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 showStandardStreams true
1857 info.events = [ TestLogEvent.FAILED ]
1860 if (OperatingSystem.current().isMacOsX()) {
1861 testTask.systemProperty "apple.awt.UIElement", "true"
1862 testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
1866 ignoreFailures = true // Always try to run all tests for all modules
1868 afterSuite { desc, result ->
1870 return // Only summarize results for whole modules
1872 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1874 rootProject.ext.testsResults.add(resultsInfo)
1877 // from original test task
1878 maxHeapSize = "1024m"
1880 workingDir = jalviewDir
1881 def testLaf = project.findProperty("test_laf")
1882 if (testLaf != null) {
1883 println("Setting Test LaF to '${testLaf}'")
1884 systemProperty "laf", testLaf
1886 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1887 if (testHiDPIScale != null) {
1888 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1889 systemProperty "sun.java2d.uiScale", testHiDPIScale
1891 sourceCompatibility = compile_source_compatibility
1892 targetCompatibility = compile_target_compatibility
1893 jvmArgs += additional_compiler_args
1896 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1897 // testTasks that include the tests, and exclude all from the others.
1898 // get --test argument
1899 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1900 // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
1901 // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
1905 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1910 /* don't fail on no matching tests (so --tests will run across all testTasks) */
1911 testTask.filter.setFailOnNoMatchingTests(false)
1913 /* ensure the "test" task dependsOn all the testTasks */
1914 test.dependsOn testTask
1917 gradle.buildFinished {
1918 def allResults = rootProject.ext.testsResults
1920 if (!allResults.isEmpty()) {
1921 printResults allResults
1922 allResults.each {r ->
1923 if (r[2].resultType == TestResult.ResultType.FAILURE)
1924 throw new GradleException("Failed tests!")
1929 private static String colString(styler, col, colour, text) {
1930 return col?"${styler[colour](text)}":text
1933 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1934 def colour = 'black'
1942 case TestResult.ResultType.SUCCESS:
1945 case TestResult.ResultType.FAILURE:
1953 StringBuilder sb = new StringBuilder()
1957 sb.append(" results: ")
1958 sb.append(colString(s, col && !nocol, colour, text))
1960 sb.append("${rc} tests, ")
1961 sb.append(colString(s, col && rs > 0, 'green', rs))
1962 sb.append(" successes, ")
1963 sb.append(colString(s, col && rf > 0, 'red', rf))
1964 sb.append(" failures, ")
1965 sb.append("${rsk} skipped) in ${t}")
1966 return sb.toString()
1969 private static void printResults(allResults) {
1971 // styler from https://stackoverflow.com/a/56139852
1972 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1975 def failedTests = false
1976 def summaryLines = []
1978 def totalsuccess = 0
1981 def totaltime = TimeCategory.getSeconds(0)
1982 // sort on project name then task name
1983 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1984 def projectName = it[0]
1985 def taskName = it[1]
1989 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1990 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1991 def reportLine = "Report file: ${report}"
1992 def ls = summaryPlain.length()
1993 def lr = reportLine.length()
1994 def m = [ls, lr].max()
1997 def info = [ls, summaryCol, reportLine]
1998 summaryLines.add(info)
1999 failedTests |= result.resultType == TestResult.ResultType.FAILURE
2000 totalcount += result.testCount
2001 totalsuccess += result.successfulTestCount
2002 totalfail += result.failedTestCount
2003 totalskip += result.skippedTestCount
2006 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
2007 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
2008 def tls = totalSummaryPlain.length()
2009 if (tls > maxLength)
2011 def info = [tls, totalSummaryCol, null]
2012 summaryLines.add(info)
2014 def allSummaries = []
2015 for(sInfo : summaryLines) {
2017 def summary = sInfo[1]
2018 def report = sInfo[2]
2020 StringBuilder sb = new StringBuilder()
2021 sb.append("│" + summary + " " * (maxLength - ls) + "│")
2022 if (report != null) {
2023 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
2025 allSummaries += sb.toString()
2028 println "┌${"${"─" * maxLength}"}┐"
2029 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
2030 println "└${"${"─" * maxLength}"}┘"
2032 /* END of test tasks results summary */
2035 task compileLinkCheck(type: JavaCompile) {
2037 classpath = files("${jalviewDir}/${utils_dir}")
2038 destinationDir = file("${jalviewDir}/${utils_dir}")
2039 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
2041 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2042 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2043 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
2044 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
2048 task linkCheck(type: JavaExec) {
2050 dependsOn compileLinkCheck
2052 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2053 classpath = files("${jalviewDir}/${utils_dir}")
2054 main = "HelpLinksChecker"
2055 workingDir = "${helpBuildDir}"
2056 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2058 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2059 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2062 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2066 inputs.dir(helpBuildDir)
2067 outputs.file(helpLinksCheckerOutFile)
2071 // import the pubhtmlhelp target
2072 ant.properties.basedir = "${jalviewDir}"
2073 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2074 ant.importBuild "${utils_dir}/publishHelp.xml"
2077 task cleanPackageDir(type: Delete) {
2079 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2089 attributes "Main-Class": main_class,
2090 "Permissions": "all-permissions",
2091 "Application-Name": applicationName,
2092 "Codebase": application_codebase,
2093 "Implementation-Version": JALVIEW_VERSION
2096 def outputDir = "${jalviewDir}/${package_dir}"
2097 destinationDirectory = file(outputDir)
2098 archiveFileName = rootProject.name+".jar"
2099 duplicatesStrategy "EXCLUDE"
2106 exclude "**/*.jar.*"
2108 inputs.dir(sourceSets.main.java.outputDir)
2109 sourceSets.main.resources.srcDirs.each{ dir ->
2112 outputs.file("${outputDir}/${archiveFileName}")
2116 task copyJars(type: Copy) {
2117 from fileTree(dir: classesDir, include: "**/*.jar").files
2118 into "${jalviewDir}/${package_dir}"
2122 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2123 task syncJars(type: Sync) {
2125 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2126 into "${jalviewDir}/${package_dir}"
2128 include jar.archiveFileName.getOrNull()
2135 description = "Put all required libraries in dist"
2136 // order of "cleanPackageDir", "copyJars", "jar" important!
