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/${jalviewjs_site_dir}_swingjs")
566 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
567 jalviewjsJalviewCoreHtmlFile = string("")
568 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
569 jalviewjsCoreClasslists = []
570 jalviewjsJalviewTemplateName = string(jalviewjs_name)
571 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
572 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
573 jalviewjsJ2sProps = null
574 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
575 jalviewjsStderrLaunchFilename = "${jalviewjsSiteDir}/"+(file(jalviewjs_stderr_launch).getName())
577 eclipseWorkspace = null
578 eclipseBinary = string("")
579 eclipseVersion = string("")
582 jalviewjsChromiumUserDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}"
583 jalviewjsChromiumProfileDir = "${ext.jalviewjsChromiumUserDir}/${jalviewjs_chromium_profile_name}"
593 outputDir = file(classesDir)
597 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
600 compileClasspath = files(sourceSets.main.java.outputDir)
601 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
603 runtimeClasspath = compileClasspath
604 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
609 srcDirs cloverInstrDir
610 outputDir = cloverClassesDir
614 srcDirs = sourceSets.main.resources.srcDirs
617 compileClasspath = files( sourceSets.clover.java.outputDir )
618 //compileClasspath += files( testClassesDir )
619 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
620 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
621 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
623 runtimeClasspath = compileClasspath
628 srcDirs testSourceDir
629 outputDir = file(testClassesDir)
633 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
636 compileClasspath = files( sourceSets.test.java.outputDir )
637 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
638 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
640 runtimeClasspath = compileClasspath
641 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
647 // eclipse project and settings files creation, also used by buildship
650 name = eclipse_project_name
652 natures 'org.eclipse.jdt.core.javanature',
653 'org.eclipse.jdt.groovy.core.groovyNature',
654 'org.eclipse.buildship.core.gradleprojectnature'
656 buildCommand 'org.eclipse.jdt.core.javabuilder'
657 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
661 //defaultOutputDir = sourceSets.main.java.outputDir
662 configurations.each{ c->
663 if (c.isCanBeResolved()) {
664 minusConfigurations += [c]
668 plusConfigurations = [ ]
672 def removeTheseToo = []
673 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
674 cp.entries.each { entry ->
675 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
676 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
677 // we add the resources and help/help dirs in as libs afterwards (see below)
678 if (entry.kind == 'src') {
679 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
680 removeTheseToo += entry
682 alreadyAddedSrcPath.putAt(entry.path, true)
687 cp.entries.removeAll(removeTheseToo)
689 //cp.entries += new Output("${eclipse_bin_dir}/main")
690 if (file(helpParentDir).isDirectory()) {
691 cp.entries += new Library(fileReference(helpParentDir))
693 if (file(resourceDir).isDirectory()) {
694 cp.entries += new Library(fileReference(resourceDir))
697 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
699 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
700 //don't want to add outputDir as eclipse is using its own output dir in bin/main
701 if (it.isDirectory() || ! it.exists()) {
702 // don't add dirs to classpath, especially if they don't exist
703 return false // groovy "continue" in .any closure
705 def itPath = it.toString()
706 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
707 // make relative path
708 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
710 if (alreadyAddedLibPath.get(itPath)) {
711 //println("Not adding duplicate entry "+itPath)
713 //println("Adding entry "+itPath)
714 cp.entries += new Library(fileReference(itPath))
715 alreadyAddedLibPath.put(itPath, true)
719 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
720 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
721 if (it.isDirectory() || ! it.exists()) {
722 // don't add dirs to classpath
723 return false // groovy "continue" in .any closure
726 def itPath = it.toString()
727 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
728 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
730 if (alreadyAddedLibPath.get(itPath)) {
733 def lib = new Library(fileReference(itPath))
734 lib.entryAttributes["test"] = "true"
736 alreadyAddedLibPath.put(itPath, true)
744 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
749 // for the IDE, use java 11 compatibility
750 sourceCompatibility = compile_source_compatibility
751 targetCompatibility = compile_target_compatibility
752 javaRuntimeName = eclipseJavaRuntimeName
754 // add in jalview project specific properties/preferences into eclipse core preferences
756 withProperties { props ->
757 def jalview_prefs = new Properties()
758 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
759 jalview_prefs.load(ins)
761 jalview_prefs.forEach { t, v ->
762 if (props.getAt(t) == null) {
766 // codestyle file -- overrides previous formatter prefs
767 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
768 if (csFile.exists()) {
769 XmlParser parser = new XmlParser()
770 def profiles = parser.parse(csFile)
771 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
772 if (profile != null) {
773 profile.'setting'.each { s ->
775 def value = s.'@value'
776 if (id != null && value != null) {
777 props.putAt(id, value)
788 // Don't want these to be activated if in headless build
789 synchronizationTasks "eclipseSynchronizationTask"
790 //autoBuildTasks "eclipseAutoBuildTask"
796 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
797 // Class to allow updating arbitrary properties files
798 class PropertiesFile extends PropertiesPersistableConfigurationObject {
799 public PropertiesFile(PropertiesTransformer t) { super(t); }
800 @Override protected void load(Properties properties) { }
801 @Override protected void store(Properties properties) { }
802 @Override protected String getDefaultResourceName() { return ""; }
803 // This is necessary, because PropertiesPersistableConfigurationObject fails
804 // if no default properties file exists.
805 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
808 // Task to update arbitrary properties files (set outputFile)
809 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
810 private final PropertiesFileContentMerger file;
811 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
812 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
813 protected void configure(PropertiesFile props) {
814 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
816 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
819 task eclipseUIPreferences(type: PropertiesFileTask) {
820 description = "Generate Eclipse additional settings"
821 def filename = "org.eclipse.jdt.ui.prefs"
822 outputFile = "$projectDir/.settings/${filename}" as File
825 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
830 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
831 description = "Generate Eclipse additional settings"
832 def filename = "org.eclipse.jdt.groovy.core.prefs"
833 outputFile = "$projectDir/.settings/${filename}" as File
836 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
841 task eclipseAllPreferences {
843 dependsOn eclipseUIPreferences
844 dependsOn eclipseGroovyCorePreferences
847 eclipseUIPreferences.mustRunAfter eclipseJdt
848 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
850 /* end of eclipse preferences hack */
858 delete cloverBuildDir
859 delete cloverReportDir
864 task cloverInstrJava(type: JavaExec) {
865 group = "Verification"
866 description = "Create clover instrumented source java files"
868 dependsOn cleanClover
870 inputs.files(sourceSets.main.allJava)
871 outputs.dir(cloverInstrDir)
873 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
874 classpath = sourceSets.clover.compileClasspath
875 main = "com.atlassian.clover.CloverInstr"
883 cloverInstrDir.getPath(),
885 def srcFiles = sourceSets.main.allJava.files
888 { file -> file.absolutePath }
891 args argsList.toArray()
894 delete cloverInstrDir
895 println("Clover: About to instrument "+srcFiles.size() +" files")
900 task cloverInstrTests(type: JavaExec) {
901 group = "Verification"
902 description = "Create clover instrumented source test files"
904 dependsOn cleanClover
906 inputs.files(testDir)
907 outputs.dir(cloverTestInstrDir)
909 classpath = sourceSets.clover.compileClasspath
910 main = "com.atlassian.clover.CloverInstr"
920 cloverTestInstrDir.getPath(),
922 args argsList.toArray()
925 delete cloverTestInstrDir
926 println("Clover: About to instrument test files")
932 group = "Verification"
933 description = "Create clover instrumented all source files"
935 dependsOn cloverInstrJava
936 dependsOn cloverInstrTests
940 cloverClasses.dependsOn cloverInstr
943 task cloverConsoleReport(type: JavaExec) {
944 group = "Verification"
945 description = "Creates clover console report"
948 file(cloverDb).exists()
951 inputs.dir cloverClassesDir
953 classpath = sourceSets.clover.runtimeClasspath
954 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
956 if (cloverreport_mem.length() > 0) {
957 maxHeapSize = cloverreport_mem
959 if (cloverreport_jvmargs.length() > 0) {
960 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
970 args argsList.toArray()
974 task cloverHtmlReport(type: JavaExec) {
975 group = "Verification"
976 description = "Creates clover HTML report"
979 file(cloverDb).exists()
982 def cloverHtmlDir = cloverReportDir
983 inputs.dir cloverClassesDir
984 outputs.dir cloverHtmlDir
986 classpath = sourceSets.clover.runtimeClasspath
987 main = "com.atlassian.clover.reporters.html.HtmlReporter"
989 if (cloverreport_mem.length() > 0) {
990 maxHeapSize = cloverreport_mem
992 if (cloverreport_jvmargs.length() > 0) {
993 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1004 if (cloverreport_html_options.length() > 0) {
1005 argsList += cloverreport_html_options.split(" ")
1008 args argsList.toArray()
1012 task cloverXmlReport(type: JavaExec) {
1013 group = "Verification"
1014 description = "Creates clover XML report"
1017 file(cloverDb).exists()
1020 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1021 inputs.dir cloverClassesDir
1022 outputs.file cloverXmlFile
1024 classpath = sourceSets.clover.runtimeClasspath
1025 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1027 if (cloverreport_mem.length() > 0) {
1028 maxHeapSize = cloverreport_mem
