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 '4.0.3'
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 /* insert more testTaskNs here -- change N to next digit or other string */
1788 task testTaskN(type: Test) {
1789 group = "Verification"
1790 description = "Tests that need to be isolated from the main test run"
1793 excludeGroups testng_excluded_groups.split(",")
1795 useDefaultListeners=true
1801 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1802 * to summarise test results from all Test tasks
1804 /* START of test tasks results summary */
1805 import groovy.time.TimeCategory
1806 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1807 import org.gradle.api.tasks.testing.logging.TestLogEvent
1808 rootProject.ext.testsResults = [] // Container for tests summaries
1810 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1812 // from original test task
1814 dependsOn cloverClasses
1816 dependsOn testClasses //?
1819 // run main tests first
1820 if (!testTask.name.equals("testTask0"))
1821 testTask.mustRunAfter "testTask0"
1823 testTask.testLogging { logging ->
1824 events TestLogEvent.FAILED
1825 // TestLogEvent.SKIPPED,
1826 // TestLogEvent.STANDARD_OUT,
1827 // TestLogEvent.STANDARD_ERROR
1829 exceptionFormat TestExceptionFormat.FULL
1832 showStackTraces true
1833 showStandardStreams true
1835 info.events = [ TestLogEvent.FAILED ]
1840 ignoreFailures = true // Always try to run all tests for all modules
1842 afterSuite { desc, result ->
1844 return // Only summarize results for whole modules
1846 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1848 rootProject.ext.testsResults.add(resultsInfo)
1851 // from original test task
1852 maxHeapSize = "1024m"
1854 workingDir = jalviewDir
1855 def testLaf = project.findProperty("test_laf")
1856 if (testLaf != null) {
1857 println("Setting Test LaF to '${testLaf}'")
1858 systemProperty "laf", testLaf
1860 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1861 if (testHiDPIScale != null) {
1862 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1863 systemProperty "sun.java2d.uiScale", testHiDPIScale
1865 sourceCompatibility = compile_source_compatibility
1866 targetCompatibility = compile_target_compatibility
1867 jvmArgs += additional_compiler_args
1870 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1871 // testTasks that include the tests, and exclude all from the others.
1872 // get --test argument
1873 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1874 // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
1875 // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
1879 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1884 /* don't fail on no matching tests (so --tests will run across all testTasks) */
1885 testTask.filter.setFailOnNoMatchingTests(false)
1887 /* ensure the "test" task dependsOn all the testTasks */
1888 test.dependsOn testTask
1891 gradle.buildFinished {
1892 def allResults = rootProject.ext.testsResults
1894 if (!allResults.isEmpty()) {
1895 printResults allResults
1896 allResults.each {r ->
1897 if (r[2].resultType == TestResult.ResultType.FAILURE)
1898 throw new GradleException("Failed tests!")
1903 private static String colString(styler, col, colour, text) {
1904 return col?"${styler[colour](text)}":text
1907 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1908 def colour = 'black'
1916 case TestResult.ResultType.SUCCESS:
1919 case TestResult.ResultType.FAILURE:
1927 StringBuilder sb = new StringBuilder()
1931 sb.append(" results: ")
1932 sb.append(colString(s, col && !nocol, colour, text))
1934 sb.append("${rc} tests, ")
1935 sb.append(colString(s, col && rs > 0, 'green', rs))
1936 sb.append(" successes, ")
1937 sb.append(colString(s, col && rf > 0, 'red', rf))
1938 sb.append(" failures, ")
1939 sb.append("${rsk} skipped) in ${t}")
1940 return sb.toString()
1943 private static void printResults(allResults) {
1945 // styler from https://stackoverflow.com/a/56139852
1946 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1949 def failedTests = false
1950 def summaryLines = []
1952 def totalsuccess = 0
1955 def totaltime = TimeCategory.getSeconds(0)
1956 // sort on project name then task name
1957 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1958 def projectName = it[0]
1959 def taskName = it[1]
1963 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1964 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1965 def reportLine = "Report file: ${report}"
1966 def ls = summaryPlain.length()
1967 def lr = reportLine.length()
1968 def m = [ls, lr].max()
1971 def info = [ls, summaryCol, reportLine]
1972 summaryLines.add(info)
1973 failedTests |= result.resultType == TestResult.ResultType.FAILURE
1974 totalcount += result.testCount
1975 totalsuccess += result.successfulTestCount
1976 totalfail += result.failedTestCount
1977 totalskip += result.skippedTestCount
1980 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
1981 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
1982 def tls = totalSummaryPlain.length()
1983 if (tls > maxLength)
1985 def info = [tls, totalSummaryCol, null]
1986 summaryLines.add(info)
1988 def allSummaries = []
1989 for(sInfo : summaryLines) {
1991 def summary = sInfo[1]
1992 def report = sInfo[2]
1994 StringBuilder sb = new StringBuilder()
1995 sb.append("│" + summary + " " * (maxLength - ls) + "│")
1996 if (report != null) {
1997 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
1999 allSummaries += sb.toString()
2002 println "┌${"${"─" * maxLength}"}┐"
2003 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
2004 println "└${"${"─" * maxLength}"}┘"
2006 /* END of test tasks results summary */
2009 task compileLinkCheck(type: JavaCompile) {
2011 classpath = files("${jalviewDir}/${utils_dir}")
2012 destinationDir = file("${jalviewDir}/${utils_dir}")
2013 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
2015 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2016 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2017 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
2018 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
2022 task linkCheck(type: JavaExec) {
2024 dependsOn compileLinkCheck
2026 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2027 classpath = files("${jalviewDir}/${utils_dir}")
2028 main = "HelpLinksChecker"
2029 workingDir = "${helpBuildDir}"
2030 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2032 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2033 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2036 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2040 inputs.dir(helpBuildDir)
2041 outputs.file(helpLinksCheckerOutFile)
2045 // import the pubhtmlhelp target
2046 ant.properties.basedir = "${jalviewDir}"
2047 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2048 ant.importBuild "${utils_dir}/publishHelp.xml"
2051 task cleanPackageDir(type: Delete) {
2053 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2063 attributes "Main-Class": main_class,
2064 "Permissions": "all-permissions",
2065 "Application-Name": applicationName,
2066 "Codebase": application_codebase,
2067 "Implementation-Version": JALVIEW_VERSION
2070 def outputDir = "${jalviewDir}/${package_dir}"
2071 destinationDirectory = file(outputDir)
2072 archiveFileName = rootProject.name+".jar"
2073 duplicatesStrategy "EXCLUDE"
2080 exclude "**/*.jar.*"
2082 inputs.dir(sourceSets.main.java.outputDir)
2083 sourceSets.main.resources.srcDirs.each{ dir ->
2086 outputs.file("${outputDir}/${archiveFileName}")
2090 task copyJars(type: Copy) {
2091 from fileTree(dir: classesDir, include: "**/*.jar").files
2092 into "${jalviewDir}/${package_dir}"
2096 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2097 task syncJars(type: Sync) {
2099 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2100 into "${jalviewDir}/${package_dir}"
2102 include jar.archiveFileName.getOrNull()
2109 description = "Put all required libraries in dist"
2110 // order of "cleanPackageDir", "copyJars", "jar" important!
