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
1834 info.events = [ TestLogEvent.FAILED ]
1839 ignoreFailures = true // Always try to run all tests for all modules
1841 afterSuite { desc, result ->
1843 return // Only summarize results for whole modules
1845 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1847 rootProject.ext.testsResults.add(resultsInfo)
1850 // from original test task
1851 maxHeapSize = "1024m"
1853 workingDir = jalviewDir
1854 def testLaf = project.findProperty("test_laf")
1855 if (testLaf != null) {
1856 println("Setting Test LaF to '${testLaf}'")
1857 systemProperty "laf", testLaf
1859 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1860 if (testHiDPIScale != null) {
1861 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1862 systemProperty "sun.java2d.uiScale", testHiDPIScale
1864 sourceCompatibility = compile_source_compatibility
1865 targetCompatibility = compile_target_compatibility
1866 jvmArgs += additional_compiler_args
1869 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1870 // testTasks that include the tests, and exclude all from the others.
1871 // get --test argument
1872 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1873 // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
1874 // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
1878 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1883 /* don't fail on no matching tests (so --tests will run across all testTasks) */
1884 testTask.filter.setFailOnNoMatchingTests(false)
1886 /* ensure the "test" task dependsOn all the testTasks */
1887 test.dependsOn testTask
1890 gradle.buildFinished {
1891 def allResults = rootProject.ext.testsResults
1893 if (!allResults.isEmpty()) {
1894 printResults allResults
1895 allResults.each {r ->
1896 if (r[2].resultType == TestResult.ResultType.FAILURE)
1897 throw new GradleException("Failed tests!")
1902 private static String colString(styler, col, colour, text) {
1903 return col?"${styler[colour](text)}":text
1906 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1907 def colour = 'black'
1915 case TestResult.ResultType.SUCCESS:
1918 case TestResult.ResultType.FAILURE:
1926 StringBuilder sb = new StringBuilder()
1930 sb.append(" results: ")
1931 sb.append(colString(s, col && !nocol, colour, text))
1933 sb.append("${rc} tests, ")
1934 sb.append(colString(s, col && rs > 0, 'green', rs))
1935 sb.append(" successes, ")
1936 sb.append(colString(s, col && rf > 0, 'red', rf))
1937 sb.append(" failures, ")
1938 sb.append("${rsk} skipped) in ${t}")
1939 return sb.toString()
1942 private static void printResults(allResults) {
1944 // styler from https://stackoverflow.com/a/56139852
1945 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1948 def failedTests = false
1949 def summaryLines = []
1951 def totalsuccess = 0
1954 def totaltime = TimeCategory.getSeconds(0)
1955 // sort on project name then task name
1956 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1957 def projectName = it[0]
1958 def taskName = it[1]
1962 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1963 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1964 def reportLine = "Report file: ${report}"
1965 def ls = summaryPlain.length()
1966 def lr = reportLine.length()
1967 def m = [ls, lr].max()
1970 def info = [ls, summaryCol, reportLine]
1971 summaryLines.add(info)
1972 failedTests |= result.resultType == TestResult.ResultType.FAILURE
1973 totalcount += result.testCount
1974 totalsuccess += result.successfulTestCount
1975 totalfail += result.failedTestCount
1976 totalskip += result.skippedTestCount
1979 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
1980 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
1981 def tls = totalSummaryPlain.length()
1982 if (tls > maxLength)
1984 def info = [tls, totalSummaryCol, null]
1985 summaryLines.add(info)
1987 def allSummaries = []
1988 for(sInfo : summaryLines) {
1990 def summary = sInfo[1]
1991 def report = sInfo[2]
1993 StringBuilder sb = new StringBuilder()
1994 sb.append("│" + summary + " " * (maxLength - ls) + "│")
1995 if (report != null) {
1996 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
1998 allSummaries += sb.toString()
2001 println "┌${"${"─" * maxLength}"}┐"
2002 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
2003 println "└${"${"─" * maxLength}"}┘"
2005 /* END of test tasks results summary */
2008 task compileLinkCheck(type: JavaCompile) {
2010 classpath = files("${jalviewDir}/${utils_dir}")
2011 destinationDir = file("${jalviewDir}/${utils_dir}")
2012 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
2014 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2015 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2016 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
2017 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
2021 task linkCheck(type: JavaExec) {
2023 dependsOn compileLinkCheck
2025 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2026 classpath = files("${jalviewDir}/${utils_dir}")
2027 main = "HelpLinksChecker"
2028 workingDir = "${helpBuildDir}"
2029 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2031 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2032 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2035 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2039 inputs.dir(helpBuildDir)
2040 outputs.file(helpLinksCheckerOutFile)
2044 // import the pubhtmlhelp target
2045 ant.properties.basedir = "${jalviewDir}"
2046 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2047 ant.importBuild "${utils_dir}/publishHelp.xml"
2050 task cleanPackageDir(type: Delete) {
2052 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2062 attributes "Main-Class": main_class,
2063 "Permissions": "all-permissions",
2064 "Application-Name": applicationName,
2065 "Codebase": application_codebase,
2066 "Implementation-Version": JALVIEW_VERSION
2069 def outputDir = "${jalviewDir}/${package_dir}"
2070 destinationDirectory = file(outputDir)
2071 archiveFileName = rootProject.name+".jar"
2072 duplicatesStrategy "EXCLUDE"
2079 exclude "**/*.jar.*"
2081 inputs.dir(sourceSets.main.java.outputDir)
2082 sourceSets.main.resources.srcDirs.each{ dir ->
2085 outputs.file("${outputDir}/${archiveFileName}")
2089 task copyJars(type: Copy) {
2090 from fileTree(dir: classesDir, include: "**/*.jar").files
2091 into "${jalviewDir}/${package_dir}"
2095 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2096 task syncJars(type: Sync) {
2098 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2099 into "${jalviewDir}/${package_dir}"
2101 include jar.archiveFileName.getOrNull()
2108 description = "Put all required libraries in dist"
2109 // order of "cleanPackageDir", "copyJars", "jar" important!