1030 if (cloverreport_jvmargs.length() > 0) {
1031 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1042 if (cloverreport_xml_options.length() > 0) {
1043 argsList += cloverreport_xml_options.split(" ")
1046 args argsList.toArray()
1051 group = "Verification"
1052 description = "Creates clover reports"
1054 dependsOn cloverXmlReport
1055 dependsOn cloverHtmlReport
1062 sourceCompatibility = compile_source_compatibility
1063 targetCompatibility = compile_target_compatibility
1064 options.compilerArgs += additional_compiler_args
1065 print ("Setting target compatibility to "+targetCompatibility+"\n")
1067 //classpath += configurations.cloverRuntime
1073 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1074 sourceCompatibility = compile_source_compatibility
1075 targetCompatibility = compile_target_compatibility
1076 options.compilerArgs += additional_compiler_args
1077 options.encoding = "UTF-8"
1079 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1086 sourceCompatibility = compile_source_compatibility
1087 targetCompatibility = compile_target_compatibility
1088 options.compilerArgs += additional_compiler_args
1090 print ("Setting target compatibility to "+targetCompatibility+"\n")
1097 delete sourceSets.main.java.outputDir
1103 dependsOn cleanClover
1105 delete sourceSets.test.java.outputDir
1110 // format is a string like date.format("dd MMMM yyyy")
1111 def getDate(format) {
1112 return date.format(format)
1116 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1117 MutableDataSet options = new MutableDataSet()
1119 def extensions = new ArrayList<>()
1120 extensions.add(AnchorLinkExtension.create())
1121 extensions.add(AutolinkExtension.create())
1122 extensions.add(StrikethroughExtension.create())
1123 extensions.add(TaskListExtension.create())
1124 extensions.add(TablesExtension.create())
1125 extensions.add(TocExtension.create())
1127 options.set(Parser.EXTENSIONS, extensions)
1129 // set GFM table parsing options
1130 options.set(TablesExtension.WITH_CAPTION, false)
1131 options.set(TablesExtension.COLUMN_SPANS, false)
1132 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1133 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1134 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1135 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1136 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1138 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1139 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1140 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1141 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1143 Parser parser = Parser.builder(options).build()
1144 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1146 mdFiles.each { mdFile ->
1147 // add table of contents
1148 def mdText = "[TOC]\n"+mdFile.text
1150 // grab the first top-level title
1152 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1153 def matcher = mdText =~ titleRegex
1154 if (matcher.size() > 0) {
1155 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1156 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1158 // or use the filename if none found
1159 if (title == null) {
1160 title = mdFile.getName()
1163 Node document = parser.parse(mdText)
1164 String htmlBody = renderer.render(document)
1165 def htmlText = '''<html>
1166 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1167 <html xmlns="http://www.w3.org/1999/xhtml">
1169 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1170 <meta http-equiv="Content-Style-Type" content="text/css" />
1171 <meta name="generator" content="flexmark" />
1173 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1175 <style type="text/css">code{white-space: pre;}</style>
1177 htmlText += ((cssFile != null) ? cssFile.text : '')
1178 htmlText += '''</head>
1181 htmlText += htmlBody
1187 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1188 def htmlFile = file(htmlFilePath)
1189 println("Creating ${htmlFilePath}")
1190 htmlFile.text = htmlText
1195 task copyDocs(type: Copy) {
1196 def inputDir = "${jalviewDir}/${doc_dir}"
1197 def outputDir = "${docBuildDir}/${doc_dir}"
1201 include('**/*.html')
1203 filter(ReplaceTokens,
1207 'Version-Rel': JALVIEW_VERSION,
1208 'Year-Rel': getDate("yyyy")
1215 exclude('**/*.html')
1220 inputs.dir(inputDir)
1221 outputs.dir(outputDir)
1225 task convertMdFiles {
1227 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1228 def cssFile = file("${jalviewDir}/${flexmark_css}")
1231 convertMdToHtml(mdFiles, cssFile)
1234 inputs.files(mdFiles)
1235 inputs.file(cssFile)
1238 mdFiles.each { mdFile ->
1239 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1240 htmlFiles.add(file(htmlFilePath))
1242 outputs.files(htmlFiles)
1246 def hugoTemplateSubstitutions(String input, Map extras=null) {
1247 def replacements = [
1248 DATE: getDate("yyyy-MM-dd"),
1249 CHANNEL: propertiesChannelName,
1250 APPLICATION_NAME: applicationName,
1252 GIT_BRANCH: gitBranch,
1253 VERSION: JALVIEW_VERSION,
1254 JAVA_VERSION: JAVA_VERSION,
1255 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1260 if (extras != null) {
1261 extras.each{ k, v ->
1262 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1265 replacements.each{ k, v ->
1266 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1271 def mdFileComponents(File mdFile, def dateOnly=false) {
1274 if (mdFile.exists()) {
1275 def inFrontMatter = false
1276 def firstLine = true
1277 mdFile.eachLine { line ->
1278 if (line.matches("---")) {
1279 def prev = inFrontMatter
1280 inFrontMatter = firstLine
1281 if (inFrontMatter != prev)
1284 if (inFrontMatter) {
1286 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1287 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1288 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1289 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1290 } else if (m = line =~ /^channel:\s*(\S+)/) {
1291 map["channel"] = m[0][1]
1292 } else if (m = line =~ /^version:\s*(\S+)/) {
1293 map["version"] = m[0][1]
1294 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1295 map[ m[0][1] ] = m[0][2]
1297 if (dateOnly && map["date"] != null) {
1303 content += line+"\n"
1308 return dateOnly ? map["date"] : [map, content]
1311 task hugoTemplates {
1313 description "Create partially populated md pages for hugo website build"
1315 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1316 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1317 def templateFiles = fileTree(dir: hugoTemplatesDir)
1318 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1319 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1320 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1321 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1324 // specific release template for version archive
1327 def givenDate = null
1328 def givenChannel = null
1329 def givenVersion = null
1330 if (CHANNEL == "RELEASE") {
1331 def (map, content) = mdFileComponents(releaseMdFile)
1332 givenDate = map.date
1333 givenChannel = map.channel
1334 givenVersion = map.version
1336 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1337 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1340 if (whatsnewMdFile.exists())
1341 whatsnew = whatsnewMdFile.text
1344 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1345 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1347 def changesHugo = null
1348 if (changes != null) {
1349 changesHugo = '<div class="release_notes">\n\n'
1350 def inSection = false
1351 changes.eachLine { line ->
1353 if (m = line =~ /^##([^#].*)$/) {
1355 changesHugo += "</div>\n\n"
1357 def section = m[0][1].trim()
1358 section = section.toLowerCase()
1359 section = section.replaceAll(/ +/, "_")
1360 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1361 changesHugo += "<div class=\"${section}\">\n\n"
1363 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1364 def comment = m[0][2].trim()
1365 if (comment != "") {
1366 comment = comment.replaceAll('"', """)
1368 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1369 def newline = m[0][1]
1370 if (comment.trim() != "")
1371 newline += "{{<comment>}}${comment}{{</comment>}} "
1372 newline += m[0][3].trim()
1373 if (issuekeys.size() > 0)
1374 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1375 if (m[0][4] != null)
1380 changesHugo += line+"\n"
1383 changesHugo += "\n</div>\n\n"
1385 changesHugo += '</div>'
1388 templateFiles.each{ templateFile ->
1389 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1390 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1391 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1393 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1397 rename(templateFile.getName(), newFileName)
1401 def newFile = file("${outPathName}/${newFileName}".toString())
1402 def content = newFile.text
1403 newFile.text = hugoTemplateSubstitutions(content,
1406 CHANGES: changesHugo,
1407 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1408 DRAFT: givenDate == null ? "true" : "false",
1409 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1410 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1417 inputs.file(oldJvlFile)
1418 inputs.dir(hugoTemplatesDir)
1419 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1420 inputs.property("CHANNEL", { CHANNEL })
1423 def getMdDate(File mdFile) {
1424 return mdFileComponents(mdFile, true)
1427 def getMdSections(String content) {
1429 def sectionContent = ""
1430 def sectionName = null
1431 content.eachLine { line ->
1433 if (m = line =~ /^##([^#].*)$/) {
1434 if (sectionName != null) {
1435 sections[sectionName] = sectionContent
1439 sectionName = m[0][1].trim()
1440 sectionName = sectionName.toLowerCase()
1441 sectionName = sectionName.replaceAll(/ +/, "_")
1442 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1443 } else if (sectionName != null) {
1444 sectionContent += line+"\n"
1447 if (sectionContent != null) {
1448 sections[sectionName] = sectionContent
1454 task copyHelp(type: Copy) {
1455 def inputDir = helpSourceDir
1456 def outputDir = "${helpBuildDir}/${help_dir}"
1460 include('**/*.html')
1464 filter(ReplaceTokens,
1468 'Version-Rel': JALVIEW_VERSION,
1469 'Year-Rel': getDate("yyyy")
1476 exclude('**/*.html')
1483 inputs.dir(inputDir)
1484 outputs.files(helpFile)
1485 outputs.dir(outputDir)
1489 task releasesTemplates {
1491 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1495 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1496 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1497 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1498 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1499 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1500 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1503 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1504 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1506 if (CHANNEL == "RELEASE") {