2111 jar.mustRunAfter cleanPackageDir
2112 syncJars.mustRunAfter cleanPackageDir
2113 dependsOn cleanPackageDir
2116 outputs.dir("${jalviewDir}/${package_dir}")
2121 dependsOn cleanPackageDir
2128 group = "distribution"
2129 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2133 from ("${jalviewDir}/${libDistDir}") {
2137 attributes "Implementation-Version": JALVIEW_VERSION,
2138 "Application-Name": applicationName
2141 duplicatesStrategy "INCLUDE"
2143 mainClassName = shadow_jar_main_class
2145 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2149 task getdownImagesCopy() {
2150 inputs.dir getdownImagesDir
2151 outputs.dir getdownImagesBuildDir
2155 from(getdownImagesDir) {
2156 include("*getdown*.png")
2158 into getdownImagesBuildDir
2163 task getdownImagesProcess() {
2164 dependsOn getdownImagesCopy
2167 if (backgroundImageText) {
2168 if (convertBinary == null) {
2169 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2171 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2172 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2174 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2176 executable convertBinary
2179 '-font', getdown_background_image_text_font,
2180 '-fill', getdown_background_image_text_colour,
2181 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2182 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2183 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2192 task getdownImages() {
2193 dependsOn getdownImagesProcess
2196 task getdownWebsite() {
2197 group = "distribution"
2198 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2200 dependsOn getdownImages
2205 def getdownWebsiteResourceFilenames = []
2206 def getdownResourceDir = getdownResourceDir
2207 def getdownResourceFilenames = []
2210 // clean the getdown website and files dir before creating getdown folders
2211 delete getdownAppBaseDir
2212 delete getdownFilesDir
2215 from buildProperties
2216 rename(file(buildProperties).getName(), getdown_build_properties)
2219 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2222 from channelPropsFile
2223 filter(ReplaceTokens,
2227 'SUFFIX': channelSuffix
2230 into getdownAppBaseDir
2232 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2234 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2235 def props = project.properties.sort { it.key }
2236 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2237 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2239 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2240 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2242 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2243 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2245 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2246 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2247 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2248 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2249 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2250 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
2251 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
2254 props.put("getdown_txt_title", jalview_name)
2255 props.put("getdown_txt_ui.name", applicationName)
2257 // start with appbase
2258 getdownTextLines += "appbase = ${getdownAppBase}"
2259 props.each{ prop, val ->
2260 if (prop.startsWith("getdown_txt_") && val != null) {
2261 if (prop.startsWith("getdown_txt_multi_")) {
2262 def key = prop.substring(18)
2263 val.split(",").each{ v ->
2264 def line = "${key} = ${v}"
2265 getdownTextLines += line
2268 // file values rationalised
2269 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2271 if (val.indexOf('/') == 0) {
2274 } else if (val.indexOf('/') > 0) {
2275 // relative path (relative to jalviewDir)
2276 r = file( "${jalviewDir}/${val}" )
2279 val = "${getdown_resource_dir}/" + r.getName()
2280 getdownWebsiteResourceFilenames += val
2281 getdownResourceFilenames += r.getPath()
2284 if (! prop.startsWith("getdown_txt_resource")) {
2285 def line = prop.substring(12) + " = ${val}"
2286 getdownTextLines += line
2292 getdownWebsiteResourceFilenames.each{ filename ->
2293 getdownTextLines += "resource = ${filename}"
2295 getdownResourceFilenames.each{ filename ->
2298 into getdownResourceDir
2302 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2303 getdownWrapperScripts.each{ script ->
2304 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2308 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2310 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2315 fileTree(file(package_dir)).each{ f ->
2316 if (f.isDirectory()) {
2317 def files = fileTree(dir: f, include: ["*"]).getFiles()
2319 } else if (f.exists()) {
2323 def jalviewJar = jar.archiveFileName.getOrNull()
2324 // put jalview.jar first for CLASSPATH and .properties files reasons
2325 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2326 def name = f.getName()
2327 def line = "code = ${getdownAppDistDir}/${name}"
2328 getdownTextLines += line
2335 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2337 if (JAVA_VERSION.equals("11")) {
2338 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2339 j11libFiles.sort().each{f ->
2340 def name = f.getName()
2341 def line = "code = ${getdown_j11lib_dir}/${name}"
2342 getdownTextLines += line
2345 into getdownJ11libDir
2351 // 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.
