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 task testTask2(type: Test) {
1787 group = "Verification"
1788 description = "Tests that need to be isolated from the main test run"
1791 excludeGroups testng_excluded_groups.split(",")
1793 useDefaultListeners=true
1796 task testTask3(type: Test) {
1797 group = "Verification"
1798 description = "Tests that need to be isolated from the main test run"
1801 excludeGroups testng_excluded_groups.split(",")
1803 useDefaultListeners=true
1807 /* insert more testTaskNs here -- change N to next digit or other string */
1809 task testTaskN(type: Test) {
1810 group = "Verification"
1811 description = "Tests that need to be isolated from the main test run"
1814 excludeGroups testng_excluded_groups.split(",")
1816 useDefaultListeners=true
1822 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1823 * to summarise test results from all Test tasks
1825 /* START of test tasks results summary */
1826 import groovy.time.TimeCategory
1827 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1828 import org.gradle.api.tasks.testing.logging.TestLogEvent
1829 rootProject.ext.testsResults = [] // Container for tests summaries
1831 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1833 // from original test task
1835 dependsOn cloverClasses
1837 dependsOn testClasses //?
1840 // run main tests first
1841 if (!testTask.name.equals("testTask0"))
1842 testTask.mustRunAfter "testTask0"
1844 testTask.testLogging { logging ->
1845 events TestLogEvent.FAILED
1846 // TestLogEvent.SKIPPED,
1847 // TestLogEvent.STANDARD_OUT,
1848 // TestLogEvent.STANDARD_ERROR
1850 exceptionFormat TestExceptionFormat.FULL
1853 showStackTraces true
1855 info.events = [ TestLogEvent.FAILED ]
1858 if (OperatingSystem.current().isMacOsX()) {
1859 testTask.systemProperty "apple.awt.UIElement", "true"
1860 testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
1864 ignoreFailures = true // Always try to run all tests for all modules
1866 afterSuite { desc, result ->
1868 return // Only summarize results for whole modules
1870 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1872 rootProject.ext.testsResults.add(resultsInfo)
1875 // from original test task
1876 maxHeapSize = "1024m"
1878 workingDir = jalviewDir
1879 def testLaf = project.findProperty("test_laf")
1880 if (testLaf != null) {
1881 println("Setting Test LaF to '${testLaf}'")
1882 systemProperty "laf", testLaf
1884 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1885 if (testHiDPIScale != null) {
1886 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1887 systemProperty "sun.java2d.uiScale", testHiDPIScale
1889 sourceCompatibility = compile_source_compatibility
1890 targetCompatibility = compile_target_compatibility
1891 jvmArgs += additional_compiler_args
1894 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1895 // testTasks that include the tests, and exclude all from the others.
1896 // get --test argument
1897 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1898 // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
1899 // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
1903 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1908 /* don't fail on no matching tests (so --tests will run across all testTasks) */
1909 testTask.filter.setFailOnNoMatchingTests(false)
1911 /* ensure the "test" task dependsOn all the testTasks */
1912 test.dependsOn testTask
1915 gradle.buildFinished {
1916 def allResults = rootProject.ext.testsResults
1918 if (!allResults.isEmpty()) {
1919 printResults allResults
1920 allResults.each {r ->
1921 if (r[2].resultType == TestResult.ResultType.FAILURE)
1922 throw new GradleException("Failed tests!")
1927 private static String colString(styler, col, colour, text) {
1928 return col?"${styler[colour](text)}":text
1931 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1932 def colour = 'black'
1940 case TestResult.ResultType.SUCCESS:
1943 case TestResult.ResultType.FAILURE:
1951 StringBuilder sb = new StringBuilder()
1955 sb.append(" results: ")
1956 sb.append(colString(s, col && !nocol, colour, text))
1958 sb.append("${rc} tests, ")
1959 sb.append(colString(s, col && rs > 0, 'green', rs))
1960 sb.append(" successes, ")
1961 sb.append(colString(s, col && rf > 0, 'red', rf))
1962 sb.append(" failures, ")
1963 sb.append("${rsk} skipped) in ${t}")
1964 return sb.toString()
1967 private static void printResults(allResults) {
1969 // styler from https://stackoverflow.com/a/56139852
1970 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1973 def failedTests = false
1974 def summaryLines = []
1976 def totalsuccess = 0
1979 def totaltime = TimeCategory.getSeconds(0)
1980 // sort on project name then task name
1981 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1982 def projectName = it[0]
1983 def taskName = it[1]
1987 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1988 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1989 def reportLine = "Report file: ${report}"
1990 def ls = summaryPlain.length()
1991 def lr = reportLine.length()
1992 def m = [ls, lr].max()
1995 def info = [ls, summaryCol, reportLine]
1996 summaryLines.add(info)
1997 failedTests |= result.resultType == TestResult.ResultType.FAILURE
1998 totalcount += result.testCount
1999 totalsuccess += result.successfulTestCount
2000 totalfail += result.failedTestCount
2001 totalskip += result.skippedTestCount
2004 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
2005 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
2006 def tls = totalSummaryPlain.length()
2007 if (tls > maxLength)
2009 def info = [tls, totalSummaryCol, null]
2010 summaryLines.add(info)
2012 def allSummaries = []
2013 for(sInfo : summaryLines) {
2015 def summary = sInfo[1]
2016 def report = sInfo[2]
2018 StringBuilder sb = new StringBuilder()
2019 sb.append("│" + summary + " " * (maxLength - ls) + "│")
2020 if (report != null) {
2021 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
2023 allSummaries += sb.toString()
2026 println "┌${"${"─" * maxLength}"}┐"
2027 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
2028 println "└${"${"─" * maxLength}"}┘"
2030 /* END of test tasks results summary */
2033 task compileLinkCheck(type: JavaCompile) {
2035 classpath = files("${jalviewDir}/${utils_dir}")
2036 destinationDir = file("${jalviewDir}/${utils_dir}")
2037 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
2039 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2040 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2041 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
2042 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
2046 task linkCheck(type: JavaExec) {
2048 dependsOn compileLinkCheck
2050 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2051 classpath = files("${jalviewDir}/${utils_dir}")
2052 main = "HelpLinksChecker"
2053 workingDir = "${helpBuildDir}"
2054 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2056 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2057 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2060 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2064 inputs.dir(helpBuildDir)
2065 outputs.file(helpLinksCheckerOutFile)
2069 // import the pubhtmlhelp target
2070 ant.properties.basedir = "${jalviewDir}"
2071 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2072 ant.importBuild "${utils_dir}/publishHelp.xml"
2075 task cleanPackageDir(type: Delete) {
2077 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2087 attributes "Main-Class": main_class,
2088 "Permissions": "all-permissions",
2089 "Application-Name": applicationName,
2090 "Codebase": application_codebase,
2091 "Implementation-Version": JALVIEW_VERSION
2094 def outputDir = "${jalviewDir}/${package_dir}"
2095 destinationDirectory = file(outputDir)
2096 archiveFileName = rootProject.name+".jar"
2097 duplicatesStrategy "EXCLUDE"
2104 exclude "**/*.jar.*"
2106 inputs.dir(sourceSets.main.java.outputDir)
2107 sourceSets.main.resources.srcDirs.each{ dir ->
2110 outputs.file("${outputDir}/${archiveFileName}")
2114 task copyJars(type: Copy) {
2115 from fileTree(dir: classesDir, include: "**/*.jar").files
2116 into "${jalviewDir}/${package_dir}"
2120 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2121 task syncJars(type: Sync) {
2123 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2124 into "${jalviewDir}/${package_dir}"
2126 include jar.archiveFileName.getOrNull()
2133 description = "Put all required libraries in dist"
2134 // order of "cleanPackageDir", "copyJars", "jar" important!
