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 groovy.transform.ExternalizeMethods
13 import groovy.util.XmlParser
14 import groovy.xml.XmlUtil
15 import groovy.json.JsonBuilder
16 import com.vladsch.flexmark.util.ast.Node
17 import com.vladsch.flexmark.html.HtmlRenderer
18 import com.vladsch.flexmark.parser.Parser
19 import com.vladsch.flexmark.util.data.MutableDataSet
20 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
21 import com.vladsch.flexmark.ext.tables.TablesExtension
22 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
23 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
24 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
25 import com.vladsch.flexmark.ext.toc.TocExtension
26 import com.google.common.hash.HashCode
27 import com.google.common.hash.Hashing
28 import com.google.common.io.Files
29 import org.jsoup.Jsoup
30 import org.jsoup.nodes.Element
38 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
39 classpath "org.jsoup:jsoup:1.14.3"
48 id "com.diffplug.gradle.spotless" version "3.28.0"
49 id 'com.github.johnrengelman.shadow' version '4.0.3'
50 id 'com.install4j.gradle' version '9.0.6'
51 id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
52 id 'com.palantir.git-version' version '0.13.0' apply false
63 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
64 def string(Object o) {
65 return o == null ? "" : o.toString()
68 def overrideProperties(String propsFileName, boolean output = false) {
69 if (propsFileName == null) {
72 def propsFile = file(propsFileName)
73 if (propsFile != null && propsFile.exists()) {
74 println("Using properties from file '${propsFileName}'")
76 def p = new Properties()
77 def localPropsFIS = new FileInputStream(propsFile)
83 if (project.hasProperty(key)) {
84 oldval = project.findProperty(key)
85 project.setProperty(key, val)
87 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
90 ext.setProperty(key, val)
92 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
96 } catch (Exception e) {
97 println("Exception reading local.properties")
104 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
105 jalviewDirRelativePath = jalviewDir
108 getdownChannelName = CHANNEL.toLowerCase()
109 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
110 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
111 // Import channel_properties
112 channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
113 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
114 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
115 overrideProperties(channelGradleProperties, false)
116 // local build environment properties
117 // can be "projectDir/local.properties"
118 overrideProperties("${projectDir}/local.properties", true)
119 // or "../projectDir_local.properties"
120 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
123 // Import releaseProps from the RELEASE file
124 // or a file specified via JALVIEW_RELEASE_FILE if defined
125 // Expect jalview.version and target release branch in jalview.release
126 releaseProps = new Properties();
127 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
128 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
130 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
131 releaseProps.load(it)
133 } catch (Exception fileLoadError) {
134 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
137 // Set JALVIEW_VERSION if it is not already set
138 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
139 JALVIEW_VERSION = releaseProps.get("jalview.version")
142 // this property set when running Eclipse headlessly
143 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
144 // this property set by Eclipse
145 eclipseApplicationProperty = string("eclipse.application")
146 // CHECK IF RUNNING FROM WITHIN ECLIPSE
147 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
148 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
149 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
150 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
151 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
155 println("WITHIN ECLIPSE IDE")
157 println("HEADLESS BUILD")
160 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
162 println("J2S ENABLED")
165 System.properties.sort { it.key }.each {
166 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
169 if (false && IN_ECLIPSE) {
170 jalviewDir = jalviewDirAbsolutePath
175 buildDate = new Date().format("yyyyMMdd")
178 bareSourceDir = string(source_dir)
179 sourceDir = string("${jalviewDir}/${bareSourceDir}")
180 resourceDir = string("${jalviewDir}/${resource_dir}")
181 bareTestSourceDir = string(test_source_dir)
182 testDir = string("${jalviewDir}/${bareTestSourceDir}")
184 classesDir = string("${jalviewDir}/${classes_dir}")
187 useClover = clover.equals("true")
188 cloverBuildDir = "${buildDir}/clover"
189 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
190 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
191 cloverReportDir = file("${buildDir}/reports/clover")
192 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
193 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
194 //cloverTestClassesDir = cloverClassesDir
195 cloverDb = string("${cloverBuildDir}/clover.db")
197 testSourceDir = useClover ? cloverTestInstrDir : testDir
198 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
200 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
201 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
202 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
203 getdownFullArchiveDir = null
204 getdownTextLines = []
205 getdownLaunchJvl = null
206 getdownVersionLaunchJvl = null
208 buildProperties = null
210 // the following values might be overridden by the CHANNEL switch
211 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
212 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
213 getdownArchiveAppBase = getdown_archive_base
214 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
215 getdownAppDistDir = getdown_app_dir_alt
216 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
217 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
218 reportRsyncCommand = false
219 jvlChannelName = CHANNEL.toLowerCase()
220 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
221 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
222 install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
223 install4jInstallerName = "${jalview_name} Non-Release Installer"
224 install4jExecutableName = install4j_executable_name
225 install4jExtraScheme = "jalviewx"
226 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
227 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
228 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
229 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