2352 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2353 getdownTextLines += "resource = ${getdown_launcher_new}"
2354 getdownTextLines += "class = ${main_class}"
2355 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2356 if (getdownSetAppBaseProperty) {
2357 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2358 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2361 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2362 getdownTxt.write(getdownTextLines.join("\n"))
2364 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2365 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2366 launchJvl.write("appbase=${getdownAppBase}")
2368 // files going into the getdown website dir: getdown-launcher.jar
2370 from getdownLauncher
2371 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2372 into getdownAppBaseDir
2375 // files going into the getdown website dir: getdown-launcher(-local).jar
2377 from getdownLauncher
2378 if (file(getdownLauncher).getName() != getdown_launcher) {
2379 rename(file(getdownLauncher).getName(), getdown_launcher)
2381 into getdownAppBaseDir
2384 // files going into the getdown website dir: ./install dir and files
2385 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2388 from getdownLauncher
2389 from "${getdownAppDir}/${getdown_build_properties}"
2390 if (file(getdownLauncher).getName() != getdown_launcher) {
2391 rename(file(getdownLauncher).getName(), getdown_launcher)
2393 into getdownInstallDir
2396 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2398 from getdownInstallDir
2399 into getdownFilesInstallDir
2403 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2407 from getdownLauncher
2408 from "${getdownAppBaseDir}/${getdown_build_properties}"
2409 from "${getdownAppBaseDir}/${channel_props}"
2410 if (file(getdownLauncher).getName() != getdown_launcher) {
2411 rename(file(getdownLauncher).getName(), getdown_launcher)
2413 into getdownFilesDir
2416 // and ./resource (not all downloaded by getdown)
2418 from getdownResourceDir
2419 into "${getdownFilesDir}/${getdown_resource_dir}"
2424 inputs.dir("${jalviewDir}/${package_dir}")
2426 outputs.dir(getdownAppBaseDir)
2427 outputs.dir(getdownFilesDir)
2431 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2432 task getdownDigestDir(type: JavaExec) {
2434 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2436 def digestDirPropertyName = "DIGESTDIR"
2438 classpath = files(getdownLauncher)
2439 def digestDir = findProperty(digestDirPropertyName)
2440 if (digestDir == null) {
2441 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2445 main = "com.threerings.getdown.tools.Digester"
2449 task getdownDigest(type: JavaExec) {
2450 group = "distribution"
2451 description = "Digest the getdown website folder"
2452 dependsOn getdownWebsite
2454 classpath = files(getdownLauncher)
2456 main = "com.threerings.getdown.tools.Digester"
2457 args getdownAppBaseDir
2458 inputs.dir(getdownAppBaseDir)
2459 outputs.file("${getdownAppBaseDir}/digest2.txt")
2464 group = "distribution"
2465 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2466 dependsOn getdownDigest
2468 if (reportRsyncCommand) {
2469 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2470 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2471 println "LIKELY RSYNC COMMAND:"
2472 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2473 if (RUNRSYNC == "true") {
2475 commandLine "mkdir", "-p", toDir
2478 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2486 task getdownArchiveBuild() {
2487 group = "distribution"
2488 description = "Put files in the archive dir to go on the website"
2490 dependsOn getdownWebsite
2492 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2493 def vDir = "${getdownArchiveDir}/${v}"
2494 getdownFullArchiveDir = "${vDir}/getdown"
2495 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2497 def vAltDir = "alt_${v}"
2498 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2501 // cleanup old "old" dir
2502 delete getdownArchiveDir
2504 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2505 getdownArchiveTxt.getParentFile().mkdirs()
2506 def getdownArchiveTextLines = []
2507 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2511 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2512 into "${getdownFullArchiveDir}/${vAltDir}"
2515 getdownTextLines.each { line ->
2516 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2517 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2518 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2519 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2520 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2521 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2522 // remove the existing resource = resource/ or bin/ lines
2523 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2524 getdownArchiveTextLines += line
2528 // the resource dir -- add these files as resource lines in getdown.txt
2530 from "${archiveImagesDir}"
2531 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2533 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2537 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2539 def vLaunchJvl = file(getdownVersionLaunchJvl)
2540 vLaunchJvl.getParentFile().mkdirs()
2541 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2542 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2543 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2544 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2545 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2546 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2548 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2550 from getdownLauncher
2551 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2552 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2553 from "${getdownAppBaseDir}/${channel_props}"
2554 if (file(getdownLauncher).getName() != getdown_launcher) {
2555 rename(file(getdownLauncher).getName(), getdown_launcher)
2557 into getdownFullArchiveDir
2563 task getdownArchiveDigest(type: JavaExec) {
2564 group = "distribution"
2565 description = "Digest the getdown archive folder"
2567 dependsOn getdownArchiveBuild
2570 classpath = files(getdownLauncher)
2571 args getdownFullArchiveDir
2573 main = "com.threerings.getdown.tools.Digester"
2574 inputs.dir(getdownFullArchiveDir)
2575 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2578 task getdownArchive() {
2579 group = "distribution"
2580 description = "Build the website archive dir with getdown digest"
2582 dependsOn getdownArchiveBuild
2583 dependsOn getdownArchiveDigest
2586 tasks.withType(JavaCompile) {
2587 options.encoding = 'UTF-8'
2593 delete getdownAppBaseDir
2594 delete getdownFilesDir
2595 delete getdownArchiveDir
2601 if (file(install4jHomeDir).exists()) {
2603 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2604 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2605 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2606 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2608 installDir(file(install4jHomeDir))
2610 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2614 task copyInstall4jTemplate {
2615 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2616 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2617 inputs.file(install4jTemplateFile)
2618 inputs.file(install4jFileAssociationsFile)
2619 inputs.property("CHANNEL", { CHANNEL })
2620 outputs.file(install4jConfFile)
2623 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2625 // turn off code signing if no OSX_KEYPASS
2626 if (OSX_KEYPASS == "") {
2627 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2628 codeSigning.'@macEnabled' = "false"
2630 install4jConfigXml.'**'.windows.each { windows ->
2631 windows.'@runPostProcessor' = "false"
2635 // disable install screen for OSX dmg (for 2.11.2.0)
2636 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2637 macosArchive.attributes().remove('executeSetupApp')
2638 macosArchive.attributes().remove('setupAppId')
2641 // turn off checksum creation for LOCAL channel
2642 def e = install4jConfigXml.application[0]
2643 e.'@createChecksums' = string(install4jCheckSums)
2645 // put file association actions where placeholder action is
2646 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2647 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2648 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2649 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2650 def parent = a.parent()
2652 fileAssociationActions.each { faa ->
2655 // don't need to continue in .any loop once replacements have been made
2660 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2661 // NB we're deleting the /other/ one!