1507 if (!releaseMdFile.exists()) {
1508 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1510 if (!whatsnewMdFile.exists()) {
1511 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1515 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1516 def releaseFilesDates = releaseFiles.collectEntries {
1517 [(it): getMdDate(it)]
1519 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1521 def releasesTemplate = releasesTemplateFile.text
1522 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1523 def versionTemplate = m[0][1]
1525 MutableDataSet options = new MutableDataSet()
1527 def extensions = new ArrayList<>()
1528 options.set(Parser.EXTENSIONS, extensions)
1529 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1531 Parser parser = Parser.builder(options).build()
1532 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1534 def actualVersions = releaseFiles.collect { rf ->
1535 def (rfMap, rfContent) = mdFileComponents(rf)
1536 return rfMap.version
1538 def versionsHtml = ""
1539 def linkedVersions = []
1540 releaseFiles.reverse().each { rFile ->
1541 def (rMap, rContent) = mdFileComponents(rFile)
1543 def versionLink = ""
1544 def partialVersion = ""
1545 def firstPart = true
1546 rMap.version.split("\\.").each { part ->
1547 def displayPart = ( firstPart ? "" : "." ) + part
1548 partialVersion += displayPart
1550 linkedVersions.contains(partialVersion)
1551 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1553 versionLink += displayPart
1555 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1556 linkedVersions += partialVersion
1560 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1563 def rContentProcessed = ""
1564 rContent.eachLine { line ->
1565 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1566 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1567 } else if (lm = line =~ /^###([^#]+.*)$/) {
1568 line = "_${lm[0][1].trim()}_"
1570 rContentProcessed += line + "\n"
1573 def rContentSections = getMdSections(rContentProcessed)
1574 def rVersion = versionTemplate
1575 if (rVersion != "") {
1576 def rNewFeatures = rContentSections["new_features"]
1577 def rIssuesResolved = rContentSections["issues_resolved"]
1578 Node newFeaturesNode = parser.parse(rNewFeatures)
1579 String newFeaturesHtml = renderer.render(newFeaturesNode)
1580 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1581 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1582 rVersion = hugoTemplateSubstitutions(rVersion,
1584 VERSION: rMap.version,
1585 VERSION_LINK: versionLink,
1586 DISPLAY_DATE: displayDate,
1587 NEW_FEATURES: newFeaturesHtml,
1588 ISSUES_RESOLVED: issuesResolvedHtml
1591 versionsHtml += rVersion
1595 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1596 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1597 releasesHtmlFile.text = releasesTemplate
1599 if (whatsnewMdFile.exists()) {
1600 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1601 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1602 Node whatsnewNode = parser.parse(whatsnewMd)
1603 String whatsnewHtml = renderer.render(whatsnewNode)
1604 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1605 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1607 VERSION: JALVIEW_VERSION,
1608 DISPLAY_DATE: wnDisplayDate
1611 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1612 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1617 inputs.file(releasesTemplateFile)
1618 inputs.file(whatsnewTemplateFile)
1619 inputs.dir(releasesMdDir)
1620 inputs.dir(whatsnewMdDir)
1621 outputs.file(releasesHtmlFile)
1622 outputs.file(whatsnewHtmlFile)
1626 task copyResources(type: Copy) {
1628 description = "Copy (and make text substitutions in) the resources dir to the build area"
1630 def inputDir = resourceDir
1631 def outputDir = resourcesBuildDir
1635 include('**/*.html')
1637 filter(ReplaceTokens,
1641 'Version-Rel': JALVIEW_VERSION,
1642 'Year-Rel': getDate("yyyy")
1649 exclude('**/*.html')
1654 inputs.dir(inputDir)
1655 outputs.dir(outputDir)
1658 task copyChannelResources(type: Copy) {
1659 dependsOn copyResources
1661 description = "Copy the channel resources dir to the build resources area"
1663 def inputDir = "${channelDir}/${resource_dir}"
1664 def outputDir = resourcesBuildDir
1666 include(channel_props)
1667 filter(ReplaceTokens,
1671 'SUFFIX': channelSuffix
1676 exclude(channel_props)
1680 inputs.dir(inputDir)
1681 outputs.dir(outputDir)
1684 task createBuildProperties(type: WriteProperties) {
1685 dependsOn copyResources
1687 description = "Create the ${buildProperties} file"
1689 inputs.dir(sourceDir)
1690 inputs.dir(resourcesBuildDir)
1691 outputFile (buildProperties)
1692 // taking time specific comment out to allow better incremental builds
1693 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1694 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1695 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1696 property "VERSION", JALVIEW_VERSION
1697 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1698 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1699 if (getdownSetAppBaseProperty) {
1700 property "GETDOWNAPPBASE", getdownAppBase
1701 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1703 outputs.file(outputFile)
1707 task buildIndices(type: JavaExec) {
1709 classpath = sourceSets.main.compileClasspath
1710 main = "com.sun.java.help.search.Indexer"
1711 workingDir = "${helpBuildDir}/${help_dir}"
1714 inputs.dir("${workingDir}/${argDir}")
1716 outputs.dir("${classesDir}/doc")
1717 outputs.dir("${classesDir}/help")
1718 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1719 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1720 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1721 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1722 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1723 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1726 task buildResources {
1727 dependsOn copyResources
1728 dependsOn copyChannelResources
1729 dependsOn createBuildProperties
1733 dependsOn buildResources
1736 dependsOn releasesTemplates
1737 dependsOn convertMdFiles
1738 dependsOn buildIndices
1742 compileJava.dependsOn prepare
1743 run.dependsOn compileJava
1744 compileTestJava.dependsOn compileJava
1749 group = "Verification"
1750 description = "Runs all testTaskN tasks)"
1753 dependsOn cloverClasses
1755 dependsOn testClasses
1758 // not running tests in this task
1761 /* testTask0 is the main test task */
1762 task testTask0(type: Test) {
1763 group = "Verification"
1764 description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
1766 includeGroups testng_groups.split(",")
1767 excludeGroups testng_excluded_groups.split(",")
1768 tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
1770 useDefaultListeners=true
1774 /* separated tests */
1775 task testTask1(type: Test) {
1776 group = "Verification"
1777 description = "Tests that need to be isolated from the main test run"
1780 excludeGroups testng_excluded_groups.split(",")
1782 useDefaultListeners=true
1786 task testTask2(type: Test) {
1787 group = "Verification"
1788 description = "Tests that need to be isolated from the main test run"
1791 excludeGroups testng_excluded_groups.split(",")
1793 useDefaultListeners=true
1796 task testTask3(type: Test) {
1797 group = "Verification"
1798 description = "Tests that need to be isolated from the main test run"
1801 excludeGroups testng_excluded_groups.split(",")
1803 useDefaultListeners=true
1807 /* insert more testTaskNs here -- change N to next digit or other string */
1809 task testTaskN(type: Test) {
1810 group = "Verification"
1811 description = "Tests that need to be isolated from the main test run"
1814 excludeGroups testng_excluded_groups.split(",")
1816 useDefaultListeners=true
1822 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1823 * to summarise test results from all Test tasks
1825 /* START of test tasks results summary */
1826 import groovy.time.TimeCategory
1827 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1828 import org.gradle.api.tasks.testing.logging.TestLogEvent
1829 rootProject.ext.testsResults = [] // Container for tests summaries
1831 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1833 // from original test task
1835 dependsOn cloverClasses
1837 dependsOn testClasses //?
1840 // run main tests first
1841 if (!testTask.name.equals("testTask0"))
1842 testTask.mustRunAfter "testTask0"
1844 testTask.testLogging { logging ->
1845 events TestLogEvent.FAILED
1846 // TestLogEvent.SKIPPED,
1847 // TestLogEvent.STANDARD_OUT,
1848 // TestLogEvent.STANDARD_ERROR
1850 exceptionFormat TestExceptionFormat.FULL
1853 showStackTraces true
1855 showStandardStreams true
1857 info.events = [ TestLogEvent.FAILED ]
1860 if (OperatingSystem.current().isMacOsX()) {
1861 testTask.systemProperty "apple.awt.UIElement", "true"
1862 testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
1866 ignoreFailures = true // Always try to run all tests for all modules
1868 afterSuite { desc, result ->
1870 return // Only summarize results for whole modules
1872 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1874 rootProject.ext.testsResults.add(resultsInfo)
1877 // from original test task
1878 maxHeapSize = "1024m"
1880 workingDir = jalviewDir
1881 def testLaf = project.findProperty("test_laf")
1882 if (testLaf != null) {
1883 println("Setting Test LaF to '${testLaf}'")
1884 systemProperty "laf", testLaf
1886 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1887 if (testHiDPIScale != null) {
1888 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1889 systemProperty "sun.java2d.uiScale", testHiDPIScale
1891 sourceCompatibility = compile_source_compatibility
1892 targetCompatibility = compile_target_compatibility
1893 jvmArgs += additional_compiler_args
1896 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1897 // testTasks that include the tests, and exclude all from the others.
1898 // get --test argument
1899 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1900 // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
1901 // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
1905 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1910 /* don't fail on no matching tests (so --tests will run across all testTasks) */
1911 testTask.filter.setFailOnNoMatchingTests(false)
1913 /* ensure the "test" task dependsOn all the testTasks */
1914 test.dependsOn testTask
1917 gradle.buildFinished {
1918 def allResults = rootProject.ext.testsResults
1920 if (!allResults.isEmpty()) {
1921 printResults allResults
1922 allResults.each {r ->
1923 if (r[2].resultType == TestResult.ResultType.FAILURE)
1924 throw new GradleException("Failed tests!")