230 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
231 install4jCheckSums = true
233 applicationName = "${jalview_name}"
237 // TODO: get bamboo build artifact URL for getdown artifacts
238 getdown_channel_base = bamboo_channelbase
239 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
240 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
241 jvlChannelName += "_${getdownChannelName}"
242 // automatically add the test group Not-bamboo for exclusion
243 if ("".equals(testng_excluded_groups)) {
244 testng_excluded_groups = "Not-bamboo"
246 install4jExtraScheme = "jalviewb"
249 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
250 getdownAppDistDir = getdown_app_dir_release
251 getdownSetAppBaseProperty = true
252 reportRsyncCommand = true
254 install4jInstallerName = "${jalview_name} Installer"
258 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
259 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
260 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
261 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
262 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
264 package_dir = string("${ARCHIVEDIR}/${package_dir}")
265 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
268 reportRsyncCommand = true
269 install4jExtraScheme = "jalviewa"
273 getdownChannelName = string("archive/${JALVIEW_VERSION}")
274 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
275 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
276 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
277 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
279 package_dir = string("${ARCHIVEDIR}/${package_dir}")
280 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
283 reportRsyncCommand = true
284 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
285 install4jSuffix = "Archive"
286 install4jExtraScheme = "jalviewa"
290 reportRsyncCommand = true
291 getdownSetAppBaseProperty = true
292 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
293 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
295 install4jSuffix = "Develop"
296 install4jExtraScheme = "jalviewd"
297 install4jInstallerName = "${jalview_name} Develop Installer"
301 reportRsyncCommand = true
302 getdownSetAppBaseProperty = true
303 // Don't ignore transpile errors for release build
304 if (jalviewjs_ignore_transpile_errors.equals("true")) {
305 jalviewjs_ignore_transpile_errors = "false"
306 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
308 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
309 install4jSuffix = "Test"
310 install4jExtraScheme = "jalviewt"
311 install4jInstallerName = "${jalview_name} Test Installer"
314 case ~/^SCRATCH(|-[-\w]*)$/:
315 getdownChannelName = CHANNEL
316 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
318 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
319 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
320 reportRsyncCommand = true
321 install4jSuffix = "Scratch"
325 if (!file("${LOCALDIR}").exists()) {
326 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
328 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
329 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
331 JALVIEW_VERSION = "TEST"
332 install4jSuffix = "Test-Local"
333 install4jExtraScheme = "jalviewt"
334 install4jInstallerName = "${jalview_name} Test Installer"
337 case [ "LOCAL", "JALVIEWJS" ]:
338 JALVIEW_VERSION = "TEST"
339 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
340 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
341 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
342 install4jExtraScheme = "jalviewl"
343 install4jCheckSums = false
346 default: // something wrong specified
347 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
351 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
352 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
353 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
354 // override getdownAppBase if requested
355 if (findProperty("getdown_appbase_override") != null) {
356 // revert to LOCAL if empty string
357 if (string(getdown_appbase_override) == "") {
358 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
359 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
360 } else if (string(getdown_appbase_override).startsWith("file://")) {
361 getdownAppBase = string(getdown_appbase_override)
362 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
364 getdownAppBase = string(getdown_appbase_override)
366 println("Overriding getdown appbase with '${getdownAppBase}'")
368 // sanitise file name for jalview launcher file for this channel
369 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
370 // install4j application and folder names
371 if (install4jSuffix == "") {
372 install4jBundleId = "${install4j_bundle_id}"
373 install4jWinApplicationId = install4j_release_win_application_id
375 applicationName = "${jalview_name} ${install4jSuffix}"
376 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
377 // add int hash of install4jSuffix to the last part of the application_id
378 def id = install4j_release_win_application_id
379 def idsplitreverse = id.split("-").reverse()
380 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
381 install4jWinApplicationId = idsplitreverse.reverse().join("-")
383 // sanitise folder and id names
384 // install4jApplicationFolder = e.g. "Jalview Build"
385 install4jApplicationFolder = applicationName
386 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
387 .replaceAll("_+", "_") // collapse __
388 install4jInternalId = applicationName
390 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
391 .replaceAll("_+", "") // collapse __
392 //.replaceAll("_*-_*", "-") // collapse _-_
393 install4jUnixApplicationFolder = applicationName
395 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
396 .replaceAll("_+", "_") // collapse __
397 .replaceAll("_*-_*", "-") // collapse _-_
400 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
401 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
402 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
403 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
404 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
405 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
406 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
407 /* compile without modules -- using classpath libraries
408 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
409 modules_runtimeClasspath = modules_compileClasspath
415 apply plugin: "com.palantir.git-version"
416 def details = versionDetails()
417 gitHash = details.gitHash
418 gitBranch = details.branchName
419 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
420 println("Not in a git repository. Using git values from RELEASE properties file.")