2135 jar.mustRunAfter cleanPackageDir
2136 syncJars.mustRunAfter cleanPackageDir
2137 dependsOn cleanPackageDir
2140 outputs.dir("${jalviewDir}/${package_dir}")
2145 dependsOn cleanPackageDir
2152 group = "distribution"
2153 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2157 from ("${jalviewDir}/${libDistDir}") {
2161 attributes "Implementation-Version": JALVIEW_VERSION,
2162 "Application-Name": applicationName
2165 duplicatesStrategy "INCLUDE"
2167 mainClassName = shadow_jar_main_class
2169 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2173 task getdownImagesCopy() {
2174 inputs.dir getdownImagesDir
2175 outputs.dir getdownImagesBuildDir
2179 from(getdownImagesDir) {
2180 include("*getdown*.png")
2182 into getdownImagesBuildDir
2187 task getdownImagesProcess() {
2188 dependsOn getdownImagesCopy
2191 if (backgroundImageText) {
2192 if (convertBinary == null) {
2193 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2195 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2196 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2198 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2200 executable convertBinary
2203 '-font', getdown_background_image_text_font,
2204 '-fill', getdown_background_image_text_colour,
2205 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2206 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2207 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2216 task getdownImages() {
2217 dependsOn getdownImagesProcess
2220 task getdownWebsite() {
2221 group = "distribution"
2222 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2224 dependsOn getdownImages
2229 def getdownWebsiteResourceFilenames = []
2230 def getdownResourceDir = getdownResourceDir
2231 def getdownResourceFilenames = []
2234 // clean the getdown website and files dir before creating getdown folders
2235 delete getdownAppBaseDir
2236 delete getdownFilesDir
2239 from buildProperties
2240 rename(file(buildProperties).getName(), getdown_build_properties)
2243 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2246 from channelPropsFile
2247 filter(ReplaceTokens,
2251 'SUFFIX': channelSuffix
2254 into getdownAppBaseDir
2256 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2258 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2259 def props = project.properties.sort { it.key }
2260 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2261 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2263 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2264 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2266 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2267 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2269 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2270 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2271 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2272 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2273 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2274 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
2275 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
2278 props.put("getdown_txt_title", jalview_name)
2279 props.put("getdown_txt_ui.name", applicationName)
2281 // start with appbase
2282 getdownTextLines += "appbase = ${getdownAppBase}"
2283 props.each{ prop, val ->
2284 if (prop.startsWith("getdown_txt_") && val != null) {
2285 if (prop.startsWith("getdown_txt_multi_")) {
2286 def key = prop.substring(18)
2287 val.split(",").each{ v ->
2288 def line = "${key} = ${v}"
2289 getdownTextLines += line
2292 // file values rationalised
2293 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2295 if (val.indexOf('/') == 0) {
2298 } else if (val.indexOf('/') > 0) {
2299 // relative path (relative to jalviewDir)
2300 r = file( "${jalviewDir}/${val}" )
2303 val = "${getdown_resource_dir}/" + r.getName()
2304 getdownWebsiteResourceFilenames += val
2305 getdownResourceFilenames += r.getPath()
2308 if (! prop.startsWith("getdown_txt_resource")) {
2309 def line = prop.substring(12) + " = ${val}"
2310 getdownTextLines += line
2316 getdownWebsiteResourceFilenames.each{ filename ->
2317 getdownTextLines += "resource = ${filename}"
2319 getdownResourceFilenames.each{ filename ->
2322 into getdownResourceDir
2326 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2327 getdownWrapperScripts.each{ script ->
2328 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2332 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2334 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2339 fileTree(file(package_dir)).each{ f ->
2340 if (f.isDirectory()) {
2341 def files = fileTree(dir: f, include: ["*"]).getFiles()
2343 } else if (f.exists()) {
2347 def jalviewJar = jar.archiveFileName.getOrNull()
2348 // put jalview.jar first for CLASSPATH and .properties files reasons
2349 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2350 def name = f.getName()
2351 def line = "code = ${getdownAppDistDir}/${name}"
2352 getdownTextLines += line
2359 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2361 if (JAVA_VERSION.equals("11")) {
2362 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2363 j11libFiles.sort().each{f ->
2364 def name = f.getName()
2365 def line = "code = ${getdown_j11lib_dir}/${name}"
2366 getdownTextLines += line
2369 into getdownJ11libDir
2375 // 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.