1929 private static String colString(styler, col, colour, text) {
1930 return col?"${styler[colour](text)}":text
1933 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1934 def colour = 'black'
1942 case TestResult.ResultType.SUCCESS:
1945 case TestResult.ResultType.FAILURE:
1953 StringBuilder sb = new StringBuilder()
1957 sb.append(" results: ")
1958 sb.append(colString(s, col && !nocol, colour, text))
1960 sb.append("${rc} tests, ")
1961 sb.append(colString(s, col && rs > 0, 'green', rs))
1962 sb.append(" successes, ")
1963 sb.append(colString(s, col && rf > 0, 'red', rf))
1964 sb.append(" failures, ")
1965 sb.append("${rsk} skipped) in ${t}")
1966 return sb.toString()
1969 private static void printResults(allResults) {
1971 // styler from https://stackoverflow.com/a/56139852
1972 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1975 def failedTests = false
1976 def summaryLines = []
1978 def totalsuccess = 0
1981 def totaltime = TimeCategory.getSeconds(0)
1982 // sort on project name then task name
1983 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1984 def projectName = it[0]
1985 def taskName = it[1]
1989 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1990 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1991 def reportLine = "Report file: ${report}"
1992 def ls = summaryPlain.length()
1993 def lr = reportLine.length()
1994 def m = [ls, lr].max()
1997 def info = [ls, summaryCol, reportLine]
1998 summaryLines.add(info)
1999 failedTests |= result.resultType == TestResult.ResultType.FAILURE
2000 totalcount += result.testCount
2001 totalsuccess += result.successfulTestCount
2002 totalfail += result.failedTestCount
2003 totalskip += result.skippedTestCount
2006 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
2007 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
2008 def tls = totalSummaryPlain.length()
2009 if (tls > maxLength)
2011 def info = [tls, totalSummaryCol, null]
2012 summaryLines.add(info)
2014 def allSummaries = []
2015 for(sInfo : summaryLines) {
2017 def summary = sInfo[1]
2018 def report = sInfo[2]
2020 StringBuilder sb = new StringBuilder()
2021 sb.append("│" + summary + " " * (maxLength - ls) + "│")
2022 if (report != null) {
2023 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
2025 allSummaries += sb.toString()
2028 println "┌${"${"─" * maxLength}"}┐"
2029 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
2030 println "└${"${"─" * maxLength}"}┘"
2032 /* END of test tasks results summary */
2035 task compileLinkCheck(type: JavaCompile) {
2037 classpath = files("${jalviewDir}/${utils_dir}")
2038 destinationDir = file("${jalviewDir}/${utils_dir}")
2039 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
2041 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2042 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2043 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
2044 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
2048 task linkCheck(type: JavaExec) {
2050 dependsOn compileLinkCheck
2052 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2053 classpath = files("${jalviewDir}/${utils_dir}")
2054 main = "HelpLinksChecker"
2055 workingDir = "${helpBuildDir}"
2056 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2058 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2059 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2062 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2066 inputs.dir(helpBuildDir)
2067 outputs.file(helpLinksCheckerOutFile)
2071 // import the pubhtmlhelp target
2072 ant.properties.basedir = "${jalviewDir}"
2073 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2074 ant.importBuild "${utils_dir}/publishHelp.xml"
2077 task cleanPackageDir(type: Delete) {
2079 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2089 attributes "Main-Class": main_class,
2090 "Permissions": "all-permissions",
2091 "Application-Name": applicationName,
2092 "Codebase": application_codebase,
2093 "Implementation-Version": JALVIEW_VERSION
2096 def outputDir = "${jalviewDir}/${package_dir}"
2097 destinationDirectory = file(outputDir)
2098 archiveFileName = rootProject.name+".jar"
2099 duplicatesStrategy "EXCLUDE"
2106 exclude "**/*.jar.*"
2108 inputs.dir(sourceSets.main.java.outputDir)
2109 sourceSets.main.resources.srcDirs.each{ dir ->
2112 outputs.file("${outputDir}/${archiveFileName}")
2116 task copyJars(type: Copy) {
2117 from fileTree(dir: classesDir, include: "**/*.jar").files
2118 into "${jalviewDir}/${package_dir}"
2122 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2123 task syncJars(type: Sync) {
2125 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2126 into "${jalviewDir}/${package_dir}"
2128 include jar.archiveFileName.getOrNull()
2135 description = "Put all required libraries in dist"
2136 // order of "cleanPackageDir", "copyJars", "jar" important!
2137 jar.mustRunAfter cleanPackageDir
2138 syncJars.mustRunAfter cleanPackageDir
2139 dependsOn cleanPackageDir
2142 outputs.dir("${jalviewDir}/${package_dir}")
2147 dependsOn cleanPackageDir
2154 group = "distribution"
2155 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2160 def jarFiles = fileTree(dir: "${jalviewDir}/${libDistDir}", include: "*.jar", exclude: "regex.jar").getFiles()
2161 def groovyJars = jarFiles.findAll {it1 -> file(it1).getName().startsWith("groovy-swing")}
2162 def otherJars = jarFiles.findAll {it2 -> !file(it2).getName().startsWith("groovy-swing")}
2166 // we need to include the groovy-swing Include-Package for it to run in the shadowJar
2168 def jarFileManifests = []
2169 groovyJars.each { jarFile ->
2170 def mf = zipTree(jarFile).getFiles().find { it.getName().equals("MANIFEST.MF") }
2172 jarFileManifests += mf
2177 attributes "Implementation-Version": JALVIEW_VERSION, "Application-Name": applicationName
2178 from (jarFileManifests) {
2179 eachEntry { details ->
2180 if (!details.key.equals("Import-Package")) {
2188 duplicatesStrategy "INCLUDE"
2190 mainClassName = shadow_jar_main_class
2192 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2196 task getdownImagesCopy() {
2197 inputs.dir getdownImagesDir
2198 outputs.dir getdownImagesBuildDir
2202 from(getdownImagesDir) {
2203 include("*getdown*.png")
2205 into getdownImagesBuildDir
2210 task getdownImagesProcess() {
2211 dependsOn getdownImagesCopy
2214 if (backgroundImageText) {
2215 if (convertBinary == null) {
2216 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2218 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2219 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2221 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2223 executable convertBinary
2226 '-font', getdown_background_image_text_font,
2227 '-fill', getdown_background_image_text_colour,
2228 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2229 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2230 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2239 task getdownImages() {
2240 dependsOn getdownImagesProcess
2243 task getdownWebsite() {
2244 group = "distribution"
2245 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2247 dependsOn getdownImages
2252 def getdownWebsiteResourceFilenames = []
2253 def getdownResourceDir = getdownResourceDir
2254 def getdownResourceFilenames = []
2257 // clean the getdown website and files dir before creating getdown folders
2258 delete getdownAppBaseDir
2259 delete getdownFilesDir
2262 from buildProperties
2263 rename(file(buildProperties).getName(), getdown_build_properties)
2266 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2269 from channelPropsFile
2270 filter(ReplaceTokens,
2274 'SUFFIX': channelSuffix
2277 into getdownAppBaseDir
2279 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2281 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2282 def props = project.properties.sort { it.key }
2283 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2284 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2286 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2287 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2289 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2290 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2292 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2293 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2294 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2295 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2296 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2297 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
2298 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
2301 props.put("getdown_txt_title", jalview_name)
2302 props.put("getdown_txt_ui.name", applicationName)
2304 // start with appbase
2305 getdownTextLines += "appbase = ${getdownAppBase}"
2306 props.each{ prop, val ->
2307 if (prop.startsWith("getdown_txt_") && val != null) {
2308 if (prop.startsWith("getdown_txt_multi_")) {
2309 def key = prop.substring(18)
2310 val.split(",").each{ v ->
2311 def line = "${key} = ${v}"
2312 getdownTextLines += line
2315 // file values rationalised
2316 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2318 if (val.indexOf('/') == 0) {
2321 } else if (val.indexOf('/') > 0) {
2322 // relative path (relative to jalviewDir)
2323 r = file( "${jalviewDir}/${val}" )
2326 val = "${getdown_resource_dir}/" + r.getName()
2327 getdownWebsiteResourceFilenames += val
2328 getdownResourceFilenames += r.getPath()
2331 if (! prop.startsWith("getdown_txt_resource")) {
2332 def line = prop.substring(12) + " = ${val}"
2333 getdownTextLines += line
2339 getdownWebsiteResourceFilenames.each{ filename ->
2340 getdownTextLines += "resource = ${filename}"
2342 getdownResourceFilenames.each{ filename ->
2345 into getdownResourceDir
2349 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2350 getdownWrapperScripts.each{ script ->
2351 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2355 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2357 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2362 fileTree(file(package_dir)).each{ f ->
2363 if (f.isDirectory()) {
2364 def files = fileTree(dir: f, include: ["*"]).getFiles()
2366 } else if (f.exists()) {
2370 def jalviewJar = jar.archiveFileName.getOrNull()
2371 // put jalview.jar first for CLASSPATH and .properties files reasons
2372 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2373 def name = f.getName()
2374 def line = "code = ${getdownAppDistDir}/${name}"
2375 getdownTextLines += line
2382 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2384 if (JAVA_VERSION.equals("11")) {
2385 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2386 j11libFiles.sort().each{f ->
2387 def name = f.getName()
2388 def line = "code = ${getdown_j11lib_dir}/${name}"
2389 getdownTextLines += line
2392 into getdownJ11libDir
2398 // 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.