2110 jar.mustRunAfter cleanPackageDir
2111 syncJars.mustRunAfter cleanPackageDir
2112 dependsOn cleanPackageDir
2115 outputs.dir("${jalviewDir}/${package_dir}")
2120 dependsOn cleanPackageDir
2127 group = "distribution"
2128 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2132 from ("${jalviewDir}/${libDistDir}") {
2136 attributes "Implementation-Version": JALVIEW_VERSION,
2137 "Application-Name": applicationName
2140 duplicatesStrategy "INCLUDE"
2142 mainClassName = shadow_jar_main_class
2144 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2148 task getdownImagesCopy() {
2149 inputs.dir getdownImagesDir
2150 outputs.dir getdownImagesBuildDir
2154 from(getdownImagesDir) {
2155 include("*getdown*.png")
2157 into getdownImagesBuildDir
2162 task getdownImagesProcess() {
2163 dependsOn getdownImagesCopy
2166 if (backgroundImageText) {
2167 if (convertBinary == null) {
2168 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2170 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2171 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2173 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2175 executable convertBinary
2178 '-font', getdown_background_image_text_font,
2179 '-fill', getdown_background_image_text_colour,
2180 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2181 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2182 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2191 task getdownImages() {
2192 dependsOn getdownImagesProcess
2195 task getdownWebsite() {
2196 group = "distribution"
2197 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2199 dependsOn getdownImages
2204 def getdownWebsiteResourceFilenames = []
2205 def getdownResourceDir = getdownResourceDir
2206 def getdownResourceFilenames = []
2209 // clean the getdown website and files dir before creating getdown folders
2210 delete getdownAppBaseDir
2211 delete getdownFilesDir
2214 from buildProperties
2215 rename(file(buildProperties).getName(), getdown_build_properties)
2218 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2221 from channelPropsFile
2222 filter(ReplaceTokens,
2226 'SUFFIX': channelSuffix
2229 into getdownAppBaseDir
2231 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2233 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2234 def props = project.properties.sort { it.key }
2235 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2236 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2238 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2239 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2241 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2242 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2244 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2245 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2246 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2247 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2248 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2249 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
2250 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
2253 props.put("getdown_txt_title", jalview_name)
2254 props.put("getdown_txt_ui.name", applicationName)
2256 // start with appbase
2257 getdownTextLines += "appbase = ${getdownAppBase}"
2258 props.each{ prop, val ->
2259 if (prop.startsWith("getdown_txt_") && val != null) {
2260 if (prop.startsWith("getdown_txt_multi_")) {
2261 def key = prop.substring(18)
2262 val.split(",").each{ v ->
2263 def line = "${key} = ${v}"
2264 getdownTextLines += line
2267 // file values rationalised
2268 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2270 if (val.indexOf('/') == 0) {
2273 } else if (val.indexOf('/') > 0) {
2274 // relative path (relative to jalviewDir)
2275 r = file( "${jalviewDir}/${val}" )
2278 val = "${getdown_resource_dir}/" + r.getName()
2279 getdownWebsiteResourceFilenames += val
2280 getdownResourceFilenames += r.getPath()
2283 if (! prop.startsWith("getdown_txt_resource")) {
2284 def line = prop.substring(12) + " = ${val}"
2285 getdownTextLines += line
2291 getdownWebsiteResourceFilenames.each{ filename ->
2292 getdownTextLines += "resource = ${filename}"
2294 getdownResourceFilenames.each{ filename ->
2297 into getdownResourceDir
2301 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2302 getdownWrapperScripts.each{ script ->
2303 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2307 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2309 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2314 fileTree(file(package_dir)).each{ f ->
2315 if (f.isDirectory()) {
2316 def files = fileTree(dir: f, include: ["*"]).getFiles()
2318 } else if (f.exists()) {
2322 def jalviewJar = jar.archiveFileName.getOrNull()
2323 // put jalview.jar first for CLASSPATH and .properties files reasons
2324 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2325 def name = f.getName()
2326 def line = "code = ${getdownAppDistDir}/${name}"
2327 getdownTextLines += line
2334 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2336 if (JAVA_VERSION.equals("11")) {
2337 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2338 j11libFiles.sort().each{f ->
2339 def name = f.getName()
2340 def line = "code = ${getdown_j11lib_dir}/${name}"
2341 getdownTextLines += line
2344 into getdownJ11libDir
2350 // 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.
2351 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2352 getdownTextLines += "resource = ${getdown_launcher_new}"
2353 getdownTextLines += "class = ${main_class}"
2354 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2355 if (getdownSetAppBaseProperty) {
2356 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2357 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2360 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2361 getdownTxt.write(getdownTextLines.join("\n"))
2363 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2364 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2365 launchJvl.write("appbase=${getdownAppBase}")
2367 // files going into the getdown website dir: getdown-launcher.jar
2369 from getdownLauncher
2370 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2371 into getdownAppBaseDir
2374 // files going into the getdown website dir: getdown-launcher(-local).jar
2376 from getdownLauncher
2377 if (file(getdownLauncher).getName() != getdown_launcher) {
2378 rename(file(getdownLauncher).getName(), getdown_launcher)
2380 into getdownAppBaseDir
2383 // files going into the getdown website dir: ./install dir and files
2384 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2387 from getdownLauncher
2388 from "${getdownAppDir}/${getdown_build_properties}"
2389 if (file(getdownLauncher).getName() != getdown_launcher) {
2390 rename(file(getdownLauncher).getName(), getdown_launcher)
2392 into getdownInstallDir
2395 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2397 from getdownInstallDir
2398 into getdownFilesInstallDir
2402 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2406 from getdownLauncher
2407 from "${getdownAppBaseDir}/${getdown_build_properties}"
2408 from "${getdownAppBaseDir}/${channel_props}"
2409 if (file(getdownLauncher).getName() != getdown_launcher) {
2410 rename(file(getdownLauncher).getName(), getdown_launcher)
2412 into getdownFilesDir
2415 // and ./resource (not all downloaded by getdown)
2417 from getdownResourceDir
2418 into "${getdownFilesDir}/${getdown_resource_dir}"
2423 inputs.dir("${jalviewDir}/${package_dir}")
2425 outputs.dir(getdownAppBaseDir)
2426 outputs.dir(getdownFilesDir)
2430 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2431 task getdownDigestDir(type: JavaExec) {
2433 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2435 def digestDirPropertyName = "DIGESTDIR"
2437 classpath = files(getdownLauncher)
2438 def digestDir = findProperty(digestDirPropertyName)
2439 if (digestDir == null) {
2440 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2444 main = "com.threerings.getdown.tools.Digester"
2448 task getdownDigest(type: JavaExec) {
2449 group = "distribution"
2450 description = "Digest the getdown website folder"
2451 dependsOn getdownWebsite