2137 jar.mustRunAfter cleanPackageDir
2138 syncJars.mustRunAfter cleanPackageDir
2139 dependsOn cleanPackageDir
2142 outputs.dir("${jalviewDir}/${package_dir}")
2147 dependsOn cleanPackageDir
2154 group = "distribution"
2155 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2159 from ("${jalviewDir}/${libDistDir}") {
2163 attributes "Implementation-Version": JALVIEW_VERSION,
2164 "Application-Name": applicationName
2167 duplicatesStrategy "INCLUDE"
2169 mainClassName = shadow_jar_main_class
2171 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2175 task getdownImagesCopy() {
2176 inputs.dir getdownImagesDir
2177 outputs.dir getdownImagesBuildDir
2181 from(getdownImagesDir) {
2182 include("*getdown*.png")
2184 into getdownImagesBuildDir
2189 task getdownImagesProcess() {
2190 dependsOn getdownImagesCopy
2193 if (backgroundImageText) {
2194 if (convertBinary == null) {
2195 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2197 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2198 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2200 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2202 executable convertBinary
2205 '-font', getdown_background_image_text_font,
2206 '-fill', getdown_background_image_text_colour,
2207 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2208 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2209 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2218 task getdownImages() {
2219 dependsOn getdownImagesProcess
2222 task getdownWebsite() {
2223 group = "distribution"
2224 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2226 dependsOn getdownImages
2231 def getdownWebsiteResourceFilenames = []
2232 def getdownResourceDir = getdownResourceDir
2233 def getdownResourceFilenames = []
2236 // clean the getdown website and files dir before creating getdown folders
2237 delete getdownAppBaseDir
2238 delete getdownFilesDir
2241 from buildProperties
2242 rename(file(buildProperties).getName(), getdown_build_properties)
2245 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2248 from channelPropsFile
2249 filter(ReplaceTokens,
2253 'SUFFIX': channelSuffix
2256 into getdownAppBaseDir
2258 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2260 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2261 def props = project.properties.sort { it.key }
2262 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2263 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2265 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2266 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2268 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2269 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2271 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2272 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2273 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2274 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2275 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2276 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
2277 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
2280 props.put("getdown_txt_title", jalview_name)
2281 props.put("getdown_txt_ui.name", applicationName)
2283 // start with appbase
2284 getdownTextLines += "appbase = ${getdownAppBase}"
2285 props.each{ prop, val ->
2286 if (prop.startsWith("getdown_txt_") && val != null) {
2287 if (prop.startsWith("getdown_txt_multi_")) {
2288 def key = prop.substring(18)
2289 val.split(",").each{ v ->
2290 def line = "${key} = ${v}"
2291 getdownTextLines += line
2294 // file values rationalised
2295 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2297 if (val.indexOf('/') == 0) {
2300 } else if (val.indexOf('/') > 0) {
2301 // relative path (relative to jalviewDir)
2302 r = file( "${jalviewDir}/${val}" )
2305 val = "${getdown_resource_dir}/" + r.getName()
2306 getdownWebsiteResourceFilenames += val
2307 getdownResourceFilenames += r.getPath()
2310 if (! prop.startsWith("getdown_txt_resource")) {
2311 def line = prop.substring(12) + " = ${val}"
2312 getdownTextLines += line
2318 getdownWebsiteResourceFilenames.each{ filename ->
2319 getdownTextLines += "resource = ${filename}"
2321 getdownResourceFilenames.each{ filename ->
2324 into getdownResourceDir
2328 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2329 getdownWrapperScripts.each{ script ->
2330 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2334 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2336 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2341 fileTree(file(package_dir)).each{ f ->
2342 if (f.isDirectory()) {
2343 def files = fileTree(dir: f, include: ["*"]).getFiles()
2345 } else if (f.exists()) {
2349 def jalviewJar = jar.archiveFileName.getOrNull()
2350 // put jalview.jar first for CLASSPATH and .properties files reasons
2351 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2352 def name = f.getName()
2353 def line = "code = ${getdownAppDistDir}/${name}"
2354 getdownTextLines += line
2361 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2363 if (JAVA_VERSION.equals("11")) {
2364 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2365 j11libFiles.sort().each{f ->
2366 def name = f.getName()
2367 def line = "code = ${getdown_j11lib_dir}/${name}"
2368 getdownTextLines += line
2371 into getdownJ11libDir
2377 // 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.
2378 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2379 getdownTextLines += "resource = ${getdown_launcher_new}"
2380 getdownTextLines += "class = ${main_class}"
2381 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2382 if (getdownSetAppBaseProperty) {
2383 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2384 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2387 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2388 getdownTxt.write(getdownTextLines.join("\n"))
2390 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2391 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2392 launchJvl.write("appbase=${getdownAppBase}")
2394 // files going into the getdown website dir: getdown-launcher.jar
2396 from getdownLauncher
2397 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2398 into getdownAppBaseDir
2401 // files going into the getdown website dir: getdown-launcher(-local).jar
2403 from getdownLauncher
2404 if (file(getdownLauncher).getName() != getdown_launcher) {
2405 rename(file(getdownLauncher).getName(), getdown_launcher)
2407 into getdownAppBaseDir
2410 // files going into the getdown website dir: ./install dir and files
2411 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2414 from getdownLauncher
2415 from "${getdownAppDir}/${getdown_build_properties}"
2416 if (file(getdownLauncher).getName() != getdown_launcher) {
2417 rename(file(getdownLauncher).getName(), getdown_launcher)
2419 into getdownInstallDir
2422 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2424 from getdownInstallDir
2425 into getdownFilesInstallDir
2429 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2433 from getdownLauncher
2434 from "${getdownAppBaseDir}/${getdown_build_properties}"
2435 from "${getdownAppBaseDir}/${channel_props}"
2436 if (file(getdownLauncher).getName() != getdown_launcher) {
2437 rename(file(getdownLauncher).getName(), getdown_launcher)
2439 into getdownFilesDir
2442 // and ./resource (not all downloaded by getdown)
2444 from getdownResourceDir
2445 into "${getdownFilesDir}/${getdown_resource_dir}"
2450 inputs.dir("${jalviewDir}/${package_dir}")
2452 outputs.dir(getdownAppBaseDir)
2453 outputs.dir(getdownFilesDir)
2457 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2458 task getdownDigestDir(type: JavaExec) {
2460 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2462 def digestDirPropertyName = "DIGESTDIR"
2464 classpath = files(getdownLauncher)
2465 def digestDir = findProperty(digestDirPropertyName)
2466 if (digestDir == null) {
2467 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2471 main = "com.threerings.getdown.tools.Digester"
2475 task getdownDigest(type: JavaExec) {
2476 group = "distribution"
2477 description = "Digest the getdown website folder"
2478 dependsOn getdownWebsite