2376 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2377 getdownTextLines += "resource = ${getdown_launcher_new}"
2378 getdownTextLines += "class = ${main_class}"
2379 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2380 if (getdownSetAppBaseProperty) {
2381 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2382 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2385 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2386 getdownTxt.write(getdownTextLines.join("\n"))
2388 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2389 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2390 launchJvl.write("appbase=${getdownAppBase}")
2392 // files going into the getdown website dir: getdown-launcher.jar
2394 from getdownLauncher
2395 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2396 into getdownAppBaseDir
2399 // files going into the getdown website dir: getdown-launcher(-local).jar
2401 from getdownLauncher
2402 if (file(getdownLauncher).getName() != getdown_launcher) {
2403 rename(file(getdownLauncher).getName(), getdown_launcher)
2405 into getdownAppBaseDir
2408 // files going into the getdown website dir: ./install dir and files
2409 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2412 from getdownLauncher
2413 from "${getdownAppDir}/${getdown_build_properties}"
2414 if (file(getdownLauncher).getName() != getdown_launcher) {
2415 rename(file(getdownLauncher).getName(), getdown_launcher)
2417 into getdownInstallDir
2420 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2422 from getdownInstallDir
2423 into getdownFilesInstallDir
2427 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2431 from getdownLauncher
2432 from "${getdownAppBaseDir}/${getdown_build_properties}"
2433 from "${getdownAppBaseDir}/${channel_props}"
2434 if (file(getdownLauncher).getName() != getdown_launcher) {
2435 rename(file(getdownLauncher).getName(), getdown_launcher)
2437 into getdownFilesDir
2440 // and ./resource (not all downloaded by getdown)
2442 from getdownResourceDir
2443 into "${getdownFilesDir}/${getdown_resource_dir}"
2448 inputs.dir("${jalviewDir}/${package_dir}")
2450 outputs.dir(getdownAppBaseDir)
2451 outputs.dir(getdownFilesDir)
2455 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2456 task getdownDigestDir(type: JavaExec) {
2458 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2460 def digestDirPropertyName = "DIGESTDIR"
2462 classpath = files(getdownLauncher)
2463 def digestDir = findProperty(digestDirPropertyName)
2464 if (digestDir == null) {
2465 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2469 main = "com.threerings.getdown.tools.Digester"
2473 task getdownDigest(type: JavaExec) {
2474 group = "distribution"
2475 description = "Digest the getdown website folder"
2476 dependsOn getdownWebsite
2478 classpath = files(getdownLauncher)
2480 main = "com.threerings.getdown.tools.Digester"
2481 args getdownAppBaseDir
2482 inputs.dir(getdownAppBaseDir)
2483 outputs.file("${getdownAppBaseDir}/digest2.txt")
2488 group = "distribution"
2489 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2490 dependsOn getdownDigest
2492 if (reportRsyncCommand) {
2493 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2494 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2495 println "LIKELY RSYNC COMMAND:"
2496 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2497 if (RUNRSYNC == "true") {
2499 commandLine "mkdir", "-p", toDir
2502 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2510 task getdownArchiveBuild() {
2511 group = "distribution"
2512 description = "Put files in the archive dir to go on the website"
2514 dependsOn getdownWebsite
2516 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2517 def vDir = "${getdownArchiveDir}/${v}"
2518 getdownFullArchiveDir = "${vDir}/getdown"
2519 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2521 def vAltDir = "alt_${v}"
2522 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2525 // cleanup old "old" dir
2526 delete getdownArchiveDir
2528 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2529 getdownArchiveTxt.getParentFile().mkdirs()
2530 def getdownArchiveTextLines = []
2531 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2535 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2536 into "${getdownFullArchiveDir}/${vAltDir}"
2539 getdownTextLines.each { line ->
2540 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2541 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2542 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2543 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2544 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2545 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2546 // remove the existing resource = resource/ or bin/ lines
2547 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2548 getdownArchiveTextLines += line
2552 // the resource dir -- add these files as resource lines in getdown.txt
2554 from "${archiveImagesDir}"
2555 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2557 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2561 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2563 def vLaunchJvl = file(getdownVersionLaunchJvl)
2564 vLaunchJvl.getParentFile().mkdirs()
2565 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2566 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2567 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2568 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2569 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2570 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2572 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2574 from getdownLauncher
2575 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2576 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2577 from "${getdownAppBaseDir}/${channel_props}"
2578 if (file(getdownLauncher).getName() != getdown_launcher) {
2579 rename(file(getdownLauncher).getName(), getdown_launcher)
2581 into getdownFullArchiveDir
2587 task getdownArchiveDigest(type: JavaExec) {
2588 group = "distribution"
2589 description = "Digest the getdown archive folder"
2591 dependsOn getdownArchiveBuild
2594 classpath = files(getdownLauncher)
2595 args getdownFullArchiveDir
2597 main = "com.threerings.getdown.tools.Digester"
2598 inputs.dir(getdownFullArchiveDir)
2599 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2602 task getdownArchive() {
2603 group = "distribution"
2604 description = "Build the website archive dir with getdown digest"
2606 dependsOn getdownArchiveBuild
2607 dependsOn getdownArchiveDigest
2610 tasks.withType(JavaCompile) {
2611 options.encoding = 'UTF-8'
2617 delete getdownAppBaseDir
2618 delete getdownFilesDir
2619 delete getdownArchiveDir
2625 if (file(install4jHomeDir).exists()) {
2627 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2628 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2629 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2630 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2632 installDir(file(install4jHomeDir))
2634 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2638 task copyInstall4jTemplate {
2639 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2640 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2641 inputs.file(install4jTemplateFile)
2642 inputs.file(install4jFileAssociationsFile)
2643 inputs.property("CHANNEL", { CHANNEL })
2644 outputs.file(install4jConfFile)
2647 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2649 // turn off code signing if no OSX_KEYPASS
2650 if (OSX_KEYPASS == "") {
2651 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2652 codeSigning.'@macEnabled' = "false"
2654 install4jConfigXml.'**'.windows.each { windows ->
2655 windows.'@runPostProcessor' = "false"
2659 // disable install screen for OSX dmg (for 2.11.2.0)
2660 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2661 macosArchive.attributes().remove('executeSetupApp')
2662 macosArchive.attributes().remove('setupAppId')
2665 // turn off checksum creation for LOCAL channel
2666 def e = install4jConfigXml.application[0]
2667 e.'@createChecksums' = string(install4jCheckSums)
2669 // put file association actions where placeholder action is
2670 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2671 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2672 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2673 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2674 def parent = a.parent()
2676 fileAssociationActions.each { faa ->
2679 // don't need to continue in .any loop once replacements have been made
2684 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2685 // NB we're deleting the /other/ one!