2453 classpath = files(getdownLauncher)
2455 main = "com.threerings.getdown.tools.Digester"
2456 args getdownAppBaseDir
2457 inputs.dir(getdownAppBaseDir)
2458 outputs.file("${getdownAppBaseDir}/digest2.txt")
2463 group = "distribution"
2464 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2465 dependsOn getdownDigest
2467 if (reportRsyncCommand) {
2468 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2469 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2470 println "LIKELY RSYNC COMMAND:"
2471 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2472 if (RUNRSYNC == "true") {
2474 commandLine "mkdir", "-p", toDir
2477 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2485 task getdownArchiveBuild() {
2486 group = "distribution"
2487 description = "Put files in the archive dir to go on the website"
2489 dependsOn getdownWebsite
2491 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2492 def vDir = "${getdownArchiveDir}/${v}"
2493 getdownFullArchiveDir = "${vDir}/getdown"
2494 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2496 def vAltDir = "alt_${v}"
2497 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2500 // cleanup old "old" dir
2501 delete getdownArchiveDir
2503 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2504 getdownArchiveTxt.getParentFile().mkdirs()
2505 def getdownArchiveTextLines = []
2506 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2510 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2511 into "${getdownFullArchiveDir}/${vAltDir}"
2514 getdownTextLines.each { line ->
2515 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2516 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2517 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2518 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2519 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2520 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2521 // remove the existing resource = resource/ or bin/ lines
2522 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2523 getdownArchiveTextLines += line
2527 // the resource dir -- add these files as resource lines in getdown.txt
2529 from "${archiveImagesDir}"
2530 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2532 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2536 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2538 def vLaunchJvl = file(getdownVersionLaunchJvl)
2539 vLaunchJvl.getParentFile().mkdirs()
2540 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2541 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2542 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2543 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2544 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2545 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2547 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2549 from getdownLauncher
2550 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2551 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2552 from "${getdownAppBaseDir}/${channel_props}"
2553 if (file(getdownLauncher).getName() != getdown_launcher) {
2554 rename(file(getdownLauncher).getName(), getdown_launcher)
2556 into getdownFullArchiveDir
2562 task getdownArchiveDigest(type: JavaExec) {
2563 group = "distribution"
2564 description = "Digest the getdown archive folder"
2566 dependsOn getdownArchiveBuild
2569 classpath = files(getdownLauncher)
2570 args getdownFullArchiveDir
2572 main = "com.threerings.getdown.tools.Digester"
2573 inputs.dir(getdownFullArchiveDir)
2574 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2577 task getdownArchive() {
2578 group = "distribution"
2579 description = "Build the website archive dir with getdown digest"
2581 dependsOn getdownArchiveBuild
2582 dependsOn getdownArchiveDigest
2585 tasks.withType(JavaCompile) {
2586 options.encoding = 'UTF-8'
2592 delete getdownAppBaseDir
2593 delete getdownFilesDir
2594 delete getdownArchiveDir
2600 if (file(install4jHomeDir).exists()) {
2602 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2603 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2604 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2605 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2607 installDir(file(install4jHomeDir))
2609 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2613 task copyInstall4jTemplate {
2614 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2615 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2616 inputs.file(install4jTemplateFile)
2617 inputs.file(install4jFileAssociationsFile)
2618 inputs.property("CHANNEL", { CHANNEL })
2619 outputs.file(install4jConfFile)
2622 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2624 // turn off code signing if no OSX_KEYPASS
2625 if (OSX_KEYPASS == "") {
2626 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2627 codeSigning.'@macEnabled' = "false"
2629 install4jConfigXml.'**'.windows.each { windows ->
2630 windows.'@runPostProcessor' = "false"
2634 // disable install screen for OSX dmg (for 2.11.2.0)
2635 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2636 macosArchive.attributes().remove('executeSetupApp')
2637 macosArchive.attributes().remove('setupAppId')
2640 // turn off checksum creation for LOCAL channel
2641 def e = install4jConfigXml.application[0]
2642 e.'@createChecksums' = string(install4jCheckSums)
2644 // put file association actions where placeholder action is
2645 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2646 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2647 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2648 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2649 def parent = a.parent()
2651 fileAssociationActions.each { faa ->
2654 // don't need to continue in .any loop once replacements have been made
2659 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2660 // NB we're deleting the /other/ one!
2661 // Also remove the examples subdir from non-release versions
2662 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2663 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2664 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2665 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2667 // remove the examples subdir from Full File Set
2668 def files = install4jConfigXml.files[0]
2669 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2670 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2671 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2672 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2673 dirEntry.parent().remove(dirEntry)
2675 install4jConfigXml.'**'.action.any { a ->
2676 if (a.'@customizedId' == customizedIdToDelete) {
2677 def parent = a.parent()
2683 // write install4j file
2684 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2691 delete install4jConfFile
2695 task cleanInstallersDataFiles {
2696 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2697 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2698 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2700 delete installersOutputTxt
2701 delete installersSha256
2702 delete hugoDataJsonFile
2706 task install4jDMGBackgroundImageCopy {
2707 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2708 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2711 from(install4jDMGBackgroundImageDir) {
2712 include(install4jDMGBackgroundImageFile)
2714 into install4jDMGBackgroundImageBuildDir
2719 task install4jDMGBackgroundImageProcess {
2720 dependsOn install4jDMGBackgroundImageCopy
2723 if (backgroundImageText) {
2724 if (convertBinary == null) {
2725 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2727 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2728 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2730 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2732 executable convertBinary
2735 '-font', install4j_background_image_text_font,
2736 '-fill', install4j_background_image_text_colour,
2737 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2738 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2739 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2748 task install4jDMGBackgroundImage {
2749 dependsOn install4jDMGBackgroundImageProcess