2480 classpath = files(getdownLauncher)
2482 main = "com.threerings.getdown.tools.Digester"
2483 args getdownAppBaseDir
2484 inputs.dir(getdownAppBaseDir)
2485 outputs.file("${getdownAppBaseDir}/digest2.txt")
2490 group = "distribution"
2491 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2492 dependsOn getdownDigest
2494 if (reportRsyncCommand) {
2495 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2496 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2497 println "LIKELY RSYNC COMMAND:"
2498 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2499 if (RUNRSYNC == "true") {
2501 commandLine "mkdir", "-p", toDir
2504 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2512 task getdownArchiveBuild() {
2513 group = "distribution"
2514 description = "Put files in the archive dir to go on the website"
2516 dependsOn getdownWebsite
2518 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2519 def vDir = "${getdownArchiveDir}/${v}"
2520 getdownFullArchiveDir = "${vDir}/getdown"
2521 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2523 def vAltDir = "alt_${v}"
2524 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2527 // cleanup old "old" dir
2528 delete getdownArchiveDir
2530 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2531 getdownArchiveTxt.getParentFile().mkdirs()
2532 def getdownArchiveTextLines = []
2533 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2537 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2538 into "${getdownFullArchiveDir}/${vAltDir}"
2541 getdownTextLines.each { line ->
2542 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2543 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2544 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2545 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2546 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2547 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2548 // remove the existing resource = resource/ or bin/ lines
2549 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2550 getdownArchiveTextLines += line
2554 // the resource dir -- add these files as resource lines in getdown.txt
2556 from "${archiveImagesDir}"
2557 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2559 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2563 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2565 def vLaunchJvl = file(getdownVersionLaunchJvl)
2566 vLaunchJvl.getParentFile().mkdirs()
2567 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2568 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2569 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2570 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2571 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2572 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2574 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2576 from getdownLauncher
2577 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2578 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2579 from "${getdownAppBaseDir}/${channel_props}"
2580 if (file(getdownLauncher).getName() != getdown_launcher) {
2581 rename(file(getdownLauncher).getName(), getdown_launcher)
2583 into getdownFullArchiveDir
2589 task getdownArchiveDigest(type: JavaExec) {
2590 group = "distribution"
2591 description = "Digest the getdown archive folder"
2593 dependsOn getdownArchiveBuild
2596 classpath = files(getdownLauncher)
2597 args getdownFullArchiveDir
2599 main = "com.threerings.getdown.tools.Digester"
2600 inputs.dir(getdownFullArchiveDir)
2601 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2604 task getdownArchive() {
2605 group = "distribution"
2606 description = "Build the website archive dir with getdown digest"
2608 dependsOn getdownArchiveBuild
2609 dependsOn getdownArchiveDigest
2612 tasks.withType(JavaCompile) {
2613 options.encoding = 'UTF-8'
2619 delete getdownAppBaseDir
2620 delete getdownFilesDir
2621 delete getdownArchiveDir
2627 if (file(install4jHomeDir).exists()) {
2629 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2630 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2631 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2632 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2634 installDir(file(install4jHomeDir))
2636 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2640 task copyInstall4jTemplate {
2641 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2642 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2643 inputs.file(install4jTemplateFile)
2644 inputs.file(install4jFileAssociationsFile)
2645 inputs.property("CHANNEL", { CHANNEL })
2646 outputs.file(install4jConfFile)
2649 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2651 // turn off code signing if no OSX_KEYPASS
2652 if (OSX_KEYPASS == "") {
2653 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2654 codeSigning.'@macEnabled' = "false"
2656 install4jConfigXml.'**'.windows.each { windows ->
2657 windows.'@runPostProcessor' = "false"
2661 // disable install screen for OSX dmg (for 2.11.2.0)
2662 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2663 macosArchive.attributes().remove('executeSetupApp')
2664 macosArchive.attributes().remove('setupAppId')
2667 // turn off checksum creation for LOCAL channel
2668 def e = install4jConfigXml.application[0]
2669 e.'@createChecksums' = string(install4jCheckSums)
2671 // put file association actions where placeholder action is
2672 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2673 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2674 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2675 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2676 def parent = a.parent()
2678 fileAssociationActions.each { faa ->
2681 // don't need to continue in .any loop once replacements have been made
2686 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2687 // NB we're deleting the /other/ one!
2688 // Also remove the examples subdir from non-release versions
2689 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2690 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2691 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2692 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2694 // remove the examples subdir from Full File Set
2695 def files = install4jConfigXml.files[0]
2696 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2697 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2698 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2699 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2700 dirEntry.parent().remove(dirEntry)
2702 install4jConfigXml.'**'.action.any { a ->
2703 if (a.'@customizedId' == customizedIdToDelete) {
2704 def parent = a.parent()
2710 // write install4j file
2711 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2718 delete install4jConfFile
2722 task cleanInstallersDataFiles {
2723 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2724 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2725 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2727 delete installersOutputTxt
2728 delete installersSha256
2729 delete hugoDataJsonFile
2733 task install4jDMGBackgroundImageCopy {
2734 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2735 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2738 from(install4jDMGBackgroundImageDir) {
2739 include(install4jDMGBackgroundImageFile)
2741 into install4jDMGBackgroundImageBuildDir
2746 task install4jDMGBackgroundImageProcess {
2747 dependsOn install4jDMGBackgroundImageCopy
2750 if (backgroundImageText) {
2751 if (convertBinary == null) {
2752 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2754 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2755 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2757 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2759 executable convertBinary
2762 '-font', install4j_background_image_text_font,
2763 '-fill', install4j_background_image_text_colour,
2764 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2765 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2766 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2775 task install4jDMGBackgroundImage {
2776 dependsOn install4jDMGBackgroundImageProcess
