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
1740 group = "Verification"
1741 description = "Runs all testTaskN tasks)"
1744 dependsOn cloverClasses
1746 dependsOn testClasses
1749 // not running tests in this task
1752 /* testTask0 is the main test task */
1753 task testTask0(type: Test) {
1754 group = "Verification"
1755 description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
1757 includeGroups testng_groups.split(",")
1758 excludeGroups testng_excluded_groups.split(",")
1759 tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
1761 useDefaultListeners=true
1765 /* separated tests */
1766 task testTask1(type: Test) {
1767 group = "Verification"
1768 description = "Tests that need to be isolated from the main test run"
1771 excludeGroups testng_excluded_groups.split(",")
1773 useDefaultListeners=true
1777 /* insert more testTaskNs here -- change N to next digit or other string */
1779 task testTaskN(type: Test) {
1780 group = "Verification"
1781 description = "Tests that need to be isolated from the main test run"
1784 excludeGroups testng_excluded_groups.split(",")
1786 useDefaultListeners=true
1792 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1793 * to summarise test results from all Test tasks
1795 /* START of test tasks results summary */
1796 import groovy.time.TimeCategory
1797 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1798 import org.gradle.api.tasks.testing.logging.TestLogEvent
1799 rootProject.ext.testsResults = [] // Container for tests summaries
1801 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1803 // from original test task
1805 dependsOn cloverClasses
1807 dependsOn testClasses //?
1810 // run main tests first
1811 if (!testTask.name.equals("testTask0"))
1812 testTask.mustRunAfter "testTask0"
1814 testTask.testLogging { logging ->
1815 events TestLogEvent.FAILED
1816 // TestLogEvent.SKIPPED,
1817 // TestLogEvent.STANDARD_OUT,
1818 // TestLogEvent.STANDARD_ERROR
1820 exceptionFormat TestExceptionFormat.FULL
1823 showStackTraces true
1825 info.events = [ TestLogEvent.FAILED ]
1830 ignoreFailures = true // Always try to run all tests for all modules
1832 afterSuite { desc, result ->
1834 return // Only summarize results for whole modules
1836 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1838 rootProject.ext.testsResults.add(resultsInfo)
1841 // from original test task
1842 maxHeapSize = "1024m"
1844 workingDir = jalviewDir
1845 def testLaf = project.findProperty("test_laf")
1846 if (testLaf != null) {
1847 println("Setting Test LaF to '${testLaf}'")
1848 systemProperty "laf", testLaf
1850 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1851 if (testHiDPIScale != null) {
1852 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1853 systemProperty "sun.java2d.uiScale", testHiDPIScale
1855 sourceCompatibility = compile_source_compatibility
1856 targetCompatibility = compile_target_compatibility
1857 jvmArgs += additional_compiler_args
1860 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1861 // testTasks that include the tests, and exclude all from the others.
1862 // get --test argument
1863 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1864 // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
1865 // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
1869 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1874 /* don't fail on no matching tests (so --tests will run across all testTasks) */
1875 testTask.filter.setFailOnNoMatchingTests(false)
1877 /* ensure the "test" task dependsOn all the testTasks */
1878 test.dependsOn testTask
1881 gradle.buildFinished {
1882 def allResults = rootProject.ext.testsResults
1884 if (!allResults.isEmpty()) {
1885 printResults allResults
1886 allResults.each {r ->
1887 if (r[2].resultType == TestResult.ResultType.FAILURE)
1888 throw new GradleException("Failed tests!")
1893 private static String colString(styler, col, colour, text) {
1894 return col?"${styler[colour](text)}":text
1897 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1898 def colour = 'black'
1906 case TestResult.ResultType.SUCCESS:
1909 case TestResult.ResultType.FAILURE:
1917 StringBuilder sb = new StringBuilder()
1921 sb.append(" results: ")
1922 sb.append(colString(s, col && !nocol, colour, text))
1924 sb.append("${rc} tests, ")
1925 sb.append(colString(s, col && rs > 0, 'green', rs))
1926 sb.append(" successes, ")
1927 sb.append(colString(s, col && rf > 0, 'red', rf))
1928 sb.append(" failures, ")
1929 sb.append("${rsk} skipped) in ${t}")
1930 return sb.toString()
1933 private static void printResults(allResults) {
1935 // styler from https://stackoverflow.com/a/56139852
1936 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1939 def failedTests = false
1940 def summaryLines = []
1942 def totalsuccess = 0
1945 def totaltime = TimeCategory.getSeconds(0)
1946 // sort on project name then task name
1947 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1948 def projectName = it[0]
1949 def taskName = it[1]
1953 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1954 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1955 def reportLine = "Report file: ${report}"
1956 def ls = summaryPlain.length()
1957 def lr = reportLine.length()
1958 def m = [ls, lr].max()
1961 def info = [ls, summaryCol, reportLine]
1962 summaryLines.add(info)
1963 failedTests |= result.resultType == TestResult.ResultType.FAILURE
1964 totalcount += result.testCount
1965 totalsuccess += result.successfulTestCount
1966 totalfail += result.failedTestCount
1967 totalskip += result.skippedTestCount
1970 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
1971 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
1972 def tls = totalSummaryPlain.length()
1973 if (tls > maxLength)
1975 def info = [tls, totalSummaryCol, null]
1976 summaryLines.add(info)
1978 def allSummaries = []
1979 for(sInfo : summaryLines) {
1981 def summary = sInfo[1]
1982 def report = sInfo[2]
1984 StringBuilder sb = new StringBuilder()
1985 sb.append("│" + summary + " " * (maxLength - ls) + "│")
1986 if (report != null) {
1987 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
1989 allSummaries += sb.toString()
1992 println "┌${"${"─" * maxLength}"}┐"
1993 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
1994 println "└${"${"─" * maxLength}"}┘"
1996 /* END of test tasks results summary */
1999 task compileLinkCheck(type: JavaCompile) {
2001 classpath = files("${jalviewDir}/${utils_dir}")
2002 destinationDir = file("${jalviewDir}/${utils_dir}")
2003 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
2005 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2006 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
2007 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
2008 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
2012 task linkCheck(type: JavaExec) {
2014 dependsOn compileLinkCheck
2016 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2017 classpath = files("${jalviewDir}/${utils_dir}")
2018 main = "HelpLinksChecker"
2019 workingDir = "${helpBuildDir}"
2020 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2022 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2023 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2026 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2030 inputs.dir(helpBuildDir)
2031 outputs.file(helpLinksCheckerOutFile)
2035 // import the pubhtmlhelp target
2036 ant.properties.basedir = "${jalviewDir}"
2037 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2038 ant.importBuild "${utils_dir}/publishHelp.xml"
2041 task cleanPackageDir(type: Delete) {
2043 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2053 attributes "Main-Class": main_class,
2054 "Permissions": "all-permissions",
2055 "Application-Name": applicationName,
2056 "Codebase": application_codebase,
2057 "Implementation-Version": JALVIEW_VERSION
2060 def outputDir = "${jalviewDir}/${package_dir}"
2061 destinationDirectory = file(outputDir)
2062 archiveFileName = rootProject.name+".jar"
2063 duplicatesStrategy "EXCLUDE"
2070 exclude "**/*.jar.*"
2072 inputs.dir(sourceSets.main.java.outputDir)
2073 sourceSets.main.resources.srcDirs.each{ dir ->
2076 outputs.file("${outputDir}/${archiveFileName}")
2080 task copyJars(type: Copy) {
2081 from fileTree(dir: classesDir, include: "**/*.jar").files
2082 into "${jalviewDir}/${package_dir}"
2086 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2087 task syncJars(type: Sync) {
2089 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2090 into "${jalviewDir}/${package_dir}"
2092 include jar.archiveFileName.getOrNull()
2099 description = "Put all required libraries in dist"
2100 // order of "cleanPackageDir", "copyJars", "jar" important!