2752 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2753 group = "distribution"
2754 description = "Create the install4j installers"
2756 dependsOn copyInstall4jTemplate
2757 dependsOn cleanInstallersDataFiles
2758 dependsOn install4jDMGBackgroundImage
2760 projectFile = install4jConfFile
2762 // create an md5 for the input files to use as version for install4j conf file
2763 def digest = MessageDigest.getInstance("MD5")
2765 (file("${install4jDir}/${install4j_template}").text +
2766 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2767 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2768 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2769 if (filesMd5.length() >= 8) {
2770 filesMd5 = filesMd5.substring(0,8)
2772 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2775 'JALVIEW_NAME': jalview_name,
2776 'JALVIEW_APPLICATION_NAME': applicationName,
2777 'JALVIEW_DIR': "../..",
2778 'OSX_KEYSTORE': OSX_KEYSTORE,
2779 'OSX_APPLEID': OSX_APPLEID,
2780 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2781 'JSIGN_SH': JSIGN_SH,
2782 'JRE_DIR': getdown_app_dir_java,
2783 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2784 'JALVIEW_VERSION': JALVIEW_VERSION,
2785 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2786 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2787 'JAVA_VERSION': JAVA_VERSION,
2788 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2789 'VERSION': JALVIEW_VERSION,
2790 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2791 'BUNDLE_ID': install4jBundleId,
2792 'INTERNAL_ID': install4jInternalId,
2793 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2794 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2795 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2796 'WRAPPER_LINK': getdownWrapperLink,
2797 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2798 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2799 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
2800 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2801 'INSTALLER_NAME': install4jInstallerName,
2802 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2803 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2804 'GETDOWN_FILES_DIR': getdown_files_dir,
2805 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2806 'GETDOWN_DIST_DIR': getdownAppDistDir,
2807 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2808 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2809 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2810 'BUILD_DIR': install4jBuildDir,
2811 'APPLICATION_CATEGORIES': install4j_application_categories,
2812 'APPLICATION_FOLDER': install4jApplicationFolder,
2813 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2814 'EXECUTABLE_NAME': install4jExecutableName,
2815 'EXTRA_SCHEME': install4jExtraScheme,
2816 'MAC_ICONS_FILE': install4jMacIconsFile,
2817 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2818 'PNG_ICON_FILE': install4jPngIconFile,
2819 'BACKGROUND': install4jBackground,
2824 'windows': 'WINDOWS',
2828 // these are the bundled OS/architecture VMs needed by install4j
2831 [ "mac", "aarch64" ],
2832 [ "windows", "x64" ],
2834 [ "linux", "aarch64" ]
2836 osArch.forEach { os, arch ->
2837 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)
2838 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2839 // otherwise running `gradle installers` generates a non-useful error:
2840 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2841 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)
2844 //println("INSTALL4J VARIABLES:")
2845 //variables.each{k,v->println("${k}=${v}")}
2847 destination = "${jalviewDir}/${install4jBuildDir}"
2848 buildSelected = true
2850 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2852 disableSigning = true
2853 disableNotarization = true
2857 macKeystorePassword = OSX_KEYPASS
2860 if (OSX_ALTOOLPASS) {
2861 appleIdPassword = OSX_ALTOOLPASS
2862 disableNotarization = false
2864 disableNotarization = true
2868 println("Using projectFile "+projectFile)
2869 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2873 inputs.dir(getdownAppBaseDir)
2874 inputs.file(install4jConfFile)
2875 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2876 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2879 def getDataHash(File myFile) {
2880 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2881 return myFile.exists()
2883 "file" : myFile.getName(),
2884 "filesize" : myFile.length(),
2885 "sha256" : hash.toString()
2890 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2892 "channel" : getdownChannelName,
2893 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2894 "git-commit" : "${gitHash} [${gitBranch}]",
2895 "version" : JALVIEW_VERSION
2897 // install4j installer files
2898 if (installersOutputTxt.exists()) {
2900 installersOutputTxt.readLines().each { def line ->
2901 if (line.startsWith("#")) {
2904 line.replaceAll("\n","")
2905 def vals = line.split("\t")
2906 def filename = vals[3]
2907 def filesize = file(filename).length()
2908 filename = filename.replaceAll(/^.*\//, "")
2909 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2910 idHash."${filename}" = vals[0]
2912 if (install4jCheckSums && installersSha256.exists()) {
2913 installersSha256.readLines().each { def line ->
2914 if (line.startsWith("#")) {
2917 line.replaceAll("\n","")
2918 def vals = line.split(/\s+\*?/)
2919 def filename = vals[1]
2920 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2926 "JAR": shadowJar.archiveFile, // executable JAR
2927 "JVL": getdownVersionLaunchJvl, // version JVL
2928 "SOURCE": sourceDist.archiveFile // source TGZ
2929 ].each { key, value ->
2930 def file = file(value)
2931 if (file.exists()) {
2932 def fileHash = getDataHash(file)
2933 if (fileHash != null) {
2934 hash."${key}" = fileHash;
2938 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2941 task staticMakeInstallersJsonFile {
2943 def output = findProperty("i4j_output")
2944 def sha256 = findProperty("i4j_sha256")
2945 def json = findProperty("i4j_json")
2946 if (output == null || sha256 == null || json == null) {
2947 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2949 writeDataJsonFile(file(output), file(sha256), file(json))
2954 dependsOn installerFiles
2960 eclipse().configFile(eclipse_codestyle_file)
2964 task createSourceReleaseProperties(type: WriteProperties) {
2965 group = "distribution"
2966 description = "Create the source RELEASE properties file"
2968 def sourceTarBuildDir = "${buildDir}/sourceTar"
2969 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2970 outputFile (sourceReleasePropertiesFile)
2973 releaseProps.each{ key, val -> property key, val }
2974 property "git.branch", gitBranch
2975 property "git.hash", gitHash
2978 outputs.file(outputFile)
2981 task sourceDist(type: Tar) {
2982 group "distribution"
2983 description "Create a source .tar.gz file for distribution"
2985 dependsOn createBuildProperties
2986 dependsOn convertMdFiles
2987 dependsOn eclipseAllPreferences
2988 dependsOn createSourceReleaseProperties
2991 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2992 archiveFileName = outputFileName
2994 compression Compression.GZIP
3009 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
3011 "utils/InstallAnywhere",
3026 "gradle.properties",
3038 ".settings/org.eclipse.buildship.core.prefs",
3039 ".settings/org.eclipse.jdt.core.prefs"
3043 exclude (EXCLUDE_FILES)
3044 include (PROCESS_FILES)
3045 filter(ReplaceTokens,
3049 'Version-Rel': JALVIEW_VERSION,
3050 'Year-Rel': getDate("yyyy")
3055 exclude (EXCLUDE_FILES)
3056 exclude (PROCESS_FILES)
3057 exclude ("appletlib")
3058 exclude ("**/*locales")
3059 exclude ("*locales/**")
3060 exclude ("utils/InstallAnywhere")
3062 exclude (getdown_files_dir)
3063 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3064 //exclude (getdown_website_dir)
3065 //exclude (getdown_archive_dir)
3067 // exluding these as not using jars as modules yet
3068 exclude ("${j11modDir}/**/*.jar")
3071 include(INCLUDE_FILES)
3073 // from (jalviewDir) {
3074 // // explicit includes for stuff that seemed to not get included
3075 // include(fileTree("test/**/*."))