2779 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2780 group = "distribution"
2781 description = "Create the install4j installers"
2783 dependsOn copyInstall4jTemplate
2784 dependsOn cleanInstallersDataFiles
2785 dependsOn install4jDMGBackgroundImage
2787 projectFile = install4jConfFile
2789 // create an md5 for the input files to use as version for install4j conf file
2790 def digest = MessageDigest.getInstance("MD5")
2792 (file("${install4jDir}/${install4j_template}").text +
2793 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2794 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2795 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2796 if (filesMd5.length() >= 8) {
2797 filesMd5 = filesMd5.substring(0,8)
2799 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2802 'JALVIEW_NAME': jalview_name,
2803 'JALVIEW_APPLICATION_NAME': applicationName,
2804 'JALVIEW_DIR': "../..",
2805 'OSX_KEYSTORE': OSX_KEYSTORE,
2806 'OSX_APPLEID': OSX_APPLEID,
2807 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2808 'JSIGN_SH': JSIGN_SH,
2809 'JRE_DIR': getdown_app_dir_java,
2810 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2811 'JALVIEW_VERSION': JALVIEW_VERSION,
2812 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2813 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2814 'JAVA_VERSION': JAVA_VERSION,
2815 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2816 'VERSION': JALVIEW_VERSION,
2817 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2818 'BUNDLE_ID': install4jBundleId,
2819 'INTERNAL_ID': install4jInternalId,
2820 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2821 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2822 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2823 'WRAPPER_LINK': getdownWrapperLink,
2824 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2825 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2826 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
2827 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2828 'INSTALLER_NAME': install4jInstallerName,
2829 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2830 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2831 'GETDOWN_FILES_DIR': getdown_files_dir,
2832 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2833 'GETDOWN_DIST_DIR': getdownAppDistDir,
2834 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2835 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2836 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2837 'BUILD_DIR': install4jBuildDir,
2838 'APPLICATION_CATEGORIES': install4j_application_categories,
2839 'APPLICATION_FOLDER': install4jApplicationFolder,
2840 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2841 'EXECUTABLE_NAME': install4jExecutableName,
2842 'EXTRA_SCHEME': install4jExtraScheme,
2843 'MAC_ICONS_FILE': install4jMacIconsFile,
2844 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2845 'PNG_ICON_FILE': install4jPngIconFile,
2846 'BACKGROUND': install4jBackground,
2851 'windows': 'WINDOWS',
2855 // these are the bundled OS/architecture VMs needed by install4j
2858 [ "mac", "aarch64" ],
2859 [ "windows", "x64" ],
2861 [ "linux", "aarch64" ]
2863 osArch.forEach { os, arch ->
2864 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)
2865 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2866 // otherwise running `gradle installers` generates a non-useful error:
2867 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2868 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)
2871 //println("INSTALL4J VARIABLES:")
2872 //variables.each{k,v->println("${k}=${v}")}
2874 destination = "${jalviewDir}/${install4jBuildDir}"
2875 buildSelected = true
2877 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2879 disableSigning = true
2880 disableNotarization = true
2884 macKeystorePassword = OSX_KEYPASS
2887 if (OSX_ALTOOLPASS) {
2888 appleIdPassword = OSX_ALTOOLPASS
2889 disableNotarization = false
2891 disableNotarization = true
2895 println("Using projectFile "+projectFile)
2896 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2900 inputs.dir(getdownAppBaseDir)
2901 inputs.file(install4jConfFile)
2902 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2903 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2906 def getDataHash(File myFile) {
2907 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2908 return myFile.exists()
2910 "file" : myFile.getName(),
2911 "filesize" : myFile.length(),
2912 "sha256" : hash.toString()
2917 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2919 "channel" : getdownChannelName,
2920 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2921 "git-commit" : "${gitHash} [${gitBranch}]",
2922 "version" : JALVIEW_VERSION
2924 // install4j installer files
2925 if (installersOutputTxt.exists()) {
2927 installersOutputTxt.readLines().each { def line ->
2928 if (line.startsWith("#")) {
2931 line.replaceAll("\n","")
2932 def vals = line.split("\t")
2933 def filename = vals[3]
2934 def filesize = file(filename).length()
2935 filename = filename.replaceAll(/^.*\//, "")
2936 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2937 idHash."${filename}" = vals[0]
2939 if (install4jCheckSums && installersSha256.exists()) {
2940 installersSha256.readLines().each { def line ->
2941 if (line.startsWith("#")) {
2944 line.replaceAll("\n","")
2945 def vals = line.split(/\s+\*?/)
2946 def filename = vals[1]
2947 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2953 "JAR": shadowJar.archiveFile, // executable JAR
2954 "JVL": getdownVersionLaunchJvl, // version JVL
2955 "SOURCE": sourceDist.archiveFile // source TGZ
2956 ].each { key, value ->
2957 def file = file(value)
2958 if (file.exists()) {
2959 def fileHash = getDataHash(file)
2960 if (fileHash != null) {
2961 hash."${key}" = fileHash;
2965 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2968 task staticMakeInstallersJsonFile {
2970 def output = findProperty("i4j_output")
2971 def sha256 = findProperty("i4j_sha256")
2972 def json = findProperty("i4j_json")
2973 if (output == null || sha256 == null || json == null) {
2974 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2976 writeDataJsonFile(file(output), file(sha256), file(json))
2981 dependsOn installerFiles
2987 eclipse().configFile(eclipse_codestyle_file)
2991 task createSourceReleaseProperties(type: WriteProperties) {
2992 group = "distribution"
2993 description = "Create the source RELEASE properties file"
2995 def sourceTarBuildDir = "${buildDir}/sourceTar"
2996 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2997 outputFile (sourceReleasePropertiesFile)
3000 releaseProps.each{ key, val -> property key, val }
3001 property "git.branch", gitBranch
3002 property "git.hash", gitHash
3005 outputs.file(outputFile)
3008 task sourceDist(type: Tar) {
3009 group "distribution"
3010 description "Create a source .tar.gz file for distribution"
3012 dependsOn createBuildProperties
3013 dependsOn convertMdFiles
3014 dependsOn eclipseAllPreferences
3015 dependsOn createSourceReleaseProperties
3018 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
3019 archiveFileName = outputFileName
3021 compression Compression.GZIP
3036 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
3038 "utils/InstallAnywhere",
3053 "gradle.properties",
3065 ".settings/org.eclipse.buildship.core.prefs",
3066 ".settings/org.eclipse.jdt.core.prefs"
3070 exclude (EXCLUDE_FILES)
3071 include (PROCESS_FILES)
3072 filter(ReplaceTokens,
3076 'Version-Rel': JALVIEW_VERSION,
3077 'Year-Rel': getDate("yyyy")
3082 exclude (EXCLUDE_FILES)
3083 exclude (PROCESS_FILES)
3084 exclude ("appletlib")
3085 exclude ("**/*locales")
3086 exclude ("*locales/**")
3087 exclude ("utils/InstallAnywhere")
3089 exclude (getdown_files_dir)
3090 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3091 //exclude (getdown_website_dir)
3092 //exclude (getdown_archive_dir)
3094 // exluding these as not using jars as modules yet
3095 exclude ("${j11modDir}/**/*.jar")
3098 include(INCLUDE_FILES)
3100 // from (jalviewDir) {
3101 // // explicit includes for stuff that seemed to not get included
3102 // include(fileTree("test/**/*."))