2399 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2400 getdownTextLines += "resource = ${getdown_launcher_new}"
2401 getdownTextLines += "class = ${main_class}"
2402 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2403 if (getdownSetAppBaseProperty) {
2404 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2405 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2408 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2409 getdownTxt.write(getdownTextLines.join("\n"))
2411 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2412 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2413 launchJvl.write("appbase=${getdownAppBase}")
2415 // files going into the getdown website dir: getdown-launcher.jar
2417 from getdownLauncher
2418 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2419 into getdownAppBaseDir
2422 // files going into the getdown website dir: getdown-launcher(-local).jar
2424 from getdownLauncher
2425 if (file(getdownLauncher).getName() != getdown_launcher) {
2426 rename(file(getdownLauncher).getName(), getdown_launcher)
2428 into getdownAppBaseDir
2431 // files going into the getdown website dir: ./install dir and files
2432 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2435 from getdownLauncher
2436 from "${getdownAppDir}/${getdown_build_properties}"
2437 if (file(getdownLauncher).getName() != getdown_launcher) {
2438 rename(file(getdownLauncher).getName(), getdown_launcher)
2440 into getdownInstallDir
2443 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2445 from getdownInstallDir
2446 into getdownFilesInstallDir
2450 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2454 from getdownLauncher
2455 from "${getdownAppBaseDir}/${getdown_build_properties}"
2456 from "${getdownAppBaseDir}/${channel_props}"
2457 if (file(getdownLauncher).getName() != getdown_launcher) {
2458 rename(file(getdownLauncher).getName(), getdown_launcher)
2460 into getdownFilesDir
2463 // and ./resource (not all downloaded by getdown)
2465 from getdownResourceDir
2466 into "${getdownFilesDir}/${getdown_resource_dir}"
2471 inputs.dir("${jalviewDir}/${package_dir}")
2473 outputs.dir(getdownAppBaseDir)
2474 outputs.dir(getdownFilesDir)
2478 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2479 task getdownDigestDir(type: JavaExec) {
2481 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2483 def digestDirPropertyName = "DIGESTDIR"
2485 classpath = files(getdownLauncher)
2486 def digestDir = findProperty(digestDirPropertyName)
2487 if (digestDir == null) {
2488 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2492 main = "com.threerings.getdown.tools.Digester"
2496 task getdownDigest(type: JavaExec) {
2497 group = "distribution"
2498 description = "Digest the getdown website folder"
2499 dependsOn getdownWebsite
2501 classpath = files(getdownLauncher)
2503 main = "com.threerings.getdown.tools.Digester"
2504 args getdownAppBaseDir
2505 inputs.dir(getdownAppBaseDir)
2506 outputs.file("${getdownAppBaseDir}/digest2.txt")
2511 group = "distribution"
2512 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2513 dependsOn getdownDigest
2515 if (reportRsyncCommand) {
2516 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2517 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2518 println "LIKELY RSYNC COMMAND:"
2519 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2520 if (RUNRSYNC == "true") {
2522 commandLine "mkdir", "-p", toDir
2525 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2533 task getdownArchiveBuild() {
2534 group = "distribution"
2535 description = "Put files in the archive dir to go on the website"
2537 dependsOn getdownWebsite
2539 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2540 def vDir = "${getdownArchiveDir}/${v}"
2541 getdownFullArchiveDir = "${vDir}/getdown"
2542 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2544 def vAltDir = "alt_${v}"
2545 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2548 // cleanup old "old" dir
2549 delete getdownArchiveDir
2551 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2552 getdownArchiveTxt.getParentFile().mkdirs()
2553 def getdownArchiveTextLines = []
2554 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2558 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2559 into "${getdownFullArchiveDir}/${vAltDir}"
2562 getdownTextLines.each { line ->
2563 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2564 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2565 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2566 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2567 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2568 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2569 // remove the existing resource = resource/ or bin/ lines
2570 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2571 getdownArchiveTextLines += line
2575 // the resource dir -- add these files as resource lines in getdown.txt
2577 from "${archiveImagesDir}"
2578 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2580 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2584 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2586 def vLaunchJvl = file(getdownVersionLaunchJvl)
2587 vLaunchJvl.getParentFile().mkdirs()
2588 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2589 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2590 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2591 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2592 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2593 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2595 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2597 from getdownLauncher
2598 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2599 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2600 from "${getdownAppBaseDir}/${channel_props}"
2601 if (file(getdownLauncher).getName() != getdown_launcher) {
2602 rename(file(getdownLauncher).getName(), getdown_launcher)
2604 into getdownFullArchiveDir
2610 task getdownArchiveDigest(type: JavaExec) {
2611 group = "distribution"
2612 description = "Digest the getdown archive folder"
2614 dependsOn getdownArchiveBuild
2617 classpath = files(getdownLauncher)
2618 args getdownFullArchiveDir
2620 main = "com.threerings.getdown.tools.Digester"
2621 inputs.dir(getdownFullArchiveDir)
2622 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2625 task getdownArchive() {
2626 group = "distribution"
2627 description = "Build the website archive dir with getdown digest"
2629 dependsOn getdownArchiveBuild
2630 dependsOn getdownArchiveDigest
2633 tasks.withType(JavaCompile) {
2634 options.encoding = 'UTF-8'
2640 delete getdownAppBaseDir
2641 delete getdownFilesDir
2642 delete getdownArchiveDir
2648 if (file(install4jHomeDir).exists()) {
2650 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2651 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2652 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2653 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2655 installDir(file(install4jHomeDir))
2657 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2661 task copyInstall4jTemplate {
2662 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2663 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2664 inputs.file(install4jTemplateFile)
2665 inputs.file(install4jFileAssociationsFile)
2666 inputs.property("CHANNEL", { CHANNEL })
2667 outputs.file(install4jConfFile)
2670 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2672 // turn off code signing if no OSX_KEYPASS
2673 if (OSX_KEYPASS == "") {
2674 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2675 codeSigning.'@macEnabled' = "false"
2677 install4jConfigXml.'**'.windows.each { windows ->
2678 windows.'@runPostProcessor' = "false"
2682 // disable install screen for OSX dmg (for 2.11.2.0)
2683 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2684 macosArchive.attributes().remove('executeSetupApp')
2685 macosArchive.attributes().remove('setupAppId')
2688 // turn off checksum creation for LOCAL channel
2689 def e = install4jConfigXml.application[0]
2690 e.'@createChecksums' = string(install4jCheckSums)
2692 // put file association actions where placeholder action is
2693 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2694 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2695 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2696 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2697 def parent = a.parent()
2699 fileAssociationActions.each { faa ->
2702 // don't need to continue in .any loop once replacements have been made
2707 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2708 // NB we're deleting the /other/ one!
2709 // Also remove the examples subdir from non-release versions
2710 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2711 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2712 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2713 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2715 // remove the examples subdir from Full File Set
2716 def files = install4jConfigXml.files[0]
2717 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2718 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2719 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2720 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2721 dirEntry.parent().remove(dirEntry)
2723 install4jConfigXml.'**'.action.any { a ->
2724 if (a.'@customizedId' == customizedIdToDelete) {
2725 def parent = a.parent()
2731 // write install4j file
2732 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2739 delete install4jConfFile
2743 task cleanInstallersDataFiles {
2744 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2745 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2746 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2748 delete installersOutputTxt
2749 delete installersSha256
2750 delete hugoDataJsonFile
2754 task install4jDMGBackgroundImageCopy {
2755 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2756 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2759 from(install4jDMGBackgroundImageDir) {
2760 include(install4jDMGBackgroundImageFile)
2762 into install4jDMGBackgroundImageBuildDir
2767 task install4jDMGBackgroundImageProcess {
2768 dependsOn install4jDMGBackgroundImageCopy
2771 if (backgroundImageText) {
2772 if (convertBinary == null) {
2773 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2775 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2776 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2778 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2780 executable convertBinary
2783 '-font', install4j_background_image_text_font,
2784 '-fill', install4j_background_image_text_colour,
2785 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2786 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2787 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2796 task install4jDMGBackgroundImage {
2797 dependsOn install4jDMGBackgroundImageProcess
2800 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2801 group = "distribution"
2802 description = "Create the install4j installers"
2804 dependsOn copyInstall4jTemplate
2805 dependsOn cleanInstallersDataFiles
2806 dependsOn install4jDMGBackgroundImage
2808 projectFile = install4jConfFile
2810 // create an md5 for the input files to use as version for install4j conf file
2811 def digest = MessageDigest.getInstance("MD5")
2813 (file("${install4jDir}/${install4j_template}").text +
2814 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2815 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2816 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2817 if (filesMd5.length() >= 8) {
2818 filesMd5 = filesMd5.substring(0,8)
2820 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2823 'JALVIEW_NAME': jalview_name,
2824 'JALVIEW_APPLICATION_NAME': applicationName,
2825 'JALVIEW_DIR': "../..",
2826 'OSX_KEYSTORE': OSX_KEYSTORE,
2827 'OSX_APPLEID': OSX_APPLEID,
2828 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2829 'JSIGN_SH': JSIGN_SH,
2830 'JRE_DIR': getdown_app_dir_java,
2831 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2832 'JALVIEW_VERSION': JALVIEW_VERSION,
2833 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2834 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2835 'JAVA_VERSION': JAVA_VERSION,
2836 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2837 'VERSION': JALVIEW_VERSION,
2838 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2839 'BUNDLE_ID': install4jBundleId,
2840 'INTERNAL_ID': install4jInternalId,
2841 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2842 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2843 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2844 'WRAPPER_LINK': getdownWrapperLink,
2845 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2846 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2847 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
2848 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2849 'INSTALLER_NAME': install4jInstallerName,
2850 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2851 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2852 'GETDOWN_FILES_DIR': getdown_files_dir,
2853 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2854 'GETDOWN_DIST_DIR': getdownAppDistDir,
2855 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2856 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2857 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2858 'BUILD_DIR': install4jBuildDir,
2859 'APPLICATION_CATEGORIES': install4j_application_categories,
2860 'APPLICATION_FOLDER': install4jApplicationFolder,
2861 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2862 'EXECUTABLE_NAME': install4jExecutableName,
2863 'EXTRA_SCHEME': install4jExtraScheme,
