs.dir(getdownWebsiteDir)
1619 outputs.dir(getdownFilesDir)
1623 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1624 task getdownDigestDir(type: JavaExec) {
1626 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1628 def digestDirPropertyName = "DIGESTDIR"
1630 classpath = files(getdownLauncher)
1631 def digestDir = findProperty(digestDirPropertyName)
1632 if (digestDir == null) {
1633 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1637 main = "com.threerings.getdown.tools.Digester"
1641 task getdownDigest(type: JavaExec) {
1642 group = "distribution"
1643 description = "Digest the getdown website folder"
1644 dependsOn getdownWebsite
1646 classpath = files(getdownLauncher)
1648 main = "com.threerings.getdown.tools.Digester"
1649 args getdownWebsiteDir
1650 inputs.dir(getdownWebsiteDir)
1651 outputs.file("${getdownWebsiteDir}/digest2.txt")
1656 group = "distribution"
1657 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1658 dependsOn getdownDigest
1660 if (reportRsyncCommand) {
1661 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1662 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1663 println "LIKELY RSYNC COMMAND:"
1664 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1665 if (RUNRSYNC == "true") {
1667 commandLine "mkdir", "-p", toDir
1670 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1678 tasks.withType(JavaCompile) {
1679 options.encoding = 'UTF-8'
1685 delete getdownWebsiteDir
1686 delete getdownFilesDir
1692 if (file(install4jHomeDir).exists()) {
1694 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1695 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1696 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1697 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1699 installDir(file(install4jHomeDir))
1701 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1705 task copyInstall4jTemplate {
1706 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1707 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1708 inputs.file(install4jTemplateFile)
1709 inputs.file(install4jFileAssociationsFile)
1710 inputs.property("CHANNEL", { CHANNEL })
1711 outputs.file(install4jConfFile)
1714 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1716 // turn off code signing if no OSX_KEYPASS
1717 if (OSX_KEYPASS == "") {
1718 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1719 codeSigning.'@macEnabled' = "false"
1721 install4jConfigXml.'**'.windows.each { windows ->
1722 windows.'@runPostProcessor' = "false"
1726 // turn off checksum creation for LOCAL channel
1727 def e = install4jConfigXml.application[0]
1728 if (CHANNEL == "LOCAL") {
1729 e.'@createChecksums' = "false"
1731 e.'@createChecksums' = "true"
1734 // put file association actions where placeholder action is
1735 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1736 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1737 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1738 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1739 def parent = a.parent()
1741 fileAssociationActions.each { faa ->
1744 // don't need to continue in .any loop once replacements have been made
1749 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1750 // NB we're deleting the /other/ one!
1751 // Also remove the examples subdir from non-release versions
1752 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1753 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1754 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1755 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1757 // remove the examples subdir from Full File Set
1758 def files = install4jConfigXml.files[0]
1759 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1760 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1761 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1762 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1763 dirEntry.parent().remove(dirEntry)
1765 install4jConfigXml.'**'.action.any { a ->
1766 if (a.'@customizedId' == customizedIdToDelete) {
1767 def parent = a.parent()
1773 // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
1774 if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
1775 def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
1776 symlink.parent().remove(symlink)
1779 // write install4j file
1780 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1787 delete install4jConfFile
1792 task installers(type: com.install4j.gradle.Install4jTask) {
1793 group = "distribution"
1794 description = "Create the install4j installers"
