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 java.util.regex.Matcher
13 import java.util.concurrent.Executors
14 import java.util.concurrent.Future
15 import java.util.concurrent.ScheduledExecutorService
16 import java.util.concurrent.TimeUnit
17 import groovy.transform.ExternalizeMethods
18 import groovy.util.XmlParser
19 import groovy.xml.XmlUtil
20 import groovy.json.JsonBuilder
21 import com.vladsch.flexmark.util.ast.Node
22 import com.vladsch.flexmark.html.HtmlRenderer
23 import com.vladsch.flexmark.parser.Parser
24 import com.vladsch.flexmark.util.data.MutableDataSet
25 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
26 import com.vladsch.flexmark.ext.tables.TablesExtension
27 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
28 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
29 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
30 import com.vladsch.flexmark.ext.toc.TocExtension
31 import com.google.common.hash.HashCode
32 import com.google.common.hash.Hashing
33 import com.google.common.io.Files
34 import org.jsoup.Jsoup
35 import org.jsoup.nodes.Element
43 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
44 classpath "org.jsoup:jsoup:1.14.3"
45 classpath "com.eowise:gradle-imagemagick:0.5.1"
54 id "com.diffplug.gradle.spotless" version "3.28.0"
55 id 'com.github.johnrengelman.shadow' version '6.0.0'
56 id 'com.install4j.gradle' version '10.0.3'
57 id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
58 id 'com.palantir.git-version' version '0.13.0' apply false
69 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
70 def string(Object o) {
71 return o == null ? "" : o.toString()
74 def overrideProperties(String propsFileName, boolean output = false) {
75 if (propsFileName == null) {
78 def propsFile = file(propsFileName)
79 if (propsFile != null && propsFile.exists()) {
80 println("Using properties from file '${propsFileName}'")
82 def p = new Properties()
83 def localPropsFIS = new FileInputStream(propsFile)
89 if (project.hasProperty(key)) {
90 oldval = project.findProperty(key)
91 project.setProperty(key, val)
93 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
96 ext.setProperty(key, val)
98 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
102 } catch (Exception e) {
103 println("Exception reading local.properties")
110 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
111 jalviewDirRelativePath = jalviewDir
114 getdownChannelName = CHANNEL.toLowerCase()
115 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
116 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
117 channelDirName = propertiesChannelName
118 // Import channel_properties
119 if (getdownChannelName.startsWith("develop-")) {
120 channelDirName = "develop-SUFFIX"
122 channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
123 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
124 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
125 overrideProperties(channelGradleProperties, false)
126 // local build environment properties
127 // can be "projectDir/local.properties"
128 overrideProperties("${projectDir}/local.properties", true)
129 // or "../projectDir_local.properties"
130 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
133 // Import releaseProps from the RELEASE file
134 // or a file specified via JALVIEW_RELEASE_FILE if defined
135 // Expect jalview.version and target release branch in jalview.release
136 releaseProps = new Properties();
137 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
138 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
140 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
141 releaseProps.load(it)
143 } catch (Exception fileLoadError) {
144 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
147 // Set JALVIEW_VERSION if it is not already set
148 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
149 JALVIEW_VERSION = releaseProps.get("jalview.version")
151 println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
153 // this property set when running Eclipse headlessly
154 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
155 // this property set by Eclipse
156 eclipseApplicationProperty = string("eclipse.application")
157 // CHECK IF RUNNING FROM WITHIN ECLIPSE
158 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
159 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
160 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
161 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
162 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
166 println("WITHIN ECLIPSE IDE")
168 println("HEADLESS BUILD")
171 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
173 println("J2S ENABLED")
176 System.properties.sort { it.key }.each {
177 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
180 if (false && IN_ECLIPSE) {
181 jalviewDir = jalviewDirAbsolutePath
186 buildDate = new Date().format("yyyyMMdd")
189 bareSourceDir = string(source_dir)
190 sourceDir = string("${jalviewDir}/${bareSourceDir}")
191 resourceDir = string("${jalviewDir}/${resource_dir}")
192 bareTestSourceDir = string(test_source_dir)
193 testDir = string("${jalviewDir}/${bareTestSourceDir}")
195 classesDir = string("${jalviewDir}/${classes_dir}")
198 useClover = clover.equals("true")
199 cloverBuildDir = "${buildDir}/clover"
200 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
201 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
202 cloverReportDir = file("${buildDir}/reports/clover")
203 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
204 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
205 //cloverTestClassesDir = cloverClassesDir
206 cloverDb = string("${cloverBuildDir}/clover.db")
208 testSourceDir = useClover ? cloverTestInstrDir : testDir
209 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
212 backgroundImageText = BACKGROUNDIMAGETEXT
213 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
214 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
215 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
216 getdownFullArchiveDir = null
217 getdownTextLines = []
218 getdownLaunchJvl = null
219 getdownVersionLaunchJvl = null
221 buildProperties = null
223 // the following values might be overridden by the CHANNEL switch
224 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
225 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
226 getdownArchiveAppBase = getdown_archive_base
227 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
228 getdownAppDistDir = getdown_app_dir_alt
229 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
230 getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
231 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
232 reportRsyncCommand = false
233 jvlChannelName = CHANNEL.toLowerCase()
234 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
235 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
236 install4jDMGBackgroundImageDir = "${install4j_images_dir}"
237 install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
238 install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
239 install4jInstallerName = "${jalview_name} Non-Release Installer"
240 install4jExecutableName = install4j_executable_name
241 install4jExtraScheme = "jalviewx"
242 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
243 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
244 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
245 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
246 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
247 install4jCheckSums = true
249 applicationName = "${jalview_name}"
253 // TODO: get bamboo build artifact URL for getdown artifacts
254 getdown_channel_base = bamboo_channelbase
255 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
256 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
257 jvlChannelName += "_${getdownChannelName}"
258 // automatically add the test group Not-bamboo for exclusion
259 if ("".equals(testng_excluded_groups)) {
260 testng_excluded_groups = "Not-bamboo"
262 install4jExtraScheme = "jalviewb"
263 backgroundImageText = true
266 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
267 getdownAppDistDir = getdown_app_dir_release
268 getdownSetAppBaseProperty = true
269 reportRsyncCommand = true
271 install4jInstallerName = "${jalview_name} Installer"
275 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
276 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
277 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
278 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
279 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
281 package_dir = string("${ARCHIVEDIR}/${package_dir}")
282 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
285 reportRsyncCommand = true
286 install4jExtraScheme = "jalviewa"
290 getdownChannelName = string("archive/${JALVIEW_VERSION}")
291 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
292 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
293 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
294 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
296 package_dir = string("${ARCHIVEDIR}/${package_dir}")
297 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
300 reportRsyncCommand = true
301 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
302 install4jSuffix = "Archive"
303 install4jExtraScheme = "jalviewa"
306 case ~/^DEVELOP-([\.\-\w]*)$/:
307 def suffix = Matcher.lastMatcher[0][1]
308 reportRsyncCommand = true
309 getdownSetAppBaseProperty = true
310 JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
311 install4jSuffix = "Develop ${suffix}"
312 install4jExtraScheme = "jalviewd"
313 install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
314 getdownChannelName = string("develop-${suffix}")
315 getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
316 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
317 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
318 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
319 channelSuffix = string(suffix)
320 backgroundImageText = true
324 reportRsyncCommand = true
325 getdownSetAppBaseProperty = true
326 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
327 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
329 install4jSuffix = "Develop"
330 install4jExtraScheme = "jalviewd"
331 install4jInstallerName = "${jalview_name} Develop Installer"
332 backgroundImageText = true
336 reportRsyncCommand = true
337 getdownSetAppBaseProperty = true
338 // Don't ignore transpile errors for release build
339 if (jalviewjs_ignore_transpile_errors.equals("true")) {
340 jalviewjs_ignore_transpile_errors = "false"
341 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
343 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
344 install4jSuffix = "Test"
345 install4jExtraScheme = "jalviewt"
346 install4jInstallerName = "${jalview_name} Test Installer"
347 backgroundImageText = true
350 case ~/^SCRATCH(|-[-\w]*)$/:
351 getdownChannelName = CHANNEL
352 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
354 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
355 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
356 reportRsyncCommand = true
357 install4jSuffix = "Scratch"
361 if (!file("${LOCALDIR}").exists()) {
362 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
364 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
365 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
367 JALVIEW_VERSION = "TEST"
368 install4jSuffix = "Test-Local"
369 install4jExtraScheme = "jalviewt"
370 install4jInstallerName = "${jalview_name} Test Installer"
371 backgroundImageText = true
374 case [ "LOCAL", "JALVIEWJS" ]:
375 JALVIEW_VERSION = "TEST"
376 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
377 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
378 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
379 install4jExtraScheme = "jalviewl"
380 install4jCheckSums = false
383 default: // something wrong specified
384 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
388 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
389 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
390 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
391 // override getdownAppBase if requested
392 if (findProperty("getdown_appbase_override") != null) {
393 // revert to LOCAL if empty string
394 if (string(getdown_appbase_override) == "") {
395 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
396 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
397 } else if (string(getdown_appbase_override).startsWith("file://")) {
398 getdownAppBase = string(getdown_appbase_override)
399 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
401 getdownAppBase = string(getdown_appbase_override)
403 println("Overriding getdown appbase with '${getdownAppBase}'")
405 // sanitise file name for jalview launcher file for this channel
406 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
407 // install4j application and folder names
408 if (install4jSuffix == "") {
409 install4jBundleId = "${install4j_bundle_id}"
410 install4jWinApplicationId = install4j_release_win_application_id
412 applicationName = "${jalview_name} ${install4jSuffix}"
413 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
414 // add int hash of install4jSuffix to the last part of the application_id
415 def id = install4j_release_win_application_id
416 def idsplitreverse = id.split("-").reverse()
417 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
418 install4jWinApplicationId = idsplitreverse.reverse().join("-")
420 // sanitise folder and id names
421 // install4jApplicationFolder = e.g. "Jalview Build"
422 install4jApplicationFolder = applicationName
423 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
424 .replaceAll("_+", "_") // collapse __
425 install4jInternalId = applicationName
427 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
428 .replaceAll("_+", "") // collapse __
429 //.replaceAll("_*-_*", "-") // collapse _-_
430 install4jUnixApplicationFolder = applicationName
432 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
433 .replaceAll("_+", "_") // collapse __
434 .replaceAll("_*-_*", "-") // collapse _-_
437 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
438 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
439 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
440 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
441 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
442 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
443 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
444 /* compile without modules -- using classpath libraries
445 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
446 modules_runtimeClasspath = modules_compileClasspath
452 apply plugin: "com.palantir.git-version"
453 def details = versionDetails()
454 gitHash = details.gitHash
455 gitBranch = details.branchName
456 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
457 println("Not in a git repository. Using git values from RELEASE properties file.")
458 gitHash = releaseProps.getProperty("git.hash")
459 gitBranch = releaseProps.getProperty("git.branch")
460 } catch(java.lang.RuntimeException e1) {
461 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
464 println("Using a ${CHANNEL} profile.")