2864 'MAC_ICONS_FILE': install4jMacIconsFile,
2865 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2866 'PNG_ICON_FILE': install4jPngIconFile,
2867 'BACKGROUND': install4jBackground,
2872 'windows': 'WINDOWS',
2876 // these are the bundled OS/architecture VMs needed by install4j
2879 [ "mac", "aarch64" ],
2880 [ "windows", "x64" ],
2882 [ "linux", "aarch64" ]
2884 osArch.forEach { os, arch ->
2885 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)
2886 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2887 // otherwise running `gradle installers` generates a non-useful error:
2888 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2889 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)
2892 //println("INSTALL4J VARIABLES:")
2893 //variables.each{k,v->println("${k}=${v}")}
2895 destination = "${jalviewDir}/${install4jBuildDir}"
2896 buildSelected = true
2898 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2900 disableSigning = true
2901 disableNotarization = true
2905 macKeystorePassword = OSX_KEYPASS
2908 if (OSX_ALTOOLPASS) {
2909 appleIdPassword = OSX_ALTOOLPASS
2910 disableNotarization = false
2912 disableNotarization = true
2916 println("Using projectFile "+projectFile)
2917 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2921 inputs.dir(getdownAppBaseDir)
2922 inputs.file(install4jConfFile)
2923 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2924 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2927 def getDataHash(File myFile) {
2928 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2929 return myFile.exists()
2931 "file" : myFile.getName(),
2932 "filesize" : myFile.length(),
2933 "sha256" : hash.toString()
2938 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2940 "channel" : getdownChannelName,
2941 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2942 "git-commit" : "${gitHash} [${gitBranch}]",
2943 "version" : JALVIEW_VERSION
2945 // install4j installer files
2946 if (installersOutputTxt.exists()) {
2948 installersOutputTxt.readLines().each { def line ->
2949 if (line.startsWith("#")) {
2952 line.replaceAll("\n","")
2953 def vals = line.split("\t")
2954 def filename = vals[3]
2955 def filesize = file(filename).length()
2956 filename = filename.replaceAll(/^.*\//, "")
2957 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2958 idHash."${filename}" = vals[0]
2960 if (install4jCheckSums && installersSha256.exists()) {
2961 installersSha256.readLines().each { def line ->
2962 if (line.startsWith("#")) {
2965 line.replaceAll("\n","")
2966 def vals = line.split(/\s+\*?/)
2967 def filename = vals[1]
2968 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2974 "JAR": shadowJar.archiveFile, // executable JAR
2975 "JVL": getdownVersionLaunchJvl, // version JVL
2976 "SOURCE": sourceDist.archiveFile // source TGZ
2977 ].each { key, value ->
2978 def file = file(value)
2979 if (file.exists()) {
2980 def fileHash = getDataHash(file)
2981 if (fileHash != null) {
2982 hash."${key}" = fileHash;
2986 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2989 task staticMakeInstallersJsonFile {
2991 def output = findProperty("i4j_output")
2992 def sha256 = findProperty("i4j_sha256")
2993 def json = findProperty("i4j_json")
2994 if (output == null || sha256 == null || json == null) {
2995 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2997 writeDataJsonFile(file(output), file(sha256), file(json))
3002 dependsOn installerFiles
3008 eclipse().configFile(eclipse_codestyle_file)
3012 task createSourceReleaseProperties(type: WriteProperties) {
3013 group = "distribution"
3014 description = "Create the source RELEASE properties file"
3016 def sourceTarBuildDir = "${buildDir}/sourceTar"
3017 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
3018 outputFile (sourceReleasePropertiesFile)
3021 releaseProps.each{ key, val -> property key, val }
3022 property "git.branch", gitBranch
3023 property "git.hash", gitHash
3026 outputs.file(outputFile)
3029 task sourceDist(type: Tar) {
3030 group "distribution"
3031 description "Create a source .tar.gz file for distribution"
3033 dependsOn createBuildProperties
3034 dependsOn convertMdFiles
3035 dependsOn eclipseAllPreferences
3036 dependsOn createSourceReleaseProperties
3039 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
3040 archiveFileName = outputFileName
3042 compression Compression.GZIP
3057 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
3059 "utils/InstallAnywhere",
3074 "gradle.properties",
3086 ".settings/org.eclipse.buildship.core.prefs",
3087 ".settings/org.eclipse.jdt.core.prefs"
3091 exclude (EXCLUDE_FILES)
3092 include (PROCESS_FILES)
3093 filter(ReplaceTokens,
3097 'Version-Rel': JALVIEW_VERSION,
3098 'Year-Rel': getDate("yyyy")
3103 exclude (EXCLUDE_FILES)
3104 exclude (PROCESS_FILES)
3105 exclude ("appletlib")
3106 exclude ("**/*locales")
3107 exclude ("*locales/**")
3108 exclude ("utils/InstallAnywhere")
3110 exclude (getdown_files_dir)
3111 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3112 //exclude (getdown_website_dir)
3113 //exclude (getdown_archive_dir)
3115 // exluding these as not using jars as modules yet
3116 exclude ("${j11modDir}/**/*.jar")
3119 include(INCLUDE_FILES)
3121 // from (jalviewDir) {
3122 // // explicit includes for stuff that seemed to not get included
3123 // include(fileTree("test/**/*."))
3124 // exclude(EXCLUDE_FILES)
3125 // exclude(PROCESS_FILES)
3128 from(file(buildProperties).getParent()) {
3129 include(file(buildProperties).getName())
3130 rename(file(buildProperties).getName(), "build_properties")
3132 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3136 def sourceTarBuildDir = "${buildDir}/sourceTar"
3137 from(sourceTarBuildDir) {
3138 // this includes the appended RELEASE properties file
3142 task dataInstallersJson {
3144 description "Create the installers-VERSION.json data file for installer files created"
3146 mustRunAfter installers
3147 mustRunAfter shadowJar
3148 mustRunAfter sourceDist
3149 mustRunAfter getdownArchive
3151 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3152 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3154 if (installersOutputTxt.exists()) {
3155 inputs.file(installersOutputTxt)
3157 if (install4jCheckSums && installersSha256.exists()) {
3158 inputs.file(installersSha256)
3161 shadowJar.archiveFile, // executable JAR
3162 getdownVersionLaunchJvl, // version JVL
3163 sourceDist.archiveFile // source TGZ
3164 ].each { fileName ->
3165 if (file(fileName).exists()) {
3166 inputs.file(fileName)
3170 outputs.file(hugoDataJsonFile)
3173 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3179 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3182 dependsOn pubhtmlhelp
3184 inputs.dir("${helpBuildDir}/${help_dir}")
3185 outputs.dir("${buildDir}/distributions/${help_dir}")
3189 task j2sSetHeadlessBuild {
3196 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3198 description "Enable the alternative J2S Config file for headless build"
3200 outputFile = jalviewjsJ2sSettingsFileName
3201 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3202 def j2sProps = new Properties()
3203 if (j2sPropsFile.exists()) {
3205 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3206 j2sProps.load(j2sPropsFileFIS)
3207 j2sPropsFileFIS.close()
3209 j2sProps.each { prop, val ->
3212 } catch (Exception e) {
3213 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3217 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3218 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3223 task jalviewjsSetEclipseWorkspace {
3224 def propKey = "jalviewjs_eclipse_workspace"
3226 if (project.hasProperty(propKey)) {
3227 propVal = project.getProperty(propKey)
3228 if (propVal.startsWith("~/")) {
3229 propVal = System.getProperty("user.home") + propVal.substring(1)
3232 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3233 def propsFile = file(propsFileName)
3234 def eclipseWsDir = propVal
3235 def props = new Properties()
3237 def writeProps = true
3238 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3239 def ins = new FileInputStream(propsFileName)
3242 if (props.getProperty(propKey, null) != null) {
3243 eclipseWsDir = props.getProperty(propKey)
3248 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3249 def tempDir = File.createTempDir()
3250 eclipseWsDir = tempDir.getAbsolutePath()
3253 eclipseWorkspace = file(eclipseWsDir)
3256 // do not run a headless transpile when we claim to be in Eclipse
3258 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3259 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3261 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3265 props.setProperty(propKey, eclipseWsDir)
3266 propsFile.parentFile.mkdirs()
3267 def bytes = new ByteArrayOutputStream()
3268 props.store(bytes, null)
3269 def propertiesString = bytes.toString()
3270 propsFile.text = propertiesString
3276 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3279 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3280 outputs.file(propsFileName)
3281 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3285 task jalviewjsEclipsePaths {
3288 def eclipseRoot = jalviewjs_eclipse_root
3289 if (eclipseRoot.startsWith("~/")) {
3290 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3292 if (OperatingSystem.current().isMacOsX()) {
3293 eclipseRoot += "/Eclipse.app"
3294 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3295 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3296 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3297 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3298 eclipseRoot += "/eclipse"
3300 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3301 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3302 } else { // linux or unix
3303 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3304 eclipseRoot += "/eclipse"
3305 println("eclipseDir exists")
3307 eclipseBinary = "${eclipseRoot}/eclipse"
3308 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3311 eclipseVersion = "4.13" // default
3312 def assumedVersion = true
3313 if (file(eclipseProduct).exists()) {
3314 def fis = new FileInputStream(eclipseProduct)
3315 def props = new Properties()
3317 eclipseVersion = props.getProperty("version")
3319 assumedVersion = false
3322 def propKey = "eclipse_debug"
3323 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3326 // do not run a headless transpile when we claim to be in Eclipse
3328 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3329 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3331 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3334 if (!assumedVersion) {
3335 println("ECLIPSE VERSION=${eclipseVersion}")
3341 task printProperties {
3343 description "Output to console all System.properties"
3345 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3351 dependsOn eclipseProject
3352 dependsOn eclipseClasspath
3353 dependsOn eclipseJdt
3357 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3358 task jalviewjsEclipseCopyDropins(type: Copy) {
3359 dependsOn jalviewjsEclipsePaths
3361 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3362 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3363 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3370 // this eclipse -clean doesn't actually work
3371 task jalviewjsCleanEclipse(type: Exec) {
3372 dependsOn eclipseSetup
3373 dependsOn jalviewjsEclipsePaths
3374 dependsOn jalviewjsEclipseCopyDropins
3376 executable(eclipseBinary)
3377 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3383 def inputString = """exit
3386 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3387 standardInput = inputByteStream
3390 /* not really working yet
3391 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3395 task jalviewjsTransferUnzipSwingJs {
3396 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3400 from zipTree(file_zip)
3401 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3405 inputs.file file_zip
3406 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3410 task jalviewjsTransferUnzipLib {
3411 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip").sort()
3414 zipFiles.each { file_zip ->
3416 from zipTree(file_zip)
3417 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3422 inputs.files zipFiles
3423 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3426 jalviewjsTransferUnzipSwingJs.mustRunAfter jalviewjsTransferUnzipLib
3429 task jalviewjsTransferUnzipAllLibs {
3430 dependsOn jalviewjsTransferUnzipLib
3431 dependsOn jalviewjsTransferUnzipSwingJs
3437 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3439 description "Create the alternative j2s file from the j2s.* properties"
3441 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3442 def siteDirProperty = "j2s.site.directory"
3443 def setSiteDir = false
3444 jalviewjsJ2sProps.each { prop, val ->
3446 if (prop == siteDirProperty) {
3447 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3448 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3454 if (!setSiteDir) { // default site location, don't override specifically set property
3455 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3458 outputFile = jalviewjsJ2sAltSettingsFileName
3461 inputs.properties(jalviewjsJ2sProps)
3462 outputs.file(jalviewjsJ2sAltSettingsFileName)
3467 task jalviewjsEclipseSetup {
3468 dependsOn jalviewjsEclipseCopyDropins
3469 dependsOn jalviewjsSetEclipseWorkspace
3470 dependsOn jalviewjsCreateJ2sSettings
3474 task jalviewjsSyncAllLibs (type: Sync) {
3475 dependsOn jalviewjsTransferUnzipAllLibs
3476 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3477 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3478 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3482 def outputFiles = []
3483 rename { filename ->
3484 outputFiles += "${outputDir}/${filename}"
3491 // should this be exclude really ?