2101 jar.mustRunAfter cleanPackageDir
2102 syncJars.mustRunAfter cleanPackageDir
2103 dependsOn cleanPackageDir
2106 outputs.dir("${jalviewDir}/${package_dir}")
2111 dependsOn cleanPackageDir
2118 group = "distribution"
2119 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2123 from ("${jalviewDir}/${libDistDir}") {
2127 attributes "Implementation-Version": JALVIEW_VERSION,
2128 "Application-Name": applicationName
2131 duplicatesStrategy "INCLUDE"
2133 mainClassName = shadow_jar_main_class
2135 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2139 task getdownImagesCopy() {
2140 inputs.dir getdownImagesDir
2141 outputs.dir getdownImagesBuildDir
2145 from(getdownImagesDir) {
2146 include("*getdown*.png")
2148 into getdownImagesBuildDir
2153 task getdownImagesProcess() {
2154 dependsOn getdownImagesCopy
2157 if (backgroundImageText) {
2158 if (convertBinary == null) {
2159 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2161 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2162 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2164 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2166 executable convertBinary
2169 '-font', getdown_background_image_text_font,
2170 '-fill', getdown_background_image_text_colour,
2171 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2172 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2173 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2182 task getdownImages() {
2183 dependsOn getdownImagesProcess
2186 task getdownWebsite() {
2187 group = "distribution"
2188 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2190 dependsOn getdownImages
2195 def getdownWebsiteResourceFilenames = []
2196 def getdownResourceDir = getdownResourceDir
2197 def getdownResourceFilenames = []
2200 // clean the getdown website and files dir before creating getdown folders
2201 delete getdownAppBaseDir
2202 delete getdownFilesDir
2205 from buildProperties
2206 rename(file(buildProperties).getName(), getdown_build_properties)
2209 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2212 from channelPropsFile
2213 filter(ReplaceTokens,
2217 'SUFFIX': channelSuffix
2220 into getdownAppBaseDir
2222 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2224 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2225 def props = project.properties.sort { it.key }
2226 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2227 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2229 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2230 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2232 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2233 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2235 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2236 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2237 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2238 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2239 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2240 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2241 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2244 props.put("getdown_txt_title", jalview_name)
2245 props.put("getdown_txt_ui.name", applicationName)
2247 // start with appbase
2248 getdownTextLines += "appbase = ${getdownAppBase}"
2249 props.each{ prop, val ->
2250 if (prop.startsWith("getdown_txt_") && val != null) {
2251 if (prop.startsWith("getdown_txt_multi_")) {
2252 def key = prop.substring(18)
2253 val.split(",").each{ v ->
2254 def line = "${key} = ${v}"
2255 getdownTextLines += line
2258 // file values rationalised
2259 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2261 if (val.indexOf('/') == 0) {
2264 } else if (val.indexOf('/') > 0) {
2265 // relative path (relative to jalviewDir)
2266 r = file( "${jalviewDir}/${val}" )
2269 val = "${getdown_resource_dir}/" + r.getName()
2270 getdownWebsiteResourceFilenames += val
2271 getdownResourceFilenames += r.getPath()
2274 if (! prop.startsWith("getdown_txt_resource")) {
2275 def line = prop.substring(12) + " = ${val}"
2276 getdownTextLines += line
2282 getdownWebsiteResourceFilenames.each{ filename ->
2283 getdownTextLines += "resource = ${filename}"
2285 getdownResourceFilenames.each{ filename ->
2288 into getdownResourceDir
2292 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2293 getdownWrapperScripts.each{ script ->
2294 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2298 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2300 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2305 fileTree(file(package_dir)).each{ f ->
2306 if (f.isDirectory()) {
2307 def files = fileTree(dir: f, include: ["*"]).getFiles()
2309 } else if (f.exists()) {
2313 def jalviewJar = jar.archiveFileName.getOrNull()
2314 // put jalview.jar first for CLASSPATH and .properties files reasons
2315 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2316 def name = f.getName()
2317 def line = "code = ${getdownAppDistDir}/${name}"
2318 getdownTextLines += line
2325 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2327 if (JAVA_VERSION.equals("11")) {
2328 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2329 j11libFiles.sort().each{f ->
2330 def name = f.getName()
2331 def line = "code = ${getdown_j11lib_dir}/${name}"
2332 getdownTextLines += line
2335 into getdownJ11libDir
2341 // 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.