466 additional_compiler_args = []
467 // configure classpath/args for j8/j11 compilation
468 if (JAVA_VERSION.equals("1.8")) {
469 JAVA_INTEGER_VERSION = string("8")
472 libDistDir = j8libDir
473 compile_source_compatibility = 1.8
474 compile_target_compatibility = 1.8
475 // these are getdown.txt properties defined dependent on the JAVA_VERSION
476 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
477 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
478 // this property is assigned below and expanded to multiple lines in the getdown task
479 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
480 // this property is for the Java library used in eclipse
481 eclipseJavaRuntimeName = string("JavaSE-1.8")
482 } else if (JAVA_VERSION.equals("11")) {
483 JAVA_INTEGER_VERSION = string("11")
485 libDistDir = j11libDir
486 compile_source_compatibility = 11
487 compile_target_compatibility = 11
488 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
489 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
490 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
491 eclipseJavaRuntimeName = string("JavaSE-11")
492 /* compile without modules -- using classpath libraries
493 additional_compiler_args += [
494 '--module-path', modules_compileClasspath.asPath,
495 '--add-modules', j11modules
498 } else if (JAVA_VERSION.equals("17")) {
499 JAVA_INTEGER_VERSION = string("17")
501 libDistDir = j17libDir
502 compile_source_compatibility = 17
503 compile_target_compatibility = 17
504 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
505 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
506 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
507 eclipseJavaRuntimeName = string("JavaSE-17")
508 /* compile without modules -- using classpath libraries
509 additional_compiler_args += [
510 '--module-path', modules_compileClasspath.asPath,
511 '--add-modules', j11modules
515 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
520 JAVA_MIN_VERSION = JAVA_VERSION
521 JAVA_MAX_VERSION = JAVA_VERSION
522 jreInstallsDir = string(jre_installs_dir)
523 if (jreInstallsDir.startsWith("~/")) {
524 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
526 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
527 install4jConfFileName = string("jalview-install4j-conf.install4j")
528 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
529 install4jHomeDir = install4j_home_dir
530 if (install4jHomeDir.startsWith("~/")) {
531 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
534 resourceBuildDir = string("${buildDir}/resources")
535 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
536 helpBuildDir = string("${resourceBuildDir}/help_build")
537 docBuildDir = string("${resourceBuildDir}/doc_build")
539 if (buildProperties == null) {
540 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
542 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
543 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
544 helpSourceDir = string("${helpParentDir}/${help_dir}")
545 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
548 convertBinaryExpectedLocation = imagemagick_convert
549 if (convertBinaryExpectedLocation.startsWith("~/")) {
550 convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
552 if (file(convertBinaryExpectedLocation).exists()) {
553 convertBinary = convertBinaryExpectedLocation
556 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
557 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
558 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
560 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
562 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
564 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
565 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
566 jalviewjsTransferSiteMergeDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_merge")
567 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
568 jalviewjsJalviewCoreHtmlFile = string("")
569 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
570 jalviewjsCoreClasslists = []
571 jalviewjsJalviewTemplateName = string(jalviewjs_name)
572 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
573 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
574 jalviewjsJ2sProps = null
575 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
576 jalviewjsStderrLaunchFilename = "${jalviewjsSiteDir}/"+(file(jalviewjs_stderr_launch).getName())
578 eclipseWorkspace = null
579 eclipseBinary = string("")
580 eclipseVersion = string("")
583 jalviewjsChromiumUserDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}"
584 jalviewjsChromiumProfileDir = "${ext.jalviewjsChromiumUserDir}/${jalviewjs_chromium_profile_name}"
594 outputDir = file(classesDir)
598 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
601 compileClasspath = files(sourceSets.main.java.outputDir)
602 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
604 runtimeClasspath = compileClasspath
605 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
610 srcDirs cloverInstrDir
611 outputDir = cloverClassesDir
615 srcDirs = sourceSets.main.resources.srcDirs
618 compileClasspath = files( sourceSets.clover.java.outputDir )
619 //compileClasspath += files( testClassesDir )
620 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
621 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
622 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
624 runtimeClasspath = compileClasspath
629 srcDirs testSourceDir
630 outputDir = file(testClassesDir)
634 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
637 compileClasspath = files( sourceSets.test.java.outputDir )
638 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
639 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
641 runtimeClasspath = compileClasspath
642 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
648 // eclipse project and settings files creation, also used by buildship
651 name = eclipse_project_name
653 natures 'org.eclipse.jdt.core.javanature',
654 'org.eclipse.jdt.groovy.core.groovyNature',
655 'org.eclipse.buildship.core.gradleprojectnature'
657 buildCommand 'org.eclipse.jdt.core.javabuilder'
658 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
662 //defaultOutputDir = sourceSets.main.java.outputDir
663 configurations.each{ c->
664 if (c.isCanBeResolved()) {
665 minusConfigurations += [c]
669 plusConfigurations = [ ]
673 def removeTheseToo = []
674 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
675 cp.entries.each { entry ->
676 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
677 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
678 // we add the resources and help/help dirs in as libs afterwards (see below)
679 if (entry.kind == 'src') {
680 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
681 removeTheseToo += entry
683 alreadyAddedSrcPath.putAt(entry.path, true)
688 cp.entries.removeAll(removeTheseToo)
690 //cp.entries += new Output("${eclipse_bin_dir}/main")
691 if (file(helpParentDir).isDirectory()) {
692 cp.entries += new Library(fileReference(helpParentDir))
694 if (file(resourceDir).isDirectory()) {
695 cp.entries += new Library(fileReference(resourceDir))
698 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
700 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
701 //don't want to add outputDir as eclipse is using its own output dir in bin/main
702 if (it.isDirectory() || ! it.exists()) {
703 // don't add dirs to classpath, especially if they don't exist
704 return false // groovy "continue" in .any closure
706 def itPath = it.toString()
707 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
708 // make relative path
709 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
711 if (alreadyAddedLibPath.get(itPath)) {
712 //println("Not adding duplicate entry "+itPath)
714 //println("Adding entry "+itPath)
715 cp.entries += new Library(fileReference(itPath))
716 alreadyAddedLibPath.put(itPath, true)
720 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
721 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
722 if (it.isDirectory() || ! it.exists()) {
723 // don't add dirs to classpath
724 return false // groovy "continue" in .any closure
727 def itPath = it.toString()
728 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
729 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
731 if (alreadyAddedLibPath.get(itPath)) {
734 def lib = new Library(fileReference(itPath))
735 lib.entryAttributes["test"] = "true"
737 alreadyAddedLibPath.put(itPath, true)
745 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
750 // for the IDE, use java 11 compatibility
751 sourceCompatibility = compile_source_compatibility
752 targetCompatibility = compile_target_compatibility
753 javaRuntimeName = eclipseJavaRuntimeName
755 // add in jalview project specific properties/preferences into eclipse core preferences
757 withProperties { props ->
758 def jalview_prefs = new Properties()
759 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
760 jalview_prefs.load(ins)
762 jalview_prefs.forEach { t, v ->
763 if (props.getAt(t) == null) {
767 // codestyle file -- overrides previous formatter prefs
768 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
769 if (csFile.exists()) {
770 XmlParser parser = new XmlParser()
771 def profiles = parser.parse(csFile)
772 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
773 if (profile != null) {
774 profile.'setting'.each { s ->
776 def value = s.'@value'
777 if (id != null && value != null) {
778 props.putAt(id, value)
789 // Don't want these to be activated if in headless build
790 synchronizationTasks "eclipseSynchronizationTask"
791 //autoBuildTasks "eclipseAutoBuildTask"
797 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
798 // Class to allow updating arbitrary properties files
799 class PropertiesFile extends PropertiesPersistableConfigurationObject {
800 public PropertiesFile(PropertiesTransformer t) { super(t); }
801 @Override protected void load(Properties properties) { }
802 @Override protected void store(Properties properties) { }
803 @Override protected String getDefaultResourceName() { return ""; }
804 // This is necessary, because PropertiesPersistableConfigurationObject fails
805 // if no default properties file exists.
806 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
809 // Task to update arbitrary properties files (set outputFile)
810 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
811 private final PropertiesFileContentMerger file;
812 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
813 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
814 protected void configure(PropertiesFile props) {
815 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
817 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
820 task eclipseUIPreferences(type: PropertiesFileTask) {
821 description = "Generate Eclipse additional settings"
822 def filename = "org.eclipse.jdt.ui.prefs"
823 outputFile = "$projectDir/.settings/${filename}" as File
826 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
831 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
832 description = "Generate Eclipse additional settings"
833 def filename = "org.eclipse.jdt.groovy.core.prefs"
834 outputFile = "$projectDir/.settings/${filename}" as File
837 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
842 task eclipseAllPreferences {
844 dependsOn eclipseUIPreferences
845 dependsOn eclipseGroovyCorePreferences
848 eclipseUIPreferences.mustRunAfter eclipseJdt
849 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
851 /* end of eclipse preferences hack */
859 delete cloverBuildDir
860 delete cloverReportDir
865 task cloverInstrJava(type: JavaExec) {
866 group = "Verification"
867 description = "Create clover instrumented source java files"
869 dependsOn cleanClover
871 inputs.files(sourceSets.main.allJava)
872 outputs.dir(cloverInstrDir)
874 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
875 classpath = sourceSets.clover.compileClasspath
876 main = "com.atlassian.clover.CloverInstr"
884 cloverInstrDir.getPath(),
886 def srcFiles = sourceSets.main.allJava.files
889 { file -> file.absolutePath }
892 args argsList.toArray()
895 delete cloverInstrDir
896 println("Clover: About to instrument "+srcFiles.size() +" files")
901 task cloverInstrTests(type: JavaExec) {
902 group = "Verification"
903 description = "Create clover instrumented source test files"
905 dependsOn cleanClover
907 inputs.files(testDir)
908 outputs.dir(cloverTestInstrDir)
910 classpath = sourceSets.clover.compileClasspath
911 main = "com.atlassian.clover.CloverInstr"
921 cloverTestInstrDir.getPath(),
923 args argsList.toArray()
926 delete cloverTestInstrDir
927 println("Clover: About to instrument test files")
933 group = "Verification"
934 description = "Create clover instrumented all source files"
936 dependsOn cloverInstrJava
937 dependsOn cloverInstrTests
941 cloverClasses.dependsOn cloverInstr
944 task cloverConsoleReport(type: JavaExec) {
945 group = "Verification"
946 description = "Creates clover console report"
949 file(cloverDb).exists()
952 inputs.dir cloverClassesDir
954 classpath = sourceSets.clover.runtimeClasspath
955 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
957 if (cloverreport_mem.length() > 0) {
958 maxHeapSize = cloverreport_mem
960 if (cloverreport_jvmargs.length() > 0) {
961 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
971 args argsList.toArray()
975 task cloverHtmlReport(type: JavaExec) {
976 group = "Verification"
977 description = "Creates clover HTML report"
980 file(cloverDb).exists()
983 def cloverHtmlDir = cloverReportDir
984 inputs.dir cloverClassesDir