1796 dependsOn copyInstall4jTemplate
1798 projectFile = install4jConfFile
1800 // create an md5 for the input files to use as version for install4j conf file
1801 def digest = MessageDigest.getInstance("MD5")
1803 (file("${install4jDir}/${install4j_template}").text +
1804 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1805 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1806 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1807 if (filesMd5.length() >= 8) {
1808 filesMd5 = filesMd5.substring(0,8)
1810 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1811 // make install4jBuildDir relative to jalviewDir
1812 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1815 'JALVIEW_NAME': jalview_name,
1816 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1817 'JALVIEW_DIR': "../..",
1818 'OSX_KEYSTORE': OSX_KEYSTORE,
1819 'JSIGN_SH': JSIGN_SH,
1820 'JRE_DIR': getdown_app_dir_java,
1821 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1822 'JALVIEW_VERSION': JALVIEW_VERSION,
1823 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1824 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1825 'JAVA_VERSION': JAVA_VERSION,
1826 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1827 'VERSION': JALVIEW_VERSION,
1828 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1829 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1830 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1831 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1832 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1833 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1834 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1835 'BUNDLE_ID': install4jBundleId,
1836 'INTERNAL_ID': install4jInternalId,
1837 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1838 'MACOS_DS_STORE': install4jDSStore,
1839 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1840 'INSTALLER_NAME': install4jInstallerName,
1841 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1842 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1843 'GETDOWN_FILES_DIR': getdown_files_dir,
1844 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1845 'GETDOWN_DIST_DIR': getdownAppDistDir,
1846 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1847 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1848 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1849 'BUILD_DIR': install4jBuildDir,
1850 'APPLICATION_CATEGORIES': install4j_application_categories,
1851 'APPLICATION_FOLDER': install4jApplicationFolder,
1852 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1853 'EXECUTABLE_NAME': install4jExecutableName,
1854 'EXTRA_SCHEME': install4jExtraScheme,
1857 //println("INSTALL4J VARIABLES:")
1858 //variables.each{k,v->println("${k}=${v}")}
1860 destination = "${jalviewDir}/${install4jBuildDir}"
1861 buildSelected = true
1863 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1865 disableSigning = true
1869 macKeystorePassword = OSX_KEYPASS
1873 println("Using projectFile "+projectFile)
1876 inputs.dir(getdownWebsiteDir)
1877 inputs.file(install4jConfFile)
1878 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1879 inputs.dir(macosJavaVMDir)
1880 inputs.dir(windowsJavaVMDir)
1881 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
1887 eclipse().configFile(eclipse_codestyle_file)
1892 task sourceDist(type: Tar) {
1893 group "distribution"
1894 description "Create a source .tar.gz file for distribution"
1896 dependsOn convertMdFiles
1898 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1899 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1900 archiveFileName = outputFileName
1902 compression Compression.GZIP
1917 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
1919 "utils/InstallAnywhere",
1934 "gradle.properties",
1945 ".settings/org.eclipse.jdt.core.jalview.prefs",
1949 exclude (EXCLUDE_FILES)
1950 include (PROCESS_FILES)
1951 filter(ReplaceTokens,
1955 'Version-Rel': JALVIEW_VERSION,
1956 'Year-Rel': getDate("yyyy")
1961 exclude (EXCLUDE_FILES)
1962 exclude (PROCESS_FILES)
1963 exclude ("appletlib")
1964 exclude ("**/*locales")
1965 exclude ("*locales/**")
1966 exclude ("utils/InstallAnywhere")
1968 exclude (getdown_files_dir)
1969 exclude (getdown_website_dir)
1971 // exluding these as not using jars as modules yet
1972 exclude ("${j11modDir}/**/*.jar")
1975 include(INCLUDE_FILES)
1977 // from (jalviewDir) {
1978 // // explicit includes for stuff that seemed to not get included
1979 // include(fileTree("test/**/*."))