2342 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2343 getdownTextLines += "resource = ${getdown_launcher_new}"
2344 getdownTextLines += "class = ${main_class}"
2345 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2346 if (getdownSetAppBaseProperty) {
2347 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2348 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2351 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2352 getdownTxt.write(getdownTextLines.join("\n"))
2354 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2355 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2356 launchJvl.write("appbase=${getdownAppBase}")
2358 // files going into the getdown website dir: getdown-launcher.jar
2360 from getdownLauncher
2361 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2362 into getdownAppBaseDir
2365 // files going into the getdown website dir: getdown-launcher(-local).jar
2367 from getdownLauncher
2368 if (file(getdownLauncher).getName() != getdown_launcher) {
2369 rename(file(getdownLauncher).getName(), getdown_launcher)
2371 into getdownAppBaseDir
2374 // files going into the getdown website dir: ./install dir and files
2375 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2378 from getdownLauncher
2379 from "${getdownAppDir}/${getdown_build_properties}"
2380 if (file(getdownLauncher).getName() != getdown_launcher) {
2381 rename(file(getdownLauncher).getName(), getdown_launcher)
2383 into getdownInstallDir
2386 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2388 from getdownInstallDir
2389 into getdownFilesInstallDir
2393 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2397 from getdownLauncher
2398 from "${getdownAppBaseDir}/${getdown_build_properties}"
2399 from "${getdownAppBaseDir}/${channel_props}"
2400 if (file(getdownLauncher).getName() != getdown_launcher) {
2401 rename(file(getdownLauncher).getName(), getdown_launcher)
2403 into getdownFilesDir
2406 // and ./resource (not all downloaded by getdown)
2408 from getdownResourceDir
2409 into "${getdownFilesDir}/${getdown_resource_dir}"
2414 inputs.dir("${jalviewDir}/${package_dir}")
2416 outputs.dir(getdownAppBaseDir)
2417 outputs.dir(getdownFilesDir)
2421 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2422 task getdownDigestDir(type: JavaExec) {
2424 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2426 def digestDirPropertyName = "DIGESTDIR"
2428 classpath = files(getdownLauncher)
2429 def digestDir = findProperty(digestDirPropertyName)
2430 if (digestDir == null) {
2431 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2435 main = "com.threerings.getdown.tools.Digester"
2439 task getdownDigest(type: JavaExec) {
2440 group = "distribution"
2441 description = "Digest the getdown website folder"
2442 dependsOn getdownWebsite
2444 classpath = files(getdownLauncher)
2446 main = "com.threerings.getdown.tools.Digester"
2447 args getdownAppBaseDir
2448 inputs.dir(getdownAppBaseDir)
2449 outputs.file("${getdownAppBaseDir}/digest2.txt")
2454 group = "distribution"
2455 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2456 dependsOn getdownDigest
2458 if (reportRsyncCommand) {
2459 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2460 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2461 println "LIKELY RSYNC COMMAND:"
2462 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2463 if (RUNRSYNC == "true") {
2465 commandLine "mkdir", "-p", toDir
2468 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2476 task getdownArchiveBuild() {
2477 group = "distribution"
2478 description = "Put files in the archive dir to go on the website"
2480 dependsOn getdownWebsite
2482 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2483 def vDir = "${getdownArchiveDir}/${v}"
2484 getdownFullArchiveDir = "${vDir}/getdown"
2485 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2487 def vAltDir = "alt_${v}"
2488 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2491 // cleanup old "old" dir
2492 delete getdownArchiveDir
2494 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2495 getdownArchiveTxt.getParentFile().mkdirs()
2496 def getdownArchiveTextLines = []
2497 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2501 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2502 into "${getdownFullArchiveDir}/${vAltDir}"
2505 getdownTextLines.each { line ->
2506 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2507 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2508 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2509 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2510 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2511 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2512 // remove the existing resource = resource/ or bin/ lines
2513 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2514 getdownArchiveTextLines += line
2518 // the resource dir -- add these files as resource lines in getdown.txt
2520 from "${archiveImagesDir}"
2521 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2523 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2527 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2529 def vLaunchJvl = file(getdownVersionLaunchJvl)
2530 vLaunchJvl.getParentFile().mkdirs()
2531 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2532 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2533 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2534 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2535 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2536 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2538 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2540 from getdownLauncher
2541 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2542 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2543 from "${getdownAppBaseDir}/${channel_props}"
2544 if (file(getdownLauncher).getName() != getdown_launcher) {
2545 rename(file(getdownLauncher).getName(), getdown_launcher)
2547 into getdownFullArchiveDir
2553 task getdownArchiveDigest(type: JavaExec) {
2554 group = "distribution"
2555 description = "Digest the getdown archive folder"
2557 dependsOn getdownArchiveBuild
2560 classpath = files(getdownLauncher)
2561 args getdownFullArchiveDir
2563 main = "com.threerings.getdown.tools.Digester"
2564 inputs.dir(getdownFullArchiveDir)
2565 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2568 task getdownArchive() {
2569 group = "distribution"
2570 description = "Build the website archive dir with getdown digest"
2572 dependsOn getdownArchiveBuild
2573 dependsOn getdownArchiveDigest
2576 tasks.withType(JavaCompile) {
2577 options.encoding = 'UTF-8'
2583 delete getdownAppBaseDir
2584 delete getdownFilesDir
2585 delete getdownArchiveDir
2591 if (file(install4jHomeDir).exists()) {
2593 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2594 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2595 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2596 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2598 installDir(file(install4jHomeDir))
2600 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2604 task copyInstall4jTemplate {
2605 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2606 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2607 inputs.file(install4jTemplateFile)
2608 inputs.file(install4jFileAssociationsFile)
2609 inputs.property("CHANNEL", { CHANNEL })
2610 outputs.file(install4jConfFile)
2613 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2615 // turn off code signing if no OSX_KEYPASS
2616 if (OSX_KEYPASS == "") {
2617 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2618 codeSigning.'@macEnabled' = "false"
2620 install4jConfigXml.'**'.windows.each { windows ->
2621 windows.'@runPostProcessor' = "false"
2625 // disable install screen for OSX dmg (for 2.11.2.0)
2626 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2627 macosArchive.attributes().remove('executeSetupApp')
2628 macosArchive.attributes().remove('setupAppId')
2631 // turn off checksum creation for LOCAL channel
2632 def e = install4jConfigXml.application[0]
2633 e.'@createChecksums' = string(install4jCheckSums)
2635 // put file association actions where placeholder action is
2636 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2637 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2638 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2639 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2640 def parent = a.parent()
2642 fileAssociationActions.each { faa ->
2645 // don't need to continue in .any loop once replacements have been made
2650 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2651 // NB we're deleting the /other/ one!
