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 groovy.transform.ExternalizeMethods
14 import groovy.util.XmlParser
15 import groovy.xml.XmlUtil
16 import groovy.json.JsonBuilder
17 import com.vladsch.flexmark.util.ast.Node
18 import com.vladsch.flexmark.html.HtmlRenderer
19 import com.vladsch.flexmark.parser.Parser
20 import com.vladsch.flexmark.util.data.MutableDataSet
21 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
22 import com.vladsch.flexmark.ext.tables.TablesExtension
23 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
24 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
25 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
26 import com.vladsch.flexmark.ext.toc.TocExtension
27 import com.google.common.hash.HashCode
28 import com.google.common.hash.Hashing
29 import com.google.common.io.Files
30 import org.jsoup.Jsoup
31 import org.jsoup.nodes.Element
39 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
40 classpath "org.jsoup:jsoup:1.14.3"
41 classpath "com.eowise:gradle-imagemagick:0.5.1"
50 id "com.diffplug.gradle.spotless" version "3.28.0"
51 id 'com.github.johnrengelman.shadow' version '4.0.3'
52 id 'com.install4j.gradle' version '10.0.3'
53 id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
54 id 'com.palantir.git-version' version '0.13.0' apply false
65 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
66 def string(Object o) {
67 return o == null ? "" : o.toString()
70 def overrideProperties(String propsFileName, boolean output = false) {
71 if (propsFileName == null) {
74 def propsFile = file(propsFileName)
75 if (propsFile != null && propsFile.exists()) {
76 println("Using properties from file '${propsFileName}'")
78 def p = new Properties()
79 def localPropsFIS = new FileInputStream(propsFile)
85 if (project.hasProperty(key)) {
86 oldval = project.findProperty(key)
87 project.setProperty(key, val)
89 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
92 ext.setProperty(key, val)
94 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
98 } catch (Exception e) {
99 println("Exception reading local.properties")
106 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
107 jalviewDirRelativePath = jalviewDir
110 getdownChannelName = CHANNEL.toLowerCase()
111 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
112 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
113 channelDirName = propertiesChannelName
114 // Import channel_properties
115 if (getdownChannelName.startsWith("develop-")) {
116 channelDirName = "develop-SUFFIX"
118 channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
119 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
120 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
121 overrideProperties(channelGradleProperties, false)
122 // local build environment properties
123 // can be "projectDir/local.properties"
124 overrideProperties("${projectDir}/local.properties", true)
125 // or "../projectDir_local.properties"
126 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
129 // Import releaseProps from the RELEASE file
130 // or a file specified via JALVIEW_RELEASE_FILE if defined
131 // Expect jalview.version and target release branch in jalview.release
132 releaseProps = new Properties();
133 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
134 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
136 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
137 releaseProps.load(it)
139 } catch (Exception fileLoadError) {
140 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
143 // Set JALVIEW_VERSION if it is not already set
144 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
145 JALVIEW_VERSION = releaseProps.get("jalview.version")
147 println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
149 // this property set when running Eclipse headlessly
150 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
151 // this property set by Eclipse
152 eclipseApplicationProperty = string("eclipse.application")
153 // CHECK IF RUNNING FROM WITHIN ECLIPSE
154 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
155 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
156 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
157 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
158 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
162 println("WITHIN ECLIPSE IDE")
164 println("HEADLESS BUILD")
167 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
169 println("J2S ENABLED")
172 System.properties.sort { it.key }.each {
173 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
176 if (false && IN_ECLIPSE) {
177 jalviewDir = jalviewDirAbsolutePath
182 buildDate = new Date().format("yyyyMMdd")
185 bareSourceDir = string(source_dir)
186 sourceDir = string("${jalviewDir}/${bareSourceDir}")
187 resourceDir = string("${jalviewDir}/${resource_dir}")
188 bareTestSourceDir = string(test_source_dir)
189 testDir = string("${jalviewDir}/${bareTestSourceDir}")
191 classesDir = string("${jalviewDir}/${classes_dir}")
194 useClover = clover.equals("true")
195 cloverBuildDir = "${buildDir}/clover"
196 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
197 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
198 cloverReportDir = file("${buildDir}/reports/clover")
199 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
200 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
201 //cloverTestClassesDir = cloverClassesDir
202 cloverDb = string("${cloverBuildDir}/clover.db")
204 testSourceDir = useClover ? cloverTestInstrDir : testDir
205 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
208 backgroundImageText = BACKGROUNDIMAGETEXT
209 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
210 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
211 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
212 getdownFullArchiveDir = null
213 getdownTextLines = []
214 getdownLaunchJvl = null
215 getdownVersionLaunchJvl = null
217 buildProperties = null
219 // the following values might be overridden by the CHANNEL switch
220 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
221 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
222 getdownArchiveAppBase = getdown_archive_base
223 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
224 getdownAppDistDir = getdown_app_dir_alt
225 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
226 getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
227 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
228 reportRsyncCommand = false
229 jvlChannelName = CHANNEL.toLowerCase()
230 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
231 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
232 install4jDMGBackgroundImageDir = "${install4j_images_dir}"
233 install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
234 install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
235 install4jInstallerName = "${jalview_name} Non-Release Installer"
236 install4jExecutableName = install4j_executable_name
237 install4jExtraScheme = "jalviewx"
238 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
239 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
240 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
241 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
242 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
243 install4jCheckSums = true
245 applicationName = "${jalview_name}"
249 // TODO: get bamboo build artifact URL for getdown artifacts
250 getdown_channel_base = bamboo_channelbase
251 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
252 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
253 jvlChannelName += "_${getdownChannelName}"
254 // automatically add the test group Not-bamboo for exclusion
255 if ("".equals(testng_excluded_groups)) {
256 testng_excluded_groups = "Not-bamboo"
258 install4jExtraScheme = "jalviewb"
259 backgroundImageText = true
262 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
263 getdownAppDistDir = getdown_app_dir_release
264 getdownSetAppBaseProperty = true
265 reportRsyncCommand = true
267 install4jInstallerName = "${jalview_name} Installer"
271 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
272 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
273 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
274 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
275 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
277 package_dir = string("${ARCHIVEDIR}/${package_dir}")
278 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
281 reportRsyncCommand = true
282 install4jExtraScheme = "jalviewa"
286 getdownChannelName = string("archive/${JALVIEW_VERSION}")
287 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
288 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
289 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
290 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
292 package_dir = string("${ARCHIVEDIR}/${package_dir}")
293 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
296 reportRsyncCommand = true
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
298 install4jSuffix = "Archive"
299 install4jExtraScheme = "jalviewa"
302 case ~/^DEVELOP-([\.\-\w]*)$/:
303 def suffix = Matcher.lastMatcher[0][1]
304 reportRsyncCommand = true
305 getdownSetAppBaseProperty = true
306 JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
307 install4jSuffix = "Develop ${suffix}"
308 install4jExtraScheme = "jalviewd"
309 install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
310 getdownChannelName = string("develop-${suffix}")
311 getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
312 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
313 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
314 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
315 channelSuffix = string(suffix)
316 backgroundImageText = true
320 reportRsyncCommand = true
321 getdownSetAppBaseProperty = true
322 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
323 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
325 install4jSuffix = "Develop"
326 install4jExtraScheme = "jalviewd"
327 install4jInstallerName = "${jalview_name} Develop Installer"
328 backgroundImageText = true
332 reportRsyncCommand = true
333 getdownSetAppBaseProperty = true
334 // Don't ignore transpile errors for release build
335 if (jalviewjs_ignore_transpile_errors.equals("true")) {
336 jalviewjs_ignore_transpile_errors = "false"
337 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
339 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
340 install4jSuffix = "Test"
341 install4jExtraScheme = "jalviewt"
342 install4jInstallerName = "${jalview_name} Test Installer"
343 backgroundImageText = true
346 case ~/^SCRATCH(|-[-\w]*)$/:
347 getdownChannelName = CHANNEL
348 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
350 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
351 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
352 reportRsyncCommand = true
353 install4jSuffix = "Scratch"
357 if (!file("${LOCALDIR}").exists()) {
358 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
360 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
361 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
363 JALVIEW_VERSION = "TEST"
364 install4jSuffix = "Test-Local"
365 install4jExtraScheme = "jalviewt"
366 install4jInstallerName = "${jalview_name} Test Installer"
367 backgroundImageText = true
370 case [ "LOCAL", "JALVIEWJS" ]:
371 JALVIEW_VERSION = "TEST"
372 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
373 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
374 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
375 install4jExtraScheme = "jalviewl"
376 install4jCheckSums = false
379 default: // something wrong specified
380 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
384 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
385 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
386 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
387 // override getdownAppBase if requested
388 if (findProperty("getdown_appbase_override") != null) {
389 // revert to LOCAL if empty string
390 if (string(getdown_appbase_override) == "") {
391 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
392 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
393 } else if (string(getdown_appbase_override).startsWith("file://")) {
394 getdownAppBase = string(getdown_appbase_override)
395 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
397 getdownAppBase = string(getdown_appbase_override)
399 println("Overriding getdown appbase with '${getdownAppBase}'")
401 // sanitise file name for jalview launcher file for this channel
402 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
403 // install4j application and folder names
404 if (install4jSuffix == "") {
405 install4jBundleId = "${install4j_bundle_id}"
406 install4jWinApplicationId = install4j_release_win_application_id
408 applicationName = "${jalview_name} ${install4jSuffix}"
409 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
410 // add int hash of install4jSuffix to the last part of the application_id
411 def id = install4j_release_win_application_id
412 def idsplitreverse = id.split("-").reverse()
413 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
414 install4jWinApplicationId = idsplitreverse.reverse().join("-")
416 // sanitise folder and id names
417 // install4jApplicationFolder = e.g. "Jalview Build"
418 install4jApplicationFolder = applicationName
419 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
420 .replaceAll("_+", "_") // collapse __
421 install4jInternalId = applicationName
423 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
424 .replaceAll("_+", "") // collapse __
425 //.replaceAll("_*-_*", "-") // collapse _-_
426 install4jUnixApplicationFolder = applicationName
428 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
429 .replaceAll("_+", "_") // collapse __
430 .replaceAll("_*-_*", "-") // collapse _-_
433 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
434 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
435 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
436 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
437 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
438 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
439 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
440 /* compile without modules -- using classpath libraries
441 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
442 modules_runtimeClasspath = modules_compileClasspath
448 apply plugin: "com.palantir.git-version"
449 def details = versionDetails()
450 gitHash = details.gitHash
451 gitBranch = details.branchName
452 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
453 println("Not in a git repository. Using git values from RELEASE properties file.")
454 gitHash = releaseProps.getProperty("git.hash")
455 gitBranch = releaseProps.getProperty("git.branch")
456 } catch(java.lang.RuntimeException e1) {
457 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
460 println("Using a ${CHANNEL} profile.")