985 outputs.dir cloverHtmlDir
987 classpath = sourceSets.clover.runtimeClasspath
988 main = "com.atlassian.clover.reporters.html.HtmlReporter"
990 if (cloverreport_mem.length() > 0) {
991 maxHeapSize = cloverreport_mem
993 if (cloverreport_jvmargs.length() > 0) {
994 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1005 if (cloverreport_html_options.length() > 0) {
1006 argsList += cloverreport_html_options.split(" ")
1009 args argsList.toArray()
1013 task cloverXmlReport(type: JavaExec) {
1014 group = "Verification"
1015 description = "Creates clover XML report"
1018 file(cloverDb).exists()
1021 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1022 inputs.dir cloverClassesDir
1023 outputs.file cloverXmlFile
1025 classpath = sourceSets.clover.runtimeClasspath
1026 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1028 if (cloverreport_mem.length() > 0) {
1029 maxHeapSize = cloverreport_mem
1031 if (cloverreport_jvmargs.length() > 0) {
1032 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1043 if (cloverreport_xml_options.length() > 0) {
1044 argsList += cloverreport_xml_options.split(" ")
1047 args argsList.toArray()
1052 group = "Verification"
1053 description = "Creates clover reports"
1055 dependsOn cloverXmlReport
1056 dependsOn cloverHtmlReport
1063 sourceCompatibility = compile_source_compatibility
1064 targetCompatibility = compile_target_compatibility
1065 options.compilerArgs += additional_compiler_args
1066 print ("Setting target compatibility to "+targetCompatibility+"\n")
1068 //classpath += configurations.cloverRuntime
1074 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1075 sourceCompatibility = compile_source_compatibility
1076 targetCompatibility = compile_target_compatibility
1077 options.compilerArgs += additional_compiler_args
1078 options.encoding = "UTF-8"
1080 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1087 sourceCompatibility = compile_source_compatibility
1088 targetCompatibility = compile_target_compatibility
1089 options.compilerArgs += additional_compiler_args
1091 print ("Setting target compatibility to "+targetCompatibility+"\n")
1098 delete sourceSets.main.java.outputDir
1104 dependsOn cleanClover
1106 delete sourceSets.test.java.outputDir
1111 // format is a string like date.format("dd MMMM yyyy")
1112 def getDate(format) {
1113 return date.format(format)
1117 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1118 MutableDataSet options = new MutableDataSet()
1120 def extensions = new ArrayList<>()
1121 extensions.add(AnchorLinkExtension.create())
1122 extensions.add(AutolinkExtension.create())
1123 extensions.add(StrikethroughExtension.create())
1124 extensions.add(TaskListExtension.create())
1125 extensions.add(TablesExtension.create())
1126 extensions.add(TocExtension.create())
1128 options.set(Parser.EXTENSIONS, extensions)
1130 // set GFM table parsing options
1131 options.set(TablesExtension.WITH_CAPTION, false)
1132 options.set(TablesExtension.COLUMN_SPANS, false)
1133 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1134 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1135 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1136 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1137 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1139 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1140 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1141 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1142 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1144 Parser parser = Parser.builder(options).build()
1145 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1147 mdFiles.each { mdFile ->
1148 // add table of contents
1149 def mdText = "[TOC]\n"+mdFile.text
1151 // grab the first top-level title
1153 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1154 def matcher = mdText =~ titleRegex
1155 if (matcher.size() > 0) {
1156 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1157 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1159 // or use the filename if none found
1160 if (title == null) {
1161 title = mdFile.getName()
1164 Node document = parser.parse(mdText)
1165 String htmlBody = renderer.render(document)
1166 def htmlText = '''<html>
1167 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1168 <html xmlns="http://www.w3.org/1999/xhtml">
1170 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1171 <meta http-equiv="Content-Style-Type" content="text/css" />
1172 <meta name="generator" content="flexmark" />
1174 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1176 <style type="text/css">code{white-space: pre;}</style>
1178 htmlText += ((cssFile != null) ? cssFile.text : '')
1179 htmlText += '''</head>
1182 htmlText += htmlBody
1188 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1189 def htmlFile = file(htmlFilePath)
1190 println("Creating ${htmlFilePath}")
1191 htmlFile.text = htmlText
1196 task copyDocs(type: Copy) {
1197 def inputDir = "${jalviewDir}/${doc_dir}"
1198 def outputDir = "${docBuildDir}/${doc_dir}"
1202 include('**/*.html')
1204 filter(ReplaceTokens,
1208 'Version-Rel': JALVIEW_VERSION,
1209 'Year-Rel': getDate("yyyy")
1216 exclude('**/*.html')
1221 inputs.dir(inputDir)
1222 outputs.dir(outputDir)
1226 task convertMdFiles {
1228 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1229 def cssFile = file("${jalviewDir}/${flexmark_css}")
1232 convertMdToHtml(mdFiles, cssFile)
1235 inputs.files(mdFiles)
1236 inputs.file(cssFile)
1239 mdFiles.each { mdFile ->
1240 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1241 htmlFiles.add(file(htmlFilePath))
1243 outputs.files(htmlFiles)
1247 def hugoTemplateSubstitutions(String input, Map extras=null) {
1248 def replacements = [
1249 DATE: getDate("yyyy-MM-dd"),
1250 CHANNEL: propertiesChannelName,
1251 APPLICATION_NAME: applicationName,
1253 GIT_BRANCH: gitBranch,
1254 VERSION: JALVIEW_VERSION,
1255 JAVA_VERSION: JAVA_VERSION,
1256 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1261 if (extras != null) {
1262 extras.each{ k, v ->
1263 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1266 replacements.each{ k, v ->
1267 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1272 def mdFileComponents(File mdFile, def dateOnly=false) {
1275 if (mdFile.exists()) {
1276 def inFrontMatter = false
1277 def firstLine = true
1278 mdFile.eachLine { line ->
1279 if (line.matches("---")) {
1280 def prev = inFrontMatter
1281 inFrontMatter = firstLine
1282 if (inFrontMatter != prev)
1285 if (inFrontMatter) {
1287 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1288 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1289 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1290 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1291 } else if (m = line =~ /^channel:\s*(\S+)/) {
1292 map["channel"] = m[0][1]
1293 } else if (m = line =~ /^version:\s*(\S+)/) {
1294 map["version"] = m[0][1]
1295 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1296 map[ m[0][1] ] = m[0][2]
1298 if (dateOnly && map["date"] != null) {
1304 content += line+"\n"
1309 return dateOnly ? map["date"] : [map, content]
1312 task hugoTemplates {
1314 description "Create partially populated md pages for hugo website build"
1316 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1317 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1318 def templateFiles = fileTree(dir: hugoTemplatesDir)
1319 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1320 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1321 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1322 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1325 // specific release template for version archive
1328 def givenDate = null
1329 def givenChannel = null
1330 def givenVersion = null
1331 if (CHANNEL == "RELEASE") {
1332 def (map, content) = mdFileComponents(releaseMdFile)
1333 givenDate = map.date
1334 givenChannel = map.channel
1335 givenVersion = map.version
1337 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1338 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1341 if (whatsnewMdFile.exists())
1342 whatsnew = whatsnewMdFile.text
1345 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1346 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1348 def changesHugo = null
1349 if (changes != null) {
1350 changesHugo = '<div class="release_notes">\n\n'
1351 def inSection = false
1352 changes.eachLine { line ->
1354 if (m = line =~ /^##([^#].*)$/) {
1356 changesHugo += "</div>\n\n"
1358 def section = m[0][1].trim()
1359 section = section.toLowerCase()
1360 section = section.replaceAll(/ +/, "_")
1361 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1362 changesHugo += "<div class=\"${section}\">\n\n"
1364 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1365 def comment = m[0][2].trim()
1366 if (comment != "") {
1367 comment = comment.replaceAll('"', """)
1369 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1370 def newline = m[0][1]
1371 if (comment.trim() != "")
1372 newline += "{{<comment>}}${comment}{{</comment>}} "
1373 newline += m[0][3].trim()
1374 if (issuekeys.size() > 0)
1375 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1376 if (m[0][4] != null)
1381 changesHugo += line+"\n"
1384 changesHugo += "\n</div>\n\n"
1386 changesHugo += '</div>'
1389 templateFiles.each{ templateFile ->
1390 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1391 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1392 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1394 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1398 rename(templateFile.getName(), newFileName)
1402 def newFile = file("${outPathName}/${newFileName}".toString())
1403 def content = newFile.text
1404 newFile.text = hugoTemplateSubstitutions(content,
1407 CHANGES: changesHugo,
1408 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1409 DRAFT: givenDate == null ? "true" : "false",
1410 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1411 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1418 inputs.file(oldJvlFile)
1419 inputs.dir(hugoTemplatesDir)
1420 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1421 inputs.property("CHANNEL", { CHANNEL })
1424 def getMdDate(File mdFile) {
1425 return mdFileComponents(mdFile, true)
1428 def getMdSections(String content) {
1430 def sectionContent = ""
1431 def sectionName = null
1432 content.eachLine { line ->
1434 if (m = line =~ /^##([^#].*)$/) {
1435 if (sectionName != null) {
1436 sections[sectionName] = sectionContent
1440 sectionName = m[0][1].trim()
1441 sectionName = sectionName.toLowerCase()
1442 sectionName = sectionName.replaceAll(/ +/, "_")
1443 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1444 } else if (sectionName != null) {
1445 sectionContent += line+"\n"
1448 if (sectionContent != null) {
1449 sections[sectionName] = sectionContent
1455 task copyHelp(type: Copy) {
1456 def inputDir = helpSourceDir
1457 def outputDir = "${helpBuildDir}/${help_dir}"
1461 include('**/*.html')
1465 filter(ReplaceTokens,
1469 'Version-Rel': JALVIEW_VERSION,
1470 'Year-Rel': getDate("yyyy")
1477 exclude('**/*.html')
1484 inputs.dir(inputDir)
1485 outputs.files(helpFile)
1486 outputs.dir(outputDir)
1490 task releasesTemplates {
1492 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1496 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1497 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1498 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1499 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1500 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1501 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1504 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1505 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1507 if (CHANNEL == "RELEASE") {
1508 if (!releaseMdFile.exists()) {
1509 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1511 if (!whatsnewMdFile.exists()) {
1512 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1516 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1517 def releaseFilesDates = releaseFiles.collectEntries {
1518 [(it): getMdDate(it)]
1520 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1522 def releasesTemplate = releasesTemplateFile.text
1523 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1524 def versionTemplate = m[0][1]
1526 MutableDataSet options = new MutableDataSet()
1528 def extensions = new ArrayList<>()
1529 options.set(Parser.EXTENSIONS, extensions)
1530 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1532 Parser parser = Parser.builder(options).build()
1533 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1535 def actualVersions = releaseFiles.collect { rf ->
1536 def (rfMap, rfContent) = mdFileComponents(rf)
1537 return rfMap.version
1539 def versionsHtml = ""
1540 def linkedVersions = []
1541 releaseFiles.reverse().each { rFile ->
1542 def (rMap, rContent) = mdFileComponents(rFile)
1544 def versionLink = ""
1545 def partialVersion = ""
1546 def firstPart = true
1547 rMap.version.split("\\.").each { part ->
1548 def displayPart = ( firstPart ? "" : "." ) + part
1549 partialVersion += displayPart
1551 linkedVersions.contains(partialVersion)
1552 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1554 versionLink += displayPart
1556 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1557 linkedVersions += partialVersion
1561 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1564 def rContentProcessed = ""
1565 rContent.eachLine { line ->
1566 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1567 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1568 } else if (lm = line =~ /^###([^#]+.*)$/) {
1569 line = "_${lm[0][1].trim()}_"