3076 // exclude(EXCLUDE_FILES)
3077 // exclude(PROCESS_FILES)
3080 from(file(buildProperties).getParent()) {
3081 include(file(buildProperties).getName())
3082 rename(file(buildProperties).getName(), "build_properties")
3084 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3088 def sourceTarBuildDir = "${buildDir}/sourceTar"
3089 from(sourceTarBuildDir) {
3090 // this includes the appended RELEASE properties file
3094 task dataInstallersJson {
3096 description "Create the installers-VERSION.json data file for installer files created"
3098 mustRunAfter installers
3099 mustRunAfter shadowJar
3100 mustRunAfter sourceDist
3101 mustRunAfter getdownArchive
3103 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3104 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3106 if (installersOutputTxt.exists()) {
3107 inputs.file(installersOutputTxt)
3109 if (install4jCheckSums && installersSha256.exists()) {
3110 inputs.file(installersSha256)
3113 shadowJar.archiveFile, // executable JAR
3114 getdownVersionLaunchJvl, // version JVL
3115 sourceDist.archiveFile // source TGZ
3116 ].each { fileName ->
3117 if (file(fileName).exists()) {
3118 inputs.file(fileName)
3122 outputs.file(hugoDataJsonFile)
3125 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3131 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3134 dependsOn pubhtmlhelp
3136 inputs.dir("${helpBuildDir}/${help_dir}")
3137 outputs.dir("${buildDir}/distributions/${help_dir}")
3141 task j2sSetHeadlessBuild {
3148 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3150 description "Enable the alternative J2S Config file for headless build"
3152 outputFile = jalviewjsJ2sSettingsFileName
3153 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3154 def j2sProps = new Properties()
3155 if (j2sPropsFile.exists()) {
3157 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3158 j2sProps.load(j2sPropsFileFIS)
3159 j2sPropsFileFIS.close()
3161 j2sProps.each { prop, val ->
3164 } catch (Exception e) {
3165 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3169 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3170 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3175 task jalviewjsSetEclipseWorkspace {
3176 def propKey = "jalviewjs_eclipse_workspace"
3178 if (project.hasProperty(propKey)) {
3179 propVal = project.getProperty(propKey)
3180 if (propVal.startsWith("~/")) {
3181 propVal = System.getProperty("user.home") + propVal.substring(1)
3184 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3185 def propsFile = file(propsFileName)
3186 def eclipseWsDir = propVal
3187 def props = new Properties()
3189 def writeProps = true
3190 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3191 def ins = new FileInputStream(propsFileName)
3194 if (props.getProperty(propKey, null) != null) {
3195 eclipseWsDir = props.getProperty(propKey)
3200 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3201 def tempDir = File.createTempDir()
3202 eclipseWsDir = tempDir.getAbsolutePath()
3205 eclipseWorkspace = file(eclipseWsDir)
3208 // do not run a headless transpile when we claim to be in Eclipse
3210 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3211 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3213 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3217 props.setProperty(propKey, eclipseWsDir)
3218 propsFile.parentFile.mkdirs()
3219 def bytes = new ByteArrayOutputStream()
3220 props.store(bytes, null)
3221 def propertiesString = bytes.toString()
3222 propsFile.text = propertiesString
3228 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3231 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3232 outputs.file(propsFileName)
3233 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3237 task jalviewjsEclipsePaths {
3240 def eclipseRoot = jalviewjs_eclipse_root
3241 if (eclipseRoot.startsWith("~/")) {
3242 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3244 if (OperatingSystem.current().isMacOsX()) {
3245 eclipseRoot += "/Eclipse.app"
3246 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3247 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3248 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3249 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3250 eclipseRoot += "/eclipse"
3252 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3253 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3254 } else { // linux or unix
3255 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3256 eclipseRoot += "/eclipse"
3257 println("eclipseDir exists")
3259 eclipseBinary = "${eclipseRoot}/eclipse"
3260 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3263 eclipseVersion = "4.13" // default
3264 def assumedVersion = true
3265 if (file(eclipseProduct).exists()) {
3266 def fis = new FileInputStream(eclipseProduct)
3267 def props = new Properties()
3269 eclipseVersion = props.getProperty("version")
3271 assumedVersion = false
3274 def propKey = "eclipse_debug"
3275 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3278 // do not run a headless transpile when we claim to be in Eclipse
3280 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3281 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3283 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3286 if (!assumedVersion) {
3287 println("ECLIPSE VERSION=${eclipseVersion}")
3293 task printProperties {
3295 description "Output to console all System.properties"
3297 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3303 dependsOn eclipseProject
3304 dependsOn eclipseClasspath
3305 dependsOn eclipseJdt
3309 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3310 task jalviewjsEclipseCopyDropins(type: Copy) {
3311 dependsOn jalviewjsEclipsePaths
3313 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3314 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3315 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3322 // this eclipse -clean doesn't actually work
3323 task jalviewjsCleanEclipse(type: Exec) {
3324 dependsOn eclipseSetup
3325 dependsOn jalviewjsEclipsePaths
3326 dependsOn jalviewjsEclipseCopyDropins
3328 executable(eclipseBinary)
3329 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3335 def inputString = """exit
3338 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3339 standardInput = inputByteStream
3342 /* not really working yet
3343 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3347 task jalviewjsTransferUnzipSwingJs {
3348 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3352 from zipTree(file_zip)
3353 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3357 inputs.file file_zip
3358 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3362 task jalviewjsTransferUnzipLib {
3363 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3366 zipFiles.each { file_zip ->
3368 from zipTree(file_zip)
3369 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3374 inputs.files zipFiles
3375 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3379 task jalviewjsTransferUnzipAllLibs {
3380 dependsOn jalviewjsTransferUnzipSwingJs
3381 dependsOn jalviewjsTransferUnzipLib
3385 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3387 description "Create the alternative j2s file from the j2s.* properties"
3389 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3390 def siteDirProperty = "j2s.site.directory"
3391 def setSiteDir = false
3392 jalviewjsJ2sProps.each { prop, val ->
3394 if (prop == siteDirProperty) {
3395 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3396 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3402 if (!setSiteDir) { // default site location, don't override specifically set property
3403 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3406 outputFile = jalviewjsJ2sAltSettingsFileName
3409 inputs.properties(jalviewjsJ2sProps)
3410 outputs.file(jalviewjsJ2sAltSettingsFileName)
3415 task jalviewjsEclipseSetup {
3416 dependsOn jalviewjsEclipseCopyDropins
3417 dependsOn jalviewjsSetEclipseWorkspace
3418 dependsOn jalviewjsCreateJ2sSettings
3422 task jalviewjsSyncAllLibs (type: Sync) {
3423 dependsOn jalviewjsTransferUnzipAllLibs
3424 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3425 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3426 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3430 def outputFiles = []
3431 rename { filename ->
3432 outputFiles += "${outputDir}/${filename}"
3439 // should this be exclude really ?