2686 // Also remove the examples subdir from non-release versions
2687 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2688 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2689 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2690 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2692 // remove the examples subdir from Full File Set
2693 def files = install4jConfigXml.files[0]
2694 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2695 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2696 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2697 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2698 dirEntry.parent().remove(dirEntry)
2700 install4jConfigXml.'**'.action.any { a ->
2701 if (a.'@customizedId' == customizedIdToDelete) {
2702 def parent = a.parent()
2708 // write install4j file
2709 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2716 delete install4jConfFile
2720 task cleanInstallersDataFiles {
2721 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2722 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2723 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2725 delete installersOutputTxt
2726 delete installersSha256
2727 delete hugoDataJsonFile
2731 task install4jDMGBackgroundImageCopy {
2732 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2733 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2736 from(install4jDMGBackgroundImageDir) {
2737 include(install4jDMGBackgroundImageFile)
2739 into install4jDMGBackgroundImageBuildDir
2744 task install4jDMGBackgroundImageProcess {
2745 dependsOn install4jDMGBackgroundImageCopy
2748 if (backgroundImageText) {
2749 if (convertBinary == null) {
2750 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2752 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2753 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2755 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2757 executable convertBinary
2760 '-font', install4j_background_image_text_font,
2761 '-fill', install4j_background_image_text_colour,
2762 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2763 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2764 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2773 task install4jDMGBackgroundImage {
2774 dependsOn install4jDMGBackgroundImageProcess
2777 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2778 group = "distribution"
2779 description = "Create the install4j installers"
2781 dependsOn copyInstall4jTemplate
2782 dependsOn cleanInstallersDataFiles
2783 dependsOn install4jDMGBackgroundImage
2785 projectFile = install4jConfFile
2787 // create an md5 for the input files to use as version for install4j conf file
2788 def digest = MessageDigest.getInstance("MD5")
2790 (file("${install4jDir}/${install4j_template}").text +
2791 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2792 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2793 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2794 if (filesMd5.length() >= 8) {
2795 filesMd5 = filesMd5.substring(0,8)
2797 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2800 'JALVIEW_NAME': jalview_name,
2801 'JALVIEW_APPLICATION_NAME': applicationName,
2802 'JALVIEW_DIR': "../..",
2803 'OSX_KEYSTORE': OSX_KEYSTORE,
2804 'OSX_APPLEID': OSX_APPLEID,
2805 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2806 'JSIGN_SH': JSIGN_SH,
2807 'JRE_DIR': getdown_app_dir_java,
2808 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2809 'JALVIEW_VERSION': JALVIEW_VERSION,
2810 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2811 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2812 'JAVA_VERSION': JAVA_VERSION,
2813 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2814 'VERSION': JALVIEW_VERSION,
2815 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2816 'BUNDLE_ID': install4jBundleId,
2817 'INTERNAL_ID': install4jInternalId,
2818 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2819 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2820 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2821 'WRAPPER_LINK': getdownWrapperLink,
2822 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2823 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2824 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
2825 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2826 'INSTALLER_NAME': install4jInstallerName,
2827 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2828 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2829 'GETDOWN_FILES_DIR': getdown_files_dir,
2830 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2831 'GETDOWN_DIST_DIR': getdownAppDistDir,
2832 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2833 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2834 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2835 'BUILD_DIR': install4jBuildDir,
2836 'APPLICATION_CATEGORIES': install4j_application_categories,
2837 'APPLICATION_FOLDER': install4jApplicationFolder,
2838 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2839 'EXECUTABLE_NAME': install4jExecutableName,
2840 'EXTRA_SCHEME': install4jExtraScheme,
2841 'MAC_ICONS_FILE': install4jMacIconsFile,
2842 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2843 'PNG_ICON_FILE': install4jPngIconFile,
2844 'BACKGROUND': install4jBackground,
2849 'windows': 'WINDOWS',
2853 // these are the bundled OS/architecture VMs needed by install4j
2856 [ "mac", "aarch64" ],
2857 [ "windows", "x64" ],
2859 [ "linux", "aarch64" ]
2861 osArch.forEach { os, arch ->
2862 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)
2863 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2864 // otherwise running `gradle installers` generates a non-useful error:
2865 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2866 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)
2869 //println("INSTALL4J VARIABLES:")
2870 //variables.each{k,v->println("${k}=${v}")}
2872 destination = "${jalviewDir}/${install4jBuildDir}"
2873 buildSelected = true
2875 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2877 disableSigning = true
2878 disableNotarization = true
2882 macKeystorePassword = OSX_KEYPASS
2885 if (OSX_ALTOOLPASS) {
2886 appleIdPassword = OSX_ALTOOLPASS
2887 disableNotarization = false
2889 disableNotarization = true
2893 println("Using projectFile "+projectFile)
2894 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2898 inputs.dir(getdownAppBaseDir)
2899 inputs.file(install4jConfFile)
2900 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2901 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2904 def getDataHash(File myFile) {
2905 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2906 return myFile.exists()
2908 "file" : myFile.getName(),
2909 "filesize" : myFile.length(),
2910 "sha256" : hash.toString()
2915 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2917 "channel" : getdownChannelName,
2918 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2919 "git-commit" : "${gitHash} [${gitBranch}]",
2920 "version" : JALVIEW_VERSION
2922 // install4j installer files
2923 if (installersOutputTxt.exists()) {
2925 installersOutputTxt.readLines().each { def line ->
2926 if (line.startsWith("#")) {
2929 line.replaceAll("\n","")
2930 def vals = line.split("\t")
2931 def filename = vals[3]
2932 def filesize = file(filename).length()
2933 filename = filename.replaceAll(/^.*\//, "")
2934 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2935 idHash."${filename}" = vals[0]
2937 if (install4jCheckSums && installersSha256.exists()) {
2938 installersSha256.readLines().each { def line ->
2939 if (line.startsWith("#")) {
2942 line.replaceAll("\n","")
2943 def vals = line.split(/\s+\*?/)
2944 def filename = vals[1]
2945 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2951 "JAR": shadowJar.archiveFile, // executable JAR
2952 "JVL": getdownVersionLaunchJvl, // version JVL
2953 "SOURCE": sourceDist.archiveFile // source TGZ
2954 ].each { key, value ->
2955 def file = file(value)
2956 if (file.exists()) {
2957 def fileHash = getDataHash(file)
2958 if (fileHash != null) {
2959 hash."${key}" = fileHash;
2963 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2966 task staticMakeInstallersJsonFile {
2968 def output = findProperty("i4j_output")
2969 def sha256 = findProperty("i4j_sha256")
2970 def json = findProperty("i4j_json")
2971 if (output == null || sha256 == null || json == null) {
2972 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2974 writeDataJsonFile(file(output), file(sha256), file(json))
2979 dependsOn installerFiles
2985 eclipse().configFile(eclipse_codestyle_file)
2989 task createSourceReleaseProperties(type: WriteProperties) {
2990 group = "distribution"
2991 description = "Create the source RELEASE properties file"
2993 def sourceTarBuildDir = "${buildDir}/sourceTar"
2994 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2995 outputFile (sourceReleasePropertiesFile)
2998 releaseProps.each{ key, val -> property key, val }
2999 property "git.branch", gitBranch
3000 property "git.hash", gitHash
3003 outputs.file(outputFile)
3006 task sourceDist(type: Tar) {
3007 group "distribution"
3008 description "Create a source .tar.gz file for distribution"
3010 dependsOn createBuildProperties
3011 dependsOn convertMdFiles
3012 dependsOn eclipseAllPreferences
3013 dependsOn createSourceReleaseProperties
3016 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
3017 archiveFileName = outputFileName
3019 compression Compression.GZIP
3034 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
3036 "utils/InstallAnywhere",
3051 "gradle.properties",
3063 ".settings/org.eclipse.buildship.core.prefs",
3064 ".settings/org.eclipse.jdt.core.prefs"
3068 exclude (EXCLUDE_FILES)
3069 include (PROCESS_FILES)
3070 filter(ReplaceTokens,
3074 'Version-Rel': JALVIEW_VERSION,
3075 'Year-Rel': getDate("yyyy")
3080 exclude (EXCLUDE_FILES)
3081 exclude (PROCESS_FILES)
3082 exclude ("appletlib")
3083 exclude ("**/*locales")
3084 exclude ("*locales/**")
3085 exclude ("utils/InstallAnywhere")
3087 exclude (getdown_files_dir)
3088 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3089 //exclude (getdown_website_dir)
3090 //exclude (getdown_archive_dir)
3092 // exluding these as not using jars as modules yet
3093 exclude ("${j11modDir}/**/*.jar")
3096 include(INCLUDE_FILES)
3098 // from (jalviewDir) {
3099 // // explicit includes for stuff that seemed to not get included
3100 // include(fileTree("test/**/*."))