1571 rContentProcessed += line + "\n"
1574 def rContentSections = getMdSections(rContentProcessed)
1575 def rVersion = versionTemplate
1576 if (rVersion != "") {
1577 def rNewFeatures = rContentSections["new_features"]
1578 def rIssuesResolved = rContentSections["issues_resolved"]
1579 Node newFeaturesNode = parser.parse(rNewFeatures)
1580 String newFeaturesHtml = renderer.render(newFeaturesNode)
1581 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1582 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1583 rVersion = hugoTemplateSubstitutions(rVersion,
1585 VERSION: rMap.version,
1586 VERSION_LINK: versionLink,
1587 DISPLAY_DATE: displayDate,
1588 NEW_FEATURES: newFeaturesHtml,
1589 ISSUES_RESOLVED: issuesResolvedHtml
1592 versionsHtml += rVersion
1596 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1597 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1598 releasesHtmlFile.text = releasesTemplate
1600 if (whatsnewMdFile.exists()) {
1601 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1602 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1603 Node whatsnewNode = parser.parse(whatsnewMd)
1604 String whatsnewHtml = renderer.render(whatsnewNode)
1605 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1606 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1608 VERSION: JALVIEW_VERSION,
1609 DISPLAY_DATE: wnDisplayDate
1612 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1613 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1618 inputs.file(releasesTemplateFile)
1619 inputs.file(whatsnewTemplateFile)
1620 inputs.dir(releasesMdDir)
1621 inputs.dir(whatsnewMdDir)
1622 outputs.file(releasesHtmlFile)
1623 outputs.file(whatsnewHtmlFile)
1627 task copyResources(type: Copy) {
1629 description = "Copy (and make text substitutions in) the resources dir to the build area"
1631 def inputDir = resourceDir
1632 def outputDir = resourcesBuildDir
1636 include('**/*.html')
1638 filter(ReplaceTokens,
1642 'Version-Rel': JALVIEW_VERSION,
1643 'Year-Rel': getDate("yyyy")
1650 exclude('**/*.html')
1655 inputs.dir(inputDir)
1656 outputs.dir(outputDir)
1659 task copyChannelResources(type: Copy) {
1660 dependsOn copyResources
1662 description = "Copy the channel resources dir to the build resources area"
1664 def inputDir = "${channelDir}/${resource_dir}"
1665 def outputDir = resourcesBuildDir
1667 include(channel_props)
1668 filter(ReplaceTokens,
1672 'SUFFIX': channelSuffix
1677 exclude(channel_props)
1681 inputs.dir(inputDir)
1682 outputs.dir(outputDir)
1685 task createBuildProperties(type: WriteProperties) {
1686 dependsOn copyResources
1688 description = "Create the ${buildProperties} file"
1690 inputs.dir(sourceDir)
1691 inputs.dir(resourcesBuildDir)
1692 outputFile (buildProperties)
1693 // taking time specific comment out to allow better incremental builds
1694 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1695 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1696 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1697 property "VERSION", JALVIEW_VERSION
1698 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1699 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1700 if (getdownSetAppBaseProperty) {
1701 property "GETDOWNAPPBASE", getdownAppBase
1702 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1704 outputs.file(outputFile)
1708 task buildIndices(type: JavaExec) {
1710 classpath = sourceSets.main.compileClasspath
1711 main = "com.sun.java.help.search.Indexer"
1712 workingDir = "${helpBuildDir}/${help_dir}"
1715 inputs.dir("${workingDir}/${argDir}")
1717 outputs.dir("${classesDir}/doc")
1718 outputs.dir("${classesDir}/help")
1719 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1720 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1721 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1722 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1723 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1724 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1727 task buildResources {
1728 dependsOn copyResources
1729 dependsOn copyChannelResources
1730 dependsOn createBuildProperties
1734 dependsOn buildResources
1737 dependsOn releasesTemplates
1738 dependsOn convertMdFiles
1739 dependsOn buildIndices
1743 compileJava.dependsOn prepare
1744 run.dependsOn compileJava
1745 compileTestJava.dependsOn compileJava
1750 group = "Verification"
1751 description = "Runs all testTaskN tasks)"
1754 dependsOn cloverClasses
1756 dependsOn testClasses
1759 // not running tests in this task
1762 /* testTask0 is the main test task */
1763 task testTask0(type: Test) {
1764 group = "Verification"
1765 description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
1767 includeGroups testng_groups.split(",")
1768 excludeGroups testng_excluded_groups.split(",")
1769 tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
1771 useDefaultListeners=true
1775 /* separated tests */
1776 task testTask1(type: Test) {
1777 group = "Verification"
1778 description = "Tests that need to be isolated from the main test run"
1781 excludeGroups testng_excluded_groups.split(",")
1783 useDefaultListeners=true
1787 task testTask2(type: Test) {
1788 group = "Verification"
1789 description = "Tests that need to be isolated from the main test run"
1792 excludeGroups testng_excluded_groups.split(",")
1794 useDefaultListeners=true
1797 task testTask3(type: Test) {
1798 group = "Verification"
1799 description = "Tests that need to be isolated from the main test run"
1802 excludeGroups testng_excluded_groups.split(",")
1804 useDefaultListeners=true
1808 /* insert more testTaskNs here -- change N to next digit or other string */
1810 task testTaskN(type: Test) {
1811 group = "Verification"
1812 description = "Tests that need to be isolated from the main test run"
1815 excludeGroups testng_excluded_groups.split(",")
1817 useDefaultListeners=true
1823 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1824 * to summarise test results from all Test tasks
1826 /* START of test tasks results summary */
1827 import groovy.time.TimeCategory
1828 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1829 import org.gradle.api.tasks.testing.logging.TestLogEvent
1830 rootProject.ext.testsResults = [] // Container for tests summaries
1832 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1834 // from original test task
1836 dependsOn cloverClasses
1838 dependsOn testClasses //?
1841 // run main tests first
1842 if (!testTask.name.equals("testTask0"))
1843 testTask.mustRunAfter "testTask0"
1845 testTask.testLogging { logging ->
1846 events TestLogEvent.FAILED
1847 // TestLogEvent.SKIPPED,
1848 // TestLogEvent.STANDARD_OUT,
1849 // TestLogEvent.STANDARD_ERROR
1851 exceptionFormat TestExceptionFormat.FULL
1854 showStackTraces true
1856 showStandardStreams true
1858 info.events = [ TestLogEvent.FAILED ]
1861 if (OperatingSystem.current().isMacOsX()) {
1862 testTask.systemProperty "apple.awt.UIElement", "true"
1863 testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
1867 ignoreFailures = true // Always try to run all tests for all modules
1869 afterSuite { desc, result ->
1871 return // Only summarize results for whole modules
1873 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1875 rootProject.ext.testsResults.add(resultsInfo)
1878 // from original test task
1879 maxHeapSize = "1024m"
1881 workingDir = jalviewDir
1882 def testLaf = project.findProperty("test_laf")
1883 if (testLaf != null) {
1884 println("Setting Test LaF to '${testLaf}'")
1885 systemProperty "laf", testLaf
1887 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1888 if (testHiDPIScale != null) {
1889 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1890 systemProperty "sun.java2d.uiScale", testHiDPIScale
1892 sourceCompatibility = compile_source_compatibility
1893 targetCompatibility = compile_target_compatibility
1894 jvmArgs += additional_compiler_args
1897 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1898 // testTasks that include the tests, and exclude all from the others.
1899 // get --test argument
1900 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1901 // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
1902 // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
1906 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1911 /* don't fail on no matching tests (so --tests will run across all testTasks) */
1912 testTask.filter.setFailOnNoMatchingTests(false)
1914 /* ensure the "test" task dependsOn all the testTasks */
1915 test.dependsOn testTask
1918 gradle.buildFinished {
1919 def allResults = rootProject.ext.testsResults
1921 if (!allResults.isEmpty()) {
1922 printResults allResults
1923 allResults.each {r ->
1924 if (r[2].resultType == TestResult.ResultType.FAILURE)
1925 throw new GradleException("Failed tests!")
1930 private static String colString(styler, col, colour, text) {
1931 return col?"${styler[colour](text)}":text
1934 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1935 def colour = 'black'
1943 case TestResult.ResultType.SUCCESS:
1946 case TestResult.ResultType.FAILURE:
1954 StringBuilder sb = new StringBuilder()
1958 sb.append(" results: ")
1959 sb.append(colString(s, col && !nocol, colour, text))
1961 sb.append("${rc} tests, ")
1962 sb.append(colString(s, col && rs > 0, 'green', rs))
1963 sb.append(" successes, ")
1964 sb.append(colString(s, col && rf > 0, 'red', rf))
1965 sb.append(" failures, ")
1966 sb.append("${rsk} skipped) in ${t}")
1967 return sb.toString()
1970 private static void printResults(allResults) {
1972 // styler from https://stackoverflow.com/a/56139852
1973 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1976 def failedTests = false
1977 def summaryLines = []
1979 def totalsuccess = 0
1982 def totaltime = TimeCategory.getSeconds(0)
1983 // sort on project name then task name
1984 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1985 def projectName = it[0]
1986 def taskName = it[1]
1990 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1991 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1992 def reportLine = "Report file: ${report}"
1993 def ls = summaryPlain.length()
1994 def lr = reportLine.length()
1995 def m = [ls, lr].max()
1998 def info = [ls, summaryCol, reportLine]
1999 summaryLines.add(info)
2000 failedTests |= result.resultType == TestResult.ResultType.FAILURE
2001 totalcount += result.testCount
2002 totalsuccess += result.successfulTestCount
2003 totalfail += result.failedTestCount
2004 totalskip += result.skippedTestCount
2007 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
2008 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
2009 def tls = totalSummaryPlain.length()
2010 if (tls > maxLength)
2012 def info = [tls, totalSummaryCol, null]
2013 summaryLines.add(info)
2015 def allSummaries = []
2016 for(sInfo : summaryLines) {
2018 def summary = sInfo[1]
2019 def report = sInfo[2]
2021 StringBuilder sb = new StringBuilder()
2022 sb.append("│" + summary + " " * (maxLength - ls) + "│")
2023 if (report != null) {
2024 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
2026 allSummaries += sb.toString()
2029 println "┌${"${"─" * maxLength}"}┐"
2030 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
2031 println "└${"${"─" * maxLength}"}┘"
2033 /* END of test tasks results summary */
2036 task compileLinkCheck(type: JavaCompile) {
2038 classpath = files("${jalviewDir}/${utils_dir}")
2039 destinationDir = file("${jalviewDir}/${utils_dir}")
2040 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
2042 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2043 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2044 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
2045 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
2049 task linkCheck(type: JavaExec) {
2051 dependsOn compileLinkCheck
2053 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2054 classpath = files("${jalviewDir}/${utils_dir}")
2055 main = "HelpLinksChecker"
2056 workingDir = "${helpBuildDir}"
2057 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2059 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2060 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2063 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2067 inputs.dir(helpBuildDir)
2068 outputs.file(helpLinksCheckerOutFile)
2072 // import the pubhtmlhelp target
2073 ant.properties.basedir = "${jalviewDir}"
2074 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2075 ant.importBuild "${utils_dir}/publishHelp.xml"
2078 task cleanPackageDir(type: Delete) {
2080 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2090 attributes "Main-Class": main_class,
2091 "Permissions": "all-permissions",
2092 "Application-Name": applicationName,
2093 "Codebase": application_codebase,
2094 "Implementation-Version": JALVIEW_VERSION
2097 def outputDir = "${jalviewDir}/${package_dir}"
2098 destinationDirectory = file(outputDir)
2099 archiveFileName = rootProject.name+".jar"
2100 duplicatesStrategy "EXCLUDE"
2107 exclude "**/*.jar.*"
2109 inputs.dir(sourceSets.main.java.outputDir)
2110 sourceSets.main.resources.srcDirs.each{ dir ->
2113 outputs.file("${outputDir}/${archiveFileName}")
2117 task copyJars(type: Copy) {
2118 from fileTree(dir: classesDir, include: "**/*.jar").files
2119 into "${jalviewDir}/${package_dir}"
2123 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2124 task syncJars(type: Sync) {
2126 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2127 into "${jalviewDir}/${package_dir}"
2129 include jar.archiveFileName.getOrNull()
2136 description = "Put all required libraries in dist"
2137 // order of "cleanPackageDir", "copyJars", "jar" important!