3492 duplicatesStrategy "INCLUDE"
3494 outputs.files outputFiles
3495 inputs.files inputFiles
3499 task jalviewjsSyncResources (type: Sync) {
3500 dependsOn buildResources
3502 def inputFiles = fileTree(dir: resourcesBuildDir)
3503 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3507 def outputFiles = []
3508 rename { filename ->
3509 outputFiles += "${outputDir}/${filename}"
3515 outputs.files outputFiles
3516 inputs.files inputFiles
3520 task jalviewjsSyncSiteResources (type: Sync) {
3521 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3522 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3526 def outputFiles = []
3527 rename { filename ->
3528 outputFiles += "${outputDir}/${filename}"
3534 outputs.files outputFiles
3535 inputs.files inputFiles
3539 task jalviewjsSyncBuildProperties (type: Sync) {
3540 dependsOn createBuildProperties
3541 def inputFiles = [file(buildProperties)]
3542 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3546 def outputFiles = []
3547 rename { filename ->
3548 outputFiles += "${outputDir}/${filename}"
3554 outputs.files outputFiles
3555 inputs.files inputFiles
3559 task jalviewjsProjectImport(type: Exec) {
3560 dependsOn eclipseSetup
3561 dependsOn jalviewjsEclipsePaths
3562 dependsOn jalviewjsEclipseSetup
3565 // do not run a headless import when we claim to be in Eclipse
3567 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3568 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3570 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3574 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3575 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3576 executable(eclipseBinary)
3577 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3581 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3583 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3584 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3587 inputs.file("${jalviewDir}/.project")
3588 outputs.upToDateWhen {
3589 file(projdir).exists()
3594 task jalviewjsTranspile(type: Exec) {
3595 dependsOn jalviewjsEclipseSetup
3596 dependsOn jalviewjsProjectImport
3597 dependsOn jalviewjsEclipsePaths
3599 dependsOn jalviewjsEnableAltFileProperty
3603 // do not run a headless transpile when we claim to be in Eclipse
3605 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3606 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3608 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3612 executable(eclipseBinary)
3613 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3617 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3619 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3620 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3626 stdout = new ByteArrayOutputStream()
3627 stderr = new ByteArrayOutputStream()
3629 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3630 def logOutFile = file(logOutFileName)
3631 logOutFile.createNewFile()
3632 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3633 BINARY: ${eclipseBinary}
3634 VERSION: ${eclipseVersion}
3635 WORKSPACE: ${eclipseWorkspace}
3636 DEBUG: ${eclipseDebug}
3639 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3640 // combine stdout and stderr
3641 def logErrFOS = logOutFOS
3643 if (jalviewjs_j2s_to_console.equals("true")) {
3644 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3645 new org.apache.tools.ant.util.TeeOutputStream(
3649 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3650 new org.apache.tools.ant.util.TeeOutputStream(
3655 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3658 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3665 if (stdout.toString().contains("Error processing ")) {
3666 // j2s did not complete transpile
3667 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3668 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3669 println("IGNORING TRANSPILE ERRORS")
3670 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3672 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3677 inputs.dir("${jalviewDir}/${sourceDir}")
3678 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3679 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3683 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3685 def stdout = new ByteArrayOutputStream()
3686 def stderr = new ByteArrayOutputStream()
3688 def coreFile = file(jsfile)
3690 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3692 logOutFile.createNewFile()
3693 logOutFile.append(msg+"\n")
3695 def coreTop = file(prefixFile)
3696 def coreBottom = file(suffixFile)
3697 coreFile.getParentFile().mkdirs()
3698 coreFile.createNewFile()
3699 coreFile.write( coreTop.getText("UTF-8") )
3703 def t = f.getText("UTF-8")
3704 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3705 coreFile.append( t )
3707 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3709 logOutFile.append(msg+"\n")
3712 coreFile.append( coreBottom.getText("UTF-8") )
3714 msg = "Generating ${zjsfile}"
3716 logOutFile.append(msg+"\n")
3717 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3718 def logErrFOS = logOutFOS
3721 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3722 main = "com.google.javascript.jscomp.CommandLineRunner"
3723 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3724 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3727 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3729 logOutFile.append(msg+"\n")
3731 if (logOutConsole) {
3732 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3733 new org.apache.tools.ant.util.TeeOutputStream(
3737 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3738 new org.apache.tools.ant.util.TeeOutputStream(
3743 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3746 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3753 logOutFile.append(msg+"\n")
3757 task jalviewjsBuildAllCores {
3759 description "Build the core js lib closures listed in the classlists dir"
3760 dependsOn jalviewjsTranspile
3761 dependsOn jalviewjsTransferUnzipSwingJs
3763 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3764 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3765 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3766 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3767 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3768 def prefixFile = "${jsDir}/core/coretop2.js"
3769 def suffixFile = "${jsDir}/core/corebottom2.js"
3771 inputs.file prefixFile
3772 inputs.file suffixFile
3774 def classlistFiles = []
3775 // add the classlists found int the jalviewjs_classlists_dir
3776 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3778 def name = file.getName() - ".txt"
3785 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3786 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3787 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3789 jalviewjsCoreClasslists = []
3791 classlistFiles.each {
3794 def file = hash['file']
3795 if (! file.exists()) {
3796 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3797 return false // this is a "continue" in groovy .each closure
3799 def name = hash['name']
3801 name = file.getName() - ".txt"
3809 def list = fileTree(dir: j2sDir, includes: filelist)
3811 def jsfile = "${outputDir}/core${name}.js"
3812 def zjsfile = "${outputDir}/core${name}.z.js"
3814 jalviewjsCoreClasslists += [
3823 outputs.file(jsfile)
3824 outputs.file(zjsfile)
3827 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3828 def stevesoftClasslistName = "_stevesoft"
3829 def stevesoftClasslist = [
3830 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3831 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3832 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3833 'name': stevesoftClasslistName
3835 jalviewjsCoreClasslists += stevesoftClasslist
3836 inputs.files(stevesoftClasslist['list'])
3837 outputs.file(stevesoftClasslist['jsfile'])
3838 outputs.file(stevesoftClasslist['zjsfile'])
3841 def allClasslistName = "_all"
3842 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3843 allJsFiles += fileTree(
3847 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3848 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3849 "**/org/jmol/export/JSExporter.js"
3852 allJsFiles += fileTree(
3856 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3857 "**/sun/misc/Unsafe.js",
3858 "**/swingjs/jquery/jquery-editable-select.js",
3859 "**/swingjs/jquery/j2sComboBox.js",
3860 "**/sun/misc/FloatingDecimal.js"
3863 def allClasslist = [
3864 'jsfile': "${outputDir}/core${allClasslistName}.js",
3865 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3867 'name': allClasslistName
3869 // not including this version of "all" core at the moment
3870 //jalviewjsCoreClasslists += allClasslist
3871 inputs.files(allClasslist['list'])
3872 outputs.file(allClasslist['jsfile'])
3873 outputs.file(allClasslist['zjsfile'])
3876 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3877 logOutFile.getParentFile().mkdirs()
3878 logOutFile.createNewFile()
3879 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3881 jalviewjsCoreClasslists.each {
3882 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3889 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3892 into file(outputFile).getParentFile()
3893 rename { filename ->
3894 if (filename.equals(inputFile.getName())) {
3895 return file(outputFile).getName()
3899 filter(ReplaceTokens,
3903 'MAIN': '"'+main_class+'"',
3905 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3906 'COREKEY': jalviewjs_core_key,
3907 'CORENAME': coreName
3914 task jalviewjsPublishCoreTemplates {
3915 dependsOn jalviewjsBuildAllCores
3916 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3917 def inputFile = file(inputFileName)
3918 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3920 def outputFiles = []
3921 jalviewjsCoreClasslists.each { cl ->
3922 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3923 cl['outputfile'] = outputFile
3924 outputFiles += outputFile
3928 jalviewjsCoreClasslists.each { cl ->
3929 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3932 inputs.file(inputFile)
3933 outputs.files(outputFiles)
3937 task jalviewjsSyncCore (type: Sync) {
3938 dependsOn jalviewjsBuildAllCores
3939 dependsOn jalviewjsPublishCoreTemplates
3940 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3941 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3945 def outputFiles = []
3946 rename { filename ->
3947 outputFiles += "${outputDir}/${filename}"
3953 outputs.files outputFiles
3954 inputs.files inputFiles
3958 // this Copy version of TransferSiteJs will delete anything else in the target dir
3959 task jalviewjsCopyTransferSiteJs(type: Copy) {
3960 dependsOn jalviewjsTranspile
3961 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3962 into "${jalviewDir}/${jalviewjsSiteDir}"
3966 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3967 task jalviewjsSyncTransferSiteJs(type: Sync) {
3968 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3970 into "${jalviewDir}/${jalviewjsSiteDir}"
3977 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3978 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3979 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3980 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3982 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3983 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3984 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3985 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3988 task jalviewjsPrepareSite {
3990 description "Prepares the website folder including unzipping files and copying resources"
3991 dependsOn jalviewjsSyncAllLibs
3992 dependsOn jalviewjsSyncResources
3993 dependsOn jalviewjsSyncSiteResources
3994 dependsOn jalviewjsSyncBuildProperties
3995 dependsOn jalviewjsSyncCore
3999 task jalviewjsBuildSite {
4001 description "Builds the whole website including transpiled code"
4002 dependsOn jalviewjsCopyTransferSiteJs
4003 dependsOn jalviewjsPrepareSite
4007 task cleanJalviewjsTransferSite {
4009 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
4010 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
4011 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
4012 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
4017 task cleanJalviewjsSite {
4018 dependsOn cleanJalviewjsTransferSite
4020 delete "${jalviewDir}/${jalviewjsSiteDir}"
4025 task jalviewjsSiteTar(type: Tar) {
4027 description "Creates a tar.gz file for the website"
4028 dependsOn jalviewjsBuildSite
4029 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
4030 archiveFileName = outputFilename
4032 compression Compression.GZIP
4034 from "${jalviewDir}/${jalviewjsSiteDir}"
4035 into jalviewjs_site_dir // this is inside the tar file
4037 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
4041 task jalviewjsServer {
4043 def filename = "jalviewjsTest.html"
4044 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
4045 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
4050 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
4051 factory = f.newInstance()
4052 } catch (ClassNotFoundException e) {
4053 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
4055 def port = Integer.valueOf(jalviewjs_server_port)
4060 while(port < start+1000 && !running) {
4062 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
4063 jalviewjsServer = factory.start(doc_root, port)
4065 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
4066 println("SERVER STARTED with document root ${doc_root}.")