3101 // exclude(EXCLUDE_FILES)
3102 // exclude(PROCESS_FILES)
3105 from(file(buildProperties).getParent()) {
3106 include(file(buildProperties).getName())
3107 rename(file(buildProperties).getName(), "build_properties")
3109 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3113 def sourceTarBuildDir = "${buildDir}/sourceTar"
3114 from(sourceTarBuildDir) {
3115 // this includes the appended RELEASE properties file
3119 task dataInstallersJson {
3121 description "Create the installers-VERSION.json data file for installer files created"
3123 mustRunAfter installers
3124 mustRunAfter shadowJar
3125 mustRunAfter sourceDist
3126 mustRunAfter getdownArchive
3128 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3129 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3131 if (installersOutputTxt.exists()) {
3132 inputs.file(installersOutputTxt)
3134 if (install4jCheckSums && installersSha256.exists()) {
3135 inputs.file(installersSha256)
3138 shadowJar.archiveFile, // executable JAR
3139 getdownVersionLaunchJvl, // version JVL
3140 sourceDist.archiveFile // source TGZ
3141 ].each { fileName ->
3142 if (file(fileName).exists()) {
3143 inputs.file(fileName)
3147 outputs.file(hugoDataJsonFile)
3150 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3156 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3159 dependsOn pubhtmlhelp
3161 inputs.dir("${helpBuildDir}/${help_dir}")
3162 outputs.dir("${buildDir}/distributions/${help_dir}")
3166 task j2sSetHeadlessBuild {
3173 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3175 description "Enable the alternative J2S Config file for headless build"
3177 outputFile = jalviewjsJ2sSettingsFileName
3178 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3179 def j2sProps = new Properties()
3180 if (j2sPropsFile.exists()) {
3182 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3183 j2sProps.load(j2sPropsFileFIS)
3184 j2sPropsFileFIS.close()
3186 j2sProps.each { prop, val ->
3189 } catch (Exception e) {
3190 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3194 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3195 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3200 task jalviewjsSetEclipseWorkspace {
3201 def propKey = "jalviewjs_eclipse_workspace"
3203 if (project.hasProperty(propKey)) {
3204 propVal = project.getProperty(propKey)
3205 if (propVal.startsWith("~/")) {
3206 propVal = System.getProperty("user.home") + propVal.substring(1)
3209 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3210 def propsFile = file(propsFileName)
3211 def eclipseWsDir = propVal
3212 def props = new Properties()
3214 def writeProps = true
3215 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3216 def ins = new FileInputStream(propsFileName)
3219 if (props.getProperty(propKey, null) != null) {
3220 eclipseWsDir = props.getProperty(propKey)
3225 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3226 def tempDir = File.createTempDir()
3227 eclipseWsDir = tempDir.getAbsolutePath()
3230 eclipseWorkspace = file(eclipseWsDir)
3233 // do not run a headless transpile when we claim to be in Eclipse
3235 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3236 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3238 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3242 props.setProperty(propKey, eclipseWsDir)
3243 propsFile.parentFile.mkdirs()
3244 def bytes = new ByteArrayOutputStream()
3245 props.store(bytes, null)
3246 def propertiesString = bytes.toString()
3247 propsFile.text = propertiesString
3253 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3256 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3257 outputs.file(propsFileName)
3258 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3262 task jalviewjsEclipsePaths {
3265 def eclipseRoot = jalviewjs_eclipse_root
3266 if (eclipseRoot.startsWith("~/")) {
3267 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3269 if (OperatingSystem.current().isMacOsX()) {
3270 eclipseRoot += "/Eclipse.app"
3271 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3272 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3273 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3274 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3275 eclipseRoot += "/eclipse"
3277 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3278 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3279 } else { // linux or unix
3280 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3281 eclipseRoot += "/eclipse"
3282 println("eclipseDir exists")
3284 eclipseBinary = "${eclipseRoot}/eclipse"
3285 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3288 eclipseVersion = "4.13" // default
3289 def assumedVersion = true
3290 if (file(eclipseProduct).exists()) {
3291 def fis = new FileInputStream(eclipseProduct)
3292 def props = new Properties()
3294 eclipseVersion = props.getProperty("version")
3296 assumedVersion = false
3299 def propKey = "eclipse_debug"
3300 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3303 // do not run a headless transpile when we claim to be in Eclipse
3305 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3306 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3308 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3311 if (!assumedVersion) {
3312 println("ECLIPSE VERSION=${eclipseVersion}")
3318 task printProperties {
3320 description "Output to console all System.properties"
3322 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3328 dependsOn eclipseProject
3329 dependsOn eclipseClasspath
3330 dependsOn eclipseJdt
3334 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3335 task jalviewjsEclipseCopyDropins(type: Copy) {
3336 dependsOn jalviewjsEclipsePaths
3338 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3339 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3340 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3347 // this eclipse -clean doesn't actually work
3348 task jalviewjsCleanEclipse(type: Exec) {
3349 dependsOn eclipseSetup
3350 dependsOn jalviewjsEclipsePaths
3351 dependsOn jalviewjsEclipseCopyDropins
3353 executable(eclipseBinary)
3354 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3360 def inputString = """exit
3363 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3364 standardInput = inputByteStream
3367 /* not really working yet
3368 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3372 task jalviewjsTransferUnzipSwingJs {
3373 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3377 from zipTree(file_zip)
3378 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3382 inputs.file file_zip
3383 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3387 task jalviewjsTransferUnzipLib {
3388 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3391 zipFiles.each { file_zip ->
3393 from zipTree(file_zip)
3394 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3399 inputs.files zipFiles
3400 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3404 task jalviewjsTransferUnzipAllLibs {
3405 dependsOn jalviewjsTransferUnzipSwingJs
3406 dependsOn jalviewjsTransferUnzipLib
3410 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3412 description "Create the alternative j2s file from the j2s.* properties"
3414 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3415 def siteDirProperty = "j2s.site.directory"
3416 def setSiteDir = false
3417 jalviewjsJ2sProps.each { prop, val ->
3419 if (prop == siteDirProperty) {
3420 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3421 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3427 if (!setSiteDir) { // default site location, don't override specifically set property
3428 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3431 outputFile = jalviewjsJ2sAltSettingsFileName
3434 inputs.properties(jalviewjsJ2sProps)
3435 outputs.file(jalviewjsJ2sAltSettingsFileName)
3440 task jalviewjsEclipseSetup {
3441 dependsOn jalviewjsEclipseCopyDropins
3442 dependsOn jalviewjsSetEclipseWorkspace
3443 dependsOn jalviewjsCreateJ2sSettings
3447 task jalviewjsSyncAllLibs (type: Sync) {
3448 dependsOn jalviewjsTransferUnzipAllLibs
3449 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3450 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3451 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3455 def outputFiles = []
3456 rename { filename ->
3457 outputFiles += "${outputDir}/${filename}"
3464 // should this be exclude really ?