2138 jar.mustRunAfter cleanPackageDir
2139 syncJars.mustRunAfter cleanPackageDir
2140 dependsOn cleanPackageDir
2143 outputs.dir("${jalviewDir}/${package_dir}")
2148 dependsOn cleanPackageDir
2155 group = "distribution"
2156 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2161 def jarFiles = fileTree(dir: "${jalviewDir}/${libDistDir}", include: "*.jar", exclude: "regex.jar").getFiles()
2162 def groovyJars = jarFiles.findAll {it1 -> file(it1).getName().startsWith("groovy-swing")}
2163 def otherJars = jarFiles.findAll {it2 -> !file(it2).getName().startsWith("groovy-swing")}
2167 // we need to include the groovy-swing Include-Package for it to run in the shadowJar
2169 def jarFileManifests = []
2170 groovyJars.each { jarFile ->
2171 def mf = zipTree(jarFile).getFiles().find { it.getName().equals("MANIFEST.MF") }
2173 jarFileManifests += mf
2178 attributes "Implementation-Version": JALVIEW_VERSION, "Application-Name": applicationName
2179 from (jarFileManifests) {
2180 eachEntry { details ->
2181 if (!details.key.equals("Import-Package")) {
2189 duplicatesStrategy "INCLUDE"
2191 mainClassName = shadow_jar_main_class
2193 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2197 task getdownImagesCopy() {
2198 inputs.dir getdownImagesDir
2199 outputs.dir getdownImagesBuildDir
2203 from(getdownImagesDir) {
2204 include("*getdown*.png")
2206 into getdownImagesBuildDir
2211 task getdownImagesProcess() {
2212 dependsOn getdownImagesCopy
2215 if (backgroundImageText) {
2216 if (convertBinary == null) {
2217 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2219 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2220 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2222 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2224 executable convertBinary
2227 '-font', getdown_background_image_text_font,
2228 '-fill', getdown_background_image_text_colour,
2229 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2230 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2231 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2240 task getdownImages() {
2241 dependsOn getdownImagesProcess
2244 task getdownWebsite() {
2245 group = "distribution"
2246 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2248 dependsOn getdownImages
2253 def getdownWebsiteResourceFilenames = []
2254 def getdownResourceDir = getdownResourceDir
2255 def getdownResourceFilenames = []
2258 // clean the getdown website and files dir before creating getdown folders
2259 delete getdownAppBaseDir
2260 delete getdownFilesDir
2263 from buildProperties
2264 rename(file(buildProperties).getName(), getdown_build_properties)
2267 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2270 from channelPropsFile
2271 filter(ReplaceTokens,
2275 'SUFFIX': channelSuffix
2278 into getdownAppBaseDir
2280 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2282 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2283 def props = project.properties.sort { it.key }
2284 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2285 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2287 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2288 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2290 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2291 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2293 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2294 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2295 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2296 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2297 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2298 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
2299 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
2302 props.put("getdown_txt_title", jalview_name)
2303 props.put("getdown_txt_ui.name", applicationName)
2305 // start with appbase
2306 getdownTextLines += "appbase = ${getdownAppBase}"
2307 props.each{ prop, val ->
2308 if (prop.startsWith("getdown_txt_") && val != null) {
2309 if (prop.startsWith("getdown_txt_multi_")) {
2310 def key = prop.substring(18)
2311 val.split(",").each{ v ->
2312 def line = "${key} = ${v}"
2313 getdownTextLines += line
2316 // file values rationalised
2317 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2319 if (val.indexOf('/') == 0) {
2322 } else if (val.indexOf('/') > 0) {
2323 // relative path (relative to jalviewDir)
2324 r = file( "${jalviewDir}/${val}" )
2327 val = "${getdown_resource_dir}/" + r.getName()
2328 getdownWebsiteResourceFilenames += val
2329 getdownResourceFilenames += r.getPath()
2332 if (! prop.startsWith("getdown_txt_resource")) {
2333 def line = prop.substring(12) + " = ${val}"
2334 getdownTextLines += line
2340 getdownWebsiteResourceFilenames.each{ filename ->
2341 getdownTextLines += "resource = ${filename}"
2343 getdownResourceFilenames.each{ filename ->
2346 into getdownResourceDir
2350 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2351 getdownWrapperScripts.each{ script ->
2352 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2356 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2358 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2363 fileTree(file(package_dir)).each{ f ->
2364 if (f.isDirectory()) {
2365 def files = fileTree(dir: f, include: ["*"]).getFiles()
2367 } else if (f.exists()) {
2371 def jalviewJar = jar.archiveFileName.getOrNull()
2372 // put jalview.jar first for CLASSPATH and .properties files reasons
2373 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2374 def name = f.getName()
2375 def line = "code = ${getdownAppDistDir}/${name}"
2376 getdownTextLines += line
2383 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2385 if (JAVA_VERSION.equals("11")) {
2386 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2387 j11libFiles.sort().each{f ->
2388 def name = f.getName()
2389 def line = "code = ${getdown_j11lib_dir}/${name}"
2390 getdownTextLines += line
2393 into getdownJ11libDir
2399 // 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.
2400 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2401 getdownTextLines += "resource = ${getdown_launcher_new}"
2402 getdownTextLines += "class = ${main_class}"
2403 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2404 if (getdownSetAppBaseProperty) {
2405 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2406 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2409 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2410 getdownTxt.write(getdownTextLines.join("\n"))
2412 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2413 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2414 launchJvl.write("appbase=${getdownAppBase}")
2416 // files going into the getdown website dir: getdown-launcher.jar
2418 from getdownLauncher
2419 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2420 into getdownAppBaseDir
2423 // files going into the getdown website dir: getdown-launcher(-local).jar
2425 from getdownLauncher
2426 if (file(getdownLauncher).getName() != getdown_launcher) {
2427 rename(file(getdownLauncher).getName(), getdown_launcher)
2429 into getdownAppBaseDir
2432 // files going into the getdown website dir: ./install dir and files
2433 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2436 from getdownLauncher
2437 from "${getdownAppDir}/${getdown_build_properties}"
2438 if (file(getdownLauncher).getName() != getdown_launcher) {
2439 rename(file(getdownLauncher).getName(), getdown_launcher)
2441 into getdownInstallDir
2444 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2446 from getdownInstallDir
2447 into getdownFilesInstallDir
2451 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2455 from getdownLauncher
2456 from "${getdownAppBaseDir}/${getdown_build_properties}"
2457 from "${getdownAppBaseDir}/${channel_props}"
2458 if (file(getdownLauncher).getName() != getdown_launcher) {
2459 rename(file(getdownLauncher).getName(), getdown_launcher)
2461 into getdownFilesDir
2464 // and ./resource (not all downloaded by getdown)
2466 from getdownResourceDir
2467 into "${getdownFilesDir}/${getdown_resource_dir}"
2472 inputs.dir("${jalviewDir}/${package_dir}")
2474 outputs.dir(getdownAppBaseDir)
2475 outputs.dir(getdownFilesDir)
2479 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2480 task getdownDigestDir(type: JavaExec) {
2482 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2484 def digestDirPropertyName = "DIGESTDIR"
2486 classpath = files(getdownLauncher)
2487 def digestDir = findProperty(digestDirPropertyName)
2488 if (digestDir == null) {
2489 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2493 main = "com.threerings.getdown.tools.Digester"
2497 task getdownDigest(type: JavaExec) {
2498 group = "distribution"
2499 description = "Digest the getdown website folder"
2500 dependsOn getdownWebsite
2502 classpath = files(getdownLauncher)
2504 main = "com.threerings.getdown.tools.Digester"
2505 args getdownAppBaseDir
2506 inputs.dir(getdownAppBaseDir)
2507 outputs.file("${getdownAppBaseDir}/digest2.txt")
2512 group = "distribution"
2513 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2514 dependsOn getdownDigest
2516 if (reportRsyncCommand) {
2517 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2518 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2519 println "LIKELY RSYNC COMMAND:"
2520 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2521 if (RUNRSYNC == "true") {
2523 commandLine "mkdir", "-p", toDir
2526 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2534 task getdownArchiveBuild() {
2535 group = "distribution"
2536 description = "Put files in the archive dir to go on the website"
2538 dependsOn getdownWebsite
2540 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2541 def vDir = "${getdownArchiveDir}/${v}"
2542 getdownFullArchiveDir = "${vDir}/getdown"
2543 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2545 def vAltDir = "alt_${v}"
2546 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2549 // cleanup old "old" dir
2550 delete getdownArchiveDir
2552 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2553 getdownArchiveTxt.getParentFile().mkdirs()
2554 def getdownArchiveTextLines = []
2555 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2559 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2560 into "${getdownFullArchiveDir}/${vAltDir}"
2563 getdownTextLines.each { line ->
2564 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2565 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2566 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2567 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2568 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2569 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2570 // remove the existing resource = resource/ or bin/ lines
2571 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2572 getdownArchiveTextLines += line
2576 // the resource dir -- add these files as resource lines in getdown.txt
2578 from "${archiveImagesDir}"
2579 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2581 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2585 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2587 def vLaunchJvl = file(getdownVersionLaunchJvl)
2588 vLaunchJvl.getParentFile().mkdirs()
2589 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2590 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2591 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2592 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2593 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2594 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2596 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2598 from getdownLauncher
2599 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2600 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2601 from "${getdownAppBaseDir}/${channel_props}"
2602 if (file(getdownLauncher).getName() != getdown_launcher) {
2603 rename(file(getdownLauncher).getName(), getdown_launcher)
2605 into getdownFullArchiveDir
2611 task getdownArchiveDigest(type: JavaExec) {
2612 group = "distribution"
2613 description = "Digest the getdown archive folder"
2615 dependsOn getdownArchiveBuild
2618 classpath = files(getdownLauncher)
2619 args getdownFullArchiveDir
2621 main = "com.threerings.getdown.tools.Digester"
2622 inputs.dir(getdownFullArchiveDir)
2623 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2626 task getdownArchive() {
2627 group = "distribution"
2628 description = "Build the website archive dir with getdown digest"
2630 dependsOn getdownArchiveBuild
2631 dependsOn getdownArchiveDigest
2634 tasks.withType(JavaCompile) {
2635 options.encoding = 'UTF-8'
2641 delete getdownAppBaseDir
2642 delete getdownFilesDir
2643 delete getdownArchiveDir
2649 if (file(install4jHomeDir).exists()) {
2651 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2652 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2653 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2654 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2656 installDir(file(install4jHomeDir))
2658 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2662 task copyInstall4jTemplate {
2663 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2664 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2665 inputs.file(install4jTemplateFile)
2666 inputs.file(install4jFileAssociationsFile)
2667 inputs.property("CHANNEL", { CHANNEL })
2668 outputs.file(install4jConfFile)
2671 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2673 // turn off code signing if no OSX_KEYPASS
2674 if (OSX_KEYPASS == "") {
2675 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2676 codeSigning.'@macEnabled' = "false"
2678 install4jConfigXml.'**'.windows.each { windows ->
2679 windows.'@runPostProcessor' = "false"
2683 // disable install screen for OSX dmg (for 2.11.2.0)
2684 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2685 macosArchive.attributes().remove('executeSetupApp')
2686 macosArchive.attributes().remove('setupAppId')
2689 // turn off checksum creation for LOCAL channel
2690 def e = install4jConfigXml.application[0]
2691 e.'@createChecksums' = string(install4jCheckSums)
2693 // put file association actions where placeholder action is
2694 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2695 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2696 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2697 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2698 def parent = a.parent()
2700 fileAssociationActions.each { faa ->
2703 // don't need to continue in .any loop once replacements have been made
2708 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2709 // NB we're deleting the /other/ one!