462 additional_compiler_args = []
463 // configure classpath/args for j8/j11 compilation
464 if (JAVA_VERSION.equals("1.8")) {
465 JAVA_INTEGER_VERSION = string("8")
468 libDistDir = j8libDir
469 compile_source_compatibility = 1.8
470 compile_target_compatibility = 1.8
471 // these are getdown.txt properties defined dependent on the JAVA_VERSION
472 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
473 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
474 // this property is assigned below and expanded to multiple lines in the getdown task
475 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
476 // this property is for the Java library used in eclipse
477 eclipseJavaRuntimeName = string("JavaSE-1.8")
478 } else if (JAVA_VERSION.equals("11")) {
479 JAVA_INTEGER_VERSION = string("11")
481 libDistDir = j11libDir
482 compile_source_compatibility = 11
483 compile_target_compatibility = 11
484 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
485 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
486 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
487 eclipseJavaRuntimeName = string("JavaSE-11")
488 /* compile without modules -- using classpath libraries
489 additional_compiler_args += [
490 '--module-path', modules_compileClasspath.asPath,
491 '--add-modules', j11modules
494 } else if (JAVA_VERSION.equals("17")) {
495 JAVA_INTEGER_VERSION = string("17")
497 libDistDir = j17libDir
498 compile_source_compatibility = 17
499 compile_target_compatibility = 17
500 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
501 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
502 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
503 eclipseJavaRuntimeName = string("JavaSE-17")
504 /* compile without modules -- using classpath libraries
505 additional_compiler_args += [
506 '--module-path', modules_compileClasspath.asPath,
507 '--add-modules', j11modules
511 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
516 JAVA_MIN_VERSION = JAVA_VERSION
517 JAVA_MAX_VERSION = JAVA_VERSION
518 jreInstallsDir = string(jre_installs_dir)
519 if (jreInstallsDir.startsWith("~/")) {
520 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
522 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
523 install4jConfFileName = string("jalview-install4j-conf.install4j")
524 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
525 install4jHomeDir = install4j_home_dir
526 if (install4jHomeDir.startsWith("~/")) {
527 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
530 resourceBuildDir = string("${buildDir}/resources")
531 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
532 helpBuildDir = string("${resourceBuildDir}/help_build")
533 docBuildDir = string("${resourceBuildDir}/doc_build")
535 if (buildProperties == null) {
536 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
538 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
539 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
540 helpSourceDir = string("${helpParentDir}/${help_dir}")
541 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
544 convertBinaryExpectedLocation = imagemagick_convert
545 if (convertBinaryExpectedLocation.startsWith("~/")) {
546 convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
548 if (file(convertBinaryExpectedLocation).exists()) {
549 convertBinary = convertBinaryExpectedLocation
552 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
553 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
554 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
556 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
558 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
560 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
561 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
562 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
563 jalviewjsJalviewCoreHtmlFile = string("")
564 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
565 jalviewjsCoreClasslists = []
566 jalviewjsJalviewTemplateName = string(jalviewjs_name)
567 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
568 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
569 jalviewjsJ2sProps = null
570 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
572 eclipseWorkspace = null
573 eclipseBinary = string("")
574 eclipseVersion = string("")
584 outputDir = file(classesDir)
588 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
591 compileClasspath = files(sourceSets.main.java.outputDir)
592 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
594 runtimeClasspath = compileClasspath
595 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
600 srcDirs cloverInstrDir
601 outputDir = cloverClassesDir
605 srcDirs = sourceSets.main.resources.srcDirs
608 compileClasspath = files( sourceSets.clover.java.outputDir )
609 //compileClasspath += files( testClassesDir )
610 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
611 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
612 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
614 runtimeClasspath = compileClasspath
619 srcDirs testSourceDir
620 outputDir = file(testClassesDir)
624 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
627 compileClasspath = files( sourceSets.test.java.outputDir )
628 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
629 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
631 runtimeClasspath = compileClasspath
632 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
638 // eclipse project and settings files creation, also used by buildship
641 name = eclipse_project_name
643 natures 'org.eclipse.jdt.core.javanature',
644 'org.eclipse.jdt.groovy.core.groovyNature',
645 'org.eclipse.buildship.core.gradleprojectnature'
647 buildCommand 'org.eclipse.jdt.core.javabuilder'
648 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
652 //defaultOutputDir = sourceSets.main.java.outputDir
653 configurations.each{ c->
654 if (c.isCanBeResolved()) {
655 minusConfigurations += [c]
659 plusConfigurations = [ ]
663 def removeTheseToo = []
664 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
665 cp.entries.each { entry ->
666 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
667 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
668 // we add the resources and help/help dirs in as libs afterwards (see below)
669 if (entry.kind == 'src') {
670 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
671 removeTheseToo += entry
673 alreadyAddedSrcPath.putAt(entry.path, true)
678 cp.entries.removeAll(removeTheseToo)
680 //cp.entries += new Output("${eclipse_bin_dir}/main")
681 if (file(helpParentDir).isDirectory()) {
682 cp.entries += new Library(fileReference(helpParentDir))
684 if (file(resourceDir).isDirectory()) {
685 cp.entries += new Library(fileReference(resourceDir))
688 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
690 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
691 //don't want to add outputDir as eclipse is using its own output dir in bin/main
692 if (it.isDirectory() || ! it.exists()) {
693 // don't add dirs to classpath, especially if they don't exist
694 return false // groovy "continue" in .any closure
696 def itPath = it.toString()
697 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
698 // make relative path
699 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
701 if (alreadyAddedLibPath.get(itPath)) {
702 //println("Not adding duplicate entry "+itPath)
704 //println("Adding entry "+itPath)
705 cp.entries += new Library(fileReference(itPath))
706 alreadyAddedLibPath.put(itPath, true)
710 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
711 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
712 if (it.isDirectory() || ! it.exists()) {
713 // don't add dirs to classpath
714 return false // groovy "continue" in .any closure
717 def itPath = it.toString()
718 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
719 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
721 if (alreadyAddedLibPath.get(itPath)) {
724 def lib = new Library(fileReference(itPath))
725 lib.entryAttributes["test"] = "true"
727 alreadyAddedLibPath.put(itPath, true)
735 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
740 // for the IDE, use java 11 compatibility
741 sourceCompatibility = compile_source_compatibility
742 targetCompatibility = compile_target_compatibility
743 javaRuntimeName = eclipseJavaRuntimeName
745 // add in jalview project specific properties/preferences into eclipse core preferences
747 withProperties { props ->
748 def jalview_prefs = new Properties()
749 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
750 jalview_prefs.load(ins)
752 jalview_prefs.forEach { t, v ->
753 if (props.getAt(t) == null) {
757 // codestyle file -- overrides previous formatter prefs
758 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
759 if (csFile.exists()) {
760 XmlParser parser = new XmlParser()
761 def profiles = parser.parse(csFile)
762 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
763 if (profile != null) {
764 profile.'setting'.each { s ->
766 def value = s.'@value'
767 if (id != null && value != null) {
768 props.putAt(id, value)
779 // Don't want these to be activated if in headless build
780 synchronizationTasks "eclipseSynchronizationTask"
781 //autoBuildTasks "eclipseAutoBuildTask"
787 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
788 // Class to allow updating arbitrary properties files
789 class PropertiesFile extends PropertiesPersistableConfigurationObject {
790 public PropertiesFile(PropertiesTransformer t) { super(t); }
791 @Override protected void load(Properties properties) { }
792 @Override protected void store(Properties properties) { }
793 @Override protected String getDefaultResourceName() { return ""; }
794 // This is necessary, because PropertiesPersistableConfigurationObject fails
795 // if no default properties file exists.