2652 // Also remove the examples subdir from non-release versions
2653 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2654 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2655 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2656 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2658 // remove the examples subdir from Full File Set
2659 def files = install4jConfigXml.files[0]
2660 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2661 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2662 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2663 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2664 dirEntry.parent().remove(dirEntry)
2666 install4jConfigXml.'**'.action.any { a ->
2667 if (a.'@customizedId' == customizedIdToDelete) {
2668 def parent = a.parent()
2674 // write install4j file
2675 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2682 delete install4jConfFile
2686 task cleanInstallersDataFiles {
2687 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2688 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2689 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2691 delete installersOutputTxt
2692 delete installersSha256
2693 delete hugoDataJsonFile
2697 task install4jDMGBackgroundImageCopy {
2698 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2699 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2702 from(install4jDMGBackgroundImageDir) {
2703 include(install4jDMGBackgroundImageFile)
2705 into install4jDMGBackgroundImageBuildDir
2710 task install4jDMGBackgroundImageProcess {
2711 dependsOn install4jDMGBackgroundImageCopy
2714 if (backgroundImageText) {
2715 if (convertBinary == null) {
2716 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2718 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2719 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2721 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2723 executable convertBinary
2726 '-font', install4j_background_image_text_font,
2727 '-fill', install4j_background_image_text_colour,
2728 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2729 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2730 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2739 task install4jDMGBackgroundImage {
2740 dependsOn install4jDMGBackgroundImageProcess
2743 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2744 group = "distribution"
2745 description = "Create the install4j installers"
2747 dependsOn copyInstall4jTemplate
2748 dependsOn cleanInstallersDataFiles
2749 dependsOn install4jDMGBackgroundImage
2751 projectFile = install4jConfFile
2753 // create an md5 for the input files to use as version for install4j conf file
2754 def digest = MessageDigest.getInstance("MD5")
2756 (file("${install4jDir}/${install4j_template}").text +
2757 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2758 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2759 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2760 if (filesMd5.length() >= 8) {
2761 filesMd5 = filesMd5.substring(0,8)
2763 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2766 'JALVIEW_NAME': jalview_name,
2767 'JALVIEW_APPLICATION_NAME': applicationName,
2768 'JALVIEW_DIR': "../..",
2769 'OSX_KEYSTORE': OSX_KEYSTORE,
2770 'OSX_APPLEID': OSX_APPLEID,
2771 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2772 'JSIGN_SH': JSIGN_SH,
2773 'JRE_DIR': getdown_app_dir_java,
2774 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2775 'JALVIEW_VERSION': JALVIEW_VERSION,
2776 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2777 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2778 'JAVA_VERSION': JAVA_VERSION,
2779 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2780 'VERSION': JALVIEW_VERSION,
2781 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2782 'BUNDLE_ID': install4jBundleId,
2783 'INTERNAL_ID': install4jInternalId,
2784 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2785 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2786 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2787 'WRAPPER_LINK': getdownWrapperLink,
2788 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2789 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2790 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2791 'INSTALLER_NAME': install4jInstallerName,
2792 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2793 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2794 'GETDOWN_FILES_DIR': getdown_files_dir,
2795 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2796 'GETDOWN_DIST_DIR': getdownAppDistDir,
2797 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2798 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2799 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2800 'BUILD_DIR': install4jBuildDir,
2801 'APPLICATION_CATEGORIES': install4j_application_categories,
2802 'APPLICATION_FOLDER': install4jApplicationFolder,
2803 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2804 'EXECUTABLE_NAME': install4jExecutableName,
2805 'EXTRA_SCHEME': install4jExtraScheme,
2806 'MAC_ICONS_FILE': install4jMacIconsFile,
2807 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2808 'PNG_ICON_FILE': install4jPngIconFile,
2809 'BACKGROUND': install4jBackground,
2814 'windows': 'WINDOWS',
2818 // these are the bundled OS/architecture VMs needed by install4j
2821 [ "mac", "aarch64" ],
2822 [ "windows", "x64" ],
2824 [ "linux", "aarch64" ]
2826 osArch.forEach { os, arch ->
2827 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)
2828 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2829 // otherwise running `gradle installers` generates a non-useful error:
2830 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2831 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)
2834 //println("INSTALL4J VARIABLES:")
2835 //variables.each{k,v->println("${k}=${v}")}
2837 destination = "${jalviewDir}/${install4jBuildDir}"
2838 buildSelected = true
2840 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2842 disableSigning = true
2843 disableNotarization = true
2847 macKeystorePassword = OSX_KEYPASS
2850 if (OSX_ALTOOLPASS) {
2851 appleIdPassword = OSX_ALTOOLPASS
2852 disableNotarization = false
2854 disableNotarization = true
2858 println("Using projectFile "+projectFile)
2859 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2863 inputs.dir(getdownAppBaseDir)
2864 inputs.file(install4jConfFile)
2865 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2866 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2869 def getDataHash(File myFile) {
2870 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2871 return myFile.exists()
2873 "file" : myFile.getName(),
2874 "filesize" : myFile.length(),
2875 "sha256" : hash.toString()
2880 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2882 "channel" : getdownChannelName,
2883 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2884 "git-commit" : "${gitHash} [${gitBranch}]",
2885 "version" : JALVIEW_VERSION
2887 // install4j installer files
2888 if (installersOutputTxt.exists()) {
2890 installersOutputTxt.readLines().each { def line ->
2891 if (line.startsWith("#")) {
2894 line.replaceAll("\n","")
2895 def vals = line.split("\t")
2896 def filename = vals[3]
2897 def filesize = file(filename).length()
2898 filename = filename.replaceAll(/^.*\//, "")
2899 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2900 idHash."${filename}" = vals[0]
2902 if (install4jCheckSums && installersSha256.exists()) {
2903 installersSha256.readLines().each { def line ->
2904 if (line.startsWith("#")) {
2907 line.replaceAll("\n","")
2908 def vals = line.split(/\s+\*?/)
2909 def filename = vals[1]
2910 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2916 "JAR": shadowJar.archiveFile, // executable JAR
2917 "JVL": getdownVersionLaunchJvl, // version JVL
2918 "SOURCE": sourceDist.archiveFile // source TGZ
2919 ].each { key, value ->
2920 def file = file(value)
2921 if (file.exists()) {
2922 def fileHash = getDataHash(file)
2923 if (fileHash != null) {
2924 hash."${key}" = fileHash;