4067 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
4068 println("For debug: "+url+"?j2sdebug")
4069 println("For verbose: "+url+"?j2sverbose")
4070 } catch (Exception e) {
4075 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
4076 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
4077 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4079 jalviewjsCoreClasslists.each { cl ->
4080 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4082 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4084 println("For core ${cl.name}: "+urlcore)
4087 file(htmlFile).text = htmlText
4090 outputs.file(htmlFile)
4091 outputs.upToDateWhen({false})
4095 task cleanJalviewjsAll {
4097 description "Delete all configuration and build artifacts to do with JalviewJS build"
4098 dependsOn cleanJalviewjsSite
4099 dependsOn jalviewjsEclipsePaths
4102 delete "${jalviewDir}/${jalviewjsBuildDir}"
4103 delete "${jalviewDir}/${eclipse_bin_dir}"
4104 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4105 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4107 delete jalviewjsJ2sAltSettingsFileName
4110 outputs.upToDateWhen( { false } )
4114 task jalviewjsIDE_checkJ2sPlugin {
4115 group "00 JalviewJS in Eclipse"
4116 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4119 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4120 def j2sPluginFile = file(j2sPlugin)
4121 def eclipseHome = System.properties["eclipse.home.location"]
4122 if (eclipseHome == null || ! IN_ECLIPSE) {
4123 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4125 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4126 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4127 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4128 eclipseJ2sPluginDirs += altPluginsDir
4130 def foundPlugin = false
4131 def j2sPluginFileName = j2sPluginFile.getName()
4132 def eclipseJ2sPlugin
4133 def eclipseJ2sPluginFile
4134 eclipseJ2sPluginDirs.any { dir ->
4135 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4136 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4137 if (eclipseJ2sPluginFile.exists()) {
4143 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4144 System.err.println(msg)
4145 throw new StopExecutionException(msg)
4148 def digest = MessageDigest.getInstance("MD5")
4150 digest.update(j2sPluginFile.text.bytes)
4151 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4153 digest.update(eclipseJ2sPluginFile.text.bytes)
4154 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4156 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4157 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4158 System.err.println(msg)
4159 throw new StopExecutionException(msg)
4161 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4167 task jalviewjsIDE_copyJ2sPlugin {
4168 group "00 JalviewJS in Eclipse"
4169 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4172 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4173 def j2sPluginFile = file(j2sPlugin)
4174 def eclipseHome = System.properties["eclipse.home.location"]
4175 if (eclipseHome == null || ! IN_ECLIPSE) {
4176 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4178 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4179 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4180 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4181 System.err.println(msg)
4184 eclipseJ2sPluginFile.getParentFile().mkdirs()
4185 into eclipseJ2sPluginFile.getParent()
4191 task jalviewjsIDE_j2sFile {
4192 group "00 JalviewJS in Eclipse"
4193 description "Creates the .j2s file"
4194 dependsOn jalviewjsCreateJ2sSettings
4198 task jalviewjsIDE_SyncCore {
4199 group "00 JalviewJS in Eclipse"
4200 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4201 dependsOn jalviewjsSyncCore
4205 task jalviewjsIDE_SyncSiteAll {
4206 dependsOn jalviewjsSyncAllLibs
4207 dependsOn jalviewjsSyncResources
4208 dependsOn jalviewjsSyncSiteResources
4209 dependsOn jalviewjsSyncBuildProperties
4213 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4216 task jalviewjsIDE_PrepareSite {
4217 group "00 JalviewJS in Eclipse"
4218 description "Sync libs and resources to site dir, but not closure cores"
4220 dependsOn jalviewjsIDE_SyncSiteAll
4221 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4225 task jalviewjsIDE_AssembleSite {
4226 group "00 JalviewJS in Eclipse"
4227 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4228 dependsOn jalviewjsPrepareSite
4232 task jalviewjsIDE_SiteClean {
4233 group "00 JalviewJS in Eclipse"
4234 description "Deletes the Eclipse transpiled site"
4235 dependsOn cleanJalviewjsSite
4239 task jalviewjsIDE_Server {
4240 group "00 JalviewJS in Eclipse"
4241 description "Starts a webserver on localhost to test the website"
4242 dependsOn jalviewjsServer
4246 // buildship runs this at import or gradle refresh
4247 task eclipseSynchronizationTask {
4248 //dependsOn eclipseSetup
4249 dependsOn createBuildProperties
4251 dependsOn jalviewjsIDE_j2sFile
4252 dependsOn jalviewjsIDE_checkJ2sPlugin
4253 dependsOn jalviewjsIDE_PrepareSite
4258 // buildship runs this at build time or project refresh
4259 task eclipseAutoBuildTask {
4260 //dependsOn jalviewjsIDE_checkJ2sPlugin
4261 //dependsOn jalviewjsIDE_PrepareSite
4265 task jalviewjsCopyStderrLaunchFile(type: Copy) {
4266 from file(jalviewjs_stderr_launch)
4267 into jalviewjsSiteDir
4269 inputs.file jalviewjs_stderr_launch
4270 outputs.file jalviewjsStderrLaunchFilename
4273 task cleanJalviewjsChromiumUserDir {
4275 delete jalviewjsChromiumUserDir
4277 outputs.dir jalviewjsChromiumUserDir
4278 // always run when depended on
4279 outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
4282 task jalviewjsChromiumProfile {
4283 dependsOn cleanJalviewjsChromiumUserDir
4284 mustRunAfter cleanJalviewjsChromiumUserDir
4286 def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
4289 mkdir jalviewjsChromiumProfileDir
4292 outputs.file firstRun
4295 task jalviewjsLaunchTest {
4297 description "Check JalviewJS opens in a browser"
4298 dependsOn jalviewjsBuildSite
4299 dependsOn jalviewjsCopyStderrLaunchFile
4300 dependsOn jalviewjsChromiumProfile
4302 def macOS = OperatingSystem.current().isMacOsX()
4303 def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
4304 if (chromiumBinary.startsWith("~/")) {
4305 chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
4311 def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
4313 def binary = file(chromiumBinary)
4314 if (!binary.exists()) {
4315 throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
4317 stdout = new ByteArrayOutputStream()
4318 stderr = new ByteArrayOutputStream()
4321 if (jalviewjs_j2s_to_console.equals("true")) {
4322 execStdout = new org.apache.tools.ant.util.TeeOutputStream(
4325 execStderr = new org.apache.tools.ant.util.TeeOutputStream(
4332 // macOS not running properly with timeout arguments
4333 def execArgs = macOS ? [] : [
4334 "--timeout=${timeoutms}",
4335 "--virtual-time-budget=${timeoutms}",
4338 "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
4341 "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
4342 "--profile-directory=${jalviewjs_chromium_profile_name}",
4343 "--allow-file-access-from-files",
4344 "--enable-logging=stderr",
4345 "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
4348 if (true || macOS) {
4349 ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
4350 Future f1 = executor.submit(
4353 standardOutput = execStdout
4354 errorOutput = execStderr
4355 executable(chromiumBinary)
4357 println "COMMAND: '"+commandLine.join(" ")+"'"
4359 executor.shutdownNow()
4363 def noChangeBytes = 0
4364 def noChangeIterations = 0
4365 executor.scheduleAtFixedRate(
4367 String stderrString = stderr.toString()
4368 // shutdown the task if we have a success string
4369 if (stderrString.contains(jalviewjs_desktop_init_string)) {
4372 executor.shutdownNow()
4374 // if no change in stderr for 10s then also end
4375 if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
4376 executor.shutdownNow()
4378 if (stderrString.length() == noChangeBytes) {
4379 noChangeIterations++
4381 noChangeBytes = stderrString.length()
4382 noChangeIterations = 0
4385 1, 1, TimeUnit.SECONDS)
4387 executor.schedule(new Runnable(){
4390 executor.shutdownNow()
4392 }, timeoutms, TimeUnit.MILLISECONDS)
4394 executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
4395 executor.shutdownNow()
4402 stderr.toString().eachLine { line ->
4403 if (line.contains(jalviewjs_desktop_init_string)) {
4404 println("Found line '"+line+"'")
4410 throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
4418 description "Build the JalviewJS site and run the launch test"
4419 dependsOn jalviewjsBuildSite
4420 dependsOn jalviewjsLaunchTest