421 gitHash = releaseProps.getProperty("git.hash")
422 gitBranch = releaseProps.getProperty("git.branch")
423 } catch(java.lang.RuntimeException e1) {
424 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
427 println("Using a ${CHANNEL} profile.")
429 additional_compiler_args = []
430 // configure classpath/args for j8/j11 compilation
431 if (JAVA_VERSION.equals("1.8")) {
432 JAVA_INTEGER_VERSION = string("8")
435 libDistDir = j8libDir
436 compile_source_compatibility = 1.8
437 compile_target_compatibility = 1.8
438 // these are getdown.txt properties defined dependent on the JAVA_VERSION
439 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
440 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
441 // this property is assigned below and expanded to multiple lines in the getdown task
442 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
443 // this property is for the Java library used in eclipse
444 eclipseJavaRuntimeName = string("JavaSE-1.8")
445 } else if (JAVA_VERSION.equals("11")) {
446 JAVA_INTEGER_VERSION = string("11")
448 libDistDir = j11libDir
449 compile_source_compatibility = 11
450 compile_target_compatibility = 11
451 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
452 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
453 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
454 eclipseJavaRuntimeName = string("JavaSE-11")
455 /* compile without modules -- using classpath libraries
456 additional_compiler_args += [
457 '--module-path', modules_compileClasspath.asPath,
458 '--add-modules', j11modules
461 } else if (JAVA_VERSION.equals("17")) {
462 JAVA_INTEGER_VERSION = string("17")
464 libDistDir = j17libDir
465 compile_source_compatibility = 17
466 compile_target_compatibility = 17
467 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
468 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
469 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
470 eclipseJavaRuntimeName = string("JavaSE-17")
471 /* compile without modules -- using classpath libraries
472 additional_compiler_args += [
473 '--module-path', modules_compileClasspath.asPath,
474 '--add-modules', j11modules
478 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
483 JAVA_MIN_VERSION = JAVA_VERSION
484 JAVA_MAX_VERSION = JAVA_VERSION
485 def jreInstallsDir = string(jre_installs_dir)
486 if (jreInstallsDir.startsWith("~/")) {
487 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
489 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
490 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
491 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
492 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz")
493 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz")
494 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz")
495 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
496 install4jConfFileName = string("jalview-install4j-conf.install4j")
497 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
498 install4jHomeDir = install4j_home_dir
499 if (install4jHomeDir.startsWith("~/")) {
500 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
503 resourceBuildDir = string("${buildDir}/resources")
504 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
505 helpBuildDir = string("${resourceBuildDir}/help_build")
506 docBuildDir = string("${resourceBuildDir}/doc_build")
508 if (buildProperties == null) {
509 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
511 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
512 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
513 helpSourceDir = string("${helpParentDir}/${help_dir}")
514 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
517 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
518 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
519 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
521 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
523 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
525 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
526 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
527 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
528 jalviewjsJalviewCoreHtmlFile = string("")
529 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
530 jalviewjsCoreClasslists = []
531 jalviewjsJalviewTemplateName = string(jalviewjs_name)
532 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
533 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
534 jalviewjsJ2sProps = null
535 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
537 eclipseWorkspace = null
538 eclipseBinary = string("")
539 eclipseVersion = string("")
549 outputDir = file(classesDir)
553 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
556 compileClasspath = files(sourceSets.main.java.outputDir)
557 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
559 runtimeClasspath = compileClasspath
560 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
565 srcDirs cloverInstrDir
566 outputDir = cloverClassesDir
570 srcDirs = sourceSets.main.resources.srcDirs
573 compileClasspath = files( sourceSets.clover.java.outputDir )