1980 // exclude(EXCLUDE_FILES)
1981 // exclude(PROCESS_FILES)
1988 dependsOn pubhtmlhelp
1990 inputs.dir("${helpBuildDir}/${help_dir}")
1991 outputs.dir("${buildDir}/distributions/${help_dir}")
1995 task j2sSetHeadlessBuild {
2002 task jalviewjsSetEclipseWorkspace {
2003 def propKey = "jalviewjs_eclipse_workspace"
2005 if (project.hasProperty(propKey)) {
2006 propVal = project.getProperty(propKey)
2007 if (propVal.startsWith("~/")) {
2008 propVal = System.getProperty("user.home") + propVal.substring(1)
2011 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2012 def propsFile = file(propsFileName)
2013 def eclipseWsDir = propVal
2014 def props = new Properties()
2016 def writeProps = true
2017 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2018 def ins = new FileInputStream(propsFileName)
2021 if (props.getProperty(propKey, null) != null) {
2022 eclipseWsDir = props.getProperty(propKey)
2027 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2028 def tempDir = File.createTempDir()
2029 eclipseWsDir = tempDir.getAbsolutePath()
2032 eclipseWorkspace = file(eclipseWsDir)
2035 // do not run a headless transpile when we claim to be in Eclipse
2037 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2038 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2040 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2044 props.setProperty(propKey, eclipseWsDir)
2045 propsFile.parentFile.mkdirs()
2046 def bytes = new ByteArrayOutputStream()
2047 props.store(bytes, null)
2048 def propertiesString = bytes.toString()
2049 propsFile.text = propertiesString
2055 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2058 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2059 outputs.file(propsFileName)
2060 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2064 task jalviewjsEclipsePaths {
2067 def eclipseRoot = jalviewjs_eclipse_root
2068 if (eclipseRoot.startsWith("~/")) {
2069 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2071 if (OperatingSystem.current().isMacOsX()) {
2072 eclipseRoot += "/Eclipse.app"
2073 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2074 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2075 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2076 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2077 eclipseRoot += "/eclipse"
2079 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2080 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2081 } else { // linux or unix
2082 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2083 eclipseRoot += "/eclipse"
2084 println("eclipseDir exists")
2086 eclipseBinary = "${eclipseRoot}/eclipse"
2087 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2090 eclipseVersion = "4.13" // default
2091 def assumedVersion = true
2092 if (file(eclipseProduct).exists()) {
2093 def fis = new FileInputStream(eclipseProduct)
2094 def props = new Properties()
2096 eclipseVersion = props.getProperty("version")
2098 assumedVersion = false
2101 def propKey = "eclipse_debug"
2102 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2105 // do not run a headless transpile when we claim to be in Eclipse
2107 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2108 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2110 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2113 if (!assumedVersion) {
2114 println("ECLIPSE VERSION=${eclipseVersion}")
2120 task printProperties {
2122 description "Output to console all System.properties"
2124 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2130 dependsOn eclipseProject
2131 dependsOn eclipseClasspath
2132 dependsOn eclipseJdt
2136 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2137 task jalviewjsEclipseCopyDropins(type: Copy) {
2138 dependsOn jalviewjsEclipsePaths
2140 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2141 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2142 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2149 // this eclipse -clean doesn't actually work
2150 task jalviewjsCleanEclipse(type: Exec) {
2151 dependsOn eclipseSetup
2152 dependsOn jalviewjsEclipsePaths
2153 dependsOn jalviewjsEclipseCopyDropins
2155 executable(eclipseBinary)
2156 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2162 def inputString = """exit
2165 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2166 standardInput = inputByteStream
2169 /* not really working yet
2170 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2174 task jalviewjsTransferUnzipSwingJs {
2175 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2179 from zipTree(file_zip)
2180 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2184 inputs.file file_zip
2185 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2189 task jalviewjsTransferUnzipLib {
2190 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2193 zipFiles.each { file_zip ->
2195 from zipTree(file_zip)