796 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
799 // Task to update arbitrary properties files (set outputFile)
800 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
801 private final PropertiesFileContentMerger file;
802 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
803 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
804 protected void configure(PropertiesFile props) {
805 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
807 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
810 task eclipseUIPreferences(type: PropertiesFileTask) {
811 description = "Generate Eclipse additional settings"
812 def filename = "org.eclipse.jdt.ui.prefs"
813 outputFile = "$projectDir/.settings/${filename}" as File
816 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
821 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
822 description = "Generate Eclipse additional settings"
823 def filename = "org.eclipse.jdt.groovy.core.prefs"
824 outputFile = "$projectDir/.settings/${filename}" as File
827 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
832 task eclipseAllPreferences {
834 dependsOn eclipseUIPreferences
835 dependsOn eclipseGroovyCorePreferences
838 eclipseUIPreferences.mustRunAfter eclipseJdt
839 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
841 /* end of eclipse preferences hack */
849 delete cloverBuildDir
850 delete cloverReportDir
855 task cloverInstrJava(type: JavaExec) {
856 group = "Verification"
857 description = "Create clover instrumented source java files"
859 dependsOn cleanClover
861 inputs.files(sourceSets.main.allJava)
862 outputs.dir(cloverInstrDir)
864 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
865 classpath = sourceSets.clover.compileClasspath
866 main = "com.atlassian.clover.CloverInstr"
874 cloverInstrDir.getPath(),
876 def srcFiles = sourceSets.main.allJava.files
879 { file -> file.absolutePath }
882 args argsList.toArray()
885 delete cloverInstrDir
886 println("Clover: About to instrument "+srcFiles.size() +" files")
891 task cloverInstrTests(type: JavaExec) {
892 group = "Verification"
893 description = "Create clover instrumented source test files"
895 dependsOn cleanClover
897 inputs.files(testDir)
898 outputs.dir(cloverTestInstrDir)
900 classpath = sourceSets.clover.compileClasspath
901 main = "com.atlassian.clover.CloverInstr"
911 cloverTestInstrDir.getPath(),
913 args argsList.toArray()
916 delete cloverTestInstrDir
917 println("Clover: About to instrument test files")
923 group = "Verification"
924 description = "Create clover instrumented all source files"
926 dependsOn cloverInstrJava
927 dependsOn cloverInstrTests
931 cloverClasses.dependsOn cloverInstr
934 task cloverConsoleReport(type: JavaExec) {
935 group = "Verification"
936 description = "Creates clover console report"
939 file(cloverDb).exists()
942 inputs.dir cloverClassesDir
944 classpath = sourceSets.clover.runtimeClasspath
945 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
947 if (cloverreport_mem.length() > 0) {
948 maxHeapSize = cloverreport_mem
950 if (cloverreport_jvmargs.length() > 0) {
951 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
961 args argsList.toArray()
965 task cloverHtmlReport(type: JavaExec) {
966 group = "Verification"
967 description = "Creates clover HTML report"
970 file(cloverDb).exists()
973 def cloverHtmlDir = cloverReportDir
974 inputs.dir cloverClassesDir
975 outputs.dir cloverHtmlDir
977 classpath = sourceSets.clover.runtimeClasspath
978 main = "com.atlassian.clover.reporters.html.HtmlReporter"
980 if (cloverreport_mem.length() > 0) {
981 maxHeapSize = cloverreport_mem
983 if (cloverreport_jvmargs.length() > 0) {
984 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
995 if (cloverreport_html_options.length() > 0) {
996 argsList += cloverreport_html_options.split(" ")
999 args argsList.toArray()
1003 task cloverXmlReport(type: JavaExec) {
1004 group = "Verification"
1005 description = "Creates clover XML report"
1008 file(cloverDb).exists()
1011 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1012 inputs.dir cloverClassesDir
1013 outputs.file cloverXmlFile
1015 classpath = sourceSets.clover.runtimeClasspath
1016 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1018 if (cloverreport_mem.length() > 0) {
1019 maxHeapSize = cloverreport_mem
1021 if (cloverreport_jvmargs.length() > 0) {
1022 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1033 if (cloverreport_xml_options.length() > 0) {
1034 argsList += cloverreport_xml_options.split(" ")
1037 args argsList.toArray()
1042 group = "Verification"
1043 description = "Creates clover reports"
1045 dependsOn cloverXmlReport
1046 dependsOn cloverHtmlReport
1053 sourceCompatibility = compile_source_compatibility
1054 targetCompatibility = compile_target_compatibility
1055 options.compilerArgs += additional_compiler_args
1056 print ("Setting target compatibility to "+targetCompatibility+"\n")
1058 //classpath += configurations.cloverRuntime
1064 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1065 sourceCompatibility = compile_source_compatibility
1066 targetCompatibility = compile_target_compatibility
1067 options.compilerArgs += additional_compiler_args
1068 options.encoding = "UTF-8"
1070 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1077 sourceCompatibility = compile_source_compatibility
1078 targetCompatibility = compile_target_compatibility
1079 options.compilerArgs += additional_compiler_args
1081 print ("Setting target compatibility to "+targetCompatibility+"\n")
1088 delete sourceSets.main.java.outputDir
1094 dependsOn cleanClover
1096 delete sourceSets.test.java.outputDir
1101 // format is a string like date.format("dd MMMM yyyy")
1102 def getDate(format) {
1103 return date.format(format)
1107 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1108 MutableDataSet options = new MutableDataSet()
1110 def extensions = new ArrayList<>()
1111 extensions.add(AnchorLinkExtension.create())
1112 extensions.add(AutolinkExtension.create())
1113 extensions.add(StrikethroughExtension.create())
1114 extensions.add(TaskListExtension.create())
1115 extensions.add(TablesExtension.create())
1116 extensions.add(TocExtension.create())
1118 options.set(Parser.EXTENSIONS, extensions)
1120 // set GFM table parsing options
1121 options.set(TablesExtension.WITH_CAPTION, false)
1122 options.set(TablesExtension.COLUMN_SPANS, false)
1123 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1124 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1125 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1126 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1127 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1129 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1130 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1131 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1132 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1134 Parser parser = Parser.builder(options).build()
1135 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1137 mdFiles.each { mdFile ->
1138 // add table of contents
1139 def mdText = "[TOC]\n"+mdFile.text
1141 // grab the first top-level title
1143 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1144 def matcher = mdText =~ titleRegex
1145 if (matcher.size() > 0) {
1146 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1147 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1149 // or use the filename if none found
1150 if (title == null) {
1151 title = mdFile.getName()
1154 Node document = parser.parse(mdText)
1155 String htmlBody = renderer.render(document)
1156 def htmlText = '''<html>
1157 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1158 <html xmlns="http://www.w3.org/1999/xhtml">
1160 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1161 <meta http-equiv="Content-Style-Type" content="text/css" />
1162 <meta name="generator" content="flexmark" />
1164 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1166 <style type="text/css">code{white-space: pre;}</style>
1168 htmlText += ((cssFile != null) ? cssFile.text : '')
1169 htmlText += '''</head>
1172 htmlText += htmlBody
1178 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1179 def htmlFile = file(htmlFilePath)
1180 println("Creating ${htmlFilePath}")
1181 htmlFile.text = htmlText
1186 task copyDocs(type: Copy) {
1187 def inputDir = "${jalviewDir}/${doc_dir}"
1188 def outputDir = "${docBuildDir}/${doc_dir}"
1192 include('**/*.html')
1194 filter(ReplaceTokens,
1198 'Version-Rel': JALVIEW_VERSION,
1199 'Year-Rel': getDate("yyyy")
1206 exclude('**/*.html')
1211 inputs.dir(inputDir)
1212 outputs.dir(outputDir)
1216 task convertMdFiles {
1218 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1219 def cssFile = file("${jalviewDir}/${flexmark_css}")
1222 convertMdToHtml(mdFiles, cssFile)
1225 inputs.files(mdFiles)
1226 inputs.file(cssFile)
1229 mdFiles.each { mdFile ->
1230 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1231 htmlFiles.add(file(htmlFilePath))
1233 outputs.files(htmlFiles)
1237 def hugoTemplateSubstitutions(String input, Map extras=null) {
1238 def replacements = [
1239 DATE: getDate("yyyy-MM-dd"),
1240 CHANNEL: propertiesChannelName,
1241 APPLICATION_NAME: applicationName,
1243 GIT_BRANCH: gitBranch,
1244 VERSION: JALVIEW_VERSION,
1245 JAVA_VERSION: JAVA_VERSION,
1246 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1251 if (extras != null) {
1252 extras.each{ k, v ->
1253 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1256 replacements.each{ k, v ->
1257 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1262 def mdFileComponents(File mdFile, def dateOnly=false) {
1265 if (mdFile.exists()) {
1266 def inFrontMatter = false
1267 def firstLine = true
1268 mdFile.eachLine { line ->
1269 if (line.matches("---")) {
1270 def prev = inFrontMatter
1271 inFrontMatter = firstLine
1272 if (inFrontMatter != prev)
1275 if (inFrontMatter) {
1277 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1278 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1279 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1280 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1281 } else if (m = line =~ /^channel:\s*(\S+)/) {
1282 map["channel"] = m[0][1]
1283 } else if (m = line =~ /^version:\s*(\S+)/) {
1284 map["version"] = m[0][1]
1285 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1286 map[ m[0][1] ] = m[0][2]
1288 if (dateOnly && map["date"] != null) {
1294 content += line+"\n"
1299 return dateOnly ? map["date"] : [map, content]
1302 task hugoTemplates {
1304 description "Create partially populated md pages for hugo website build"
1306 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1307 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1308 def templateFiles = fileTree(dir: hugoTemplatesDir)
1309 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1310 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1311 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1312 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1315 // specific release template for version archive
1318 def givenDate = null
1319 def givenChannel = null
1320 def givenVersion = null
1321 if (CHANNEL == "RELEASE") {
1322 def (map, content) = mdFileComponents(releaseMdFile)
1323 givenDate = map.date
1324 givenChannel = map.channel
1325 givenVersion = map.version
1327 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1328 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1331 if (whatsnewMdFile.exists())
1332 whatsnew = whatsnewMdFile.text
1335 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1336 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1338 def changesHugo = null
1339 if (changes != null) {
1340 changesHugo = '<div class="release_notes">\n\n'
1341 def inSection = false
1342 changes.eachLine { line ->
1344 if (m = line =~ /^##([^#].*)$/) {
1346 changesHugo += "</div>\n\n"
1348 def section = m[0][1].trim()
1349 section = section.toLowerCase()
1350 section = section.replaceAll(/ +/, "_")
1351 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1352 changesHugo += "<div class=\"${section}\">\n\n"
1354 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1355 def comment = m[0][2].trim()
1356 if (comment != "") {
1357 comment = comment.replaceAll('"', """)
1359 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1360 def newline = m[0][1]
1361 if (comment.trim() != "")
1362 newline += "{{<comment>}}${comment}{{</comment>}} "
1363 newline += m[0][3].trim()
1364 if (issuekeys.size() > 0)
1365 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1366 if (m[0][4] != null)
1371 changesHugo += line+"\n"
1374 changesHugo += "\n</div>\n\n"
1376 changesHugo += '</div>'
1379 templateFiles.each{ templateFile ->
1380 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1381 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1382 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1384 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1388 rename(templateFile.getName(), newFileName)
1392 def newFile = file("${outPathName}/${newFileName}".toString())
1393 def content = newFile.text
1394 newFile.text = hugoTemplateSubstitutions(content,
1397 CHANGES: changesHugo,