3440 duplicatesStrategy "INCLUDE"
3442 outputs.files outputFiles
3443 inputs.files inputFiles
3447 task jalviewjsSyncResources (type: Sync) {
3448 dependsOn buildResources
3450 def inputFiles = fileTree(dir: resourcesBuildDir)
3451 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3455 def outputFiles = []
3456 rename { filename ->
3457 outputFiles += "${outputDir}/${filename}"
3463 outputs.files outputFiles
3464 inputs.files inputFiles
3468 task jalviewjsSyncSiteResources (type: Sync) {
3469 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3470 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3474 def outputFiles = []
3475 rename { filename ->
3476 outputFiles += "${outputDir}/${filename}"
3482 outputs.files outputFiles
3483 inputs.files inputFiles
3487 task jalviewjsSyncBuildProperties (type: Sync) {
3488 dependsOn createBuildProperties
3489 def inputFiles = [file(buildProperties)]
3490 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3494 def outputFiles = []
3495 rename { filename ->
3496 outputFiles += "${outputDir}/${filename}"
3502 outputs.files outputFiles
3503 inputs.files inputFiles
3507 task jalviewjsProjectImport(type: Exec) {
3508 dependsOn eclipseSetup
3509 dependsOn jalviewjsEclipsePaths
3510 dependsOn jalviewjsEclipseSetup
3513 // do not run a headless import when we claim to be in Eclipse
3515 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3516 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3518 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3522 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3523 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3524 executable(eclipseBinary)
3525 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3529 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3531 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3532 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3535 inputs.file("${jalviewDir}/.project")
3536 outputs.upToDateWhen {
3537 file(projdir).exists()
3542 task jalviewjsTranspile(type: Exec) {
3543 dependsOn jalviewjsEclipseSetup
3544 dependsOn jalviewjsProjectImport
3545 dependsOn jalviewjsEclipsePaths
3547 dependsOn jalviewjsEnableAltFileProperty
3551 // do not run a headless transpile when we claim to be in Eclipse
3553 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3554 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3556 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3560 executable(eclipseBinary)
3561 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3565 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3567 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3568 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3574 stdout = new ByteArrayOutputStream()
3575 stderr = new ByteArrayOutputStream()
3577 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3578 def logOutFile = file(logOutFileName)
3579 logOutFile.createNewFile()
3580 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3581 BINARY: ${eclipseBinary}
3582 VERSION: ${eclipseVersion}
3583 WORKSPACE: ${eclipseWorkspace}
3584 DEBUG: ${eclipseDebug}
3587 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3588 // combine stdout and stderr
3589 def logErrFOS = logOutFOS
3591 if (jalviewjs_j2s_to_console.equals("true")) {
3592 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3593 new org.apache.tools.ant.util.TeeOutputStream(
3597 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3598 new org.apache.tools.ant.util.TeeOutputStream(
3603 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3606 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3613 if (stdout.toString().contains("Error processing ")) {
3614 // j2s did not complete transpile
3615 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3616 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3617 println("IGNORING TRANSPILE ERRORS")
3618 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3620 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3625 inputs.dir("${jalviewDir}/${sourceDir}")
3626 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3627 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3631 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3633 def stdout = new ByteArrayOutputStream()
3634 def stderr = new ByteArrayOutputStream()
3636 def coreFile = file(jsfile)
3638 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3640 logOutFile.createNewFile()
3641 logOutFile.append(msg+"\n")
3643 def coreTop = file(prefixFile)
3644 def coreBottom = file(suffixFile)
3645 coreFile.getParentFile().mkdirs()
3646 coreFile.createNewFile()
3647 coreFile.write( coreTop.getText("UTF-8") )
3651 def t = f.getText("UTF-8")
3652 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3653 coreFile.append( t )
3655 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3657 logOutFile.append(msg+"\n")
3660 coreFile.append( coreBottom.getText("UTF-8") )
3662 msg = "Generating ${zjsfile}"
3664 logOutFile.append(msg+"\n")
3665 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3666 def logErrFOS = logOutFOS
3669 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3670 main = "com.google.javascript.jscomp.CommandLineRunner"
3671 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3672 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3675 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3677 logOutFile.append(msg+"\n")
3679 if (logOutConsole) {
3680 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3681 new org.apache.tools.ant.util.TeeOutputStream(
3685 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3686 new org.apache.tools.ant.util.TeeOutputStream(
3691 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3694 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3701 logOutFile.append(msg+"\n")
3705 task jalviewjsBuildAllCores {
3707 description "Build the core js lib closures listed in the classlists dir"
3708 dependsOn jalviewjsTranspile
3709 dependsOn jalviewjsTransferUnzipSwingJs
3711 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3712 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3713 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3714 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3715 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3716 def prefixFile = "${jsDir}/core/coretop2.js"
3717 def suffixFile = "${jsDir}/core/corebottom2.js"
3719 inputs.file prefixFile
3720 inputs.file suffixFile
3722 def classlistFiles = []
3723 // add the classlists found int the jalviewjs_classlists_dir
3724 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3726 def name = file.getName() - ".txt"
3733 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3734 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3735 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3737 jalviewjsCoreClasslists = []