574 //compileClasspath += files( testClassesDir )
575 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
576 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
577 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
579 runtimeClasspath = compileClasspath
584 srcDirs testSourceDir
585 outputDir = file(testClassesDir)
589 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
592 compileClasspath = files( sourceSets.test.java.outputDir )
593 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
594 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
596 runtimeClasspath = compileClasspath
597 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
603 // eclipse project and settings files creation, also used by buildship
606 name = eclipse_project_name
608 natures 'org.eclipse.jdt.core.javanature',
609 'org.eclipse.jdt.groovy.core.groovyNature',
610 'org.eclipse.buildship.core.gradleprojectnature'
612 buildCommand 'org.eclipse.jdt.core.javabuilder'
613 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
617 //defaultOutputDir = sourceSets.main.java.outputDir
618 configurations.each{ c->
619 if (c.isCanBeResolved()) {
620 minusConfigurations += [c]
624 plusConfigurations = [ ]
628 def removeTheseToo = []
629 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
630 cp.entries.each { entry ->
631 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
632 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
633 // we add the resources and help/help dirs in as libs afterwards (see below)
634 if (entry.kind == 'src') {
635 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
636 removeTheseToo += entry
638 alreadyAddedSrcPath.putAt(entry.path, true)
643 cp.entries.removeAll(removeTheseToo)
645 //cp.entries += new Output("${eclipse_bin_dir}/main")
646 if (file(helpParentDir).isDirectory()) {
647 cp.entries += new Library(fileReference(helpParentDir))
649 if (file(resourceDir).isDirectory()) {
650 cp.entries += new Library(fileReference(resourceDir))
653 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
655 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
656 //don't want to add outputDir as eclipse is using its own output dir in bin/main
657 if (it.isDirectory() || ! it.exists()) {
658 // don't add dirs to classpath, especially if they don't exist
659 return false // groovy "continue" in .any closure
661 def itPath = it.toString()
662 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
663 // make relative path
664 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
666 if (alreadyAddedLibPath.get(itPath)) {
667 //println("Not adding duplicate entry "+itPath)
669 //println("Adding entry "+itPath)
670 cp.entries += new Library(fileReference(itPath))
671 alreadyAddedLibPath.put(itPath, true)
675 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
676 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
677 if (it.isDirectory() || ! it.exists()) {
678 // don't add dirs to classpath
679 return false // groovy "continue" in .any closure
682 def itPath = it.toString()
683 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
684 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
686 if (alreadyAddedLibPath.get(itPath)) {
689 def lib = new Library(fileReference(itPath))
690 lib.entryAttributes["test"] = "true"
692 alreadyAddedLibPath.put(itPath, true)
700 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
705 // for the IDE, use java 11 compatibility
706 sourceCompatibility = compile_source_compatibility
707 targetCompatibility = compile_target_compatibility
708 javaRuntimeName = eclipseJavaRuntimeName
710 // add in jalview project specific properties/preferences into eclipse core preferences
712 withProperties { props ->
713 def jalview_prefs = new Properties()
714 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
715 jalview_prefs.load(ins)
717 jalview_prefs.forEach { t, v ->
718 if (props.getAt(t) == null) {
722 // codestyle file -- overrides previous formatter prefs
723 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
724 if (csFile.exists()) {
725 XmlParser parser = new XmlParser()
726 def profiles = parser.parse(csFile)
727 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
728 if (profile != null) {
729 profile.'setting'.each { s ->
731 def value = s.'@value'
732 if (id != null && value != null) {
733 props.putAt(id, value)
744 // Don't want these to be activated if in headless build
745 synchronizationTasks "eclipseSynchronizationTask"
746 //autoBuildTasks "eclipseAutoBuildTask"
752 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
753 // Class to allow updating arbitrary properties files
754 class PropertiesFile extends PropertiesPersistableConfigurationObject {
755 public PropertiesFile(PropertiesTransformer t) { super(t); }
756 @Override protected void load(Properties properties) { }
757 @Override protected void store(Properties properties) { }
758 @Override protected String getDefaultResourceName() { return ""; }
759 // This is necessary, because PropertiesPersistableConfigurationObject fails
760 // if no default properties file exists.