1398 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1399 DRAFT: givenDate == null ? "true" : "false",
1400 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1401 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1408 inputs.file(oldJvlFile)
1409 inputs.dir(hugoTemplatesDir)
1410 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1411 inputs.property("CHANNEL", { CHANNEL })
1414 def getMdDate(File mdFile) {
1415 return mdFileComponents(mdFile, true)
1418 def getMdSections(String content) {
1420 def sectionContent = ""
1421 def sectionName = null
1422 content.eachLine { line ->
1424 if (m = line =~ /^##([^#].*)$/) {
1425 if (sectionName != null) {
1426 sections[sectionName] = sectionContent
1430 sectionName = m[0][1].trim()
1431 sectionName = sectionName.toLowerCase()
1432 sectionName = sectionName.replaceAll(/ +/, "_")
1433 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1434 } else if (sectionName != null) {
1435 sectionContent += line+"\n"
1438 if (sectionContent != null) {
1439 sections[sectionName] = sectionContent
1445 task copyHelp(type: Copy) {
1446 def inputDir = helpSourceDir
1447 def outputDir = "${helpBuildDir}/${help_dir}"
1451 include('**/*.html')
1455 filter(ReplaceTokens,
1459 'Version-Rel': JALVIEW_VERSION,
1460 'Year-Rel': getDate("yyyy")
1467 exclude('**/*.html')
1474 inputs.dir(inputDir)
1475 outputs.files(helpFile)
1476 outputs.dir(outputDir)
1480 task releasesTemplates {
1482 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1486 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1487 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1488 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1489 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1490 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1491 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1494 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1495 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1497 if (CHANNEL == "RELEASE") {
1498 if (!releaseMdFile.exists()) {
1499 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1501 if (!whatsnewMdFile.exists()) {
1502 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1506 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1507 def releaseFilesDates = releaseFiles.collectEntries {
1508 [(it): getMdDate(it)]
1510 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1512 def releasesTemplate = releasesTemplateFile.text
1513 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1514 def versionTemplate = m[0][1]
1516 MutableDataSet options = new MutableDataSet()
1518 def extensions = new ArrayList<>()
1519 options.set(Parser.EXTENSIONS, extensions)
1520 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1522 Parser parser = Parser.builder(options).build()
1523 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1525 def actualVersions = releaseFiles.collect { rf ->
1526 def (rfMap, rfContent) = mdFileComponents(rf)
1527 return rfMap.version
1529 def versionsHtml = ""
1530 def linkedVersions = []
1531 releaseFiles.reverse().each { rFile ->
1532 def (rMap, rContent) = mdFileComponents(rFile)
1534 def versionLink = ""
1535 def partialVersion = ""
1536 def firstPart = true
1537 rMap.version.split("\\.").each { part ->
1538 def displayPart = ( firstPart ? "" : "." ) + part
1539 partialVersion += displayPart
1541 linkedVersions.contains(partialVersion)
1542 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1544 versionLink += displayPart
1546 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1547 linkedVersions += partialVersion
1551 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1554 def rContentProcessed = ""
1555 rContent.eachLine { line ->
1556 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1557 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1558 } else if (lm = line =~ /^###([^#]+.*)$/) {
1559 line = "_${lm[0][1].trim()}_"
1561 rContentProcessed += line + "\n"
1564 def rContentSections = getMdSections(rContentProcessed)
1565 def rVersion = versionTemplate
1566 if (rVersion != "") {
1567 def rNewFeatures = rContentSections["new_features"]
1568 def rIssuesResolved = rContentSections["issues_resolved"]
1569 Node newFeaturesNode = parser.parse(rNewFeatures)
1570 String newFeaturesHtml = renderer.render(newFeaturesNode)
1571 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1572 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1573 rVersion = hugoTemplateSubstitutions(rVersion,
1575 VERSION: rMap.version,
1576 VERSION_LINK: versionLink,
1577 DISPLAY_DATE: displayDate,
1578 NEW_FEATURES: newFeaturesHtml,
1579 ISSUES_RESOLVED: issuesResolvedHtml
1582 versionsHtml += rVersion
1586 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1587 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1588 releasesHtmlFile.text = releasesTemplate
1590 if (whatsnewMdFile.exists()) {
1591 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1592 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1593 Node whatsnewNode = parser.parse(whatsnewMd)
1594 String whatsnewHtml = renderer.render(whatsnewNode)
1595 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1596 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1598 VERSION: JALVIEW_VERSION,
1599 DISPLAY_DATE: wnDisplayDate
1602 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1603 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1608 inputs.file(releasesTemplateFile)
1609 inputs.file(whatsnewTemplateFile)
1610 inputs.dir(releasesMdDir)
1611 inputs.dir(whatsnewMdDir)
1612 outputs.file(releasesHtmlFile)
1613 outputs.file(whatsnewHtmlFile)
1617 task copyResources(type: Copy) {
1619 description = "Copy (and make text substitutions in) the resources dir to the build area"
1621 def inputDir = resourceDir
1622 def outputDir = resourcesBuildDir
1626 include('**/*.html')
1628 filter(ReplaceTokens,
1632 'Version-Rel': JALVIEW_VERSION,
1633 'Year-Rel': getDate("yyyy")
1640 exclude('**/*.html')
1645 inputs.dir(inputDir)
1646 outputs.dir(outputDir)
1649 task copyChannelResources(type: Copy) {
1650 dependsOn copyResources
1652 description = "Copy the channel resources dir to the build resources area"
1654 def inputDir = "${channelDir}/${resource_dir}"
1655 def outputDir = resourcesBuildDir
1657 include(channel_props)
1658 filter(ReplaceTokens,
1662 'SUFFIX': channelSuffix
1667 exclude(channel_props)
1671 inputs.dir(inputDir)
1672 outputs.dir(outputDir)
1675 task createBuildProperties(type: WriteProperties) {
1676 dependsOn copyResources
1678 description = "Create the ${buildProperties} file"
1680 inputs.dir(sourceDir)
1681 inputs.dir(resourcesBuildDir)
1682 outputFile (buildProperties)
1683 // taking time specific comment out to allow better incremental builds
1684 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1685 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1686 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1687 property "VERSION", JALVIEW_VERSION
1688 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1689 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1690 if (getdownSetAppBaseProperty) {
1691 property "GETDOWNAPPBASE", getdownAppBase
1692 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1694 outputs.file(outputFile)
1698 task buildIndices(type: JavaExec) {
1700 classpath = sourceSets.main.compileClasspath
1701 main = "com.sun.java.help.search.Indexer"
1702 workingDir = "${helpBuildDir}/${help_dir}"
1705 inputs.dir("${workingDir}/${argDir}")
1707 outputs.dir("${classesDir}/doc")
1708 outputs.dir("${classesDir}/help")
1709 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1710 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1711 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1712 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1713 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1714 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1717 task buildResources {
1718 dependsOn copyResources
1719 dependsOn copyChannelResources
1720 dependsOn createBuildProperties
1724 dependsOn buildResources
1727 dependsOn releasesTemplates
1728 dependsOn convertMdFiles
1729 dependsOn buildIndices
1733 compileJava.dependsOn prepare
1734 run.dependsOn compileJava
1735 compileTestJava.dependsOn compileJava
1738 ext.testsFailed = false
1739 /* testTask0 is the main test task */
1740 task testTask0(type: Test) {
1741 group = "Verification"
1742 description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
1744 includeGroups testng_groups.split(",")
1745 excludeGroups testng_excluded_groups.split(",")
1746 tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
1748 useDefaultListeners=true
1752 /* separated tests */
1753 task testTask1(type: Test) {
1754 group = "Verification"
1755 description = "Tests that need to be isolated from the main test run"
1758 excludeGroups testng_excluded_groups.split(",")
1760 useDefaultListeners=true
1765 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1766 * to summarise test results from all Test tasks
1768 /* START of test tasks results summary */
1769 import groovy.time.TimeCategory
1770 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1771 import org.gradle.api.tasks.testing.logging.TestLogEvent
1772 rootProject.ext.testsResults = [] // Container for tests summaries
1774 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1776 // from original test task
1778 dependsOn cloverClasses
1780 dependsOn testClasses //?
1783 // run main tests first
1784 if (!testTask.name.equals("testTask0"))
1785 testTask.mustRunAfter "testTask0"
1787 testTask.testLogging { logging ->
1788 events TestLogEvent.FAILED,
1789 TestLogEvent.SKIPPED,
1790 TestLogEvent.STANDARD_OUT,
1791 TestLogEvent.STANDARD_ERROR
1793 exceptionFormat TestExceptionFormat.FULL
1796 showStackTraces true
1799 ignoreFailures = true // Always try to run all tests for all modules
1801 afterSuite { desc, result ->
1803 if (desc.parent) return // Only summarize results for whole modules
1805 def summary = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1807 // Add reports in `testsResults`, keep failed suites at the end
1808 if (result.resultType == TestResult.ResultType.SUCCESS) {
1809 rootProject.ext.testsResults.add(0, summary)
1811 rootProject.ext.testsResults.add(summary)
1814 if (result.resultType == TestResult.ResultType.FAILURE) {
1819 // from original test task
1820 maxHeapSize = "1024m"
1822 workingDir = jalviewDir
1823 def testLaf = project.findProperty("test_laf")
1824 if (testLaf != null) {
1825 println("Setting Test LaF to '${testLaf}'")
1826 systemProperty "laf", testLaf
1828 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1829 if (testHiDPIScale != null) {
1830 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1831 systemProperty "sun.java2d.uiScale", testHiDPIScale
1833 sourceCompatibility = compile_source_compatibility
1834 targetCompatibility = compile_target_compatibility
1835 jvmArgs += additional_compiler_args
1839 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1845 gradle.buildFinished {
1846 def allResults = rootProject.ext.testsResults
1848 if (!allResults.isEmpty()) {
1849 printResults allResults
1850 allResults.each {r ->
1851 if (r[2].resultType == TestResult.ResultType.FAILURE)
1852 throw GradleException("Failed tests (buildFinished)!")
1857 private static void printResults(allResults) {
1858 // styler from https://stackoverflow.com/a/56139852
1859 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1862 def failedTests = false
1863 def summaryLines = []
1865 def projectName = it[0]
1866 def taskName = it[1]
1870 def colour = 'black'
1871 switch(result.resultType) {
1872 case TestResult.ResultType.SUCCESS:
1875 case TestResult.ResultType.FAILURE:
1883 def summaryCol = "${projectName}:${taskName} results: ${styler[colour](result.resultType)} (" +
1884 "${result.testCount} tests, " +
1885 (result.successfulTestCount > 0 ? "${styler['green'](result.successfulTestCount)} successes" : "${result.successfulTestCount} successes") + ", " +
1886 (result.failedTestCount > 0 ? "${styler['red'](result.failedTestCount)} failures" : "${result.failedTestCount} failures") + ", " +
1887 "${result.skippedTestCount} skipped" +
1889 def summaryPlain = "${projectName}:${taskName} results: ${result.resultType} (" +
1890 "${result.testCount} tests, " +
1891 "${result.successfulTestCount} successes, " +
1892 "${result.failedTestCount} failures, " +
1893 "${result.skippedTestCount} skipped" +
1895 def reportLine = "Report file: ${report}"
1896 def ls = summaryPlain.length()
1897 def lr = reportLine.length()
1898 def m = [ls, lr].max()
1901 def info = [ls, summaryCol, reportLine]
1902 summaryLines.add(info)
1905 println "┌${"${"─" * maxLength}"}┐"
1907 println summaryLines.collect {info ->
1909 def summary = info[1]
1910 def report = info[2]
1912 return "│" + summary + " " * (maxLength - ls) + "│" + "\n" +
1913 "│" + report + " " * (maxLength - report.length()) + "│"
1915 }.join("\n├${"${"─" * maxLength}"}┤\n")
1917 println "└${"${"─" * maxLength}"}┘"
1919 /* END of test tasks results summary */
1921 task verifyTestStatus {
1922 group = "Verification"
1923 description = "Task that FAILs the build if any tests failed"
1926 throw new GradleException("There were failing tests!")