2662 // Also remove the examples subdir from non-release versions
2663 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2664 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2665 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2666 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2668 // remove the examples subdir from Full File Set
2669 def files = install4jConfigXml.files[0]
2670 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2671 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2672 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2673 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2674 dirEntry.parent().remove(dirEntry)
2676 install4jConfigXml.'**'.action.any { a ->
2677 if (a.'@customizedId' == customizedIdToDelete) {
2678 def parent = a.parent()
2684 // write install4j file
2685 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2692 delete install4jConfFile
2696 task cleanInstallersDataFiles {
2697 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2698 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2699 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2701 delete installersOutputTxt
2702 delete installersSha256
2703 delete hugoDataJsonFile
2707 task install4jDMGBackgroundImageCopy {
2708 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2709 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2712 from(install4jDMGBackgroundImageDir) {
2713 include(install4jDMGBackgroundImageFile)
2715 into install4jDMGBackgroundImageBuildDir
2720 task install4jDMGBackgroundImageProcess {
2721 dependsOn install4jDMGBackgroundImageCopy
2724 if (backgroundImageText) {
2725 if (convertBinary == null) {
2726 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2728 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2729 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2731 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2733 executable convertBinary
2736 '-font', install4j_background_image_text_font,
2737 '-fill', install4j_background_image_text_colour,
2738 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2739 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2740 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2749 task install4jDMGBackgroundImage {
2750 dependsOn install4jDMGBackgroundImageProcess
2753 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2754 group = "distribution"
2755 description = "Create the install4j installers"
2757 dependsOn copyInstall4jTemplate
2758 dependsOn cleanInstallersDataFiles
2759 dependsOn install4jDMGBackgroundImage
2761 projectFile = install4jConfFile
2763 // create an md5 for the input files to use as version for install4j conf file
2764 def digest = MessageDigest.getInstance("MD5")
2766 (file("${install4jDir}/${install4j_template}").text +
2767 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2768 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2769 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2770 if (filesMd5.length() >= 8) {
2771 filesMd5 = filesMd5.substring(0,8)
2773 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2776 'JALVIEW_NAME': jalview_name,
2777 'JALVIEW_APPLICATION_NAME': applicationName,
2778 'JALVIEW_DIR': "../..",
2779 'OSX_KEYSTORE': OSX_KEYSTORE,
2780 'OSX_APPLEID': OSX_APPLEID,
2781 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2782 'JSIGN_SH': JSIGN_SH,
2783 'JRE_DIR': getdown_app_dir_java,
2784 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2785 'JALVIEW_VERSION': JALVIEW_VERSION,
2786 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2787 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2788 'JAVA_VERSION': JAVA_VERSION,
2789 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2790 'VERSION': JALVIEW_VERSION,
2791 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2792 'BUNDLE_ID': install4jBundleId,
2793 'INTERNAL_ID': install4jInternalId,
2794 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2795 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2796 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2797 'WRAPPER_LINK': getdownWrapperLink,
2798 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2799 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2800 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
2801 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2802 'INSTALLER_NAME': install4jInstallerName,
2803 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2804 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2805 'GETDOWN_FILES_DIR': getdown_files_dir,
2806 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2807 'GETDOWN_DIST_DIR': getdownAppDistDir,
2808 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2809 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2810 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2811 'BUILD_DIR': install4jBuildDir,
2812 'APPLICATION_CATEGORIES': install4j_application_categories,
2813 'APPLICATION_FOLDER': install4jApplicationFolder,
2814 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2815 'EXECUTABLE_NAME': install4jExecutableName,
2816 'EXTRA_SCHEME': install4jExtraScheme,
2817 'MAC_ICONS_FILE': install4jMacIconsFile,
2818 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2819 'PNG_ICON_FILE': install4jPngIconFile,
2820 'BACKGROUND': install4jBackground,
2825 'windows': 'WINDOWS',
2829 // these are the bundled OS/architecture VMs needed by install4j
2832 [ "mac", "aarch64" ],
2833 [ "windows", "x64" ],
2835 [ "linux", "aarch64" ]
2837 osArch.forEach { os, arch ->
2838 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)
2839 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2840 // otherwise running `gradle installers` generates a non-useful error:
2841 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2842 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)
2845 //println("INSTALL4J VARIABLES:")
2846 //variables.each{k,v->println("${k}=${v}")}
2848 destination = "${jalviewDir}/${install4jBuildDir}"
2849 buildSelected = true
2851 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2853 disableSigning = true
2854 disableNotarization = true
2858 macKeystorePassword = OSX_KEYPASS
2861 if (OSX_ALTOOLPASS) {
2862 appleIdPassword = OSX_ALTOOLPASS
2863 disableNotarization = false
2865 disableNotarization = true
2869 println("Using projectFile "+projectFile)
2870 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2874 inputs.dir(getdownAppBaseDir)
2875 inputs.file(install4jConfFile)
2876 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2877 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2880 def getDataHash(File myFile) {
2881 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2882 return myFile.exists()
2884 "file" : myFile.getName(),
2885 "filesize" : myFile.length(),
2886 "sha256" : hash.toString()
2891 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2893 "channel" : getdownChannelName,
2894 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2895 "git-commit" : "${gitHash} [${gitBranch}]",
2896 "version" : JALVIEW_VERSION
2898 // install4j installer files
2899 if (installersOutputTxt.exists()) {
2901 installersOutputTxt.readLines().each { def line ->
2902 if (line.startsWith("#")) {
2905 line.replaceAll("\n","")
2906 def vals = line.split("\t")
2907 def filename = vals[3]
2908 def filesize = file(filename).length()
2909 filename = filename.replaceAll(/^.*\//, "")
2910 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2911 idHash."${filename}" = vals[0]
2913 if (install4jCheckSums && installersSha256.exists()) {
2914 installersSha256.readLines().each { def line ->
2915 if (line.startsWith("#")) {
2918 line.replaceAll("\n","")
2919 def vals = line.split(/\s+\*?/)
2920 def filename = vals[1]
2921 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2927 "JAR": shadowJar.archiveFile, // executable JAR
2928 "JVL": getdownVersionLaunchJvl, // version JVL
2929 "SOURCE": sourceDist.archiveFile // source TGZ
2930 ].each { key, value ->
2931 def file = file(value)
2932 if (file.exists()) {
2933 def fileHash = getDataHash(file)
2934 if (fileHash != null) {
2935 hash."${key}" = fileHash;
2939 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2942 task staticMakeInstallersJsonFile {
2944 def output = findProperty("i4j_output")
2945 def sha256 = findProperty("i4j_sha256")
2946 def json = findProperty("i4j_json")
2947 if (output == null || sha256 == null || json == null) {
2948 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2950 writeDataJsonFile(file(output), file(sha256), file(json))
2955 dependsOn installerFiles
2961 eclipse().configFile(eclipse_codestyle_file)
2965 task createSourceReleaseProperties(type: WriteProperties) {
2966 group = "distribution"
2967 description = "Create the source RELEASE properties file"
2969 def sourceTarBuildDir = "${buildDir}/sourceTar"
2970 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2971 outputFile (sourceReleasePropertiesFile)
2974 releaseProps.each{ key, val -> property key, val }
2975 property "git.branch", gitBranch
2976 property "git.hash", gitHash
2979 outputs.file(outputFile)
2982 task sourceDist(type: Tar) {
2983 group "distribution"
2984 description "Create a source .tar.gz file for distribution"
2986 dependsOn createBuildProperties
2987 dependsOn convertMdFiles
2988 dependsOn eclipseAllPreferences
2989 dependsOn createSourceReleaseProperties
2992 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2993 archiveFileName = outputFileName
2995 compression Compression.GZIP
3010 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
3012 "utils/InstallAnywhere",
3027 "gradle.properties",
3039 ".settings/org.eclipse.buildship.core.prefs",
3040 ".settings/org.eclipse.jdt.core.prefs"
3044 exclude (EXCLUDE_FILES)
3045 include (PROCESS_FILES)
3046 filter(ReplaceTokens,
3050 'Version-Rel': JALVIEW_VERSION,
3051 'Year-Rel': getDate("yyyy")
3056 exclude (EXCLUDE_FILES)
3057 exclude (PROCESS_FILES)
3058 exclude ("appletlib")
3059 exclude ("**/*locales")
3060 exclude ("*locales/**")
3061 exclude ("utils/InstallAnywhere")
3063 exclude (getdown_files_dir)
3064 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3065 //exclude (getdown_website_dir)
3066 //exclude (getdown_archive_dir)
3068 // exluding these as not using jars as modules yet
3069 exclude ("${j11modDir}/**/*.jar")
3072 include(INCLUDE_FILES)
3074 // from (jalviewDir) {
3075 // // explicit includes for stuff that seemed to not get included
3076 // include(fileTree("test/**/*."))