3103 // exclude(EXCLUDE_FILES)
3104 // exclude(PROCESS_FILES)
3107 from(file(buildProperties).getParent()) {
3108 include(file(buildProperties).getName())
3109 rename(file(buildProperties).getName(), "build_properties")
3111 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3115 def sourceTarBuildDir = "${buildDir}/sourceTar"
3116 from(sourceTarBuildDir) {
3117 // this includes the appended RELEASE properties file
3121 task dataInstallersJson {
3123 description "Create the installers-VERSION.json data file for installer files created"
3125 mustRunAfter installers
3126 mustRunAfter shadowJar
3127 mustRunAfter sourceDist
3128 mustRunAfter getdownArchive
3130 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3131 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3133 if (installersOutputTxt.exists()) {
3134 inputs.file(installersOutputTxt)
3136 if (install4jCheckSums && installersSha256.exists()) {
3137 inputs.file(installersSha256)
3140 shadowJar.archiveFile, // executable JAR
3141 getdownVersionLaunchJvl, // version JVL
3142 sourceDist.archiveFile // source TGZ
3143 ].each { fileName ->
3144 if (file(fileName).exists()) {
3145 inputs.file(fileName)
3149 outputs.file(hugoDataJsonFile)
3152 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3158 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3161 dependsOn pubhtmlhelp
3163 inputs.dir("${helpBuildDir}/${help_dir}")
3164 outputs.dir("${buildDir}/distributions/${help_dir}")
3168 task j2sSetHeadlessBuild {
3175 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3177 description "Enable the alternative J2S Config file for headless build"
3179 outputFile = jalviewjsJ2sSettingsFileName
3180 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3181 def j2sProps = new Properties()
3182 if (j2sPropsFile.exists()) {
3184 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3185 j2sProps.load(j2sPropsFileFIS)
3186 j2sPropsFileFIS.close()
3188 j2sProps.each { prop, val ->
3191 } catch (Exception e) {
3192 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3196 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3197 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3202 task jalviewjsSetEclipseWorkspace {
3203 def propKey = "jalviewjs_eclipse_workspace"
3205 if (project.hasProperty(propKey)) {
3206 propVal = project.getProperty(propKey)
3207 if (propVal.startsWith("~/")) {
3208 propVal = System.getProperty("user.home") + propVal.substring(1)
3211 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3212 def propsFile = file(propsFileName)
3213 def eclipseWsDir = propVal
3214 def props = new Properties()
3216 def writeProps = true
3217 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3218 def ins = new FileInputStream(propsFileName)
3221 if (props.getProperty(propKey, null) != null) {
3222 eclipseWsDir = props.getProperty(propKey)
3227 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3228 def tempDir = File.createTempDir()
3229 eclipseWsDir = tempDir.getAbsolutePath()
3232 eclipseWorkspace = file(eclipseWsDir)
3235 // do not run a headless transpile when we claim to be in Eclipse
3237 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3238 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3240 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3244 props.setProperty(propKey, eclipseWsDir)
3245 propsFile.parentFile.mkdirs()
3246 def bytes = new ByteArrayOutputStream()
3247 props.store(bytes, null)
3248 def propertiesString = bytes.toString()
3249 propsFile.text = propertiesString
3255 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3258 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3259 outputs.file(propsFileName)
3260 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3264 task jalviewjsEclipsePaths {
3267 def eclipseRoot = jalviewjs_eclipse_root
3268 if (eclipseRoot.startsWith("~/")) {
3269 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3271 if (OperatingSystem.current().isMacOsX()) {
3272 eclipseRoot += "/Eclipse.app"
3273 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3274 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3275 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3276 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3277 eclipseRoot += "/eclipse"
3279 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3280 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3281 } else { // linux or unix
3282 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3283 eclipseRoot += "/eclipse"
3284 println("eclipseDir exists")
3286 eclipseBinary = "${eclipseRoot}/eclipse"
3287 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3290 eclipseVersion = "4.13" // default
3291 def assumedVersion = true
3292 if (file(eclipseProduct).exists()) {
3293 def fis = new FileInputStream(eclipseProduct)
3294 def props = new Properties()
3296 eclipseVersion = props.getProperty("version")
3298 assumedVersion = false
3301 def propKey = "eclipse_debug"
3302 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3305 // do not run a headless transpile when we claim to be in Eclipse
3307 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3308 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3310 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3313 if (!assumedVersion) {
3314 println("ECLIPSE VERSION=${eclipseVersion}")
3320 task printProperties {
3322 description "Output to console all System.properties"
3324 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3330 dependsOn eclipseProject
3331 dependsOn eclipseClasspath
3332 dependsOn eclipseJdt
3336 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3337 task jalviewjsEclipseCopyDropins(type: Copy) {
3338 dependsOn jalviewjsEclipsePaths
3340 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3341 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3342 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3349 // this eclipse -clean doesn't actually work
3350 task jalviewjsCleanEclipse(type: Exec) {
3351 dependsOn eclipseSetup
3352 dependsOn jalviewjsEclipsePaths
3353 dependsOn jalviewjsEclipseCopyDropins
3355 executable(eclipseBinary)
3356 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3362 def inputString = """exit
3365 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3366 standardInput = inputByteStream
3369 /* not really working yet
3370 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3374 task jalviewjsTransferUnzipSwingJs {
3375 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3379 from zipTree(file_zip)
3380 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3384 inputs.file file_zip
3385 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3389 task jalviewjsTransferUnzipLib {
3390 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3393 zipFiles.each { file_zip ->
3395 from zipTree(file_zip)
3396 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3401 inputs.files zipFiles
3402 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3406 task jalviewjsTransferUnzipAllLibs {
3407 dependsOn jalviewjsTransferUnzipSwingJs
3408 dependsOn jalviewjsTransferUnzipLib
3412 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3414 description "Create the alternative j2s file from the j2s.* properties"
3416 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3417 def siteDirProperty = "j2s.site.directory"
3418 def setSiteDir = false
3419 jalviewjsJ2sProps.each { prop, val ->
3421 if (prop == siteDirProperty) {
3422 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3423 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3429 if (!setSiteDir) { // default site location, don't override specifically set property
3430 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3433 outputFile = jalviewjsJ2sAltSettingsFileName
3436 inputs.properties(jalviewjsJ2sProps)
3437 outputs.file(jalviewjsJ2sAltSettingsFileName)
3442 task jalviewjsEclipseSetup {
3443 dependsOn jalviewjsEclipseCopyDropins
3444 dependsOn jalviewjsSetEclipseWorkspace
3445 dependsOn jalviewjsCreateJ2sSettings
3449 task jalviewjsSyncAllLibs (type: Sync) {
3450 dependsOn jalviewjsTransferUnzipAllLibs
3451 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3452 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3453 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3457 def outputFiles = []
3458 rename { filename ->
3459 outputFiles += "${outputDir}/${filename}"
3466 // should this be exclude really ?