1932 // from original test task
1934 dependsOn cloverClasses
1936 dependsOn testClasses
1938 dependsOn tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}
1939 finalizedBy verifyTestStatus
1942 // not running tests in this task
1947 task compileLinkCheck(type: JavaCompile) {
1949 classpath = files("${jalviewDir}/${utils_dir}")
1950 destinationDir = file("${jalviewDir}/${utils_dir}")
1951 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1953 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1954 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1955 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1956 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1960 task linkCheck(type: JavaExec) {
1962 dependsOn compileLinkCheck
1964 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1965 classpath = files("${jalviewDir}/${utils_dir}")
1966 main = "HelpLinksChecker"
1967 workingDir = "${helpBuildDir}"
1968 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1970 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1971 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1974 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1978 inputs.dir(helpBuildDir)
1979 outputs.file(helpLinksCheckerOutFile)
1983 // import the pubhtmlhelp target
1984 ant.properties.basedir = "${jalviewDir}"
1985 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1986 ant.importBuild "${utils_dir}/publishHelp.xml"
1989 task cleanPackageDir(type: Delete) {
1991 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2001 attributes "Main-Class": main_class,
2002 "Permissions": "all-permissions",
2003 "Application-Name": applicationName,
2004 "Codebase": application_codebase,
2005 "Implementation-Version": JALVIEW_VERSION
2008 def outputDir = "${jalviewDir}/${package_dir}"
2009 destinationDirectory = file(outputDir)
2010 archiveFileName = rootProject.name+".jar"
2011 duplicatesStrategy "EXCLUDE"
2018 exclude "**/*.jar.*"
2020 inputs.dir(sourceSets.main.java.outputDir)
2021 sourceSets.main.resources.srcDirs.each{ dir ->
2024 outputs.file("${outputDir}/${archiveFileName}")
2028 task copyJars(type: Copy) {
2029 from fileTree(dir: classesDir, include: "**/*.jar").files
2030 into "${jalviewDir}/${package_dir}"
2034 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2035 task syncJars(type: Sync) {
2037 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2038 into "${jalviewDir}/${package_dir}"
2040 include jar.archiveFileName.getOrNull()
2047 description = "Put all required libraries in dist"
2048 // order of "cleanPackageDir", "copyJars", "jar" important!
2049 jar.mustRunAfter cleanPackageDir
2050 syncJars.mustRunAfter cleanPackageDir
2051 dependsOn cleanPackageDir
2054 outputs.dir("${jalviewDir}/${package_dir}")
2059 dependsOn cleanPackageDir
2066 group = "distribution"
2067 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2071 from ("${jalviewDir}/${libDistDir}") {
2075 attributes "Implementation-Version": JALVIEW_VERSION,
2076 "Application-Name": applicationName
2079 duplicatesStrategy "INCLUDE"
2081 mainClassName = shadow_jar_main_class
2083 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2087 task getdownImagesCopy() {
2088 inputs.dir getdownImagesDir
2089 outputs.dir getdownImagesBuildDir
2093 from(getdownImagesDir) {
2094 include("*getdown*.png")
2096 into getdownImagesBuildDir
2101 task getdownImagesProcess() {
2102 dependsOn getdownImagesCopy
2105 if (backgroundImageText) {
2106 if (convertBinary == null) {
2107 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2109 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2110 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2112 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2114 executable convertBinary
2117 '-font', getdown_background_image_text_font,
2118 '-fill', getdown_background_image_text_colour,
2119 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2120 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2121 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2130 task getdownImages() {
2131 dependsOn getdownImagesProcess
2134 task getdownWebsite() {
2135 group = "distribution"
2136 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2138 dependsOn getdownImages
2143 def getdownWebsiteResourceFilenames = []
2144 def getdownResourceDir = getdownResourceDir
2145 def getdownResourceFilenames = []
2148 // clean the getdown website and files dir before creating getdown folders
2149 delete getdownAppBaseDir
2150 delete getdownFilesDir
2153 from buildProperties
2154 rename(file(buildProperties).getName(), getdown_build_properties)
2157 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2160 from channelPropsFile
2161 filter(ReplaceTokens,
2165 'SUFFIX': channelSuffix
2168 into getdownAppBaseDir
2170 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2172 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2173 def props = project.properties.sort { it.key }
2174 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2175 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2177 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2178 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2180 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2181 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2183 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2184 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2185 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2186 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2187 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2188 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2189 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2192 props.put("getdown_txt_title", jalview_name)
2193 props.put("getdown_txt_ui.name", applicationName)
2195 // start with appbase
2196 getdownTextLines += "appbase = ${getdownAppBase}"
2197 props.each{ prop, val ->
2198 if (prop.startsWith("getdown_txt_") && val != null) {
2199 if (prop.startsWith("getdown_txt_multi_")) {
2200 def key = prop.substring(18)
2201 val.split(",").each{ v ->
2202 def line = "${key} = ${v}"
2203 getdownTextLines += line
2206 // file values rationalised
2207 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2209 if (val.indexOf('/') == 0) {
2212 } else if (val.indexOf('/') > 0) {
2213 // relative path (relative to jalviewDir)
2214 r = file( "${jalviewDir}/${val}" )
2217 val = "${getdown_resource_dir}/" + r.getName()
2218 getdownWebsiteResourceFilenames += val
2219 getdownResourceFilenames += r.getPath()
2222 if (! prop.startsWith("getdown_txt_resource")) {
2223 def line = prop.substring(12) + " = ${val}"
2224 getdownTextLines += line
2230 getdownWebsiteResourceFilenames.each{ filename ->
2231 getdownTextLines += "resource = ${filename}"
2233 getdownResourceFilenames.each{ filename ->
2236 into getdownResourceDir
2240 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2241 getdownWrapperScripts.each{ script ->
2242 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2246 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2248 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2253 fileTree(file(package_dir)).each{ f ->
2254 if (f.isDirectory()) {
2255 def files = fileTree(dir: f, include: ["*"]).getFiles()
2257 } else if (f.exists()) {
2261 def jalviewJar = jar.archiveFileName.getOrNull()
2262 // put jalview.jar first for CLASSPATH and .properties files reasons
2263 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2264 def name = f.getName()
2265 def line = "code = ${getdownAppDistDir}/${name}"
2266 getdownTextLines += line
2273 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2275 if (JAVA_VERSION.equals("11")) {
2276 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2277 j11libFiles.sort().each{f ->
2278 def name = f.getName()
2279 def line = "code = ${getdown_j11lib_dir}/${name}"
2280 getdownTextLines += line
2283 into getdownJ11libDir
2289 // 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.
2290 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2291 getdownTextLines += "resource = ${getdown_launcher_new}"
2292 getdownTextLines += "class = ${main_class}"
2293 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2294 if (getdownSetAppBaseProperty) {
2295 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2296 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2299 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2300 getdownTxt.write(getdownTextLines.join("\n"))
2302 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2303 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2304 launchJvl.write("appbase=${getdownAppBase}")
2306 // files going into the getdown website dir: getdown-launcher.jar
2308 from getdownLauncher
2309 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2310 into getdownAppBaseDir
2313 // files going into the getdown website dir: getdown-launcher(-local).jar
2315 from getdownLauncher
2316 if (file(getdownLauncher).getName() != getdown_launcher) {
2317 rename(file(getdownLauncher).getName(), getdown_launcher)
2319 into getdownAppBaseDir
2322 // files going into the getdown website dir: ./install dir and files
2323 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2326 from getdownLauncher
2327 from "${getdownAppDir}/${getdown_build_properties}"
2328 if (file(getdownLauncher).getName() != getdown_launcher) {
2329 rename(file(getdownLauncher).getName(), getdown_launcher)
2331 into getdownInstallDir
2334 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2336 from getdownInstallDir
2337 into getdownFilesInstallDir
2341 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2345 from getdownLauncher
2346 from "${getdownAppBaseDir}/${getdown_build_properties}"
2347 from "${getdownAppBaseDir}/${channel_props}"
2348 if (file(getdownLauncher).getName() != getdown_launcher) {
2349 rename(file(getdownLauncher).getName(), getdown_launcher)
2351 into getdownFilesDir
2354 // and ./resource (not all downloaded by getdown)
2356 from getdownResourceDir
2357 into "${getdownFilesDir}/${getdown_resource_dir}"
2362 inputs.dir("${jalviewDir}/${package_dir}")
2364 outputs.dir(getdownAppBaseDir)
2365 outputs.dir(getdownFilesDir)
2369 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2370 task getdownDigestDir(type: JavaExec) {
2372 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2374 def digestDirPropertyName = "DIGESTDIR"
2376 classpath = files(getdownLauncher)
2377 def digestDir = findProperty(digestDirPropertyName)
2378 if (digestDir == null) {
2379 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2383 main = "com.threerings.getdown.tools.Digester"
2387 task getdownDigest(type: JavaExec) {
2388 group = "distribution"
2389 description = "Digest the getdown website folder"
2390 dependsOn getdownWebsite
2392 classpath = files(getdownLauncher)
2394 main = "com.threerings.getdown.tools.Digester"
2395 args getdownAppBaseDir
2396 inputs.dir(getdownAppBaseDir)
2397 outputs.file("${getdownAppBaseDir}/digest2.txt")
2402 group = "distribution"
2403 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2404 dependsOn getdownDigest
2406 if (reportRsyncCommand) {
2407 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2408 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2409 println "LIKELY RSYNC COMMAND:"
2410 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2411 if (RUNRSYNC == "true") {
2413 commandLine "mkdir", "-p", toDir
2416 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2424 task getdownArchiveBuild() {
2425 group = "distribution"
2426 description = "Put files in the archive dir to go on the website"
2428 dependsOn getdownWebsite
2430 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2431 def vDir = "${getdownArchiveDir}/${v}"
2432 getdownFullArchiveDir = "${vDir}/getdown"
2433 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2435 def vAltDir = "alt_${v}"
2436 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2439 // cleanup old "old" dir
2440 delete getdownArchiveDir
2442 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2443 getdownArchiveTxt.getParentFile().mkdirs()
2444 def getdownArchiveTextLines = []
2445 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2449 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2450 into "${getdownFullArchiveDir}/${vAltDir}"
2453 getdownTextLines.each { line ->
2454 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2455 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2456 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2457 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2458 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2459 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2460 // remove the existing resource = resource/ or bin/ lines
2461 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2462 getdownArchiveTextLines += line
2466 // the resource dir -- add these files as resource lines in getdown.txt
2468 from "${archiveImagesDir}"
2469 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2471 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2475 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2477 def vLaunchJvl = file(getdownVersionLaunchJvl)
2478 vLaunchJvl.getParentFile().mkdirs()
2479 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2480 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2481 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2482 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2483 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2484 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2486 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2488 from getdownLauncher
2489 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2490 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2491 from "${getdownAppBaseDir}/${channel_props}"
2492 if (file(getdownLauncher).getName() != getdown_launcher) {
2493 rename(file(getdownLauncher).getName(), getdown_launcher)
2495 into getdownFullArchiveDir
2501 task getdownArchiveDigest(type: JavaExec) {
2502 group = "distribution"
2503 description = "Digest the getdown archive folder"
2505 dependsOn getdownArchiveBuild
2508 classpath = files(getdownLauncher)
2509 args getdownFullArchiveDir
2511 main = "com.threerings.getdown.tools.Digester"
2512 inputs.dir(getdownFullArchiveDir)
2513 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2516 task getdownArchive() {
2517 group = "distribution"
2518 description = "Build the website archive dir with getdown digest"
2520 dependsOn getdownArchiveBuild
2521 dependsOn getdownArchiveDigest
2524 tasks.withType(JavaCompile) {
2525 options.encoding = 'UTF-8'
2531 delete getdownAppBaseDir
2532 delete getdownFilesDir
2533 delete getdownArchiveDir
2539 if (file(install4jHomeDir).exists()) {
2541 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2542 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2543 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2544 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2546 installDir(file(install4jHomeDir))
2548 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2552 task copyInstall4jTemplate {
2553 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2554 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2555 inputs.file(install4jTemplateFile)
2556 inputs.file(install4jFileAssociationsFile)
2557 inputs.property("CHANNEL", { CHANNEL })
2558 outputs.file(install4jConfFile)
2561 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2563 // turn off code signing if no OSX_KEYPASS
2564 if (OSX_KEYPASS == "") {
2565 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2566 codeSigning.'@macEnabled' = "false"
2568 install4jConfigXml.'**'.windows.each { windows ->
2569 windows.'@runPostProcessor' = "false"
2573 // disable install screen for OSX dmg (for 2.11.2.0)
2574 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2575 macosArchive.attributes().remove('executeSetupApp')
2576 macosArchive.attributes().remove('setupAppId')
2579 // turn off checksum creation for LOCAL channel
2580 def e = install4jConfigXml.application[0]
2581 e.'@createChecksums' = string(install4jCheckSums)
2583 // put file association actions where placeholder action is
2584 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2585 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2586 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2587 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2588 def parent = a.parent()
2590 fileAssociationActions.each { faa ->
2593 // don't need to continue in .any loop once replacements have been made
2598 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2599 // NB we're deleting the /other/ one!