3077 // exclude(EXCLUDE_FILES)
3078 // exclude(PROCESS_FILES)
3081 from(file(buildProperties).getParent()) {
3082 include(file(buildProperties).getName())
3083 rename(file(buildProperties).getName(), "build_properties")
3085 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3089 def sourceTarBuildDir = "${buildDir}/sourceTar"
3090 from(sourceTarBuildDir) {
3091 // this includes the appended RELEASE properties file
3095 task dataInstallersJson {
3097 description "Create the installers-VERSION.json data file for installer files created"
3099 mustRunAfter installers
3100 mustRunAfter shadowJar
3101 mustRunAfter sourceDist
3102 mustRunAfter getdownArchive
3104 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3105 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3107 if (installersOutputTxt.exists()) {
3108 inputs.file(installersOutputTxt)
3110 if (install4jCheckSums && installersSha256.exists()) {
3111 inputs.file(installersSha256)
3114 shadowJar.archiveFile, // executable JAR
3115 getdownVersionLaunchJvl, // version JVL
3116 sourceDist.archiveFile // source TGZ
3117 ].each { fileName ->
3118 if (file(fileName).exists()) {
3119 inputs.file(fileName)
3123 outputs.file(hugoDataJsonFile)
3126 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3132 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3135 dependsOn pubhtmlhelp
3137 inputs.dir("${helpBuildDir}/${help_dir}")
3138 outputs.dir("${buildDir}/distributions/${help_dir}")
3142 task j2sSetHeadlessBuild {
3149 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3151 description "Enable the alternative J2S Config file for headless build"
3153 outputFile = jalviewjsJ2sSettingsFileName
3154 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3155 def j2sProps = new Properties()
3156 if (j2sPropsFile.exists()) {
3158 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3159 j2sProps.load(j2sPropsFileFIS)
3160 j2sPropsFileFIS.close()
3162 j2sProps.each { prop, val ->
3165 } catch (Exception e) {
3166 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3170 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3171 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3176 task jalviewjsSetEclipseWorkspace {
3177 def propKey = "jalviewjs_eclipse_workspace"
3179 if (project.hasProperty(propKey)) {
3180 propVal = project.getProperty(propKey)
3181 if (propVal.startsWith("~/")) {
3182 propVal = System.getProperty("user.home") + propVal.substring(1)
3185 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3186 def propsFile = file(propsFileName)
3187 def eclipseWsDir = propVal
3188 def props = new Properties()
3190 def writeProps = true
3191 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3192 def ins = new FileInputStream(propsFileName)
3195 if (props.getProperty(propKey, null) != null) {
3196 eclipseWsDir = props.getProperty(propKey)
3201 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3202 def tempDir = File.createTempDir()
3203 eclipseWsDir = tempDir.getAbsolutePath()
3206 eclipseWorkspace = file(eclipseWsDir)
3209 // do not run a headless transpile when we claim to be in Eclipse
3211 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3212 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3214 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3218 props.setProperty(propKey, eclipseWsDir)
3219 propsFile.parentFile.mkdirs()
3220 def bytes = new ByteArrayOutputStream()
3221 props.store(bytes, null)
3222 def propertiesString = bytes.toString()
3223 propsFile.text = propertiesString
3229 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3232 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3233 outputs.file(propsFileName)
3234 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3238 task jalviewjsEclipsePaths {
3241 def eclipseRoot = jalviewjs_eclipse_root
3242 if (eclipseRoot.startsWith("~/")) {
3243 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3245 if (OperatingSystem.current().isMacOsX()) {
3246 eclipseRoot += "/Eclipse.app"
3247 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3248 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3249 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3250 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3251 eclipseRoot += "/eclipse"
3253 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3254 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3255 } else { // linux or unix
3256 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3257 eclipseRoot += "/eclipse"
3258 println("eclipseDir exists")
3260 eclipseBinary = "${eclipseRoot}/eclipse"
3261 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3264 eclipseVersion = "4.13" // default
3265 def assumedVersion = true
3266 if (file(eclipseProduct).exists()) {
3267 def fis = new FileInputStream(eclipseProduct)
3268 def props = new Properties()
3270 eclipseVersion = props.getProperty("version")
3272 assumedVersion = false
3275 def propKey = "eclipse_debug"
3276 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3279 // do not run a headless transpile when we claim to be in Eclipse
3281 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3282 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3284 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3287 if (!assumedVersion) {
3288 println("ECLIPSE VERSION=${eclipseVersion}")
3294 task printProperties {
3296 description "Output to console all System.properties"
3298 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3304 dependsOn eclipseProject
3305 dependsOn eclipseClasspath
3306 dependsOn eclipseJdt
3310 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3311 task jalviewjsEclipseCopyDropins(type: Copy) {
3312 dependsOn jalviewjsEclipsePaths
3314 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3315 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3316 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3323 // this eclipse -clean doesn't actually work
3324 task jalviewjsCleanEclipse(type: Exec) {
3325 dependsOn eclipseSetup
3326 dependsOn jalviewjsEclipsePaths
3327 dependsOn jalviewjsEclipseCopyDropins
3329 executable(eclipseBinary)
3330 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3336 def inputString = """exit
3339 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3340 standardInput = inputByteStream
3343 /* not really working yet
3344 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3348 task jalviewjsTransferUnzipSwingJs {
3349 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3353 from zipTree(file_zip)
3354 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3358 inputs.file file_zip
3359 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3363 task jalviewjsTransferUnzipLib {
3364 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3367 zipFiles.each { file_zip ->
3369 from zipTree(file_zip)
3370 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3375 inputs.files zipFiles
3376 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3380 task jalviewjsTransferUnzipAllLibs {
3381 dependsOn jalviewjsTransferUnzipSwingJs
3382 dependsOn jalviewjsTransferUnzipLib
3386 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3388 description "Create the alternative j2s file from the j2s.* properties"
3390 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3391 def siteDirProperty = "j2s.site.directory"
3392 def setSiteDir = false
3393 jalviewjsJ2sProps.each { prop, val ->
3395 if (prop == siteDirProperty) {
3396 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3397 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3403 if (!setSiteDir) { // default site location, don't override specifically set property
3404 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3407 outputFile = jalviewjsJ2sAltSettingsFileName
3410 inputs.properties(jalviewjsJ2sProps)
3411 outputs.file(jalviewjsJ2sAltSettingsFileName)
3416 task jalviewjsEclipseSetup {
3417 dependsOn jalviewjsEclipseCopyDropins
3418 dependsOn jalviewjsSetEclipseWorkspace
3419 dependsOn jalviewjsCreateJ2sSettings
3423 task jalviewjsSyncAllLibs (type: Sync) {
3424 dependsOn jalviewjsTransferUnzipAllLibs
3425 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3426 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3427 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3431 def outputFiles = []
3432 rename { filename ->
3433 outputFiles += "${outputDir}/${filename}"
3440 // should this be exclude really ?