2196 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2201 inputs.files zipFiles
2202 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2206 task jalviewjsTransferUnzipAllLibs {
2207 dependsOn jalviewjsTransferUnzipSwingJs
2208 dependsOn jalviewjsTransferUnzipLib
2212 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2214 description "Create the .j2s file from the j2s.* properties"
2216 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2217 def siteDirProperty = "j2s.site.directory"
2218 def setSiteDir = false
2219 jalviewjsJ2sProps.each { prop, val ->
2221 if (prop == siteDirProperty) {
2222 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2223 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2229 if (!setSiteDir) { // default site location, don't override specifically set property
2230 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2233 outputFile = jalviewjsJ2sSettingsFileName
2236 inputs.properties(jalviewjsJ2sProps)
2237 outputs.file(jalviewjsJ2sSettingsFileName)
2242 task jalviewjsEclipseSetup {
2243 dependsOn jalviewjsEclipseCopyDropins
2244 dependsOn jalviewjsSetEclipseWorkspace
2245 dependsOn jalviewjsCreateJ2sSettings
2249 task jalviewjsSyncAllLibs (type: Sync) {
2250 dependsOn jalviewjsTransferUnzipAllLibs
2251 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2252 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2253 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2257 def outputFiles = []
2258 rename { filename ->
2259 outputFiles += "${outputDir}/${filename}"
2265 outputs.files outputFiles
2266 inputs.files inputFiles
2270 task jalviewjsSyncResources (type: Sync) {
2271 def inputFiles = fileTree(dir: resourceDir)
2272 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2276 def outputFiles = []
2277 rename { filename ->
2278 outputFiles += "${outputDir}/${filename}"
2284 outputs.files outputFiles
2285 inputs.files inputFiles
2289 task jalviewjsSyncSiteResources (type: Sync) {
2290 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2291 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2295 def outputFiles = []
2296 rename { filename ->
2297 outputFiles += "${outputDir}/${filename}"
2303 outputs.files outputFiles
2304 inputs.files inputFiles
2308 task jalviewjsSyncBuildProperties (type: Sync) {
2309 dependsOn createBuildProperties
2310 def inputFiles = [file(buildProperties)]
2311 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2315 def outputFiles = []
2316 rename { filename ->
2317 outputFiles += "${outputDir}/${filename}"
2323 outputs.files outputFiles
2324 inputs.files inputFiles
2328 task jalviewjsProjectImport(type: Exec) {
2329 dependsOn eclipseSetup
2330 dependsOn jalviewjsEclipsePaths
2331 dependsOn jalviewjsEclipseSetup
2334 // do not run a headless import when we claim to be in Eclipse
2336 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2337 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2339 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2343 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2344 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2345 executable(eclipseBinary)
2346 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2350 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2352 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2355 inputs.file("${jalviewDir}/.project")
2356 outputs.upToDateWhen {
2357 file(projdir).exists()
2362 task jalviewjsTranspile(type: Exec) {
2363 dependsOn jalviewjsEclipseSetup
2364 dependsOn jalviewjsProjectImport
2365 dependsOn jalviewjsEclipsePaths
2368 // do not run a headless transpile when we claim to be in Eclipse
2370 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2371 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2373 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2377 executable(eclipseBinary)
2378 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2382 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2384 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2390 stdout = new ByteArrayOutputStream()
2391 stderr = new ByteArrayOutputStream()
2393 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2394 def logOutFile = file(logOutFileName)
2395 logOutFile.createNewFile()
2396 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2397 BINARY: ${eclipseBinary}
2398 VERSION: ${eclipseVersion}
2399 WORKSPACE: ${eclipseWorkspace}
2400 DEBUG: ${eclipseDebug}
2403 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2404 // combine stdout and stderr
2405 def logErrFOS = logOutFOS
2407 if (jalviewjs_j2s_to_console.equals("true")) {
2408 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2409 new org.apache.tools.ant.util.TeeOutputStream(
2413 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2414 new org.apache.tools.ant.util.TeeOutputStream(