2600 // Also remove the examples subdir from non-release versions
2601 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2602 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2603 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2604 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2606 // remove the examples subdir from Full File Set
2607 def files = install4jConfigXml.files[0]
2608 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2609 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2610 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2611 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2612 dirEntry.parent().remove(dirEntry)
2614 install4jConfigXml.'**'.action.any { a ->
2615 if (a.'@customizedId' == customizedIdToDelete) {
2616 def parent = a.parent()
2622 // write install4j file
2623 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2630 delete install4jConfFile
2634 task cleanInstallersDataFiles {
2635 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2636 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2637 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2639 delete installersOutputTxt
2640 delete installersSha256
2641 delete hugoDataJsonFile
2645 task install4jDMGBackgroundImageCopy {
2646 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2647 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2650 from(install4jDMGBackgroundImageDir) {
2651 include(install4jDMGBackgroundImageFile)
2653 into install4jDMGBackgroundImageBuildDir
2658 task install4jDMGBackgroundImageProcess {
2659 dependsOn install4jDMGBackgroundImageCopy
2662 if (backgroundImageText) {
2663 if (convertBinary == null) {
2664 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2666 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2667 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2669 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2671 executable convertBinary
2674 '-font', install4j_background_image_text_font,
2675 '-fill', install4j_background_image_text_colour,
2676 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2677 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2678 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2687 task install4jDMGBackgroundImage {
2688 dependsOn install4jDMGBackgroundImageProcess
2691 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2692 group = "distribution"
2693 description = "Create the install4j installers"
2695 dependsOn copyInstall4jTemplate
2696 dependsOn cleanInstallersDataFiles
2697 dependsOn install4jDMGBackgroundImage
2699 projectFile = install4jConfFile
2701 // create an md5 for the input files to use as version for install4j conf file
2702 def digest = MessageDigest.getInstance("MD5")
2704 (file("${install4jDir}/${install4j_template}").text +
2705 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2706 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2707 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2708 if (filesMd5.length() >= 8) {
2709 filesMd5 = filesMd5.substring(0,8)
2711 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2714 'JALVIEW_NAME': jalview_name,
2715 'JALVIEW_APPLICATION_NAME': applicationName,
2716 'JALVIEW_DIR': "../..",
2717 'OSX_KEYSTORE': OSX_KEYSTORE,
2718 'OSX_APPLEID': OSX_APPLEID,
2719 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2720 'JSIGN_SH': JSIGN_SH,
2721 'JRE_DIR': getdown_app_dir_java,
2722 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2723 'JALVIEW_VERSION': JALVIEW_VERSION,
2724 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2725 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2726 'JAVA_VERSION': JAVA_VERSION,
2727 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2728 'VERSION': JALVIEW_VERSION,
2729 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2730 'BUNDLE_ID': install4jBundleId,
2731 'INTERNAL_ID': install4jInternalId,
2732 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2733 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2734 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2735 'WRAPPER_LINK': getdownWrapperLink,
2736 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2737 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2738 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2739 'INSTALLER_NAME': install4jInstallerName,
2740 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2741 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2742 'GETDOWN_FILES_DIR': getdown_files_dir,
2743 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2744 'GETDOWN_DIST_DIR': getdownAppDistDir,
2745 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2746 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2747 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2748 'BUILD_DIR': install4jBuildDir,
2749 'APPLICATION_CATEGORIES': install4j_application_categories,
2750 'APPLICATION_FOLDER': install4jApplicationFolder,
2751 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2752 'EXECUTABLE_NAME': install4jExecutableName,
2753 'EXTRA_SCHEME': install4jExtraScheme,
2754 'MAC_ICONS_FILE': install4jMacIconsFile,
2755 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2756 'PNG_ICON_FILE': install4jPngIconFile,
2757 'BACKGROUND': install4jBackground,
2762 'windows': 'WINDOWS',
2766 // these are the bundled OS/architecture VMs needed by install4j
2769 [ "mac", "aarch64" ],
2770 [ "windows", "x64" ],
2772 [ "linux", "aarch64" ]
2774 osArch.forEach { os, arch ->
2775 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)
2776 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2777 // otherwise running `gradle installers` generates a non-useful error:
2778 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2779 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)
2782 //println("INSTALL4J VARIABLES:")
2783 //variables.each{k,v->println("${k}=${v}")}
2785 destination = "${jalviewDir}/${install4jBuildDir}"
2786 buildSelected = true
2788 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2790 disableSigning = true
2791 disableNotarization = true
2795 macKeystorePassword = OSX_KEYPASS
2798 if (OSX_ALTOOLPASS) {
2799 appleIdPassword = OSX_ALTOOLPASS
2800 disableNotarization = false
2802 disableNotarization = true
2806 println("Using projectFile "+projectFile)
2807 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2811 inputs.dir(getdownAppBaseDir)
2812 inputs.file(install4jConfFile)
2813 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2814 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2817 def getDataHash(File myFile) {
2818 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2819 return myFile.exists()
2821 "file" : myFile.getName(),
2822 "filesize" : myFile.length(),
2823 "sha256" : hash.toString()
2828 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2830 "channel" : getdownChannelName,
2831 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2832 "git-commit" : "${gitHash} [${gitBranch}]",
2833 "version" : JALVIEW_VERSION
2835 // install4j installer files
2836 if (installersOutputTxt.exists()) {
2838 installersOutputTxt.readLines().each { def line ->
2839 if (line.startsWith("#")) {
2842 line.replaceAll("\n","")
2843 def vals = line.split("\t")
2844 def filename = vals[3]
2845 def filesize = file(filename).length()
2846 filename = filename.replaceAll(/^.*\//, "")
2847 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2848 idHash."${filename}" = vals[0]
2850 if (install4jCheckSums && installersSha256.exists()) {
2851 installersSha256.readLines().each { def line ->
2852 if (line.startsWith("#")) {
2855 line.replaceAll("\n","")
2856 def vals = line.split(/\s+\*?/)
2857 def filename = vals[1]
2858 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2864 "JAR": shadowJar.archiveFile, // executable JAR
2865 "JVL": getdownVersionLaunchJvl, // version JVL
2866 "SOURCE": sourceDist.archiveFile // source TGZ
2867 ].each { key, value ->
2868 def file = file(value)
2869 if (file.exists()) {
2870 def fileHash = getDataHash(file)
2871 if (fileHash != null) {
2872 hash."${key}" = fileHash;
2876 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2879 task staticMakeInstallersJsonFile {
2881 def output = findProperty("i4j_output")
2882 def sha256 = findProperty("i4j_sha256")
2883 def json = findProperty("i4j_json")
2884 if (output == null || sha256 == null || json == null) {
2885 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2887 writeDataJsonFile(file(output), file(sha256), file(json))
2892 dependsOn installerFiles
2898 eclipse().configFile(eclipse_codestyle_file)
2902 task createSourceReleaseProperties(type: WriteProperties) {
2903 group = "distribution"
2904 description = "Create the source RELEASE properties file"
2906 def sourceTarBuildDir = "${buildDir}/sourceTar"
2907 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2908 outputFile (sourceReleasePropertiesFile)
2911 releaseProps.each{ key, val -> property key, val }
2912 property "git.branch", gitBranch
2913 property "git.hash", gitHash
2916 outputs.file(outputFile)
2919 task sourceDist(type: Tar) {
2920 group "distribution"
2921 description "Create a source .tar.gz file for distribution"
2923 dependsOn createBuildProperties
2924 dependsOn convertMdFiles
2925 dependsOn eclipseAllPreferences
2926 dependsOn createSourceReleaseProperties
2929 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2930 archiveFileName = outputFileName
2932 compression Compression.GZIP
2947 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2949 "utils/InstallAnywhere",
2964 "gradle.properties",
2976 ".settings/org.eclipse.buildship.core.prefs",
2977 ".settings/org.eclipse.jdt.core.prefs"
2981 exclude (EXCLUDE_FILES)
2982 include (PROCESS_FILES)
2983 filter(ReplaceTokens,
2987 'Version-Rel': JALVIEW_VERSION,
2988 'Year-Rel': getDate("yyyy")
2993 exclude (EXCLUDE_FILES)
2994 exclude (PROCESS_FILES)
2995 exclude ("appletlib")
2996 exclude ("**/*locales")
2997 exclude ("*locales/**")
2998 exclude ("utils/InstallAnywhere")
3000 exclude (getdown_files_dir)
3001 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3002 //exclude (getdown_website_dir)
3003 //exclude (getdown_archive_dir)
3005 // exluding these as not using jars as modules yet
3006 exclude ("${j11modDir}/**/*.jar")
3009 include(INCLUDE_FILES)
3011 // from (jalviewDir) {
3012 // // explicit includes for stuff that seemed to not get included
3013 // include(fileTree("test/**/*."))