2928 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2931 task staticMakeInstallersJsonFile {
2933 def output = findProperty("i4j_output")
2934 def sha256 = findProperty("i4j_sha256")
2935 def json = findProperty("i4j_json")
2936 if (output == null || sha256 == null || json == null) {
2937 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2939 writeDataJsonFile(file(output), file(sha256), file(json))
2944 dependsOn installerFiles
2950 eclipse().configFile(eclipse_codestyle_file)
2954 task createSourceReleaseProperties(type: WriteProperties) {
2955 group = "distribution"
2956 description = "Create the source RELEASE properties file"
2958 def sourceTarBuildDir = "${buildDir}/sourceTar"
2959 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2960 outputFile (sourceReleasePropertiesFile)
2963 releaseProps.each{ key, val -> property key, val }
2964 property "git.branch", gitBranch
2965 property "git.hash", gitHash
2968 outputs.file(outputFile)
2971 task sourceDist(type: Tar) {
2972 group "distribution"
2973 description "Create a source .tar.gz file for distribution"
2975 dependsOn createBuildProperties
2976 dependsOn convertMdFiles
2977 dependsOn eclipseAllPreferences
2978 dependsOn createSourceReleaseProperties
2981 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2982 archiveFileName = outputFileName
2984 compression Compression.GZIP
2999 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
3001 "utils/InstallAnywhere",
3016 "gradle.properties",
3028 ".settings/org.eclipse.buildship.core.prefs",
3029 ".settings/org.eclipse.jdt.core.prefs"
3033 exclude (EXCLUDE_FILES)
3034 include (PROCESS_FILES)
3035 filter(ReplaceTokens,
3039 'Version-Rel': JALVIEW_VERSION,
3040 'Year-Rel': getDate("yyyy")
3045 exclude (EXCLUDE_FILES)
3046 exclude (PROCESS_FILES)
3047 exclude ("appletlib")
3048 exclude ("**/*locales")
3049 exclude ("*locales/**")
3050 exclude ("utils/InstallAnywhere")
3052 exclude (getdown_files_dir)
3053 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3054 //exclude (getdown_website_dir)
3055 //exclude (getdown_archive_dir)
3057 // exluding these as not using jars as modules yet
3058 exclude ("${j11modDir}/**/*.jar")
3061 include(INCLUDE_FILES)
3063 // from (jalviewDir) {
3064 // // explicit includes for stuff that seemed to not get included
3065 // include(fileTree("test/**/*."))
3066 // exclude(EXCLUDE_FILES)
3067 // exclude(PROCESS_FILES)
3070 from(file(buildProperties).getParent()) {
3071 include(file(buildProperties).getName())
3072 rename(file(buildProperties).getName(), "build_properties")
3074 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3078 def sourceTarBuildDir = "${buildDir}/sourceTar"
3079 from(sourceTarBuildDir) {
3080 // this includes the appended RELEASE properties file
3084 task dataInstallersJson {
3086 description "Create the installers-VERSION.json data file for installer files created"
3088 mustRunAfter installers
3089 mustRunAfter shadowJar
3090 mustRunAfter sourceDist
3091 mustRunAfter getdownArchive
3093 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3094 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3096 if (installersOutputTxt.exists()) {
3097 inputs.file(installersOutputTxt)
3099 if (install4jCheckSums && installersSha256.exists()) {
3100 inputs.file(installersSha256)
3103 shadowJar.archiveFile, // executable JAR
3104 getdownVersionLaunchJvl, // version JVL
3105 sourceDist.archiveFile // source TGZ
3106 ].each { fileName ->
3107 if (file(fileName).exists()) {
3108 inputs.file(fileName)
3112 outputs.file(hugoDataJsonFile)
3115 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3121 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3124 dependsOn pubhtmlhelp
3126 inputs.dir("${helpBuildDir}/${help_dir}")
3127 outputs.dir("${buildDir}/distributions/${help_dir}")
3131 task j2sSetHeadlessBuild {
3138 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3140 description "Enable the alternative J2S Config file for headless build"
3142 outputFile = jalviewjsJ2sSettingsFileName
3143 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3144 def j2sProps = new Properties()
3145 if (j2sPropsFile.exists()) {
3147 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3148 j2sProps.load(j2sPropsFileFIS)
3149 j2sPropsFileFIS.close()
3151 j2sProps.each { prop, val ->
3154 } catch (Exception e) {
3155 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3159 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3160 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3165 task jalviewjsSetEclipseWorkspace {
3166 def propKey = "jalviewjs_eclipse_workspace"
3168 if (project.hasProperty(propKey)) {
3169 propVal = project.getProperty(propKey)
3170 if (propVal.startsWith("~/")) {
3171 propVal = System.getProperty("user.home") + propVal.substring(1)
3174 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3175 def propsFile = file(propsFileName)
3176 def eclipseWsDir = propVal
3177 def props = new Properties()
3179 def writeProps = true
3180 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3181 def ins = new FileInputStream(propsFileName)
3184 if (props.getProperty(propKey, null) != null) {
3185 eclipseWsDir = props.getProperty(propKey)
3190 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3191 def tempDir = File.createTempDir()
3192 eclipseWsDir = tempDir.getAbsolutePath()
3195 eclipseWorkspace = file(eclipseWsDir)
3198 // do not run a headless transpile when we claim to be in Eclipse
3200 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3201 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3203 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3207 props.setProperty(propKey, eclipseWsDir)
3208 propsFile.parentFile.mkdirs()
3209 def bytes = new ByteArrayOutputStream()
3210 props.store(bytes, null)
3211 def propertiesString = bytes.toString()
3212 propsFile.text = propertiesString
3218 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3221 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3222 outputs.file(propsFileName)
3223 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3227 task jalviewjsEclipsePaths {
3230 def eclipseRoot = jalviewjs_eclipse_root
3231 if (eclipseRoot.startsWith("~/")) {
3232 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3234 if (OperatingSystem.current().isMacOsX()) {
3235 eclipseRoot += "/Eclipse.app"
3236 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3237 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3238 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3239 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3240 eclipseRoot += "/eclipse"
3242 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3243 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3244 } else { // linux or unix
3245 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3246 eclipseRoot += "/eclipse"
3247 println("eclipseDir exists")
3249 eclipseBinary = "${eclipseRoot}/eclipse"
3250 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3253 eclipseVersion = "4.13" // default
3254 def assumedVersion = true
3255 if (file(eclipseProduct).exists()) {
3256 def fis = new FileInputStream(eclipseProduct)
3257 def props = new Properties()
3259 eclipseVersion = props.getProperty("version")
3261 assumedVersion = false
3264 def propKey = "eclipse_debug"
3265 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3268 // do not run a headless transpile when we claim to be in Eclipse
3270 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3271 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3273 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3276 if (!assumedVersion) {
3277 println("ECLIPSE VERSION=${eclipseVersion}")
3283 task printProperties {
3285 description "Output to console all System.properties"
3287 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3293 dependsOn eclipseProject
3294 dependsOn eclipseClasspath
3295 dependsOn eclipseJdt
3299 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3300 task jalviewjsEclipseCopyDropins(type: Copy) {
3301 dependsOn jalviewjsEclipsePaths