3441 duplicatesStrategy "INCLUDE"
3443 outputs.files outputFiles
3444 inputs.files inputFiles
3448 task jalviewjsSyncResources (type: Sync) {
3449 dependsOn buildResources
3451 def inputFiles = fileTree(dir: resourcesBuildDir)
3452 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3456 def outputFiles = []
3457 rename { filename ->
3458 outputFiles += "${outputDir}/${filename}"
3464 outputs.files outputFiles
3465 inputs.files inputFiles
3469 task jalviewjsSyncSiteResources (type: Sync) {
3470 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3471 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3475 def outputFiles = []
3476 rename { filename ->
3477 outputFiles += "${outputDir}/${filename}"
3483 outputs.files outputFiles
3484 inputs.files inputFiles
3488 task jalviewjsSyncBuildProperties (type: Sync) {
3489 dependsOn createBuildProperties
3490 def inputFiles = [file(buildProperties)]
3491 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3495 def outputFiles = []
3496 rename { filename ->
3497 outputFiles += "${outputDir}/${filename}"
3503 outputs.files outputFiles
3504 inputs.files inputFiles
3508 task jalviewjsProjectImport(type: Exec) {
3509 dependsOn eclipseSetup
3510 dependsOn jalviewjsEclipsePaths
3511 dependsOn jalviewjsEclipseSetup
3514 // do not run a headless import when we claim to be in Eclipse
3516 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3517 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3519 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3523 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3524 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3525 executable(eclipseBinary)
3526 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3530 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3532 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3533 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3536 inputs.file("${jalviewDir}/.project")
3537 outputs.upToDateWhen {
3538 file(projdir).exists()
3543 task jalviewjsTranspile(type: Exec) {
3544 dependsOn jalviewjsEclipseSetup
3545 dependsOn jalviewjsProjectImport
3546 dependsOn jalviewjsEclipsePaths
3548 dependsOn jalviewjsEnableAltFileProperty
3552 // do not run a headless transpile when we claim to be in Eclipse
3554 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3555 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3557 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3561 executable(eclipseBinary)
3562 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3566 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3568 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3569 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3575 stdout = new ByteArrayOutputStream()
3576 stderr = new ByteArrayOutputStream()
3578 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3579 def logOutFile = file(logOutFileName)
3580 logOutFile.createNewFile()
3581 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3582 BINARY: ${eclipseBinary}
3583 VERSION: ${eclipseVersion}
3584 WORKSPACE: ${eclipseWorkspace}
3585 DEBUG: ${eclipseDebug}
3588 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3589 // combine stdout and stderr
3590 def logErrFOS = logOutFOS
3592 if (jalviewjs_j2s_to_console.equals("true")) {
3593 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3594 new org.apache.tools.ant.util.TeeOutputStream(
3598 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3599 new org.apache.tools.ant.util.TeeOutputStream(
3604 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3607 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3614 if (stdout.toString().contains("Error processing ")) {
3615 // j2s did not complete transpile
3616 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3617 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3618 println("IGNORING TRANSPILE ERRORS")
3619 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3621 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3626 inputs.dir("${jalviewDir}/${sourceDir}")
3627 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3628 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3632 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3634 def stdout = new ByteArrayOutputStream()
3635 def stderr = new ByteArrayOutputStream()
3637 def coreFile = file(jsfile)
3639 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3641 logOutFile.createNewFile()
3642 logOutFile.append(msg+"\n")
3644 def coreTop = file(prefixFile)
3645 def coreBottom = file(suffixFile)
3646 coreFile.getParentFile().mkdirs()
3647 coreFile.createNewFile()
3648 coreFile.write( coreTop.getText("UTF-8") )
3652 def t = f.getText("UTF-8")
3653 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3654 coreFile.append( t )
3656 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3658 logOutFile.append(msg+"\n")
3661 coreFile.append( coreBottom.getText("UTF-8") )
3663 msg = "Generating ${zjsfile}"
3665 logOutFile.append(msg+"\n")
3666 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3667 def logErrFOS = logOutFOS
3670 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3671 main = "com.google.javascript.jscomp.CommandLineRunner"
3672 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3673 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3676 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3678 logOutFile.append(msg+"\n")
3680 if (logOutConsole) {
3681 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3682 new org.apache.tools.ant.util.TeeOutputStream(
3686 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3687 new org.apache.tools.ant.util.TeeOutputStream(
3692 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3695 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3702 logOutFile.append(msg+"\n")
3706 task jalviewjsBuildAllCores {
3708 description "Build the core js lib closures listed in the classlists dir"
3709 dependsOn jalviewjsTranspile
3710 dependsOn jalviewjsTransferUnzipSwingJs
3712 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3713 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3714 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3715 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3716 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3717 def prefixFile = "${jsDir}/core/coretop2.js"
3718 def suffixFile = "${jsDir}/core/corebottom2.js"
3720 inputs.file prefixFile
3721 inputs.file suffixFile
3723 def classlistFiles = []
3724 // add the classlists found int the jalviewjs_classlists_dir
3725 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3727 def name = file.getName() - ".txt"
3734 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3735 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3736 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3738 jalviewjsCoreClasslists = []