3465 duplicatesStrategy "INCLUDE"
3467 outputs.files outputFiles
3468 inputs.files inputFiles
3472 task jalviewjsSyncResources (type: Sync) {
3473 dependsOn buildResources
3475 def inputFiles = fileTree(dir: resourcesBuildDir)
3476 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3480 def outputFiles = []
3481 rename { filename ->
3482 outputFiles += "${outputDir}/${filename}"
3488 outputs.files outputFiles
3489 inputs.files inputFiles
3493 task jalviewjsSyncSiteResources (type: Sync) {
3494 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3495 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3499 def outputFiles = []
3500 rename { filename ->
3501 outputFiles += "${outputDir}/${filename}"
3507 outputs.files outputFiles
3508 inputs.files inputFiles
3512 task jalviewjsSyncBuildProperties (type: Sync) {
3513 dependsOn createBuildProperties
3514 def inputFiles = [file(buildProperties)]
3515 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3519 def outputFiles = []
3520 rename { filename ->
3521 outputFiles += "${outputDir}/${filename}"
3527 outputs.files outputFiles
3528 inputs.files inputFiles
3532 task jalviewjsProjectImport(type: Exec) {
3533 dependsOn eclipseSetup
3534 dependsOn jalviewjsEclipsePaths
3535 dependsOn jalviewjsEclipseSetup
3538 // do not run a headless import when we claim to be in Eclipse
3540 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3541 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3543 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3547 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3548 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3549 executable(eclipseBinary)
3550 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3554 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3556 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3557 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3560 inputs.file("${jalviewDir}/.project")
3561 outputs.upToDateWhen {
3562 file(projdir).exists()
3567 task jalviewjsTranspile(type: Exec) {
3568 dependsOn jalviewjsEclipseSetup
3569 dependsOn jalviewjsProjectImport
3570 dependsOn jalviewjsEclipsePaths
3572 dependsOn jalviewjsEnableAltFileProperty
3576 // do not run a headless transpile when we claim to be in Eclipse
3578 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3579 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3581 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3585 executable(eclipseBinary)
3586 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3590 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3592 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3593 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3599 stdout = new ByteArrayOutputStream()
3600 stderr = new ByteArrayOutputStream()
3602 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3603 def logOutFile = file(logOutFileName)
3604 logOutFile.createNewFile()
3605 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3606 BINARY: ${eclipseBinary}
3607 VERSION: ${eclipseVersion}
3608 WORKSPACE: ${eclipseWorkspace}
3609 DEBUG: ${eclipseDebug}
3612 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3613 // combine stdout and stderr
3614 def logErrFOS = logOutFOS
3616 if (jalviewjs_j2s_to_console.equals("true")) {
3617 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3618 new org.apache.tools.ant.util.TeeOutputStream(
3622 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3623 new org.apache.tools.ant.util.TeeOutputStream(
3628 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3631 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3638 if (stdout.toString().contains("Error processing ")) {
3639 // j2s did not complete transpile
3640 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3641 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3642 println("IGNORING TRANSPILE ERRORS")
3643 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3645 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3650 inputs.dir("${jalviewDir}/${sourceDir}")
3651 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3652 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3656 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3658 def stdout = new ByteArrayOutputStream()
3659 def stderr = new ByteArrayOutputStream()
3661 def coreFile = file(jsfile)
3663 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3665 logOutFile.createNewFile()
3666 logOutFile.append(msg+"\n")
3668 def coreTop = file(prefixFile)
3669 def coreBottom = file(suffixFile)
3670 coreFile.getParentFile().mkdirs()
3671 coreFile.createNewFile()
3672 coreFile.write( coreTop.getText("UTF-8") )
3676 def t = f.getText("UTF-8")
3677 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3678 coreFile.append( t )
3680 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3682 logOutFile.append(msg+"\n")
3685 coreFile.append( coreBottom.getText("UTF-8") )
3687 msg = "Generating ${zjsfile}"
3689 logOutFile.append(msg+"\n")
3690 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3691 def logErrFOS = logOutFOS
3694 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3695 main = "com.google.javascript.jscomp.CommandLineRunner"
3696 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3697 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3700 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3702 logOutFile.append(msg+"\n")
3704 if (logOutConsole) {
3705 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3706 new org.apache.tools.ant.util.TeeOutputStream(
3710 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3711 new org.apache.tools.ant.util.TeeOutputStream(
3716 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3719 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3726 logOutFile.append(msg+"\n")
3730 task jalviewjsBuildAllCores {
3732 description "Build the core js lib closures listed in the classlists dir"
3733 dependsOn jalviewjsTranspile
3734 dependsOn jalviewjsTransferUnzipSwingJs
3736 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3737 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3738 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3739 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3740 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3741 def prefixFile = "${jsDir}/core/coretop2.js"
3742 def suffixFile = "${jsDir}/core/corebottom2.js"
3744 inputs.file prefixFile
3745 inputs.file suffixFile
3747 def classlistFiles = []
3748 // add the classlists found int the jalviewjs_classlists_dir
3749 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3751 def name = file.getName() - ".txt"
3758 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3759 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3760 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3762 jalviewjsCoreClasslists = []