2710 // Also remove the examples subdir from non-release versions
2711 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2712 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2713 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2714 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2716 // remove the examples subdir from Full File Set
2717 def files = install4jConfigXml.files[0]
2718 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2719 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2720 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2721 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2722 dirEntry.parent().remove(dirEntry)
2724 install4jConfigXml.'**'.action.any { a ->
2725 if (a.'@customizedId' == customizedIdToDelete) {
2726 def parent = a.parent()
2732 // write install4j file
2733 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2740 delete install4jConfFile
2744 task cleanInstallersDataFiles {
2745 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2746 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2747 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2749 delete installersOutputTxt
2750 delete installersSha256
2751 delete hugoDataJsonFile
2755 task install4jDMGBackgroundImageCopy {
2756 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2757 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2760 from(install4jDMGBackgroundImageDir) {
2761 include(install4jDMGBackgroundImageFile)
2763 into install4jDMGBackgroundImageBuildDir
2768 task install4jDMGBackgroundImageProcess {
2769 dependsOn install4jDMGBackgroundImageCopy
2772 if (backgroundImageText) {
2773 if (convertBinary == null) {
2774 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2776 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2777 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2779 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2781 executable convertBinary
2784 '-font', install4j_background_image_text_font,
2785 '-fill', install4j_background_image_text_colour,
2786 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2787 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2788 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2797 task install4jDMGBackgroundImage {
2798 dependsOn install4jDMGBackgroundImageProcess
2801 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2802 group = "distribution"
2803 description = "Create the install4j installers"
2805 dependsOn copyInstall4jTemplate
2806 dependsOn cleanInstallersDataFiles
2807 dependsOn install4jDMGBackgroundImage
2809 projectFile = install4jConfFile
2811 // create an md5 for the input files to use as version for install4j conf file
2812 def digest = MessageDigest.getInstance("MD5")
2814 (file("${install4jDir}/${install4j_template}").text +
2815 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2816 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2817 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2818 if (filesMd5.length() >= 8) {
2819 filesMd5 = filesMd5.substring(0,8)
2821 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2824 'JALVIEW_NAME': jalview_name,
2825 'JALVIEW_APPLICATION_NAME': applicationName,
2826 'JALVIEW_DIR': "../..",
2827 'OSX_KEYSTORE': OSX_KEYSTORE,
2828 'OSX_APPLEID': OSX_APPLEID,
2829 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2830 'JSIGN_SH': JSIGN_SH,
2831 'JRE_DIR': getdown_app_dir_java,
2832 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2833 'JALVIEW_VERSION': JALVIEW_VERSION,
2834 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2835 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2836 'JAVA_VERSION': JAVA_VERSION,
2837 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2838 'VERSION': JALVIEW_VERSION,
2839 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2840 'BUNDLE_ID': install4jBundleId,
2841 'INTERNAL_ID': install4jInternalId,
2842 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2843 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2844 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2845 'WRAPPER_LINK': getdownWrapperLink,
2846 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2847 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2848 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
2849 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2850 'INSTALLER_NAME': install4jInstallerName,
2851 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2852 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2853 'GETDOWN_FILES_DIR': getdown_files_dir,
2854 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2855 'GETDOWN_DIST_DIR': getdownAppDistDir,
2856 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2857 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2858 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2859 'BUILD_DIR': install4jBuildDir,
2860 'APPLICATION_CATEGORIES': install4j_application_categories,
2861 'APPLICATION_FOLDER': install4jApplicationFolder,
2862 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2863 'EXECUTABLE_NAME': install4jExecutableName,
2864 'EXTRA_SCHEME': install4jExtraScheme,
2865 'MAC_ICONS_FILE': install4jMacIconsFile,
2866 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2867 'PNG_ICON_FILE': install4jPngIconFile,
2868 'BACKGROUND': install4jBackground,
2873 'windows': 'WINDOWS',
2877 // these are the bundled OS/architecture VMs needed by install4j
2880 [ "mac", "aarch64" ],
2881 [ "windows", "x64" ],
2883 [ "linux", "aarch64" ]
2885 osArch.forEach { os, arch ->
2886 variables[ sprintf("%s_%s_JAVA_VM_DIR", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/jre-%s-%s-%s/jre", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
2887 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2888 // otherwise running `gradle installers` generates a non-useful error:
2889 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2890 variables[ sprintf("%s_%s_JAVA_VM_TGZ", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/tgz/jre_%s_%s_%s.tar.gz", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
2893 //println("INSTALL4J VARIABLES:")
2894 //variables.each{k,v->println("${k}=${v}")}
2896 destination = "${jalviewDir}/${install4jBuildDir}"
2897 buildSelected = true
2899 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2901 disableSigning = true
2902 disableNotarization = true
2906 macKeystorePassword = OSX_KEYPASS
2909 if (OSX_ALTOOLPASS) {
2910 appleIdPassword = OSX_ALTOOLPASS
2911 disableNotarization = false
2913 disableNotarization = true
2917 println("Using projectFile "+projectFile)
2918 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2922 inputs.dir(getdownAppBaseDir)
2923 inputs.file(install4jConfFile)
2924 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2925 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2928 def getDataHash(File myFile) {
2929 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2930 return myFile.exists()
2932 "file" : myFile.getName(),
2933 "filesize" : myFile.length(),
2934 "sha256" : hash.toString()
2939 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2941 "channel" : getdownChannelName,
2942 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2943 "git-commit" : "${gitHash} [${gitBranch}]",
2944 "version" : JALVIEW_VERSION
2946 // install4j installer files
2947 if (installersOutputTxt.exists()) {
2949 installersOutputTxt.readLines().each { def line ->
2950 if (line.startsWith("#")) {
2953 line.replaceAll("\n","")
2954 def vals = line.split("\t")
2955 def filename = vals[3]
2956 def filesize = file(filename).length()
2957 filename = filename.replaceAll(/^.*\//, "")
2958 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2959 idHash."${filename}" = vals[0]
2961 if (install4jCheckSums && installersSha256.exists()) {
2962 installersSha256.readLines().each { def line ->
2963 if (line.startsWith("#")) {
2966 line.replaceAll("\n","")
2967 def vals = line.split(/\s+\*?/)
2968 def filename = vals[1]
2969 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2975 "JAR": shadowJar.archiveFile, // executable JAR
2976 "JVL": getdownVersionLaunchJvl, // version JVL
2977 "SOURCE": sourceDist.archiveFile // source TGZ
2978 ].each { key, value ->
2979 def file = file(value)
2980 if (file.exists()) {
2981 def fileHash = getDataHash(file)
2982 if (fileHash != null) {
2983 hash."${key}" = fileHash;
2987 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2990 task staticMakeInstallersJsonFile {
2992 def output = findProperty("i4j_output")
2993 def sha256 = findProperty("i4j_sha256")
2994 def json = findProperty("i4j_json")
2995 if (output == null || sha256 == null || json == null) {
2996 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2998 writeDataJsonFile(file(output), file(sha256), file(json))
3003 dependsOn installerFiles
3009 eclipse().configFile(eclipse_codestyle_file)
3013 task createSourceReleaseProperties(type: WriteProperties) {
3014 group = "distribution"
3015 description = "Create the source RELEASE properties file"
3017 def sourceTarBuildDir = "${buildDir}/sourceTar"
3018 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
3019 outputFile (sourceReleasePropertiesFile)
3022 releaseProps.each{ key, val -> property key, val }
3023 property "git.branch", gitBranch
3024 property "git.hash", gitHash
3027 outputs.file(outputFile)
3030 task sourceDist(type: Tar) {
3031 group "distribution"
3032 description "Create a source .tar.gz file for distribution"
3034 dependsOn createBuildProperties
3035 dependsOn convertMdFiles
3036 dependsOn eclipseAllPreferences
3037 dependsOn createSourceReleaseProperties
3040 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
3041 archiveFileName = outputFileName
3043 compression Compression.GZIP
3059 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
3061 "utils/InstallAnywhere",
3076 "gradle.properties",
3088 ".settings/org.eclipse.buildship.core.prefs",
3089 ".settings/org.eclipse.jdt.core.prefs"
3093 exclude (EXCLUDE_FILES)
3094 include (PROCESS_FILES)
3095 filter(ReplaceTokens,
3099 'Version-Rel': JALVIEW_VERSION,
3100 'Year-Rel': getDate("yyyy")
3105 exclude (EXCLUDE_FILES)
3106 exclude (PROCESS_FILES)
3107 exclude ("appletlib")
3108 exclude ("**/*locales")
3109 exclude ("*locales/**")
3110 exclude ("utils/InstallAnywhere")
3112 exclude (getdown_files_dir)
3113 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3114 //exclude (getdown_website_dir)
3115 //exclude (getdown_archive_dir)
3117 // exluding these as not using jars as modules yet
3118 exclude ("${j11modDir}/**/*.jar")
3121 include(INCLUDE_FILES)
3123 // from (jalviewDir) {
3124 // // explicit includes for stuff that seemed to not get included
3125 // include(fileTree("test/**/*."))
3126 // exclude(EXCLUDE_FILES)
3127 // exclude(PROCESS_FILES)
3130 from(file(buildProperties).getParent()) {
3131 include(file(buildProperties).getName())
3132 rename(file(buildProperties).getName(), "build_properties")
3134 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3138 def sourceTarBuildDir = "${buildDir}/sourceTar"
3139 from(sourceTarBuildDir) {
3140 // this includes the appended RELEASE properties file
3144 task dataInstallersJson {
3146 description "Create the installers-VERSION.json data file for installer files created"
3148 mustRunAfter installers
3149 mustRunAfter shadowJar
3150 mustRunAfter sourceDist
3151 mustRunAfter getdownArchive
3153 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3154 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3156 if (installersOutputTxt.exists()) {
3157 inputs.file(installersOutputTxt)
3159 if (install4jCheckSums && installersSha256.exists()) {
3160 inputs.file(installersSha256)
3163 shadowJar.archiveFile, // executable JAR
3164 getdownVersionLaunchJvl, // version JVL
3165 sourceDist.archiveFile // source TGZ
3166 ].each { fileName ->
3167 if (file(fileName).exists()) {
3168 inputs.file(fileName)
3172 outputs.file(hugoDataJsonFile)
3175 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3181 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3184 dependsOn pubhtmlhelp
3186 inputs.dir("${helpBuildDir}/${help_dir}")
3187 outputs.dir("${buildDir}/distributions/${help_dir}")
3191 task j2sSetHeadlessBuild {
3198 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3200 description "Enable the alternative J2S Config file for headless build"
3202 outputFile = jalviewjsJ2sSettingsFileName
3203 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3204 def j2sProps = new Properties()
3205 if (j2sPropsFile.exists()) {
3207 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3208 j2sProps.load(j2sPropsFileFIS)
3209 j2sPropsFileFIS.close()
3211 j2sProps.each { prop, val ->
3214 } catch (Exception e) {
3215 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3219 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3220 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3225 task jalviewjsSetEclipseWorkspace {
3226 def propKey = "jalviewjs_eclipse_workspace"
3228 if (project.hasProperty(propKey)) {
3229 propVal = project.getProperty(propKey)
3230 if (propVal.startsWith("~/")) {
3231 propVal = System.getProperty("user.home") + propVal.substring(1)
3234 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3235 def propsFile = file(propsFileName)
3236 def eclipseWsDir = propVal
3237 def props = new Properties()
3239 def writeProps = true
3240 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3241 def ins = new FileInputStream(propsFileName)
3244 if (props.getProperty(propKey, null) != null) {
3245 eclipseWsDir = props.getProperty(propKey)
3250 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3251 def tempDir = File.createTempDir()
3252 eclipseWsDir = tempDir.getAbsolutePath()
3255 eclipseWorkspace = file(eclipseWsDir)
3258 // do not run a headless transpile when we claim to be in Eclipse
3260 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3261 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3263 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3267 props.setProperty(propKey, eclipseWsDir)
3268 propsFile.parentFile.mkdirs()
3269 def bytes = new ByteArrayOutputStream()
3270 props.store(bytes, null)
3271 def propertiesString = bytes.toString()
3272 propsFile.text = propertiesString
3278 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3281 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3282 outputs.file(propsFileName)
3283 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3287 task jalviewjsEclipsePaths {