3014 // exclude(EXCLUDE_FILES)
3015 // exclude(PROCESS_FILES)
3018 from(file(buildProperties).getParent()) {
3019 include(file(buildProperties).getName())
3020 rename(file(buildProperties).getName(), "build_properties")
3022 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3026 def sourceTarBuildDir = "${buildDir}/sourceTar"
3027 from(sourceTarBuildDir) {
3028 // this includes the appended RELEASE properties file
3032 task dataInstallersJson {
3034 description "Create the installers-VERSION.json data file for installer files created"
3036 mustRunAfter installers
3037 mustRunAfter shadowJar
3038 mustRunAfter sourceDist
3039 mustRunAfter getdownArchive
3041 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3042 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3044 if (installersOutputTxt.exists()) {
3045 inputs.file(installersOutputTxt)
3047 if (install4jCheckSums && installersSha256.exists()) {
3048 inputs.file(installersSha256)
3051 shadowJar.archiveFile, // executable JAR
3052 getdownVersionLaunchJvl, // version JVL
3053 sourceDist.archiveFile // source TGZ
3054 ].each { fileName ->
3055 if (file(fileName).exists()) {
3056 inputs.file(fileName)
3060 outputs.file(hugoDataJsonFile)
3063 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3069 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3072 dependsOn pubhtmlhelp
3074 inputs.dir("${helpBuildDir}/${help_dir}")
3075 outputs.dir("${buildDir}/distributions/${help_dir}")
3079 task j2sSetHeadlessBuild {
3086 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3088 description "Enable the alternative J2S Config file for headless build"
3090 outputFile = jalviewjsJ2sSettingsFileName
3091 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3092 def j2sProps = new Properties()
3093 if (j2sPropsFile.exists()) {
3095 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3096 j2sProps.load(j2sPropsFileFIS)
3097 j2sPropsFileFIS.close()
3099 j2sProps.each { prop, val ->
3102 } catch (Exception e) {
3103 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3107 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3108 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3113 task jalviewjsSetEclipseWorkspace {
3114 def propKey = "jalviewjs_eclipse_workspace"
3116 if (project.hasProperty(propKey)) {
3117 propVal = project.getProperty(propKey)
3118 if (propVal.startsWith("~/")) {
3119 propVal = System.getProperty("user.home") + propVal.substring(1)
3122 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3123 def propsFile = file(propsFileName)
3124 def eclipseWsDir = propVal
3125 def props = new Properties()
3127 def writeProps = true
3128 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3129 def ins = new FileInputStream(propsFileName)
3132 if (props.getProperty(propKey, null) != null) {
3133 eclipseWsDir = props.getProperty(propKey)
3138 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3139 def tempDir = File.createTempDir()
3140 eclipseWsDir = tempDir.getAbsolutePath()
3143 eclipseWorkspace = file(eclipseWsDir)
3146 // do not run a headless transpile when we claim to be in Eclipse
3148 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3149 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3151 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3155 props.setProperty(propKey, eclipseWsDir)
3156 propsFile.parentFile.mkdirs()
3157 def bytes = new ByteArrayOutputStream()
3158 props.store(bytes, null)
3159 def propertiesString = bytes.toString()
3160 propsFile.text = propertiesString
3166 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3169 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3170 outputs.file(propsFileName)
3171 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3175 task jalviewjsEclipsePaths {
3178 def eclipseRoot = jalviewjs_eclipse_root
3179 if (eclipseRoot.startsWith("~/")) {
3180 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3182 if (OperatingSystem.current().isMacOsX()) {
3183 eclipseRoot += "/Eclipse.app"
3184 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3185 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3186 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3187 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3188 eclipseRoot += "/eclipse"
3190 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3191 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3192 } else { // linux or unix
3193 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3194 eclipseRoot += "/eclipse"
3195 println("eclipseDir exists")
3197 eclipseBinary = "${eclipseRoot}/eclipse"
3198 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3201 eclipseVersion = "4.13" // default
3202 def assumedVersion = true
3203 if (file(eclipseProduct).exists()) {
3204 def fis = new FileInputStream(eclipseProduct)
3205 def props = new Properties()
3207 eclipseVersion = props.getProperty("version")
3209 assumedVersion = false
3212 def propKey = "eclipse_debug"
3213 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3216 // do not run a headless transpile when we claim to be in Eclipse
3218 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3219 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3221 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3224 if (!assumedVersion) {
3225 println("ECLIPSE VERSION=${eclipseVersion}")
3231 task printProperties {
3233 description "Output to console all System.properties"
3235 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3241 dependsOn eclipseProject
3242 dependsOn eclipseClasspath
3243 dependsOn eclipseJdt
3247 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3248 task jalviewjsEclipseCopyDropins(type: Copy) {
3249 dependsOn jalviewjsEclipsePaths
3251 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3252 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3253 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3260 // this eclipse -clean doesn't actually work
3261 task jalviewjsCleanEclipse(type: Exec) {
3262 dependsOn eclipseSetup
3263 dependsOn jalviewjsEclipsePaths
3264 dependsOn jalviewjsEclipseCopyDropins
3266 executable(eclipseBinary)
3267 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3273 def inputString = """exit
3276 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3277 standardInput = inputByteStream
3280 /* not really working yet
3281 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3285 task jalviewjsTransferUnzipSwingJs {
3286 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3290 from zipTree(file_zip)
3291 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3295 inputs.file file_zip
3296 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3300 task jalviewjsTransferUnzipLib {
3301 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3304 zipFiles.each { file_zip ->
3306 from zipTree(file_zip)
3307 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3312 inputs.files zipFiles
3313 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3317 task jalviewjsTransferUnzipAllLibs {
3318 dependsOn jalviewjsTransferUnzipSwingJs
3319 dependsOn jalviewjsTransferUnzipLib
3323 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3325 description "Create the alternative j2s file from the j2s.* properties"
3327 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3328 def siteDirProperty = "j2s.site.directory"
3329 def setSiteDir = false
3330 jalviewjsJ2sProps.each { prop, val ->
3332 if (prop == siteDirProperty) {
3333 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3334 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3340 if (!setSiteDir) { // default site location, don't override specifically set property
3341 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3344 outputFile = jalviewjsJ2sAltSettingsFileName
3347 inputs.properties(jalviewjsJ2sProps)
3348 outputs.file(jalviewjsJ2sAltSettingsFileName)
3353 task jalviewjsEclipseSetup {
3354 dependsOn jalviewjsEclipseCopyDropins
3355 dependsOn jalviewjsSetEclipseWorkspace
3356 dependsOn jalviewjsCreateJ2sSettings
3360 task jalviewjsSyncAllLibs (type: Sync) {
3361 dependsOn jalviewjsTransferUnzipAllLibs
3362 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3363 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3364 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3368 def outputFiles = []
3369 rename { filename ->
3370 outputFiles += "${outputDir}/${filename}"
3377 // should this be exclude really ?
3378 duplicatesStrategy "INCLUDE"
3380 outputs.files outputFiles
3381 inputs.files inputFiles
3385 task jalviewjsSyncResources (type: Sync) {
3386 dependsOn buildResources
3388 def inputFiles = fileTree(dir: resourcesBuildDir)
3389 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3393 def outputFiles = []
3394 rename { filename ->
3395 outputFiles += "${outputDir}/${filename}"
3401 outputs.files outputFiles
3402 inputs.files inputFiles
3406 task jalviewjsSyncSiteResources (type: Sync) {
3407 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3408 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3412 def outputFiles = []
3413 rename { filename ->
3414 outputFiles += "${outputDir}/${filename}"
3420 outputs.files outputFiles
3421 inputs.files inputFiles
3425 task jalviewjsSyncBuildProperties (type: Sync) {
3426 dependsOn createBuildProperties
3427 def inputFiles = [file(buildProperties)]
3428 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3432 def outputFiles = []
3433 rename { filename ->
3434 outputFiles += "${outputDir}/${filename}"
3440 outputs.files outputFiles
3441 inputs.files inputFiles
3445 task jalviewjsProjectImport(type: Exec) {
3446 dependsOn eclipseSetup
3447 dependsOn jalviewjsEclipsePaths
3448 dependsOn jalviewjsEclipseSetup
3451 // do not run a headless import when we claim to be in Eclipse
3453 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3454 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3456 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3460 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3461 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3462 executable(eclipseBinary)
3463 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3467 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3469 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3470 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3473 inputs.file("${jalviewDir}/.project")
3474 outputs.upToDateWhen {
3475 file(projdir).exists()
3480 task jalviewjsTranspile(type: Exec) {
3481 dependsOn jalviewjsEclipseSetup
3482 dependsOn jalviewjsProjectImport
3483 dependsOn jalviewjsEclipsePaths
3485 dependsOn jalviewjsEnableAltFileProperty
3489 // do not run a headless transpile when we claim to be in Eclipse
3491 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3492 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3494 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3498 executable(eclipseBinary)
3499 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3503 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3505 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3506 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3512 stdout = new ByteArrayOutputStream()
3513 stderr = new ByteArrayOutputStream()
3515 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3516 def logOutFile = file(logOutFileName)
3517 logOutFile.createNewFile()
3518 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3519 BINARY: ${eclipseBinary}
3520 VERSION: ${eclipseVersion}
3521 WORKSPACE: ${eclipseWorkspace}
3522 DEBUG: ${eclipseDebug}
3525 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3526 // combine stdout and stderr
3527 def logErrFOS = logOutFOS
3529 if (jalviewjs_j2s_to_console.equals("true")) {
3530 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3531 new org.apache.tools.ant.util.TeeOutputStream(
3535 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3536 new org.apache.tools.ant.util.TeeOutputStream(
3541 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3544 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3551 if (stdout.toString().contains("Error processing ")) {
3552 // j2s did not complete transpile
3553 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3554 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3555 println("IGNORING TRANSPILE ERRORS")
3556 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3558 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3563 inputs.dir("${jalviewDir}/${sourceDir}")
3564 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3565 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3569 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3571 def stdout = new ByteArrayOutputStream()
3572 def stderr = new ByteArrayOutputStream()
3574 def coreFile = file(jsfile)
3576 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3578 logOutFile.createNewFile()
3579 logOutFile.append(msg+"\n")
3581 def coreTop = file(prefixFile)
3582 def coreBottom = file(suffixFile)
3583 coreFile.getParentFile().mkdirs()
3584 coreFile.createNewFile()
3585 coreFile.write( coreTop.getText("UTF-8") )
3589 def t = f.getText("UTF-8")
3590 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3591 coreFile.append( t )
3593 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3595 logOutFile.append(msg+"\n")
3598 coreFile.append( coreBottom.getText("UTF-8") )
3600 msg = "Generating ${zjsfile}"
3602 logOutFile.append(msg+"\n")
3603 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3604 def logErrFOS = logOutFOS
3607 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3608 main = "com.google.javascript.jscomp.CommandLineRunner"