2419 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2422 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2429 if (stdout.toString().contains("Error processing ")) {
2430 // j2s did not complete transpile
2431 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2432 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2433 println("IGNORING TRANSPILE ERRORS")
2434 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2436 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2441 inputs.dir("${jalviewDir}/${sourceDir}")
2442 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2443 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2447 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2449 def stdout = new ByteArrayOutputStream()
2450 def stderr = new ByteArrayOutputStream()
2452 def coreFile = file(jsfile)
2454 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2456 logOutFile.createNewFile()
2457 logOutFile.append(msg+"\n")
2459 def coreTop = file(prefixFile)
2460 def coreBottom = file(suffixFile)
2461 coreFile.getParentFile().mkdirs()
2462 coreFile.createNewFile()
2463 coreFile.write( coreTop.getText("UTF-8") )
2467 def t = f.getText("UTF-8")
2468 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2469 coreFile.append( t )
2471 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2473 logOutFile.append(msg+"\n")
2476 coreFile.append( coreBottom.getText("UTF-8") )
2478 msg = "Generating ${zjsfile}"
2480 logOutFile.append(msg+"\n")
2481 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2482 def logErrFOS = logOutFOS
2485 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2486 main = "com.google.javascript.jscomp.CommandLineRunner"
2487 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2488 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2491 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2493 logOutFile.append(msg+"\n")
2495 if (logOutConsole) {
2496 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2497 new org.apache.tools.ant.util.TeeOutputStream(
2501 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2502 new org.apache.tools.ant.util.TeeOutputStream(
2507 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2510 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2517 logOutFile.append(msg+"\n")
2521 task jalviewjsBuildAllCores {
2523 description "Build the core js lib closures listed in the classlists dir"
2524 dependsOn jalviewjsTranspile
2525 dependsOn jalviewjsTransferUnzipSwingJs
2527 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2528 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2529 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2530 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2531 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2532 def prefixFile = "${jsDir}/core/coretop2.js"
2533 def suffixFile = "${jsDir}/core/corebottom2.js"
2535 inputs.file prefixFile
2536 inputs.file suffixFile
2538 def classlistFiles = []
2539 // add the classlists found int the jalviewjs_classlists_dir
2540 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2542 def name = file.getName() - ".txt"
2549 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2550 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2551 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2553 jalviewjsCoreClasslists = []
2555 classlistFiles.each {
2558 def file = hash['file']
2559 if (! file.exists()) {
2560 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2561 return false // this is a "continue" in groovy .each closure
2563 def name = hash['name']
2565 name = file.getName() - ".txt"
2573 def list = fileTree(dir: j2sDir, includes: filelist)
2575 def jsfile = "${outputDir}/core${name}.js"
2576 def zjsfile = "${outputDir}/core${name}.z.js"
2578 jalviewjsCoreClasslists += [
2587 outputs.file(jsfile)
2588 outputs.file(zjsfile)
2591 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2592 def stevesoftClasslistName = "_stevesoft"
2593 def stevesoftClasslist = [
2594 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2595 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2596 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2597 'name': stevesoftClasslistName
2599 jalviewjsCoreClasslists += stevesoftClasslist
2600 inputs.files(stevesoftClasslist['list'])
2601 outputs.file(stevesoftClasslist['jsfile'])
2602 outputs.file(stevesoftClasslist['zjsfile'])
2605 def allClasslistName = "_all"
2606 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2607 allJsFiles += fileTree(
2611 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2612 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2613 "**/org/jmol/export/JSExporter.js"
2616 allJsFiles += fileTree(
2620 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2621 "**/sun/misc/Unsafe.js",
2622 "**/swingjs/jquery/jquery-editable-select.js",
2623 "**/swingjs/jquery/j2sComboBox.js",
2624 "**/sun/misc/FloatingDecimal.js"
2627 def allClasslist = [