3290 def eclipseRoot = jalviewjs_eclipse_root
3291 if (eclipseRoot.startsWith("~/")) {
3292 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3294 if (OperatingSystem.current().isMacOsX()) {
3295 eclipseRoot += "/Eclipse.app"
3296 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3297 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3298 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3299 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3300 eclipseRoot += "/eclipse"
3302 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3303 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3304 } else { // linux or unix
3305 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3306 eclipseRoot += "/eclipse"
3307 println("eclipseDir exists")
3309 eclipseBinary = "${eclipseRoot}/eclipse"
3310 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3313 eclipseVersion = "4.13" // default
3314 def assumedVersion = true
3315 if (file(eclipseProduct).exists()) {
3316 def fis = new FileInputStream(eclipseProduct)
3317 def props = new Properties()
3319 eclipseVersion = props.getProperty("version")
3321 assumedVersion = false
3324 def propKey = "eclipse_debug"
3325 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3328 // do not run a headless transpile when we claim to be in Eclipse
3330 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3331 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3333 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3336 if (!assumedVersion) {
3337 println("ECLIPSE VERSION=${eclipseVersion}")
3343 task printProperties {
3345 description "Output to console all System.properties"
3347 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3353 dependsOn eclipseProject
3354 dependsOn eclipseClasspath
3355 dependsOn eclipseJdt
3359 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3360 task jalviewjsEclipseCopyDropins(type: Copy) {
3361 dependsOn jalviewjsEclipsePaths
3363 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3364 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3365 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3372 // this eclipse -clean doesn't actually work
3373 task jalviewjsCleanEclipse(type: Exec) {
3374 dependsOn eclipseSetup
3375 dependsOn jalviewjsEclipsePaths
3376 dependsOn jalviewjsEclipseCopyDropins
3378 executable(eclipseBinary)
3379 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3385 def inputString = """exit
3388 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3389 standardInput = inputByteStream
3392 /* not really working yet
3393 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3397 task jalviewjsTransferUnzipSwingJs {
3398 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3402 from zipTree(file_zip)
3403 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3407 inputs.file file_zip
3408 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3412 task jalviewjsTransferUnzipLib {
3413 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip").sort()
3416 zipFiles.each { file_zip ->
3418 from zipTree(file_zip)
3419 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3421 // The following replace() is needed due to a mismatch in Jmol calls to
3422 // colorPtToFFRGB$javajs_util_T3d when only colorPtToFFRGB$javajs_util_T3 is defined
3423 // in the SwingJS.zip (github or the one distributed with JSmol)
3424 if (file_zip.getName().equals("Jmol-SwingJS.zip")) {
3427 while(!line.equals(l)) {
3428 line = line.replace('colorPtToFFRGB$javajs_util_T3d', 'colorPtToFFRGB$javajs_util_T3')
3438 inputs.files zipFiles
3439 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3443 task jalviewjsTransferUnzipAllLibs {
3444 dependsOn jalviewjsTransferUnzipLib
3445 dependsOn jalviewjsTransferUnzipSwingJs
3449 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3451 description "Create the alternative j2s file from the j2s.* properties"
3453 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3454 def siteDirProperty = "j2s.site.directory"
3455 def setSiteDir = false
3456 jalviewjsJ2sProps.each { prop, val ->
3458 if (prop == siteDirProperty) {
3459 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3460 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3466 if (!setSiteDir) { // default site location, don't override specifically set property
3467 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3470 outputFile = jalviewjsJ2sAltSettingsFileName
3473 inputs.properties(jalviewjsJ2sProps)
3474 outputs.file(jalviewjsJ2sAltSettingsFileName)
3479 task jalviewjsEclipseSetup {
3480 dependsOn jalviewjsEclipseCopyDropins
3481 dependsOn jalviewjsSetEclipseWorkspace
3482 dependsOn jalviewjsCreateJ2sSettings
3486 task jalviewjsSyncAllLibs (type: Sync) {
3487 dependsOn jalviewjsTransferUnzipAllLibs
3488 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3489 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3490 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3494 def outputFiles = []
3495 rename { filename ->
3496 outputFiles += "${outputDir}/${filename}"
3503 // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
3504 duplicatesStrategy "INCLUDE"
3506 outputs.files outputFiles
3507 inputs.files inputFiles
3511 task jalviewjsSyncResources (type: Sync) {
3512 dependsOn buildResources
3514 def inputFiles = fileTree(dir: resourcesBuildDir)
3515 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3519 def outputFiles = []
3520 rename { filename ->
3521 outputFiles += "${outputDir}/${filename}"
3527 outputs.files outputFiles
3528 inputs.files inputFiles
3532 task jalviewjsSyncSiteResources (type: Sync) {
3533 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3534 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3538 def outputFiles = []
3539 rename { filename ->
3540 outputFiles += "${outputDir}/${filename}"
3546 outputs.files outputFiles
3547 inputs.files inputFiles
3551 task jalviewjsSyncBuildProperties (type: Sync) {
3552 dependsOn createBuildProperties
3553 def inputFiles = [file(buildProperties)]
3554 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3558 def outputFiles = []
3559 rename { filename ->
3560 outputFiles += "${outputDir}/${filename}"
3566 outputs.files outputFiles
3567 inputs.files inputFiles
3571 task jalviewjsProjectImport(type: Exec) {
3572 dependsOn eclipseSetup
3573 dependsOn jalviewjsEclipsePaths
3574 dependsOn jalviewjsEclipseSetup
3577 // do not run a headless import when we claim to be in Eclipse
3579 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3580 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3582 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3586 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3587 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3588 executable(eclipseBinary)
3589 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3593 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3595 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3596 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3599 inputs.file("${jalviewDir}/.project")
3600 outputs.upToDateWhen {
3601 file(projdir).exists()
3606 task jalviewjsTranspile(type: Exec) {
3607 dependsOn jalviewjsEclipseSetup
3608 dependsOn jalviewjsProjectImport
3609 dependsOn jalviewjsEclipsePaths
3611 dependsOn jalviewjsEnableAltFileProperty
3615 // do not run a headless transpile when we claim to be in Eclipse
3617 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3618 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3620 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3624 executable(eclipseBinary)
3625 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3629 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3631 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3632 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3638 stdout = new ByteArrayOutputStream()
3639 stderr = new ByteArrayOutputStream()
3641 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3642 def logOutFile = file(logOutFileName)
3643 logOutFile.createNewFile()
3644 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3645 BINARY: ${eclipseBinary}
3646 VERSION: ${eclipseVersion}
3647 WORKSPACE: ${eclipseWorkspace}
3648 DEBUG: ${eclipseDebug}
3651 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3652 // combine stdout and stderr
3653 def logErrFOS = logOutFOS
3655 if (jalviewjs_j2s_to_console.equals("true")) {
3656 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3657 new org.apache.tools.ant.util.TeeOutputStream(
3661 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3662 new org.apache.tools.ant.util.TeeOutputStream(
3667 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3670 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3677 if (stdout.toString().contains("Error processing ")) {
3678 // j2s did not complete transpile
3679 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3680 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3681 println("IGNORING TRANSPILE ERRORS")
3682 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3684 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3689 inputs.dir("${jalviewDir}/${sourceDir}")
3690 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3691 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3695 task jalviewjsTranserSiteMergeLibDirs (type: Sync) {
3696 dependsOn jalviewjsTransferUnzipAllLibs
3697 dependsOn jalviewjsTransferUnzipSwingJs
3698 dependsOn jalviewjsTranspile
3700 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3701 // merge swingjs lib last
3702 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3704 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
3708 def outputFiles = []
3709 rename { filename ->
3710 outputFiles += "${outputDir}/${filename}"
3717 // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
3718 duplicatesStrategy "INCLUDE"
3720 outputs.files outputFiles
3721 inputs.files inputFiles
3725 task jalviewjsTranserSiteMergeSwingDir (type: Sync) {
3726 dependsOn jalviewjsTransferUnzipAllLibs
3727 dependsOn jalviewjsTransferUnzipSwingJs
3728 dependsOn jalviewjsTranspile
3730 // merge jalview files very last
3731 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3733 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
3737 def outputFiles = []
3738 rename { filename ->
3739 outputFiles += "${outputDir}/${filename}"
3746 // should this be exclude really ? No, jalview dir should be transferred last (and overwrite)
3747 duplicatesStrategy "INCLUDE"
3749 outputs.files outputFiles
3750 inputs.files inputFiles
3754 task jalviewjsTranserSiteMergeDirs {
3755 dependsOn jalviewjsTranserSiteMergeLibDirs
3756 dependsOn jalviewjsTranserSiteMergeSwingDir
3760 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3762 def stdout = new ByteArrayOutputStream()
3763 def stderr = new ByteArrayOutputStream()
3765 def coreFile = file(jsfile)
3767 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3769 logOutFile.createNewFile()
3770 logOutFile.append(msg+"\n")
3772 def coreTop = file(prefixFile)
3773 def coreBottom = file(suffixFile)
3774 def missingFiles = []
3775 coreFile.getParentFile().mkdirs()
3776 coreFile.createNewFile()
3777 coreFile.write( coreTop.getText("UTF-8") )
3781 def t = f.getText("UTF-8")
3782 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3783 coreFile.append( t )
3785 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3787 logOutFile.append(msg+"\n")
3791 coreFile.append( coreBottom.getText("UTF-8") )
3793 msg = "Generating ${zjsfile}"
3795 logOutFile.append(msg+"\n")
3796 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3797 def logErrFOS = logOutFOS
3800 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3801 main = "com.google.javascript.jscomp.CommandLineRunner"
3802 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3803 args = [ "--compilation_level", jalviewjs_closure_compiler_optimization_level, "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3806 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3808 logOutFile.append(msg+"\n")
3810 if (logOutConsole) {
3811 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3812 new org.apache.tools.ant.util.TeeOutputStream(
3816 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3817 new org.apache.tools.ant.util.TeeOutputStream(
3822 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3825 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3831 if (missingFiles.size() > 0) {
3832 msg += "\n!!! These files were listed but missing:\n"
3833 missingFiles.each { file -> msg += "!!! " + file.getPath() + "\n" }
3837 logOutFile.append(msg+"\n")
3841 task jalviewjsBuildAllCores {
3843 description "Build the core js lib closures listed in the classlists dir"
3844 dependsOn jalviewjsTranserSiteMergeDirs
3846 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
3847 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
3848 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
3849 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_js_subdir}"
3850 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3851 def prefixFile = "${jsDir}/core/coretop2.js"
3852 def suffixFile = "${jsDir}/core/corebottom2.js"
3854 inputs.file prefixFile
3855 inputs.file suffixFile
3857 def classlistFiles = []
3858 // add the classlists found int the jalviewjs_classlists_dir
3859 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3861 def name = file.getName() - ".txt"
3868 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3869 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3870 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3872 jalviewjsCoreClasslists = []
3874 classlistFiles.each {
3877 def file = hash['file']
3878 if (! file.exists()) {
3879 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3880 return false // this is a "continue" in groovy .each closure
3882 def name = hash['name']
3884 name = file.getName() - ".txt"
3892 def list = fileTree(dir: j2sDir, includes: filelist)
3894 def jsfile = "${outputDir}/core${name}.js"
3895 def zjsfile = "${outputDir}/core${name}.z.js"
3897 jalviewjsCoreClasslists += [
3906 outputs.file(jsfile)
3907 outputs.file(zjsfile)
3911 def allClasslistName = "_all"
3912 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3913 allJsFiles += fileTree(
3917 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3918 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3919 "**/org/jmol/export/JSExporter.js"