3303 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3304 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3305 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3312 // this eclipse -clean doesn't actually work
3313 task jalviewjsCleanEclipse(type: Exec) {
3314 dependsOn eclipseSetup
3315 dependsOn jalviewjsEclipsePaths
3316 dependsOn jalviewjsEclipseCopyDropins
3318 executable(eclipseBinary)
3319 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3325 def inputString = """exit
3328 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3329 standardInput = inputByteStream
3332 /* not really working yet
3333 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3337 task jalviewjsTransferUnzipSwingJs {
3338 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3342 from zipTree(file_zip)
3343 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3347 inputs.file file_zip
3348 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3352 task jalviewjsTransferUnzipLib {
3353 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3356 zipFiles.each { file_zip ->
3358 from zipTree(file_zip)
3359 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3364 inputs.files zipFiles
3365 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3369 task jalviewjsTransferUnzipAllLibs {
3370 dependsOn jalviewjsTransferUnzipSwingJs
3371 dependsOn jalviewjsTransferUnzipLib
3375 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3377 description "Create the alternative j2s file from the j2s.* properties"
3379 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3380 def siteDirProperty = "j2s.site.directory"
3381 def setSiteDir = false
3382 jalviewjsJ2sProps.each { prop, val ->
3384 if (prop == siteDirProperty) {
3385 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3386 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3392 if (!setSiteDir) { // default site location, don't override specifically set property
3393 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3396 outputFile = jalviewjsJ2sAltSettingsFileName
3399 inputs.properties(jalviewjsJ2sProps)
3400 outputs.file(jalviewjsJ2sAltSettingsFileName)
3405 task jalviewjsEclipseSetup {
3406 dependsOn jalviewjsEclipseCopyDropins
3407 dependsOn jalviewjsSetEclipseWorkspace
3408 dependsOn jalviewjsCreateJ2sSettings
3412 task jalviewjsSyncAllLibs (type: Sync) {
3413 dependsOn jalviewjsTransferUnzipAllLibs
3414 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3415 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3416 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3420 def outputFiles = []
3421 rename { filename ->
3422 outputFiles += "${outputDir}/${filename}"
3429 // should this be exclude really ?
3430 duplicatesStrategy "INCLUDE"
3432 outputs.files outputFiles
3433 inputs.files inputFiles
3437 task jalviewjsSyncResources (type: Sync) {
3438 dependsOn buildResources
3440 def inputFiles = fileTree(dir: resourcesBuildDir)
3441 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3445 def outputFiles = []
3446 rename { filename ->
3447 outputFiles += "${outputDir}/${filename}"
3453 outputs.files outputFiles
3454 inputs.files inputFiles
3458 task jalviewjsSyncSiteResources (type: Sync) {
3459 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3460 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3464 def outputFiles = []
3465 rename { filename ->
3466 outputFiles += "${outputDir}/${filename}"
3472 outputs.files outputFiles
3473 inputs.files inputFiles
3477 task jalviewjsSyncBuildProperties (type: Sync) {
3478 dependsOn createBuildProperties
3479 def inputFiles = [file(buildProperties)]
3480 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3484 def outputFiles = []
3485 rename { filename ->
3486 outputFiles += "${outputDir}/${filename}"
3492 outputs.files outputFiles
3493 inputs.files inputFiles
3497 task jalviewjsProjectImport(type: Exec) {
3498 dependsOn eclipseSetup
3499 dependsOn jalviewjsEclipsePaths
3500 dependsOn jalviewjsEclipseSetup
3503 // do not run a headless import when we claim to be in Eclipse
3505 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3506 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3508 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3512 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3513 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3514 executable(eclipseBinary)
3515 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3519 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3521 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3522 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3525 inputs.file("${jalviewDir}/.project")
3526 outputs.upToDateWhen {
3527 file(projdir).exists()
3532 task jalviewjsTranspile(type: Exec) {
3533 dependsOn jalviewjsEclipseSetup
3534 dependsOn jalviewjsProjectImport
3535 dependsOn jalviewjsEclipsePaths
3537 dependsOn jalviewjsEnableAltFileProperty
3541 // do not run a headless transpile when we claim to be in Eclipse
3543 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3544 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3546 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3550 executable(eclipseBinary)
3551 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3555 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3557 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3558 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3564 stdout = new ByteArrayOutputStream()
3565 stderr = new ByteArrayOutputStream()
3567 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3568 def logOutFile = file(logOutFileName)
3569 logOutFile.createNewFile()
3570 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3571 BINARY: ${eclipseBinary}
3572 VERSION: ${eclipseVersion}
3573 WORKSPACE: ${eclipseWorkspace}
3574 DEBUG: ${eclipseDebug}
3577 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3578 // combine stdout and stderr
3579 def logErrFOS = logOutFOS
3581 if (jalviewjs_j2s_to_console.equals("true")) {
3582 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3583 new org.apache.tools.ant.util.TeeOutputStream(
3587 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3588 new org.apache.tools.ant.util.TeeOutputStream(
3593 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3596 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3603 if (stdout.toString().contains("Error processing ")) {
3604 // j2s did not complete transpile
3605 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3606 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3607 println("IGNORING TRANSPILE ERRORS")
3608 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3610 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3615 inputs.dir("${jalviewDir}/${sourceDir}")
3616 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3617 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3621 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3623 def stdout = new ByteArrayOutputStream()
3624 def stderr = new ByteArrayOutputStream()
3626 def coreFile = file(jsfile)
3628 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3630 logOutFile.createNewFile()
3631 logOutFile.append(msg+"\n")
3633 def coreTop = file(prefixFile)
3634 def coreBottom = file(suffixFile)
3635 coreFile.getParentFile().mkdirs()
3636 coreFile.createNewFile()
3637 coreFile.write( coreTop.getText("UTF-8") )
3641 def t = f.getText("UTF-8")
3642 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3643 coreFile.append( t )
3645 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3647 logOutFile.append(msg+"\n")
3650 coreFile.append( coreBottom.getText("UTF-8") )
3652 msg = "Generating ${zjsfile}"
3654 logOutFile.append(msg+"\n")
3655 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3656 def logErrFOS = logOutFOS
3659 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3660 main = "com.google.javascript.jscomp.CommandLineRunner"
3661 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3662 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3665 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3667 logOutFile.append(msg+"\n")