3467 duplicatesStrategy "INCLUDE"
3469 outputs.files outputFiles
3470 inputs.files inputFiles
3474 task jalviewjsSyncResources (type: Sync) {
3475 dependsOn buildResources
3477 def inputFiles = fileTree(dir: resourcesBuildDir)
3478 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3482 def outputFiles = []
3483 rename { filename ->
3484 outputFiles += "${outputDir}/${filename}"
3490 outputs.files outputFiles
3491 inputs.files inputFiles
3495 task jalviewjsSyncSiteResources (type: Sync) {
3496 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3497 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3501 def outputFiles = []
3502 rename { filename ->
3503 outputFiles += "${outputDir}/${filename}"
3509 outputs.files outputFiles
3510 inputs.files inputFiles
3514 task jalviewjsSyncBuildProperties (type: Sync) {
3515 dependsOn createBuildProperties
3516 def inputFiles = [file(buildProperties)]
3517 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3521 def outputFiles = []
3522 rename { filename ->
3523 outputFiles += "${outputDir}/${filename}"
3529 outputs.files outputFiles
3530 inputs.files inputFiles
3534 task jalviewjsProjectImport(type: Exec) {
3535 dependsOn eclipseSetup
3536 dependsOn jalviewjsEclipsePaths
3537 dependsOn jalviewjsEclipseSetup
3540 // do not run a headless import when we claim to be in Eclipse
3542 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3543 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3545 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3549 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3550 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3551 executable(eclipseBinary)
3552 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3556 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3558 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3559 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3562 inputs.file("${jalviewDir}/.project")
3563 outputs.upToDateWhen {
3564 file(projdir).exists()
3569 task jalviewjsTranspile(type: Exec) {
3570 dependsOn jalviewjsEclipseSetup
3571 dependsOn jalviewjsProjectImport
3572 dependsOn jalviewjsEclipsePaths
3574 dependsOn jalviewjsEnableAltFileProperty
3578 // do not run a headless transpile when we claim to be in Eclipse
3580 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3581 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3583 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3587 executable(eclipseBinary)
3588 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3592 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3594 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3595 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3601 stdout = new ByteArrayOutputStream()
3602 stderr = new ByteArrayOutputStream()
3604 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3605 def logOutFile = file(logOutFileName)
3606 logOutFile.createNewFile()
3607 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3608 BINARY: ${eclipseBinary}
3609 VERSION: ${eclipseVersion}
3610 WORKSPACE: ${eclipseWorkspace}
3611 DEBUG: ${eclipseDebug}
3614 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3615 // combine stdout and stderr
3616 def logErrFOS = logOutFOS
3618 if (jalviewjs_j2s_to_console.equals("true")) {
3619 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3620 new org.apache.tools.ant.util.TeeOutputStream(
3624 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3625 new org.apache.tools.ant.util.TeeOutputStream(
3630 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3633 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3640 if (stdout.toString().contains("Error processing ")) {
3641 // j2s did not complete transpile
3642 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3643 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3644 println("IGNORING TRANSPILE ERRORS")
3645 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3647 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3652 inputs.dir("${jalviewDir}/${sourceDir}")
3653 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3654 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3658 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3660 def stdout = new ByteArrayOutputStream()
3661 def stderr = new ByteArrayOutputStream()
3663 def coreFile = file(jsfile)
3665 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3667 logOutFile.createNewFile()
3668 logOutFile.append(msg+"\n")
3670 def coreTop = file(prefixFile)
3671 def coreBottom = file(suffixFile)
3672 coreFile.getParentFile().mkdirs()
3673 coreFile.createNewFile()
3674 coreFile.write( coreTop.getText("UTF-8") )
3678 def t = f.getText("UTF-8")
3679 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3680 coreFile.append( t )
3682 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3684 logOutFile.append(msg+"\n")
3687 coreFile.append( coreBottom.getText("UTF-8") )
3689 msg = "Generating ${zjsfile}"
3691 logOutFile.append(msg+"\n")
3692 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3693 def logErrFOS = logOutFOS
3696 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3697 main = "com.google.javascript.jscomp.CommandLineRunner"
3698 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3699 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3702 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3704 logOutFile.append(msg+"\n")
3706 if (logOutConsole) {
3707 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3708 new org.apache.tools.ant.util.TeeOutputStream(
3712 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3713 new org.apache.tools.ant.util.TeeOutputStream(
3718 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3721 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3728 logOutFile.append(msg+"\n")
3732 task jalviewjsBuildAllCores {
3734 description "Build the core js lib closures listed in the classlists dir"
3735 dependsOn jalviewjsTranspile
3736 dependsOn jalviewjsTransferUnzipSwingJs
3738 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3739 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3740 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3741 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3742 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3743 def prefixFile = "${jsDir}/core/coretop2.js"
3744 def suffixFile = "${jsDir}/core/corebottom2.js"
3746 inputs.file prefixFile
3747 inputs.file suffixFile
3749 def classlistFiles = []
3750 // add the classlists found int the jalviewjs_classlists_dir
3751 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3753 def name = file.getName() - ".txt"
3760 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3761 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3762 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3764 jalviewjsCoreClasslists = []