3739 classlistFiles.each {
3742 def file = hash['file']
3743 if (! file.exists()) {
3744 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3745 return false // this is a "continue" in groovy .each closure
3747 def name = hash['name']
3749 name = file.getName() - ".txt"
3757 def list = fileTree(dir: j2sDir, includes: filelist)
3759 def jsfile = "${outputDir}/core${name}.js"
3760 def zjsfile = "${outputDir}/core${name}.z.js"
3762 jalviewjsCoreClasslists += [
3771 outputs.file(jsfile)
3772 outputs.file(zjsfile)
3775 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3776 def stevesoftClasslistName = "_stevesoft"
3777 def stevesoftClasslist = [
3778 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3779 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3780 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3781 'name': stevesoftClasslistName
3783 jalviewjsCoreClasslists += stevesoftClasslist
3784 inputs.files(stevesoftClasslist['list'])
3785 outputs.file(stevesoftClasslist['jsfile'])
3786 outputs.file(stevesoftClasslist['zjsfile'])
3789 def allClasslistName = "_all"
3790 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3791 allJsFiles += fileTree(
3795 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3796 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3797 "**/org/jmol/export/JSExporter.js"
3800 allJsFiles += fileTree(
3804 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3805 "**/sun/misc/Unsafe.js",
3806 "**/swingjs/jquery/jquery-editable-select.js",
3807 "**/swingjs/jquery/j2sComboBox.js",
3808 "**/sun/misc/FloatingDecimal.js"
3811 def allClasslist = [
3812 'jsfile': "${outputDir}/core${allClasslistName}.js",
3813 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3815 'name': allClasslistName
3817 // not including this version of "all" core at the moment
3818 //jalviewjsCoreClasslists += allClasslist
3819 inputs.files(allClasslist['list'])
3820 outputs.file(allClasslist['jsfile'])
3821 outputs.file(allClasslist['zjsfile'])
3824 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3825 logOutFile.getParentFile().mkdirs()
3826 logOutFile.createNewFile()
3827 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3829 jalviewjsCoreClasslists.each {
3830 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3837 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3840 into file(outputFile).getParentFile()
3841 rename { filename ->
3842 if (filename.equals(inputFile.getName())) {
3843 return file(outputFile).getName()
3847 filter(ReplaceTokens,
3851 'MAIN': '"'+main_class+'"',
3853 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3854 'COREKEY': jalviewjs_core_key,
3855 'CORENAME': coreName
3862 task jalviewjsPublishCoreTemplates {
3863 dependsOn jalviewjsBuildAllCores
3864 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3865 def inputFile = file(inputFileName)
3866 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3868 def outputFiles = []
3869 jalviewjsCoreClasslists.each { cl ->
3870 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3871 cl['outputfile'] = outputFile
3872 outputFiles += outputFile
3876 jalviewjsCoreClasslists.each { cl ->
3877 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3880 inputs.file(inputFile)
3881 outputs.files(outputFiles)
3885 task jalviewjsSyncCore (type: Sync) {
3886 dependsOn jalviewjsBuildAllCores
3887 dependsOn jalviewjsPublishCoreTemplates
3888 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3889 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3893 def outputFiles = []
3894 rename { filename ->
3895 outputFiles += "${outputDir}/${filename}"
3901 outputs.files outputFiles
3902 inputs.files inputFiles
3906 // this Copy version of TransferSiteJs will delete anything else in the target dir
3907 task jalviewjsCopyTransferSiteJs(type: Copy) {
3908 dependsOn jalviewjsTranspile
3909 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3910 into "${jalviewDir}/${jalviewjsSiteDir}"
3914 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3915 task jalviewjsSyncTransferSiteJs(type: Sync) {
3916 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3918 into "${jalviewDir}/${jalviewjsSiteDir}"
3925 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3926 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3927 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3928 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3930 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3931 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3932 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3933 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3936 task jalviewjsPrepareSite {
3938 description "Prepares the website folder including unzipping files and copying resources"
3939 dependsOn jalviewjsSyncAllLibs
3940 dependsOn jalviewjsSyncResources
3941 dependsOn jalviewjsSyncSiteResources
3942 dependsOn jalviewjsSyncBuildProperties
3943 dependsOn jalviewjsSyncCore
3947 task jalviewjsBuildSite {
3949 description "Builds the whole website including transpiled code"
3950 dependsOn jalviewjsCopyTransferSiteJs
3951 dependsOn jalviewjsPrepareSite
3955 task cleanJalviewjsTransferSite {
3957 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3958 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3959 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3960 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3965 task cleanJalviewjsSite {
3966 dependsOn cleanJalviewjsTransferSite
3968 delete "${jalviewDir}/${jalviewjsSiteDir}"
3973 task jalviewjsSiteTar(type: Tar) {
3975 description "Creates a tar.gz file for the website"
3976 dependsOn jalviewjsBuildSite
3977 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3978 archiveFileName = outputFilename
3980 compression Compression.GZIP
3982 from "${jalviewDir}/${jalviewjsSiteDir}"
3983 into jalviewjs_site_dir // this is inside the tar file
3985 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3989 task jalviewjsServer {
3991 def filename = "jalviewjsTest.html"
3992 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3993 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3998 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3999 factory = f.newInstance()
4000 } catch (ClassNotFoundException e) {
4001 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
4003 def port = Integer.valueOf(jalviewjs_server_port)
4008 while(port < start+1000 && !running) {
4010 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
4011 jalviewjsServer = factory.start(doc_root, port)
4013 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
4014 println("SERVER STARTED with document root ${doc_root}.")