3669 if (logOutConsole) {
3670 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3671 new org.apache.tools.ant.util.TeeOutputStream(
3675 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3676 new org.apache.tools.ant.util.TeeOutputStream(
3681 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3684 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3691 logOutFile.append(msg+"\n")
3695 task jalviewjsBuildAllCores {
3697 description "Build the core js lib closures listed in the classlists dir"
3698 dependsOn jalviewjsTranspile
3699 dependsOn jalviewjsTransferUnzipSwingJs
3701 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3702 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3703 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3704 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3705 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3706 def prefixFile = "${jsDir}/core/coretop2.js"
3707 def suffixFile = "${jsDir}/core/corebottom2.js"
3709 inputs.file prefixFile
3710 inputs.file suffixFile
3712 def classlistFiles = []
3713 // add the classlists found int the jalviewjs_classlists_dir
3714 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3716 def name = file.getName() - ".txt"
3723 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3724 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3725 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3727 jalviewjsCoreClasslists = []
3729 classlistFiles.each {
3732 def file = hash['file']
3733 if (! file.exists()) {
3734 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3735 return false // this is a "continue" in groovy .each closure
3737 def name = hash['name']
3739 name = file.getName() - ".txt"
3747 def list = fileTree(dir: j2sDir, includes: filelist)
3749 def jsfile = "${outputDir}/core${name}.js"
3750 def zjsfile = "${outputDir}/core${name}.z.js"
3752 jalviewjsCoreClasslists += [
3761 outputs.file(jsfile)
3762 outputs.file(zjsfile)
3765 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3766 def stevesoftClasslistName = "_stevesoft"
3767 def stevesoftClasslist = [
3768 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3769 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3770 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3771 'name': stevesoftClasslistName
3773 jalviewjsCoreClasslists += stevesoftClasslist
3774 inputs.files(stevesoftClasslist['list'])
3775 outputs.file(stevesoftClasslist['jsfile'])
3776 outputs.file(stevesoftClasslist['zjsfile'])
3779 def allClasslistName = "_all"
3780 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3781 allJsFiles += fileTree(
3785 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3786 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3787 "**/org/jmol/export/JSExporter.js"
3790 allJsFiles += fileTree(
3794 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3795 "**/sun/misc/Unsafe.js",
3796 "**/swingjs/jquery/jquery-editable-select.js",
3797 "**/swingjs/jquery/j2sComboBox.js",
3798 "**/sun/misc/FloatingDecimal.js"
3801 def allClasslist = [
3802 'jsfile': "${outputDir}/core${allClasslistName}.js",
3803 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3805 'name': allClasslistName
3807 // not including this version of "all" core at the moment
3808 //jalviewjsCoreClasslists += allClasslist
3809 inputs.files(allClasslist['list'])
3810 outputs.file(allClasslist['jsfile'])
3811 outputs.file(allClasslist['zjsfile'])
3814 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3815 logOutFile.getParentFile().mkdirs()
3816 logOutFile.createNewFile()
3817 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3819 jalviewjsCoreClasslists.each {
3820 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3827 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3830 into file(outputFile).getParentFile()
3831 rename { filename ->
3832 if (filename.equals(inputFile.getName())) {
3833 return file(outputFile).getName()
3837 filter(ReplaceTokens,
3841 'MAIN': '"'+main_class+'"',
3843 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3844 'COREKEY': jalviewjs_core_key,
3845 'CORENAME': coreName
3852 task jalviewjsPublishCoreTemplates {
3853 dependsOn jalviewjsBuildAllCores
3854 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3855 def inputFile = file(inputFileName)
3856 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3858 def outputFiles = []
3859 jalviewjsCoreClasslists.each { cl ->
3860 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3861 cl['outputfile'] = outputFile
3862 outputFiles += outputFile
3866 jalviewjsCoreClasslists.each { cl ->
3867 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3870 inputs.file(inputFile)
3871 outputs.files(outputFiles)
3875 task jalviewjsSyncCore (type: Sync) {
3876 dependsOn jalviewjsBuildAllCores
3877 dependsOn jalviewjsPublishCoreTemplates
3878 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3879 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3883 def outputFiles = []
3884 rename { filename ->
3885 outputFiles += "${outputDir}/${filename}"
3891 outputs.files outputFiles
3892 inputs.files inputFiles
3896 // this Copy version of TransferSiteJs will delete anything else in the target dir
3897 task jalviewjsCopyTransferSiteJs(type: Copy) {
3898 dependsOn jalviewjsTranspile
3899 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3900 into "${jalviewDir}/${jalviewjsSiteDir}"
3904 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3905 task jalviewjsSyncTransferSiteJs(type: Sync) {
3906 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3908 into "${jalviewDir}/${jalviewjsSiteDir}"
3915 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3916 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3917 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3918 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3920 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3921 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3922 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3923 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3926 task jalviewjsPrepareSite {
3928 description "Prepares the website folder including unzipping files and copying resources"
3929 dependsOn jalviewjsSyncAllLibs
3930 dependsOn jalviewjsSyncResources
3931 dependsOn jalviewjsSyncSiteResources
3932 dependsOn jalviewjsSyncBuildProperties
3933 dependsOn jalviewjsSyncCore
3937 task jalviewjsBuildSite {
3939 description "Builds the whole website including transpiled code"
3940 dependsOn jalviewjsCopyTransferSiteJs
3941 dependsOn jalviewjsPrepareSite
3945 task cleanJalviewjsTransferSite {
3947 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3948 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3949 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3950 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3955 task cleanJalviewjsSite {
3956 dependsOn cleanJalviewjsTransferSite
3958 delete "${jalviewDir}/${jalviewjsSiteDir}"
3963 task jalviewjsSiteTar(type: Tar) {
3965 description "Creates a tar.gz file for the website"
3966 dependsOn jalviewjsBuildSite
3967 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3968 archiveFileName = outputFilename
3970 compression Compression.GZIP
3972 from "${jalviewDir}/${jalviewjsSiteDir}"
3973 into jalviewjs_site_dir // this is inside the tar file
3975 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3979 task jalviewjsServer {
3981 def filename = "jalviewjsTest.html"
3982 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3983 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3988 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3989 factory = f.newInstance()
3990 } catch (ClassNotFoundException e) {
3991 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3993 def port = Integer.valueOf(jalviewjs_server_port)
3998 while(port < start+1000 && !running) {
4000 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
4001 jalviewjsServer = factory.start(doc_root, port)
4003 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
4004 println("SERVER STARTED with document root ${doc_root}.")