2628 'jsfile': "${outputDir}/core${allClasslistName}.js",
2629 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2631 'name': allClasslistName
2633 // not including this version of "all" core at the moment
2634 //jalviewjsCoreClasslists += allClasslist
2635 inputs.files(allClasslist['list'])
2636 outputs.file(allClasslist['jsfile'])
2637 outputs.file(allClasslist['zjsfile'])
2640 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2641 logOutFile.getParentFile().mkdirs()
2642 logOutFile.createNewFile()
2643 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2645 jalviewjsCoreClasslists.each {
2646 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2653 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2656 into file(outputFile).getParentFile()
2657 rename { filename ->
2658 if (filename.equals(inputFile.getName())) {
2659 return file(outputFile).getName()
2663 filter(ReplaceTokens,
2667 'MAIN': '"'+main_class+'"',
2669 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2670 'COREKEY': jalviewjs_core_key,
2671 'CORENAME': coreName
2678 task jalviewjsPublishCoreTemplates {
2679 dependsOn jalviewjsBuildAllCores
2680 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2681 def inputFile = file(inputFileName)
2682 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2684 def outputFiles = []
2685 jalviewjsCoreClasslists.each { cl ->
2686 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2687 cl['outputfile'] = outputFile
2688 outputFiles += outputFile
2692 jalviewjsCoreClasslists.each { cl ->
2693 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2696 inputs.file(inputFile)
2697 outputs.files(outputFiles)
2701 task jalviewjsSyncCore (type: Sync) {
2702 dependsOn jalviewjsBuildAllCores
2703 dependsOn jalviewjsPublishCoreTemplates
2704 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2705 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2709 def outputFiles = []
2710 rename { filename ->
2711 outputFiles += "${outputDir}/${filename}"
2717 outputs.files outputFiles
2718 inputs.files inputFiles
2722 // this Copy version of TransferSiteJs will delete anything else in the target dir
2723 task jalviewjsCopyTransferSiteJs(type: Copy) {
2724 dependsOn jalviewjsTranspile
2725 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2726 into "${jalviewDir}/${jalviewjsSiteDir}"
2730 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2731 task jalviewjsSyncTransferSiteJs(type: Sync) {
2732 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2734 into "${jalviewDir}/${jalviewjsSiteDir}"
2741 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2742 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2743 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2744 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2746 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2747 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2748 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2749 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2752 task jalviewjsPrepareSite {
2754 description "Prepares the website folder including unzipping files and copying resources"
2755 dependsOn jalviewjsSyncAllLibs
2756 dependsOn jalviewjsSyncResources
2757 dependsOn jalviewjsSyncSiteResources
2758 dependsOn jalviewjsSyncBuildProperties
2759 dependsOn jalviewjsSyncCore
2763 task jalviewjsBuildSite {
2765 description "Builds the whole website including transpiled code"
2766 dependsOn jalviewjsCopyTransferSiteJs
2767 dependsOn jalviewjsPrepareSite
2771 task cleanJalviewjsTransferSite {
2773 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2774 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2775 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2776 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2781 task cleanJalviewjsSite {
2782 dependsOn cleanJalviewjsTransferSite
2784 delete "${jalviewDir}/${jalviewjsSiteDir}"
2789 task jalviewjsSiteTar(type: Tar) {
2791 description "Creates a tar.gz file for the website"
2792 dependsOn jalviewjsBuildSite
2793 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2794 archiveFileName = outputFilename
2796 compression Compression.GZIP
2798 from "${jalviewDir}/${jalviewjsSiteDir}"
2799 into jalviewjs_site_dir // this is inside the tar file
2801 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
2805 task jalviewjsServer {
2807 def filename = "jalviewjsTest.html"
2808 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
2809 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
2812 SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
2813 def port = Integer.valueOf(jalviewjs_server_port)
2818 while(port < start+1000 && !running) {
2820 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
2821 jalviewjsServer = factory.start(doc_root, port)
2823 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
2824 println("SERVER STARTED with document root ${doc_root}.")