4015 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
4016 println("For debug: "+url+"?j2sdebug")
4017 println("For verbose: "+url+"?j2sverbose")
4018 } catch (Exception e) {
4023 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
4024 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
4025 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4027 jalviewjsCoreClasslists.each { cl ->
4028 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4030 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4032 println("For core ${cl.name}: "+urlcore)
4035 file(htmlFile).text = htmlText
4038 outputs.file(htmlFile)
4039 outputs.upToDateWhen({false})
4043 task cleanJalviewjsAll {
4045 description "Delete all configuration and build artifacts to do with JalviewJS build"
4046 dependsOn cleanJalviewjsSite
4047 dependsOn jalviewjsEclipsePaths
4050 delete "${jalviewDir}/${jalviewjsBuildDir}"
4051 delete "${jalviewDir}/${eclipse_bin_dir}"
4052 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4053 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4055 delete jalviewjsJ2sAltSettingsFileName
4058 outputs.upToDateWhen( { false } )
4062 task jalviewjsIDE_checkJ2sPlugin {
4063 group "00 JalviewJS in Eclipse"
4064 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4067 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4068 def j2sPluginFile = file(j2sPlugin)
4069 def eclipseHome = System.properties["eclipse.home.location"]
4070 if (eclipseHome == null || ! IN_ECLIPSE) {
4071 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4073 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4074 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4075 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4076 eclipseJ2sPluginDirs += altPluginsDir
4078 def foundPlugin = false
4079 def j2sPluginFileName = j2sPluginFile.getName()
4080 def eclipseJ2sPlugin
4081 def eclipseJ2sPluginFile
4082 eclipseJ2sPluginDirs.any { dir ->
4083 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4084 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4085 if (eclipseJ2sPluginFile.exists()) {
4091 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4092 System.err.println(msg)
4093 throw new StopExecutionException(msg)
4096 def digest = MessageDigest.getInstance("MD5")
4098 digest.update(j2sPluginFile.text.bytes)
4099 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4101 digest.update(eclipseJ2sPluginFile.text.bytes)
4102 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4104 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4105 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4106 System.err.println(msg)
4107 throw new StopExecutionException(msg)
4109 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4115 task jalviewjsIDE_copyJ2sPlugin {
4116 group "00 JalviewJS in Eclipse"
4117 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4120 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4121 def j2sPluginFile = file(j2sPlugin)
4122 def eclipseHome = System.properties["eclipse.home.location"]
4123 if (eclipseHome == null || ! IN_ECLIPSE) {
4124 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4126 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4127 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4128 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4129 System.err.println(msg)
4132 eclipseJ2sPluginFile.getParentFile().mkdirs()
4133 into eclipseJ2sPluginFile.getParent()
4139 task jalviewjsIDE_j2sFile {
4140 group "00 JalviewJS in Eclipse"
4141 description "Creates the .j2s file"
4142 dependsOn jalviewjsCreateJ2sSettings
4146 task jalviewjsIDE_SyncCore {
4147 group "00 JalviewJS in Eclipse"
4148 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4149 dependsOn jalviewjsSyncCore
4153 task jalviewjsIDE_SyncSiteAll {
4154 dependsOn jalviewjsSyncAllLibs
4155 dependsOn jalviewjsSyncResources
4156 dependsOn jalviewjsSyncSiteResources
4157 dependsOn jalviewjsSyncBuildProperties
4161 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4164 task jalviewjsIDE_PrepareSite {
4165 group "00 JalviewJS in Eclipse"
4166 description "Sync libs and resources to site dir, but not closure cores"
4168 dependsOn jalviewjsIDE_SyncSiteAll
4169 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4173 task jalviewjsIDE_AssembleSite {
4174 group "00 JalviewJS in Eclipse"
4175 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4176 dependsOn jalviewjsPrepareSite
4180 task jalviewjsIDE_SiteClean {
4181 group "00 JalviewJS in Eclipse"
4182 description "Deletes the Eclipse transpiled site"
4183 dependsOn cleanJalviewjsSite
4187 task jalviewjsIDE_Server {
4188 group "00 JalviewJS in Eclipse"
4189 description "Starts a webserver on localhost to test the website"
4190 dependsOn jalviewjsServer
4194 // buildship runs this at import or gradle refresh
4195 task eclipseSynchronizationTask {
4196 //dependsOn eclipseSetup
4197 dependsOn createBuildProperties
4199 dependsOn jalviewjsIDE_j2sFile
4200 dependsOn jalviewjsIDE_checkJ2sPlugin
4201 dependsOn jalviewjsIDE_PrepareSite
4206 // buildship runs this at build time or project refresh
4207 task eclipseAutoBuildTask {
4208 //dependsOn jalviewjsIDE_checkJ2sPlugin
4209 //dependsOn jalviewjsIDE_PrepareSite
4213 task jalviewjsCopyStderrLaunchFile(type: Copy) {
4214 from file(jalviewjs_stderr_launch)
4215 into jalviewjsSiteDir
4217 inputs.file jalviewjs_stderr_launch
4218 outputs.file jalviewjsStderrLaunchFilename
4221 task cleanJalviewjsChromiumUserDir {
4223 delete jalviewjsChromiumUserDir
4225 outputs.dir jalviewjsChromiumUserDir
4226 // always run when depended on
4227 outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
4230 task jalviewjsChromiumProfile {
4231 dependsOn cleanJalviewjsChromiumUserDir
4232 mustRunAfter cleanJalviewjsChromiumUserDir
4234 def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
4237 mkdir jalviewjsChromiumProfileDir
4240 outputs.file firstRun
4243 task jalviewjsLaunchTest {
4245 description "Check JalviewJS opens in a browser"
4246 dependsOn jalviewjsBuildSite
4247 dependsOn jalviewjsCopyStderrLaunchFile
4248 dependsOn jalviewjsChromiumProfile
4250 def macOS = OperatingSystem.current().isMacOsX()
4251 def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
4252 if (chromiumBinary.startsWith("~/")) {
4253 chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
4259 def timeoutms = Integer.valueOf(jalviewjs_chromium_timeout) * 1000
4261 def binary = file(chromiumBinary)
4262 if (!binary.exists()) {
4263 throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
4265 stdout = new ByteArrayOutputStream()
4266 stderr = new ByteArrayOutputStream()
4269 if (jalviewjs_j2s_to_console.equals("true")) {
4270 execStdout = new org.apache.tools.ant.util.TeeOutputStream(
4273 execStderr = new org.apache.tools.ant.util.TeeOutputStream(
4281 "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
4284 "--timeout=${timeoutms}",
4285 "--virtual-time-budget=${timeoutms}",
4286 "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
4287 "--profile-directory=${jalviewjs_chromium_profile_name}",
4288 "--allow-file-access-from-files",
4289 "--enable-logging=stderr",
4290 "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
4293 if (true || macOS) {
4294 ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
4295 Future f1 = executor.submit(
4298 standardOutput = execStdout
4299 errorOutput = execStderr
4300 executable(chromiumBinary)
4303 executor.shutdownNow()
4307 def noChangeBytes = 0
4308 def noChangeIterations = 0
4309 executor.scheduleAtFixedRate(
4311 String stderrString = stderr.toString()
4312 // shutdown the task if we have a success string
4313 if (stderrString.contains(jalviewjs_desktop_init_string)) {
4316 executor.shutdownNow()
4318 // if no change in stderr for 10s then also end
4319 if (noChangeIterations >= 10) {
4320 executor.shutdownNow()
4322 if (stderrString.length() == noChangeBytes) {
4323 noChangeIterations++
4325 noChangeBytes = stderrString.length()
4326 noChangeIterations = 0
4329 1, 1, TimeUnit.SECONDS)
4331 executor.schedule(new Runnable(){
4334 executor.shutdownNow()
4336 }, timeoutms, TimeUnit.MILLISECONDS)
4338 executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
4339 executor.shutdownNow()
4346 stderr.toString().eachLine { line ->
4347 if (line.contains(jalviewjs_desktop_init_string)) {
4348 println("Found line '"+line+"'")
4354 throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
4362 description "Build the JalviewJS site and run the launch test"
4363 dependsOn jalviewjsBuildSite
4364 dependsOn jalviewjsLaunchTest