4005 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
4006 println("For debug: "+url+"?j2sdebug")
4007 println("For verbose: "+url+"?j2sverbose")
4008 } catch (Exception e) {
4013 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
4014 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
4015 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4017 jalviewjsCoreClasslists.each { cl ->
4018 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4020 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4022 println("For core ${cl.name}: "+urlcore)
4025 file(htmlFile).text = htmlText
4028 outputs.file(htmlFile)
4029 outputs.upToDateWhen({false})
4033 task cleanJalviewjsAll {
4035 description "Delete all configuration and build artifacts to do with JalviewJS build"
4036 dependsOn cleanJalviewjsSite
4037 dependsOn jalviewjsEclipsePaths
4040 delete "${jalviewDir}/${jalviewjsBuildDir}"
4041 delete "${jalviewDir}/${eclipse_bin_dir}"
4042 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4043 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4045 delete jalviewjsJ2sAltSettingsFileName
4048 outputs.upToDateWhen( { false } )
4052 task jalviewjsIDE_checkJ2sPlugin {
4053 group "00 JalviewJS in Eclipse"
4054 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4057 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4058 def j2sPluginFile = file(j2sPlugin)
4059 def eclipseHome = System.properties["eclipse.home.location"]
4060 if (eclipseHome == null || ! IN_ECLIPSE) {
4061 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4063 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4064 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4065 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4066 eclipseJ2sPluginDirs += altPluginsDir
4068 def foundPlugin = false
4069 def j2sPluginFileName = j2sPluginFile.getName()
4070 def eclipseJ2sPlugin
4071 def eclipseJ2sPluginFile
4072 eclipseJ2sPluginDirs.any { dir ->
4073 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4074 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4075 if (eclipseJ2sPluginFile.exists()) {
4081 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4082 System.err.println(msg)
4083 throw new StopExecutionException(msg)
4086 def digest = MessageDigest.getInstance("MD5")
4088 digest.update(j2sPluginFile.text.bytes)
4089 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4091 digest.update(eclipseJ2sPluginFile.text.bytes)
4092 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4094 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4095 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4096 System.err.println(msg)
4097 throw new StopExecutionException(msg)
4099 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4105 task jalviewjsIDE_copyJ2sPlugin {
4106 group "00 JalviewJS in Eclipse"
4107 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4110 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4111 def j2sPluginFile = file(j2sPlugin)
4112 def eclipseHome = System.properties["eclipse.home.location"]
4113 if (eclipseHome == null || ! IN_ECLIPSE) {
4114 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4116 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4117 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4118 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4119 System.err.println(msg)
4122 eclipseJ2sPluginFile.getParentFile().mkdirs()
4123 into eclipseJ2sPluginFile.getParent()
4129 task jalviewjsIDE_j2sFile {
4130 group "00 JalviewJS in Eclipse"
4131 description "Creates the .j2s file"
4132 dependsOn jalviewjsCreateJ2sSettings
4136 task jalviewjsIDE_SyncCore {
4137 group "00 JalviewJS in Eclipse"
4138 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4139 dependsOn jalviewjsSyncCore
4143 task jalviewjsIDE_SyncSiteAll {
4144 dependsOn jalviewjsSyncAllLibs
4145 dependsOn jalviewjsSyncResources
4146 dependsOn jalviewjsSyncSiteResources
4147 dependsOn jalviewjsSyncBuildProperties
4151 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4154 task jalviewjsIDE_PrepareSite {
4155 group "00 JalviewJS in Eclipse"
4156 description "Sync libs and resources to site dir, but not closure cores"
4158 dependsOn jalviewjsIDE_SyncSiteAll
4159 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4163 task jalviewjsIDE_AssembleSite {
4164 group "00 JalviewJS in Eclipse"
4165 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4166 dependsOn jalviewjsPrepareSite
4170 task jalviewjsIDE_SiteClean {
4171 group "00 JalviewJS in Eclipse"
4172 description "Deletes the Eclipse transpiled site"
4173 dependsOn cleanJalviewjsSite
4177 task jalviewjsIDE_Server {
4178 group "00 JalviewJS in Eclipse"
4179 description "Starts a webserver on localhost to test the website"
4180 dependsOn jalviewjsServer
4184 // buildship runs this at import or gradle refresh
4185 task eclipseSynchronizationTask {
4186 //dependsOn eclipseSetup
4187 dependsOn createBuildProperties
4189 dependsOn jalviewjsIDE_j2sFile
4190 dependsOn jalviewjsIDE_checkJ2sPlugin
4191 dependsOn jalviewjsIDE_PrepareSite
4196 // buildship runs this at build time or project refresh
4197 task eclipseAutoBuildTask {
4198 //dependsOn jalviewjsIDE_checkJ2sPlugin
4199 //dependsOn jalviewjsIDE_PrepareSite
4205 description "Build the site"
4206 dependsOn jalviewjsBuildSite