3766 classlistFiles.each {
3769 def file = hash['file']
3770 if (! file.exists()) {
3771 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3772 return false // this is a "continue" in groovy .each closure
3774 def name = hash['name']
3776 name = file.getName() - ".txt"
3784 def list = fileTree(dir: j2sDir, includes: filelist)
3786 def jsfile = "${outputDir}/core${name}.js"
3787 def zjsfile = "${outputDir}/core${name}.z.js"
3789 jalviewjsCoreClasslists += [
3798 outputs.file(jsfile)
3799 outputs.file(zjsfile)
3802 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3803 def stevesoftClasslistName = "_stevesoft"
3804 def stevesoftClasslist = [
3805 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3806 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3807 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3808 'name': stevesoftClasslistName
3810 jalviewjsCoreClasslists += stevesoftClasslist
3811 inputs.files(stevesoftClasslist['list'])
3812 outputs.file(stevesoftClasslist['jsfile'])
3813 outputs.file(stevesoftClasslist['zjsfile'])
3816 def allClasslistName = "_all"
3817 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3818 allJsFiles += fileTree(
3822 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3823 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3824 "**/org/jmol/export/JSExporter.js"
3827 allJsFiles += fileTree(
3831 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3832 "**/sun/misc/Unsafe.js",
3833 "**/swingjs/jquery/jquery-editable-select.js",
3834 "**/swingjs/jquery/j2sComboBox.js",
3835 "**/sun/misc/FloatingDecimal.js"
3838 def allClasslist = [
3839 'jsfile': "${outputDir}/core${allClasslistName}.js",
3840 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3842 'name': allClasslistName
3844 // not including this version of "all" core at the moment
3845 //jalviewjsCoreClasslists += allClasslist
3846 inputs.files(allClasslist['list'])
3847 outputs.file(allClasslist['jsfile'])
3848 outputs.file(allClasslist['zjsfile'])
3851 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3852 logOutFile.getParentFile().mkdirs()
3853 logOutFile.createNewFile()
3854 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3856 jalviewjsCoreClasslists.each {
3857 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3864 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3867 into file(outputFile).getParentFile()
3868 rename { filename ->
3869 if (filename.equals(inputFile.getName())) {
3870 return file(outputFile).getName()
3874 filter(ReplaceTokens,
3878 'MAIN': '"'+main_class+'"',
3880 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3881 'COREKEY': jalviewjs_core_key,
3882 'CORENAME': coreName
3889 task jalviewjsPublishCoreTemplates {
3890 dependsOn jalviewjsBuildAllCores
3891 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3892 def inputFile = file(inputFileName)
3893 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3895 def outputFiles = []
3896 jalviewjsCoreClasslists.each { cl ->
3897 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3898 cl['outputfile'] = outputFile
3899 outputFiles += outputFile
3903 jalviewjsCoreClasslists.each { cl ->
3904 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3907 inputs.file(inputFile)
3908 outputs.files(outputFiles)
3912 task jalviewjsSyncCore (type: Sync) {
3913 dependsOn jalviewjsBuildAllCores
3914 dependsOn jalviewjsPublishCoreTemplates
3915 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3916 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3920 def outputFiles = []
3921 rename { filename ->
3922 outputFiles += "${outputDir}/${filename}"
3928 outputs.files outputFiles
3929 inputs.files inputFiles
3933 // this Copy version of TransferSiteJs will delete anything else in the target dir
3934 task jalviewjsCopyTransferSiteJs(type: Copy) {
3935 dependsOn jalviewjsTranspile
3936 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3937 into "${jalviewDir}/${jalviewjsSiteDir}"
3941 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3942 task jalviewjsSyncTransferSiteJs(type: Sync) {
3943 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3945 into "${jalviewDir}/${jalviewjsSiteDir}"
3952 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3953 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3954 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3955 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3957 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3958 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3959 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3960 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3963 task jalviewjsPrepareSite {
3965 description "Prepares the website folder including unzipping files and copying resources"
3966 dependsOn jalviewjsSyncAllLibs
3967 dependsOn jalviewjsSyncResources
3968 dependsOn jalviewjsSyncSiteResources
3969 dependsOn jalviewjsSyncBuildProperties
3970 dependsOn jalviewjsSyncCore
3974 task jalviewjsBuildSite {
3976 description "Builds the whole website including transpiled code"
3977 dependsOn jalviewjsCopyTransferSiteJs
3978 dependsOn jalviewjsPrepareSite
3982 task cleanJalviewjsTransferSite {
3984 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3985 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3986 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3987 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3992 task cleanJalviewjsSite {
3993 dependsOn cleanJalviewjsTransferSite
3995 delete "${jalviewDir}/${jalviewjsSiteDir}"
4000 task jalviewjsSiteTar(type: Tar) {
4002 description "Creates a tar.gz file for the website"
4003 dependsOn jalviewjsBuildSite
4004 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
4005 archiveFileName = outputFilename
4007 compression Compression.GZIP
4009 from "${jalviewDir}/${jalviewjsSiteDir}"
4010 into jalviewjs_site_dir // this is inside the tar file
4012 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
4016 task jalviewjsServer {
4018 def filename = "jalviewjsTest.html"
4019 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
4020 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
4025 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
4026 factory = f.newInstance()
4027 } catch (ClassNotFoundException e) {
4028 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
4030 def port = Integer.valueOf(jalviewjs_server_port)
4035 while(port < start+1000 && !running) {
4037 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
4038 jalviewjsServer = factory.start(doc_root, port)
4040 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
4041 println("SERVER STARTED with document root ${doc_root}.")