3764 classlistFiles.each {
3767 def file = hash['file']
3768 if (! file.exists()) {
3769 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3770 return false // this is a "continue" in groovy .each closure
3772 def name = hash['name']
3774 name = file.getName() - ".txt"
3782 def list = fileTree(dir: j2sDir, includes: filelist)
3784 def jsfile = "${outputDir}/core${name}.js"
3785 def zjsfile = "${outputDir}/core${name}.z.js"
3787 jalviewjsCoreClasslists += [
3796 outputs.file(jsfile)
3797 outputs.file(zjsfile)
3800 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3801 def stevesoftClasslistName = "_stevesoft"
3802 def stevesoftClasslist = [
3803 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3804 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3805 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3806 'name': stevesoftClasslistName
3808 jalviewjsCoreClasslists += stevesoftClasslist
3809 inputs.files(stevesoftClasslist['list'])
3810 outputs.file(stevesoftClasslist['jsfile'])
3811 outputs.file(stevesoftClasslist['zjsfile'])
3814 def allClasslistName = "_all"
3815 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3816 allJsFiles += fileTree(
3820 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3821 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3822 "**/org/jmol/export/JSExporter.js"
3825 allJsFiles += fileTree(
3829 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3830 "**/sun/misc/Unsafe.js",
3831 "**/swingjs/jquery/jquery-editable-select.js",
3832 "**/swingjs/jquery/j2sComboBox.js",
3833 "**/sun/misc/FloatingDecimal.js"
3836 def allClasslist = [
3837 'jsfile': "${outputDir}/core${allClasslistName}.js",
3838 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3840 'name': allClasslistName
3842 // not including this version of "all" core at the moment
3843 //jalviewjsCoreClasslists += allClasslist
3844 inputs.files(allClasslist['list'])
3845 outputs.file(allClasslist['jsfile'])
3846 outputs.file(allClasslist['zjsfile'])
3849 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3850 logOutFile.getParentFile().mkdirs()
3851 logOutFile.createNewFile()
3852 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3854 jalviewjsCoreClasslists.each {
3855 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3862 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3865 into file(outputFile).getParentFile()
3866 rename { filename ->
3867 if (filename.equals(inputFile.getName())) {
3868 return file(outputFile).getName()
3872 filter(ReplaceTokens,
3876 'MAIN': '"'+main_class+'"',
3878 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3879 'COREKEY': jalviewjs_core_key,
3880 'CORENAME': coreName
3887 task jalviewjsPublishCoreTemplates {
3888 dependsOn jalviewjsBuildAllCores
3889 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3890 def inputFile = file(inputFileName)
3891 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3893 def outputFiles = []
3894 jalviewjsCoreClasslists.each { cl ->
3895 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3896 cl['outputfile'] = outputFile
3897 outputFiles += outputFile
3901 jalviewjsCoreClasslists.each { cl ->
3902 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3905 inputs.file(inputFile)
3906 outputs.files(outputFiles)
3910 task jalviewjsSyncCore (type: Sync) {
3911 dependsOn jalviewjsBuildAllCores
3912 dependsOn jalviewjsPublishCoreTemplates
3913 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3914 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3918 def outputFiles = []
3919 rename { filename ->
3920 outputFiles += "${outputDir}/${filename}"
3926 outputs.files outputFiles
3927 inputs.files inputFiles
3931 // this Copy version of TransferSiteJs will delete anything else in the target dir
3932 task jalviewjsCopyTransferSiteJs(type: Copy) {
3933 dependsOn jalviewjsTranspile
3934 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3935 into "${jalviewDir}/${jalviewjsSiteDir}"
3939 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3940 task jalviewjsSyncTransferSiteJs(type: Sync) {
3941 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3943 into "${jalviewDir}/${jalviewjsSiteDir}"
3950 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3951 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3952 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3953 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3955 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3956 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3957 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3958 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3961 task jalviewjsPrepareSite {
3963 description "Prepares the website folder including unzipping files and copying resources"
3964 dependsOn jalviewjsSyncAllLibs
3965 dependsOn jalviewjsSyncResources
3966 dependsOn jalviewjsSyncSiteResources
3967 dependsOn jalviewjsSyncBuildProperties
3968 dependsOn jalviewjsSyncCore
3972 task jalviewjsBuildSite {
3974 description "Builds the whole website including transpiled code"
3975 dependsOn jalviewjsCopyTransferSiteJs
3976 dependsOn jalviewjsPrepareSite
3980 task cleanJalviewjsTransferSite {
3982 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3983 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3984 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3985 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3990 task cleanJalviewjsSite {
3991 dependsOn cleanJalviewjsTransferSite
3993 delete "${jalviewDir}/${jalviewjsSiteDir}"
3998 task jalviewjsSiteTar(type: Tar) {
4000 description "Creates a tar.gz file for the website"
4001 dependsOn jalviewjsBuildSite
4002 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
4003 archiveFileName = outputFilename
4005 compression Compression.GZIP
4007 from "${jalviewDir}/${jalviewjsSiteDir}"
4008 into jalviewjs_site_dir // this is inside the tar file
4010 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
4014 task jalviewjsServer {
4016 def filename = "jalviewjsTest.html"
4017 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
4018 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
4023 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
4024 factory = f.newInstance()
4025 } catch (ClassNotFoundException e) {
4026 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
4028 def port = Integer.valueOf(jalviewjs_server_port)
4033 while(port < start+1000 && !running) {
4035 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
4036 jalviewjsServer = factory.start(doc_root, port)
4038 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
4039 println("SERVER STARTED with document root ${doc_root}.")