3740 classlistFiles.each {
3743 def file = hash['file']
3744 if (! file.exists()) {
3745 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3746 return false // this is a "continue" in groovy .each closure
3748 def name = hash['name']
3750 name = file.getName() - ".txt"
3758 def list = fileTree(dir: j2sDir, includes: filelist)
3760 def jsfile = "${outputDir}/core${name}.js"
3761 def zjsfile = "${outputDir}/core${name}.z.js"
3763 jalviewjsCoreClasslists += [
3772 outputs.file(jsfile)
3773 outputs.file(zjsfile)
3776 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3777 def stevesoftClasslistName = "_stevesoft"
3778 def stevesoftClasslist = [
3779 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3780 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3781 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3782 'name': stevesoftClasslistName
3784 jalviewjsCoreClasslists += stevesoftClasslist
3785 inputs.files(stevesoftClasslist['list'])
3786 outputs.file(stevesoftClasslist['jsfile'])
3787 outputs.file(stevesoftClasslist['zjsfile'])
3790 def allClasslistName = "_all"
3791 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3792 allJsFiles += fileTree(
3796 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3797 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3798 "**/org/jmol/export/JSExporter.js"
3801 allJsFiles += fileTree(
3805 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3806 "**/sun/misc/Unsafe.js",
3807 "**/swingjs/jquery/jquery-editable-select.js",
3808 "**/swingjs/jquery/j2sComboBox.js",
3809 "**/sun/misc/FloatingDecimal.js"
3812 def allClasslist = [
3813 'jsfile': "${outputDir}/core${allClasslistName}.js",
3814 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3816 'name': allClasslistName
3818 // not including this version of "all" core at the moment
3819 //jalviewjsCoreClasslists += allClasslist
3820 inputs.files(allClasslist['list'])
3821 outputs.file(allClasslist['jsfile'])
3822 outputs.file(allClasslist['zjsfile'])
3825 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3826 logOutFile.getParentFile().mkdirs()
3827 logOutFile.createNewFile()
3828 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3830 jalviewjsCoreClasslists.each {
3831 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3838 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3841 into file(outputFile).getParentFile()
3842 rename { filename ->
3843 if (filename.equals(inputFile.getName())) {
3844 return file(outputFile).getName()
3848 filter(ReplaceTokens,
3852 'MAIN': '"'+main_class+'"',
3854 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3855 'COREKEY': jalviewjs_core_key,
3856 'CORENAME': coreName
3863 task jalviewjsPublishCoreTemplates {
3864 dependsOn jalviewjsBuildAllCores
3865 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3866 def inputFile = file(inputFileName)
3867 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3869 def outputFiles = []
3870 jalviewjsCoreClasslists.each { cl ->
3871 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3872 cl['outputfile'] = outputFile
3873 outputFiles += outputFile
3877 jalviewjsCoreClasslists.each { cl ->
3878 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3881 inputs.file(inputFile)
3882 outputs.files(outputFiles)
3886 task jalviewjsSyncCore (type: Sync) {
3887 dependsOn jalviewjsBuildAllCores
3888 dependsOn jalviewjsPublishCoreTemplates
3889 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3890 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3894 def outputFiles = []
3895 rename { filename ->
3896 outputFiles += "${outputDir}/${filename}"
3902 outputs.files outputFiles
3903 inputs.files inputFiles
3907 // this Copy version of TransferSiteJs will delete anything else in the target dir
3908 task jalviewjsCopyTransferSiteJs(type: Copy) {
3909 dependsOn jalviewjsTranspile
3910 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3911 into "${jalviewDir}/${jalviewjsSiteDir}"
3915 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3916 task jalviewjsSyncTransferSiteJs(type: Sync) {
3917 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3919 into "${jalviewDir}/${jalviewjsSiteDir}"
3926 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3927 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3928 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3929 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3931 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3932 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3933 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3934 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3937 task jalviewjsPrepareSite {
3939 description "Prepares the website folder including unzipping files and copying resources"
3940 dependsOn jalviewjsSyncAllLibs
3941 dependsOn jalviewjsSyncResources
3942 dependsOn jalviewjsSyncSiteResources
3943 dependsOn jalviewjsSyncBuildProperties
3944 dependsOn jalviewjsSyncCore
3948 task jalviewjsBuildSite {
3950 description "Builds the whole website including transpiled code"
3951 dependsOn jalviewjsCopyTransferSiteJs
3952 dependsOn jalviewjsPrepareSite
3956 task cleanJalviewjsTransferSite {
3958 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3959 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3960 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3961 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3966 task cleanJalviewjsSite {
3967 dependsOn cleanJalviewjsTransferSite
3969 delete "${jalviewDir}/${jalviewjsSiteDir}"
3974 task jalviewjsSiteTar(type: Tar) {
3976 description "Creates a tar.gz file for the website"
3977 dependsOn jalviewjsBuildSite
3978 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3979 archiveFileName = outputFilename
3981 compression Compression.GZIP
3983 from "${jalviewDir}/${jalviewjsSiteDir}"
3984 into jalviewjs_site_dir // this is inside the tar file
3986 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3990 task jalviewjsServer {
3992 def filename = "jalviewjsTest.html"
3993 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3994 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3999 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
4000 factory = f.newInstance()
4001 } catch (ClassNotFoundException e) {
4002 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
4004 def port = Integer.valueOf(jalviewjs_server_port)
4009 while(port < start+1000 && !running) {
4011 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
4012 jalviewjsServer = factory.start(doc_root, port)
4014 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
4015 println("SERVER STARTED with document root ${doc_root}.")