4042 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
4043 println("For debug: "+url+"?j2sdebug")
4044 println("For verbose: "+url+"?j2sverbose")
4045 } catch (Exception e) {
4050 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
4051 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
4052 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4054 jalviewjsCoreClasslists.each { cl ->
4055 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4057 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4059 println("For core ${cl.name}: "+urlcore)
4062 file(htmlFile).text = htmlText
4065 outputs.file(htmlFile)
4066 outputs.upToDateWhen({false})
4070 task cleanJalviewjsAll {
4072 description "Delete all configuration and build artifacts to do with JalviewJS build"
4073 dependsOn cleanJalviewjsSite
4074 dependsOn jalviewjsEclipsePaths
4077 delete "${jalviewDir}/${jalviewjsBuildDir}"
4078 delete "${jalviewDir}/${eclipse_bin_dir}"
4079 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4080 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4082 delete jalviewjsJ2sAltSettingsFileName
4085 outputs.upToDateWhen( { false } )
4089 task jalviewjsIDE_checkJ2sPlugin {
4090 group "00 JalviewJS in Eclipse"
4091 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4094 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4095 def j2sPluginFile = file(j2sPlugin)
4096 def eclipseHome = System.properties["eclipse.home.location"]
4097 if (eclipseHome == null || ! IN_ECLIPSE) {
4098 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4100 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4101 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4102 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4103 eclipseJ2sPluginDirs += altPluginsDir
4105 def foundPlugin = false
4106 def j2sPluginFileName = j2sPluginFile.getName()
4107 def eclipseJ2sPlugin
4108 def eclipseJ2sPluginFile
4109 eclipseJ2sPluginDirs.any { dir ->
4110 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4111 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4112 if (eclipseJ2sPluginFile.exists()) {
4118 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4119 System.err.println(msg)
4120 throw new StopExecutionException(msg)
4123 def digest = MessageDigest.getInstance("MD5")
4125 digest.update(j2sPluginFile.text.bytes)
4126 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4128 digest.update(eclipseJ2sPluginFile.text.bytes)
4129 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4131 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4132 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4133 System.err.println(msg)
4134 throw new StopExecutionException(msg)
4136 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4142 task jalviewjsIDE_copyJ2sPlugin {
4143 group "00 JalviewJS in Eclipse"
4144 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4147 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4148 def j2sPluginFile = file(j2sPlugin)
4149 def eclipseHome = System.properties["eclipse.home.location"]
4150 if (eclipseHome == null || ! IN_ECLIPSE) {
4151 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4153 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4154 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4155 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4156 System.err.println(msg)
4159 eclipseJ2sPluginFile.getParentFile().mkdirs()
4160 into eclipseJ2sPluginFile.getParent()
4166 task jalviewjsIDE_j2sFile {
4167 group "00 JalviewJS in Eclipse"
4168 description "Creates the .j2s file"
4169 dependsOn jalviewjsCreateJ2sSettings
4173 task jalviewjsIDE_SyncCore {
4174 group "00 JalviewJS in Eclipse"
4175 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4176 dependsOn jalviewjsSyncCore
4180 task jalviewjsIDE_SyncSiteAll {
4181 dependsOn jalviewjsSyncAllLibs
4182 dependsOn jalviewjsSyncResources
4183 dependsOn jalviewjsSyncSiteResources
4184 dependsOn jalviewjsSyncBuildProperties
4188 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4191 task jalviewjsIDE_PrepareSite {
4192 group "00 JalviewJS in Eclipse"
4193 description "Sync libs and resources to site dir, but not closure cores"
4195 dependsOn jalviewjsIDE_SyncSiteAll
4196 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4200 task jalviewjsIDE_AssembleSite {
4201 group "00 JalviewJS in Eclipse"
4202 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4203 dependsOn jalviewjsPrepareSite
4207 task jalviewjsIDE_SiteClean {
4208 group "00 JalviewJS in Eclipse"
4209 description "Deletes the Eclipse transpiled site"
4210 dependsOn cleanJalviewjsSite
4214 task jalviewjsIDE_Server {
4215 group "00 JalviewJS in Eclipse"
4216 description "Starts a webserver on localhost to test the website"
4217 dependsOn jalviewjsServer
4221 // buildship runs this at import or gradle refresh
4222 task eclipseSynchronizationTask {
4223 //dependsOn eclipseSetup
4224 dependsOn createBuildProperties
4226 dependsOn jalviewjsIDE_j2sFile
4227 dependsOn jalviewjsIDE_checkJ2sPlugin
4228 dependsOn jalviewjsIDE_PrepareSite
4233 // buildship runs this at build time or project refresh
4234 task eclipseAutoBuildTask {
4235 //dependsOn jalviewjsIDE_checkJ2sPlugin
4236 //dependsOn jalviewjsIDE_PrepareSite
4240 task jalviewjsCopyStderrLaunchFile(type: Copy) {
4241 from file(jalviewjs_stderr_launch)
4242 into jalviewjsSiteDir
4244 inputs.file jalviewjs_stderr_launch
4245 outputs.file jalviewjsStderrLaunchFilename
4248 task cleanJalviewjsChromiumUserDir {
4250 delete jalviewjsChromiumUserDir
4252 outputs.dir jalviewjsChromiumUserDir
4253 // always run when depended on
4254 outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
4257 task jalviewjsChromiumProfile {
4258 dependsOn cleanJalviewjsChromiumUserDir
4259 mustRunAfter cleanJalviewjsChromiumUserDir
4261 def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
4264 mkdir jalviewjsChromiumProfileDir
4267 outputs.file firstRun
4270 task jalviewjsLaunchTest {
4272 description "Check JalviewJS opens in a browser"
4273 dependsOn jalviewjsBuildSite
4274 dependsOn jalviewjsCopyStderrLaunchFile
4275 dependsOn jalviewjsChromiumProfile
4277 def macOS = OperatingSystem.current().isMacOsX()
4278 def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
4279 if (chromiumBinary.startsWith("~/")) {
4280 chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
4286 def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
4288 def binary = file(chromiumBinary)
4289 if (!binary.exists()) {
4290 throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
4292 stdout = new ByteArrayOutputStream()
4293 stderr = new ByteArrayOutputStream()
4296 if (jalviewjs_j2s_to_console.equals("true")) {
4297 execStdout = new org.apache.tools.ant.util.TeeOutputStream(
4300 execStderr = new org.apache.tools.ant.util.TeeOutputStream(
4308 "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
4311 "--timeout=${timeoutms}",
4312 "--virtual-time-budget=${timeoutms}",
4313 "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
4314 "--profile-directory=${jalviewjs_chromium_profile_name}",
4315 "--allow-file-access-from-files",
4316 "--enable-logging=stderr",
4317 "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
4320 if (true || macOS) {
4321 ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
4322 Future f1 = executor.submit(
4325 standardOutput = execStdout
4326 errorOutput = execStderr
4327 executable(chromiumBinary)
4329 println "COMMAND: '"+commandLine.join(" ")+"'"
4331 executor.shutdownNow()
4335 def noChangeBytes = 0
4336 def noChangeIterations = 0
4337 executor.scheduleAtFixedRate(
4339 String stderrString = stderr.toString()
4340 // shutdown the task if we have a success string
4341 if (stderrString.contains(jalviewjs_desktop_init_string)) {
4344 executor.shutdownNow()
4346 // if no change in stderr for 10s then also end
4347 if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
4348 executor.shutdownNow()
4350 if (stderrString.length() == noChangeBytes) {
4351 noChangeIterations++
4353 noChangeBytes = stderrString.length()
4354 noChangeIterations = 0
4357 1, 1, TimeUnit.SECONDS)
4359 executor.schedule(new Runnable(){
4362 executor.shutdownNow()
4364 }, timeoutms, TimeUnit.MILLISECONDS)
4366 executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
4367 executor.shutdownNow()
4374 stderr.toString().eachLine { line ->
4375 if (line.contains(jalviewjs_desktop_init_string)) {
4376 println("Found line '"+line+"'")
4382 throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
4390 description "Build the JalviewJS site and run the launch test"
4391 dependsOn jalviewjsBuildSite
4392 dependsOn jalviewjsLaunchTest