4040 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
4041 println("For debug: "+url+"?j2sdebug")
4042 println("For verbose: "+url+"?j2sverbose")
4043 } catch (Exception e) {
4048 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
4049 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
4050 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4052 jalviewjsCoreClasslists.each { cl ->
4053 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4055 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4057 println("For core ${cl.name}: "+urlcore)
4060 file(htmlFile).text = htmlText
4063 outputs.file(htmlFile)
4064 outputs.upToDateWhen({false})
4068 task cleanJalviewjsAll {
4070 description "Delete all configuration and build artifacts to do with JalviewJS build"
4071 dependsOn cleanJalviewjsSite
4072 dependsOn jalviewjsEclipsePaths
4075 delete "${jalviewDir}/${jalviewjsBuildDir}"
4076 delete "${jalviewDir}/${eclipse_bin_dir}"
4077 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4078 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4080 delete jalviewjsJ2sAltSettingsFileName
4083 outputs.upToDateWhen( { false } )
4087 task jalviewjsIDE_checkJ2sPlugin {
4088 group "00 JalviewJS in Eclipse"
4089 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4092 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4093 def j2sPluginFile = file(j2sPlugin)
4094 def eclipseHome = System.properties["eclipse.home.location"]
4095 if (eclipseHome == null || ! IN_ECLIPSE) {
4096 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4098 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4099 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4100 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4101 eclipseJ2sPluginDirs += altPluginsDir
4103 def foundPlugin = false
4104 def j2sPluginFileName = j2sPluginFile.getName()
4105 def eclipseJ2sPlugin
4106 def eclipseJ2sPluginFile
4107 eclipseJ2sPluginDirs.any { dir ->
4108 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4109 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4110 if (eclipseJ2sPluginFile.exists()) {
4116 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4117 System.err.println(msg)
4118 throw new StopExecutionException(msg)
4121 def digest = MessageDigest.getInstance("MD5")
4123 digest.update(j2sPluginFile.text.bytes)
4124 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4126 digest.update(eclipseJ2sPluginFile.text.bytes)
4127 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4129 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4130 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4131 System.err.println(msg)
4132 throw new StopExecutionException(msg)
4134 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4140 task jalviewjsIDE_copyJ2sPlugin {
4141 group "00 JalviewJS in Eclipse"
4142 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4145 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4146 def j2sPluginFile = file(j2sPlugin)
4147 def eclipseHome = System.properties["eclipse.home.location"]
4148 if (eclipseHome == null || ! IN_ECLIPSE) {
4149 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4151 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4152 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4153 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4154 System.err.println(msg)
4157 eclipseJ2sPluginFile.getParentFile().mkdirs()
4158 into eclipseJ2sPluginFile.getParent()
4164 task jalviewjsIDE_j2sFile {
4165 group "00 JalviewJS in Eclipse"
4166 description "Creates the .j2s file"
4167 dependsOn jalviewjsCreateJ2sSettings
4171 task jalviewjsIDE_SyncCore {
4172 group "00 JalviewJS in Eclipse"
4173 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4174 dependsOn jalviewjsSyncCore
4178 task jalviewjsIDE_SyncSiteAll {
4179 dependsOn jalviewjsSyncAllLibs
4180 dependsOn jalviewjsSyncResources
4181 dependsOn jalviewjsSyncSiteResources
4182 dependsOn jalviewjsSyncBuildProperties
4186 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4189 task jalviewjsIDE_PrepareSite {
4190 group "00 JalviewJS in Eclipse"
4191 description "Sync libs and resources to site dir, but not closure cores"
4193 dependsOn jalviewjsIDE_SyncSiteAll
4194 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4198 task jalviewjsIDE_AssembleSite {
4199 group "00 JalviewJS in Eclipse"
4200 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4201 dependsOn jalviewjsPrepareSite
4205 task jalviewjsIDE_SiteClean {
4206 group "00 JalviewJS in Eclipse"
4207 description "Deletes the Eclipse transpiled site"
4208 dependsOn cleanJalviewjsSite
4212 task jalviewjsIDE_Server {
4213 group "00 JalviewJS in Eclipse"
4214 description "Starts a webserver on localhost to test the website"
4215 dependsOn jalviewjsServer
4219 // buildship runs this at import or gradle refresh
4220 task eclipseSynchronizationTask {
4221 //dependsOn eclipseSetup
4222 dependsOn createBuildProperties
4224 dependsOn jalviewjsIDE_j2sFile
4225 dependsOn jalviewjsIDE_checkJ2sPlugin
4226 dependsOn jalviewjsIDE_PrepareSite
4231 // buildship runs this at build time or project refresh
4232 task eclipseAutoBuildTask {
4233 //dependsOn jalviewjsIDE_checkJ2sPlugin
4234 //dependsOn jalviewjsIDE_PrepareSite
4238 task jalviewjsCopyStderrLaunchFile(type: Copy) {
4239 from file(jalviewjs_stderr_launch)
4240 into jalviewjsSiteDir
4242 inputs.file jalviewjs_stderr_launch
4243 outputs.file jalviewjsStderrLaunchFilename
4246 task cleanJalviewjsChromiumUserDir {
4248 delete jalviewjsChromiumUserDir
4250 outputs.dir jalviewjsChromiumUserDir
4251 // always run when depended on
4252 outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
4255 task jalviewjsChromiumProfile {
4256 dependsOn cleanJalviewjsChromiumUserDir
4257 mustRunAfter cleanJalviewjsChromiumUserDir
4259 def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
4262 mkdir jalviewjsChromiumProfileDir
4265 outputs.file firstRun
4268 task jalviewjsLaunchTest {
4270 description "Check JalviewJS opens in a browser"
4271 dependsOn jalviewjsBuildSite
4272 dependsOn jalviewjsCopyStderrLaunchFile
4273 dependsOn jalviewjsChromiumProfile
4275 def macOS = OperatingSystem.current().isMacOsX()
4276 def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
4277 if (chromiumBinary.startsWith("~/")) {
4278 chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
4284 def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
4286 def binary = file(chromiumBinary)
4287 if (!binary.exists()) {
4288 throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
4290 stdout = new ByteArrayOutputStream()
4291 stderr = new ByteArrayOutputStream()
4294 if (jalviewjs_j2s_to_console.equals("true")) {
4295 execStdout = new org.apache.tools.ant.util.TeeOutputStream(
4298 execStderr = new org.apache.tools.ant.util.TeeOutputStream(
4306 "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
4309 "--timeout=${timeoutms}",
4310 "--virtual-time-budget=${timeoutms}",
4311 "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
4312 "--profile-directory=${jalviewjs_chromium_profile_name}",
4313 "--allow-file-access-from-files",
4314 "--enable-logging=stderr",
4315 "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
4318 if (true || macOS) {
4319 ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
4320 Future f1 = executor.submit(
4323 standardOutput = execStdout
4324 errorOutput = execStderr
4325 executable(chromiumBinary)
4327 println "COMMAND: '"+commandLine.join(" ")+"'"
4329 executor.shutdownNow()
4333 def noChangeBytes = 0
4334 def noChangeIterations = 0
4335 executor.scheduleAtFixedRate(
4337 String stderrString = stderr.toString()
4338 // shutdown the task if we have a success string
4339 if (stderrString.contains(jalviewjs_desktop_init_string)) {
4342 executor.shutdownNow()
4344 // if no change in stderr for 10s then also end
4345 if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
4346 executor.shutdownNow()
4348 if (stderrString.length() == noChangeBytes) {
4349 noChangeIterations++
4351 noChangeBytes = stderrString.length()
4352 noChangeIterations = 0
4355 1, 1, TimeUnit.SECONDS)
4357 executor.schedule(new Runnable(){
4360 executor.shutdownNow()
4362 }, timeoutms, TimeUnit.MILLISECONDS)
4364 executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
4365 executor.shutdownNow()
4372 stderr.toString().eachLine { line ->
4373 if (line.contains(jalviewjs_desktop_init_string)) {
4374 println("Found line '"+line+"'")
4380 throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
4388 description "Build the JalviewJS site and run the launch test"
4389 dependsOn jalviewjsBuildSite
4390 dependsOn jalviewjsLaunchTest