4016 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
4017 println("For debug: "+url+"?j2sdebug")
4018 println("For verbose: "+url+"?j2sverbose")
4019 } catch (Exception e) {
4024 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
4025 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
4026 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4028 jalviewjsCoreClasslists.each { cl ->
4029 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4031 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4033 println("For core ${cl.name}: "+urlcore)
4036 file(htmlFile).text = htmlText
4039 outputs.file(htmlFile)
4040 outputs.upToDateWhen({false})
4044 task cleanJalviewjsAll {
4046 description "Delete all configuration and build artifacts to do with JalviewJS build"
4047 dependsOn cleanJalviewjsSite
4048 dependsOn jalviewjsEclipsePaths
4051 delete "${jalviewDir}/${jalviewjsBuildDir}"
4052 delete "${jalviewDir}/${eclipse_bin_dir}"
4053 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4054 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4056 delete jalviewjsJ2sAltSettingsFileName
4059 outputs.upToDateWhen( { false } )
4063 task jalviewjsIDE_checkJ2sPlugin {
4064 group "00 JalviewJS in Eclipse"
4065 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4068 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4069 def j2sPluginFile = file(j2sPlugin)
4070 def eclipseHome = System.properties["eclipse.home.location"]
4071 if (eclipseHome == null || ! IN_ECLIPSE) {
4072 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4074 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4075 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4076 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4077 eclipseJ2sPluginDirs += altPluginsDir
4079 def foundPlugin = false
4080 def j2sPluginFileName = j2sPluginFile.getName()
4081 def eclipseJ2sPlugin
4082 def eclipseJ2sPluginFile
4083 eclipseJ2sPluginDirs.any { dir ->
4084 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4085 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4086 if (eclipseJ2sPluginFile.exists()) {
4092 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4093 System.err.println(msg)
4094 throw new StopExecutionException(msg)
4097 def digest = MessageDigest.getInstance("MD5")
4099 digest.update(j2sPluginFile.text.bytes)
4100 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4102 digest.update(eclipseJ2sPluginFile.text.bytes)
4103 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4105 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4106 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4107 System.err.println(msg)
4108 throw new StopExecutionException(msg)
4110 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4116 task jalviewjsIDE_copyJ2sPlugin {
4117 group "00 JalviewJS in Eclipse"
4118 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4121 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4122 def j2sPluginFile = file(j2sPlugin)
4123 def eclipseHome = System.properties["eclipse.home.location"]
4124 if (eclipseHome == null || ! IN_ECLIPSE) {
4125 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4127 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4128 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4129 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4130 System.err.println(msg)
4133 eclipseJ2sPluginFile.getParentFile().mkdirs()
4134 into eclipseJ2sPluginFile.getParent()
4140 task jalviewjsIDE_j2sFile {
4141 group "00 JalviewJS in Eclipse"
4142 description "Creates the .j2s file"
4143 dependsOn jalviewjsCreateJ2sSettings
4147 task jalviewjsIDE_SyncCore {
4148 group "00 JalviewJS in Eclipse"
4149 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4150 dependsOn jalviewjsSyncCore
4154 task jalviewjsIDE_SyncSiteAll {
4155 dependsOn jalviewjsSyncAllLibs
4156 dependsOn jalviewjsSyncResources
4157 dependsOn jalviewjsSyncSiteResources
4158 dependsOn jalviewjsSyncBuildProperties
4162 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4165 task jalviewjsIDE_PrepareSite {
4166 group "00 JalviewJS in Eclipse"
4167 description "Sync libs and resources to site dir, but not closure cores"
4169 dependsOn jalviewjsIDE_SyncSiteAll
4170 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4174 task jalviewjsIDE_AssembleSite {
4175 group "00 JalviewJS in Eclipse"
4176 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4177 dependsOn jalviewjsPrepareSite
4181 task jalviewjsIDE_SiteClean {
4182 group "00 JalviewJS in Eclipse"
4183 description "Deletes the Eclipse transpiled site"
4184 dependsOn cleanJalviewjsSite
4188 task jalviewjsIDE_Server {
4189 group "00 JalviewJS in Eclipse"
4190 description "Starts a webserver on localhost to test the website"
4191 dependsOn jalviewjsServer
4195 // buildship runs this at import or gradle refresh
4196 task eclipseSynchronizationTask {
4197 //dependsOn eclipseSetup
4198 dependsOn createBuildProperties
4200 dependsOn jalviewjsIDE_j2sFile
4201 dependsOn jalviewjsIDE_checkJ2sPlugin
4202 dependsOn jalviewjsIDE_PrepareSite
4207 // buildship runs this at build time or project refresh
4208 task eclipseAutoBuildTask {
4209 //dependsOn jalviewjsIDE_checkJ2sPlugin
4210 //dependsOn jalviewjsIDE_PrepareSite
4214 task jalviewjsCopyStderrLaunchFile(type: Copy) {
4215 from file(jalviewjs_stderr_launch)
4216 into jalviewjsSiteDir
4218 inputs.file jalviewjs_stderr_launch
4219 outputs.file jalviewjsStderrLaunchFilename
4222 task cleanJalviewjsChromiumUserDir {
4224 delete jalviewjsChromiumUserDir
4226 outputs.dir jalviewjsChromiumUserDir
4227 // always run when depended on
4228 outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
4231 task jalviewjsChromiumProfile {
4232 dependsOn cleanJalviewjsChromiumUserDir
4233 mustRunAfter cleanJalviewjsChromiumUserDir
4235 def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
4238 mkdir jalviewjsChromiumProfileDir
4241 outputs.file firstRun
4244 task jalviewjsLaunchTest {
4246 description "Check JalviewJS opens in a browser"
4247 dependsOn jalviewjsBuildSite
4248 dependsOn jalviewjsCopyStderrLaunchFile
4249 dependsOn jalviewjsChromiumProfile
4251 def macOS = OperatingSystem.current().isMacOsX()
4252 def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
4253 if (chromiumBinary.startsWith("~/")) {
4254 chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
4260 def timeoutms = Integer.valueOf(jalviewjs_chromium_timeout) * 1000
4262 def binary = file(chromiumBinary)
4263 if (!binary.exists()) {
4264 throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
4266 stdout = new ByteArrayOutputStream()
4267 stderr = new ByteArrayOutputStream()
4270 if (jalviewjs_j2s_to_console.equals("true")) {
4271 execStdout = new org.apache.tools.ant.util.TeeOutputStream(
4274 execStderr = new org.apache.tools.ant.util.TeeOutputStream(
4282 "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
4285 "--timeout=${timeoutms}",
4286 "--virtual-time-budget=${timeoutms}",
4287 "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
4288 "--profile-directory=${jalviewjs_chromium_profile_name}",
4289 "--allow-file-access-from-files",
4290 "--enable-logging=stderr",
4291 "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
4294 if (true || macOS) {
4295 ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
4296 Future f1 = executor.submit(
4299 standardOutput = execStdout
4300 errorOutput = execStderr
4301 executable(chromiumBinary)
4304 executor.shutdownNow()
4308 def noChangeBytes = 0
4309 def noChangeIterations = 0
4310 executor.scheduleAtFixedRate(
4312 String stderrString = stderr.toString()
4313 // shutdown the task if we have a success string
4314 if (stderrString.contains(jalviewjs_desktop_init_string)) {
4317 executor.shutdownNow()
4319 // if no change in stderr for 10s then also end
4320 if (noChangeIterations >= 10) {
4321 executor.shutdownNow()
4323 if (stderrString.length() == noChangeBytes) {
4324 noChangeIterations++
4326 noChangeBytes = stderrString.length()
4327 noChangeIterations = 0
4330 1, 1, TimeUnit.SECONDS)
4332 executor.schedule(new Runnable(){
4335 executor.shutdownNow()
4337 }, timeoutms, TimeUnit.MILLISECONDS)
4339 executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
4340 executor.shutdownNow()
4347 stderr.toString().eachLine { line ->
4348 if (line.contains(jalviewjs_desktop_init_string)) {
4349 println("Found line '"+line+"'")
4355 throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
4363 description "Build the JalviewJS site and run the launch test"
4364 dependsOn jalviewjsBuildSite
4365 dependsOn jalviewjsLaunchTest