3609 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3610 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3613 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3615 logOutFile.append(msg+"\n")
3617 if (logOutConsole) {
3618 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3619 new org.apache.tools.ant.util.TeeOutputStream(
3623 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3624 new org.apache.tools.ant.util.TeeOutputStream(
3629 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3632 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3639 logOutFile.append(msg+"\n")
3643 task jalviewjsBuildAllCores {
3645 description "Build the core js lib closures listed in the classlists dir"
3646 dependsOn jalviewjsTranspile
3647 dependsOn jalviewjsTransferUnzipSwingJs
3649 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3650 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3651 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3652 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3653 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3654 def prefixFile = "${jsDir}/core/coretop2.js"
3655 def suffixFile = "${jsDir}/core/corebottom2.js"
3657 inputs.file prefixFile
3658 inputs.file suffixFile
3660 def classlistFiles = []
3661 // add the classlists found int the jalviewjs_classlists_dir
3662 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3664 def name = file.getName() - ".txt"
3671 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3672 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3673 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3675 jalviewjsCoreClasslists = []
3677 classlistFiles.each {
3680 def file = hash['file']
3681 if (! file.exists()) {
3682 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3683 return false // this is a "continue" in groovy .each closure
3685 def name = hash['name']
3687 name = file.getName() - ".txt"
3695 def list = fileTree(dir: j2sDir, includes: filelist)
3697 def jsfile = "${outputDir}/core${name}.js"
3698 def zjsfile = "${outputDir}/core${name}.z.js"
3700 jalviewjsCoreClasslists += [
3709 outputs.file(jsfile)
3710 outputs.file(zjsfile)
3713 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3714 def stevesoftClasslistName = "_stevesoft"
3715 def stevesoftClasslist = [
3716 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3717 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3718 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3719 'name': stevesoftClasslistName
3721 jalviewjsCoreClasslists += stevesoftClasslist
3722 inputs.files(stevesoftClasslist['list'])
3723 outputs.file(stevesoftClasslist['jsfile'])
3724 outputs.file(stevesoftClasslist['zjsfile'])
3727 def allClasslistName = "_all"
3728 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3729 allJsFiles += fileTree(
3733 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3734 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3735 "**/org/jmol/export/JSExporter.js"
3738 allJsFiles += fileTree(
3742 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3743 "**/sun/misc/Unsafe.js",
3744 "**/swingjs/jquery/jquery-editable-select.js",
3745 "**/swingjs/jquery/j2sComboBox.js",
3746 "**/sun/misc/FloatingDecimal.js"
3749 def allClasslist = [
3750 'jsfile': "${outputDir}/core${allClasslistName}.js",
3751 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3753 'name': allClasslistName
3755 // not including this version of "all" core at the moment
3756 //jalviewjsCoreClasslists += allClasslist
3757 inputs.files(allClasslist['list'])
3758 outputs.file(allClasslist['jsfile'])
3759 outputs.file(allClasslist['zjsfile'])
3762 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3763 logOutFile.getParentFile().mkdirs()
3764 logOutFile.createNewFile()
3765 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3767 jalviewjsCoreClasslists.each {
3768 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3775 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3778 into file(outputFile).getParentFile()
3779 rename { filename ->
3780 if (filename.equals(inputFile.getName())) {
3781 return file(outputFile).getName()
3785 filter(ReplaceTokens,
3789 'MAIN': '"'+main_class+'"',
3791 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3792 'COREKEY': jalviewjs_core_key,
3793 'CORENAME': coreName
3800 task jalviewjsPublishCoreTemplates {
3801 dependsOn jalviewjsBuildAllCores
3802 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3803 def inputFile = file(inputFileName)
3804 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3806 def outputFiles = []
3807 jalviewjsCoreClasslists.each { cl ->
3808 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3809 cl['outputfile'] = outputFile
3810 outputFiles += outputFile
3814 jalviewjsCoreClasslists.each { cl ->
3815 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3818 inputs.file(inputFile)
3819 outputs.files(outputFiles)
3823 task jalviewjsSyncCore (type: Sync) {
3824 dependsOn jalviewjsBuildAllCores
3825 dependsOn jalviewjsPublishCoreTemplates
3826 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3827 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3831 def outputFiles = []
3832 rename { filename ->
3833 outputFiles += "${outputDir}/${filename}"
3839 outputs.files outputFiles
3840 inputs.files inputFiles
3844 // this Copy version of TransferSiteJs will delete anything else in the target dir
3845 task jalviewjsCopyTransferSiteJs(type: Copy) {
3846 dependsOn jalviewjsTranspile
3847 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3848 into "${jalviewDir}/${jalviewjsSiteDir}"
3852 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3853 task jalviewjsSyncTransferSiteJs(type: Sync) {
3854 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3856 into "${jalviewDir}/${jalviewjsSiteDir}"
3863 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3864 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3865 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3866 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3868 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3869 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3870 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3871 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3874 task jalviewjsPrepareSite {
3876 description "Prepares the website folder including unzipping files and copying resources"
3877 dependsOn jalviewjsSyncAllLibs
3878 dependsOn jalviewjsSyncResources
3879 dependsOn jalviewjsSyncSiteResources
3880 dependsOn jalviewjsSyncBuildProperties
3881 dependsOn jalviewjsSyncCore
3885 task jalviewjsBuildSite {
3887 description "Builds the whole website including transpiled code"
3888 dependsOn jalviewjsCopyTransferSiteJs
3889 dependsOn jalviewjsPrepareSite
3893 task cleanJalviewjsTransferSite {
3895 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3896 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3897 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3898 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3903 task cleanJalviewjsSite {
3904 dependsOn cleanJalviewjsTransferSite
3906 delete "${jalviewDir}/${jalviewjsSiteDir}"
3911 task jalviewjsSiteTar(type: Tar) {
3913 description "Creates a tar.gz file for the website"
3914 dependsOn jalviewjsBuildSite
3915 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3916 archiveFileName = outputFilename
3918 compression Compression.GZIP
3920 from "${jalviewDir}/${jalviewjsSiteDir}"
3921 into jalviewjs_site_dir // this is inside the tar file
3923 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3927 task jalviewjsServer {
3929 def filename = "jalviewjsTest.html"
3930 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3931 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3936 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3937 factory = f.newInstance()
3938 } catch (ClassNotFoundException e) {
3939 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3941 def port = Integer.valueOf(jalviewjs_server_port)
3946 while(port < start+1000 && !running) {
3948 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3949 jalviewjsServer = factory.start(doc_root, port)
3951 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3952 println("SERVER STARTED with document root ${doc_root}.")
3953 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3954 println("For debug: "+url+"?j2sdebug")
3955 println("For verbose: "+url+"?j2sverbose")
3956 } catch (Exception e) {
3961 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3962 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3963 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3965 jalviewjsCoreClasslists.each { cl ->
3966 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3968 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3970 println("For core ${cl.name}: "+urlcore)
3973 file(htmlFile).text = htmlText
3976 outputs.file(htmlFile)
3977 outputs.upToDateWhen({false})
3981 task cleanJalviewjsAll {
3983 description "Delete all configuration and build artifacts to do with JalviewJS build"
3984 dependsOn cleanJalviewjsSite
3985 dependsOn jalviewjsEclipsePaths
3988 delete "${jalviewDir}/${jalviewjsBuildDir}"
3989 delete "${jalviewDir}/${eclipse_bin_dir}"
3990 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3991 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3993 delete jalviewjsJ2sAltSettingsFileName
3996 outputs.upToDateWhen( { false } )
4000 task jalviewjsIDE_checkJ2sPlugin {
4001 group "00 JalviewJS in Eclipse"
4002 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4005 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4006 def j2sPluginFile = file(j2sPlugin)
4007 def eclipseHome = System.properties["eclipse.home.location"]
4008 if (eclipseHome == null || ! IN_ECLIPSE) {
4009 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4011 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4012 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4013 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4014 eclipseJ2sPluginDirs += altPluginsDir
4016 def foundPlugin = false
4017 def j2sPluginFileName = j2sPluginFile.getName()
4018 def eclipseJ2sPlugin
4019 def eclipseJ2sPluginFile
4020 eclipseJ2sPluginDirs.any { dir ->
4021 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4022 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4023 if (eclipseJ2sPluginFile.exists()) {
4029 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4030 System.err.println(msg)
4031 throw new StopExecutionException(msg)
4034 def digest = MessageDigest.getInstance("MD5")
4036 digest.update(j2sPluginFile.text.bytes)
4037 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4039 digest.update(eclipseJ2sPluginFile.text.bytes)
4040 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4042 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4043 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4044 System.err.println(msg)
4045 throw new StopExecutionException(msg)
4047 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4053 task jalviewjsIDE_copyJ2sPlugin {
4054 group "00 JalviewJS in Eclipse"
4055 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4058 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4059 def j2sPluginFile = file(j2sPlugin)
4060 def eclipseHome = System.properties["eclipse.home.location"]
4061 if (eclipseHome == null || ! IN_ECLIPSE) {
4062 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4064 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4065 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4066 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4067 System.err.println(msg)
4070 eclipseJ2sPluginFile.getParentFile().mkdirs()
4071 into eclipseJ2sPluginFile.getParent()
4077 task jalviewjsIDE_j2sFile {
4078 group "00 JalviewJS in Eclipse"
4079 description "Creates the .j2s file"
4080 dependsOn jalviewjsCreateJ2sSettings
4084 task jalviewjsIDE_SyncCore {
4085 group "00 JalviewJS in Eclipse"
4086 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4087 dependsOn jalviewjsSyncCore
4091 task jalviewjsIDE_SyncSiteAll {
4092 dependsOn jalviewjsSyncAllLibs
4093 dependsOn jalviewjsSyncResources
4094 dependsOn jalviewjsSyncSiteResources
4095 dependsOn jalviewjsSyncBuildProperties
4099 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4102 task jalviewjsIDE_PrepareSite {
4103 group "00 JalviewJS in Eclipse"
4104 description "Sync libs and resources to site dir, but not closure cores"
4106 dependsOn jalviewjsIDE_SyncSiteAll
4107 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4111 task jalviewjsIDE_AssembleSite {
4112 group "00 JalviewJS in Eclipse"
4113 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4114 dependsOn jalviewjsPrepareSite
4118 task jalviewjsIDE_SiteClean {
4119 group "00 JalviewJS in Eclipse"
4120 description "Deletes the Eclipse transpiled site"
4121 dependsOn cleanJalviewjsSite
4125 task jalviewjsIDE_Server {
4126 group "00 JalviewJS in Eclipse"
4127 description "Starts a webserver on localhost to test the website"
4128 dependsOn jalviewjsServer
4132 // buildship runs this at import or gradle refresh
4133 task eclipseSynchronizationTask {
4134 //dependsOn eclipseSetup
4135 dependsOn createBuildProperties
4137 dependsOn jalviewjsIDE_j2sFile
4138 dependsOn jalviewjsIDE_checkJ2sPlugin
4139 dependsOn jalviewjsIDE_PrepareSite
4144 // buildship runs this at build time or project refresh
4145 task eclipseAutoBuildTask {
4146 //dependsOn jalviewjsIDE_checkJ2sPlugin
4147 //dependsOn jalviewjsIDE_PrepareSite
4153 description "Build the site"
4154 dependsOn jalviewjsBuildSite