3922 allJsFiles += fileTree(
3926 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3927 "**/sun/misc/Unsafe.js",
3928 "**/swingjs/jquery/jquery-editable-select.js",
3929 "**/swingjs/jquery/j2sComboBox.js",
3930 "**/sun/misc/FloatingDecimal.js"
3933 def allClasslist = [
3934 'jsfile': "${outputDir}/core${allClasslistName}.js",
3935 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3937 'name': allClasslistName
3939 // not including this version of "all" core at the moment
3940 //jalviewjsCoreClasslists += allClasslist
3941 inputs.files(allClasslist['list'])
3942 outputs.file(allClasslist['jsfile'])
3943 outputs.file(allClasslist['zjsfile'])
3946 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3947 logOutFile.getParentFile().mkdirs()
3948 logOutFile.createNewFile()
3949 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3951 jalviewjsCoreClasslists.each {
3952 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3959 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3962 into file(outputFile).getParentFile()
3963 rename { filename ->
3964 if (filename.equals(inputFile.getName())) {
3965 return file(outputFile).getName()
3969 filter(ReplaceTokens,
3973 'MAIN': '"'+main_class+'"',
3975 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3976 'COREKEY': jalviewjs_core_key,
3977 'CORENAME': coreName
3984 task jalviewjsPublishCoreTemplates {
3985 dependsOn jalviewjsBuildAllCores
3987 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3988 def inputFile = file(inputFileName)
3989 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3991 def outputFiles = []
3992 jalviewjsCoreClasslists.each { cl ->
3993 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3994 cl['outputfile'] = outputFile
3995 outputFiles += outputFile
3999 jalviewjsCoreClasslists.each { cl ->
4000 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
4003 inputs.file(inputFile)
4004 outputs.files(outputFiles)
4008 task jalviewjsSyncCore (type: Sync) {
4009 dependsOn jalviewjsBuildAllCores
4010 dependsOn jalviewjsPublishCoreTemplates
4012 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
4013 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
4017 def outputFiles = []
4018 rename { filename ->
4019 outputFiles += "${outputDir}/${filename}"
4025 outputs.files outputFiles
4026 inputs.files inputFiles
4030 // this Copy version of TransferSiteJs will delete anything else in the target dir
4031 task jalviewjsCopyTransferSiteMergeDir(type: Copy) {
4032 dependsOn jalviewjsTranserSiteMergeDirs
4034 from "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
4035 into "${jalviewDir}/${jalviewjsSiteDir}"
4039 // this Copy version of TransferSiteJs will delete anything else in the target dir
4040 task jalviewjsCopyTransferSiteJs(type: Copy) {
4041 dependsOn jalviewjsTranspile
4043 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
4044 into "${jalviewDir}/${jalviewjsSiteDir}"
4048 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
4049 task jalviewjsSyncTransferSiteJs(type: Sync) {
4050 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
4052 into "${jalviewDir}/${jalviewjsSiteDir}"
4059 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
4060 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
4061 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
4062 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
4064 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
4065 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
4066 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
4067 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
4070 task jalviewjsPrepareSite {
4072 description "Prepares the website folder including unzipping files and copying resources"
4073 //dependsOn jalviewjsSyncAllLibs // now using jalviewjsCopyTransferSiteMergeDir
4074 dependsOn jalviewjsSyncResources
4075 dependsOn jalviewjsSyncSiteResources
4076 dependsOn jalviewjsSyncBuildProperties
4077 dependsOn jalviewjsSyncCore
4081 task jalviewjsBuildSite {
4083 description "Builds the whole website including transpiled code"
4084 dependsOn jalviewjsCopyTransferSiteMergeDir
4085 dependsOn jalviewjsPrepareSite
4089 task cleanJalviewjsTransferSite {
4091 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
4092 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
4093 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
4094 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
4099 task cleanJalviewjsSite {
4100 dependsOn cleanJalviewjsTransferSite
4102 delete "${jalviewDir}/${jalviewjsSiteDir}"
4107 task jalviewjsSiteTar(type: Tar) {
4109 description "Creates a tar.gz file for the website"
4110 dependsOn jalviewjsBuildSite
4111 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
4112 archiveFileName = outputFilename
4114 compression Compression.GZIP
4116 from "${jalviewDir}/${jalviewjsSiteDir}"
4117 into jalviewjs_site_dir // this is inside the tar file
4119 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
4123 task jalviewjsServer {
4125 def filename = "jalviewjsTest.html"
4126 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
4127 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
4132 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
4133 factory = f.newInstance()
4134 } catch (ClassNotFoundException e) {
4135 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
4137 def port = Integer.valueOf(jalviewjs_server_port)
4142 while(port < start+1000 && !running) {
4144 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
4145 jalviewjsServer = factory.start(doc_root, port)
4147 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
4148 println("SERVER STARTED with document root ${doc_root}.")
4149 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
4150 println("For debug: "+url+"?j2sdebug")
4151 println("For verbose: "+url+"?j2sverbose")
4152 } catch (Exception e) {
4157 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
4158 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
4159 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4161 jalviewjsCoreClasslists.each { cl ->
4162 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4164 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4166 println("For core ${cl.name}: "+urlcore)
4169 file(htmlFile).text = htmlText
4172 outputs.file(htmlFile)
4173 outputs.upToDateWhen({false})
4177 task cleanJalviewjsAll {
4179 description "Delete all configuration and build artifacts to do with JalviewJS build"
4180 dependsOn cleanJalviewjsSite
4181 dependsOn jalviewjsEclipsePaths
4184 delete "${jalviewDir}/${jalviewjsBuildDir}"
4185 delete "${jalviewDir}/${eclipse_bin_dir}"
4186 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4187 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4189 delete jalviewjsJ2sAltSettingsFileName
4192 outputs.upToDateWhen( { false } )
4196 task jalviewjsIDE_checkJ2sPlugin {
4197 group "00 JalviewJS in Eclipse"
4198 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4201 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4202 def j2sPluginFile = file(j2sPlugin)
4203 def eclipseHome = System.properties["eclipse.home.location"]
4204 if (eclipseHome == null || ! IN_ECLIPSE) {
4205 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4207 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4208 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4209 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4210 eclipseJ2sPluginDirs += altPluginsDir
4212 def foundPlugin = false
4213 def j2sPluginFileName = j2sPluginFile.getName()
4214 def eclipseJ2sPlugin
4215 def eclipseJ2sPluginFile
4216 eclipseJ2sPluginDirs.any { dir ->
4217 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4218 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4219 if (eclipseJ2sPluginFile.exists()) {
4225 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4226 System.err.println(msg)
4227 throw new StopExecutionException(msg)
4230 def digest = MessageDigest.getInstance("MD5")
4232 digest.update(j2sPluginFile.text.bytes)
4233 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4235 digest.update(eclipseJ2sPluginFile.text.bytes)
4236 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4238 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4239 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4240 System.err.println(msg)
4241 throw new StopExecutionException(msg)
4243 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4249 task jalviewjsIDE_copyJ2sPlugin {
4250 group "00 JalviewJS in Eclipse"
4251 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4254 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4255 def j2sPluginFile = file(j2sPlugin)
4256 def eclipseHome = System.properties["eclipse.home.location"]
4257 if (eclipseHome == null || ! IN_ECLIPSE) {
4258 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4260 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4261 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4262 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4263 System.err.println(msg)
4266 eclipseJ2sPluginFile.getParentFile().mkdirs()
4267 into eclipseJ2sPluginFile.getParent()
4273 task jalviewjsIDE_j2sFile {
4274 group "00 JalviewJS in Eclipse"
4275 description "Creates the .j2s file"
4276 dependsOn jalviewjsCreateJ2sSettings
4280 task jalviewjsIDE_SyncCore {
4281 group "00 JalviewJS in Eclipse"
4282 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4283 dependsOn jalviewjsSyncCore
4287 task jalviewjsIDE_SyncSiteAll {
4288 dependsOn jalviewjsSyncAllLibs
4289 dependsOn jalviewjsSyncResources
4290 dependsOn jalviewjsSyncSiteResources
4291 dependsOn jalviewjsSyncBuildProperties
4295 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4298 task jalviewjsIDE_PrepareSite {
4299 group "00 JalviewJS in Eclipse"
4300 description "Sync libs and resources to site dir, but not closure cores"
4302 dependsOn jalviewjsIDE_SyncSiteAll
4303 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4307 task jalviewjsIDE_AssembleSite {
4308 group "00 JalviewJS in Eclipse"
4309 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4310 dependsOn jalviewjsPrepareSite
4314 task jalviewjsIDE_SiteClean {
4315 group "00 JalviewJS in Eclipse"
4316 description "Deletes the Eclipse transpiled site"
4317 dependsOn cleanJalviewjsSite
4321 task jalviewjsIDE_Server {
4322 group "00 JalviewJS in Eclipse"
4323 description "Starts a webserver on localhost to test the website"
4324 dependsOn jalviewjsServer
4328 // buildship runs this at import or gradle refresh
4329 task eclipseSynchronizationTask {
4330 //dependsOn eclipseSetup
4331 dependsOn createBuildProperties
4333 dependsOn jalviewjsIDE_j2sFile
4334 dependsOn jalviewjsIDE_checkJ2sPlugin
4335 dependsOn jalviewjsIDE_PrepareSite
4340 // buildship runs this at build time or project refresh
4341 task eclipseAutoBuildTask {
4342 //dependsOn jalviewjsIDE_checkJ2sPlugin
4343 //dependsOn jalviewjsIDE_PrepareSite
4347 task jalviewjsCopyStderrLaunchFile(type: Copy) {
4348 from file(jalviewjs_stderr_launch)
4349 into jalviewjsSiteDir
4351 inputs.file jalviewjs_stderr_launch
4352 outputs.file jalviewjsStderrLaunchFilename
4355 task cleanJalviewjsChromiumUserDir {
4357 delete jalviewjsChromiumUserDir
4359 outputs.dir jalviewjsChromiumUserDir
4360 // always run when depended on
4361 outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
4364 task jalviewjsChromiumProfile {
4365 dependsOn cleanJalviewjsChromiumUserDir
4366 mustRunAfter cleanJalviewjsChromiumUserDir
4368 def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
4371 mkdir jalviewjsChromiumProfileDir
4374 outputs.file firstRun
4377 task jalviewjsLaunchTest {
4379 description "Check JalviewJS opens in a browser"
4380 dependsOn jalviewjsBuildSite
4381 dependsOn jalviewjsCopyStderrLaunchFile
4382 dependsOn jalviewjsChromiumProfile
4384 def macOS = OperatingSystem.current().isMacOsX()
4385 def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
4386 if (chromiumBinary.startsWith("~/")) {
4387 chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
4393 def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
4395 def binary = file(chromiumBinary)
4396 if (!binary.exists()) {
4397 throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
4399 stdout = new ByteArrayOutputStream()
4400 stderr = new ByteArrayOutputStream()
4403 if (jalviewjs_j2s_to_console.equals("true")) {
4404 execStdout = new org.apache.tools.ant.util.TeeOutputStream(
4407 execStderr = new org.apache.tools.ant.util.TeeOutputStream(
4414 // macOS not running properly with timeout arguments
4415 def execArgs = macOS ? [] : [
4416 "--virtual-time-budget=${timeoutms}",
4419 "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
4422 "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
4423 "--profile-directory=${jalviewjs_chromium_profile_name}",
4424 "--allow-file-access-from-files",
4425 "--enable-logging=stderr",
4426 "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
4429 if (true || macOS) {
4430 ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
4431 Future f1 = executor.submit(
4434 standardOutput = execStdout
4435 errorOutput = execStderr
4436 executable(chromiumBinary)
4438 println "COMMAND: '"+commandLine.join(" ")+"'"
4440 executor.shutdownNow()
4444 def noChangeBytes = 0
4445 def noChangeIterations = 0
4446 executor.scheduleAtFixedRate(
4448 String stderrString = stderr.toString()
4449 // shutdown the task if we have a success string
4450 if (stderrString.contains(jalviewjs_desktop_init_string)) {
4453 executor.shutdownNow()
4455 // if no change in stderr for 10s then also end
4456 if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
4457 executor.shutdownNow()
4459 if (stderrString.length() == noChangeBytes) {
4460 noChangeIterations++
4462 noChangeBytes = stderrString.length()
4463 noChangeIterations = 0
4466 1, 1, TimeUnit.SECONDS)
4468 executor.schedule(new Runnable(){
4471 executor.shutdownNow()
4473 }, timeoutms, TimeUnit.MILLISECONDS)
4475 executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
4476 executor.shutdownNow()
4483 stderr.toString().eachLine { line ->
4484 if (line.contains(jalviewjs_desktop_init_string)) {
4485 println("Found line '"+line+"'")
4491 throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
4499 description "Build the JalviewJS site and run the launch test"
4500 dependsOn jalviewjsBuildSite
4501 dependsOn jalviewjsLaunchTest