2825 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
2826 println("For debug: "+url+"?j2sdebug")
2827 println("For verbose: "+url+"?j2sverbose")
2828 } catch (Exception e) {
2833 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
2834 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
2835 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
2837 jalviewjsCoreClasslists.each { cl ->
2838 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
2840 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
2842 println("For core ${cl.name}: "+urlcore)
2845 file(htmlFile).text = htmlText
2848 outputs.file(htmlFile)
2849 outputs.upToDateWhen({false})
2853 task cleanJalviewjsAll {
2855 description "Delete all configuration and build artifacts to do with JalviewJS build"
2856 dependsOn cleanJalviewjsSite
2857 dependsOn jalviewjsEclipsePaths
2860 delete "${jalviewDir}/${jalviewjsBuildDir}"
2861 delete "${jalviewDir}/${eclipse_bin_dir}"
2862 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
2863 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
2865 delete "${jalviewDir}/${jalviewjs_j2s_settings}"
2868 outputs.upToDateWhen( { false } )
2872 task jalviewjsIDE_checkJ2sPlugin {
2873 group "00 JalviewJS in Eclipse"
2874 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
2877 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
2878 def j2sPluginFile = file(j2sPlugin)
2879 def eclipseHome = System.properties["eclipse.home.location"]
2880 if (eclipseHome == null || ! IN_ECLIPSE) {
2881 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
2883 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
2884 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
2885 if (altPluginsDir != null && file(altPluginsDir).exists()) {
2886 eclipseJ2sPluginDirs += altPluginsDir
2888 def foundPlugin = false
2889 def j2sPluginFileName = j2sPluginFile.getName()
2890 def eclipseJ2sPlugin
2891 def eclipseJ2sPluginFile
2892 eclipseJ2sPluginDirs.any { dir ->
2893 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
2894 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
2895 if (eclipseJ2sPluginFile.exists()) {
2901 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
2902 System.err.println(msg)
2903 throw new StopExecutionException(msg)
2906 def digest = MessageDigest.getInstance("MD5")
2908 digest.update(j2sPluginFile.text.bytes)
2909 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
2911 digest.update(eclipseJ2sPluginFile.text.bytes)
2912 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
2914 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
2915 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
2916 System.err.println(msg)
2917 throw new StopExecutionException(msg)
2919 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
2925 task jalviewjsIDE_copyJ2sPlugin {
2926 group "00 JalviewJS in Eclipse"
2927 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
2930 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
2931 def j2sPluginFile = file(j2sPlugin)
2932 def eclipseHome = System.properties["eclipse.home.location"]
2933 if (eclipseHome == null || ! IN_ECLIPSE) {
2934 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
2936 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
2937 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
2938 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
2939 System.err.println(msg)
2942 eclipseJ2sPluginFile.getParentFile().mkdirs()
2943 into eclipseJ2sPluginFile.getParent()
2949 task jalviewjsIDE_j2sFile {
2950 group "00 JalviewJS in Eclipse"
2951 description "Creates the .j2s file"
2952 dependsOn jalviewjsCreateJ2sSettings
2956 task jalviewjsIDE_SyncCore {
2957 group "00 JalviewJS in Eclipse"
2958 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
2959 dependsOn jalviewjsSyncCore
2963 task jalviewjsIDE_SyncSiteAll {
2964 dependsOn jalviewjsSyncAllLibs
2965 dependsOn jalviewjsSyncResources
2966 dependsOn jalviewjsSyncSiteResources
2967 dependsOn jalviewjsSyncBuildProperties
2971 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
2974 task jalviewjsIDE_PrepareSite {
2975 group "00 JalviewJS in Eclipse"
2976 description "Sync libs and resources to site dir, but not closure cores"
2978 dependsOn jalviewjsIDE_SyncSiteAll
2979 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
2983 task jalviewjsIDE_AssembleSite {
2984 group "00 JalviewJS in Eclipse"
2985 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
2986 dependsOn jalviewjsPrepareSite
2990 task jalviewjsIDE_SiteClean {
2991 group "00 JalviewJS in Eclipse"
2992 description "Deletes the Eclipse transpiled site"
2993 dependsOn cleanJalviewjsSite
2997 task jalviewjsIDE_Server {
2998 group "00 JalviewJS in Eclipse"
2999 description "Starts a webserver on localhost to test the website"
3000 dependsOn jalviewjsServer
3004 // buildship runs this at import or gradle refresh
3005 task eclipseSynchronizationTask {
3006 //dependsOn eclipseSetup
3007 dependsOn createBuildProperties
3009 dependsOn jalviewjsIDE_j2sFile
3010 dependsOn jalviewjsIDE_checkJ2sPlugin
3011 dependsOn jalviewjsIDE_PrepareSite
3016 // buildship runs this at build time or project refresh
3017 task eclipseAutoBuildTask {
3018 //dependsOn jalviewjsIDE_checkJ2sPlugin
3019 //dependsOn jalviewjsIDE_PrepareSite
3025 description "Build the site"
3026 dependsOn jalviewjsBuildSite