761 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
764 // Task to update arbitrary properties files (set outputFile)
765 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
766 private final PropertiesFileContentMerger file;
767 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
768 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
769 protected void configure(PropertiesFile props) {
770 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
772 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
775 task eclipseUIPreferences(type: PropertiesFileTask) {
776 description = "Generate Eclipse additional settings"
777 def filename = "org.eclipse.jdt.ui.prefs"
778 outputFile = "$projectDir/.settings/${filename}" as File
781 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
786 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
787 description = "Generate Eclipse additional settings"
788 def filename = "org.eclipse.jdt.groovy.core.prefs"
789 outputFile = "$projectDir/.settings/${filename}" as File
792 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
797 task eclipseAllPreferences {
799 dependsOn eclipseUIPreferences
800 dependsOn eclipseGroovyCorePreferences
803 eclipseUIPreferences.mustRunAfter eclipseJdt
804 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
806 /* end of eclipse preferences hack */
814 delete cloverBuildDir
815 delete cloverReportDir
820 task cloverInstrJava(type: JavaExec) {
821 group = "Verification"
822 description = "Create clover instrumented source java files"
824 dependsOn cleanClover
826 inputs.files(sourceSets.main.allJava)
827 outputs.dir(cloverInstrDir)
829 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
830 classpath = sourceSets.clover.compileClasspath
831 main = "com.atlassian.clover.CloverInstr"
839 cloverInstrDir.getPath(),
841 def srcFiles = sourceSets.main.allJava.files
844 { file -> file.absolutePath }
847 args argsList.toArray()
850 delete cloverInstrDir
851 println("Clover: About to instrument "+srcFiles.size() +" files")
856 task cloverInstrTests(type: JavaExec) {
857 group = "Verification"
858 description = "Create clover instrumented source test files"
860 dependsOn cleanClover
862 inputs.files(testDir)
863 outputs.dir(cloverTestInstrDir)
865 classpath = sourceSets.clover.compileClasspath
866 main = "com.atlassian.clover.CloverInstr"
876 cloverTestInstrDir.getPath(),
878 args argsList.toArray()
881 delete cloverTestInstrDir
882 println("Clover: About to instrument test files")
888 group = "Verification"
889 description = "Create clover instrumented all source files"
891 dependsOn cloverInstrJava
892 dependsOn cloverInstrTests
896 cloverClasses.dependsOn cloverInstr
899 task cloverConsoleReport(type: JavaExec) {
900 group = "Verification"
901 description = "Creates clover console report"
904 file(cloverDb).exists()
907 inputs.dir cloverClassesDir
909 classpath = sourceSets.clover.runtimeClasspath
910 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
912 if (cloverreport_mem.length() > 0) {
913 maxHeapSize = cloverreport_mem
915 if (cloverreport_jvmargs.length() > 0) {
916 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
926 args argsList.toArray()
930 task cloverHtmlReport(type: JavaExec) {
931 group = "Verification"
932 description = "Creates clover HTML report"
935 file(cloverDb).exists()
938 def cloverHtmlDir = cloverReportDir
939 inputs.dir cloverClassesDir
940 outputs.dir cloverHtmlDir
942 classpath = sourceSets.clover.runtimeClasspath
943 main = "com.atlassian.clover.reporters.html.HtmlReporter"
945 if (cloverreport_mem.length() > 0) {
946 maxHeapSize = cloverreport_mem
948 if (cloverreport_jvmargs.length() > 0) {
949 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
960 if (cloverreport_html_options.length() > 0) {
961 argsList += cloverreport_html_options.split(" ")
964 args argsList.toArray()
968 task cloverXmlReport(type: JavaExec) {
969 group = "Verification"
970 description = "Creates clover XML report"
973 file(cloverDb).exists()
976 def cloverXmlFile = "${cloverReportDir}/clover.xml"
977 inputs.dir cloverClassesDir
978 outputs.file cloverXmlFile
980 classpath = sourceSets.clover.runtimeClasspath
981 main = "com.atlassian.clover.reporters.xml.XMLReporter"
983 if (cloverreport_mem.length() > 0) {
984 maxHeapSize = cloverreport_mem
986 if (cloverreport_jvmargs.length() > 0) {
987 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
998 if (cloverreport_xml_options.length() > 0) {
999 argsList += cloverreport_xml_options.split(" ")
1002 args argsList.toArray()
1007 group = "Verification"
1008 description = "Creates clover reports"
1010 dependsOn cloverXmlReport
1011 dependsOn cloverHtmlReport
1018 sourceCompatibility = compile_source_compatibility
1019 targetCompatibility = compile_target_compatibility
1020 options.compilerArgs += additional_compiler_args
1021 print ("Setting target compatibility to "+targetCompatibility+"\n")
1023 //classpath += configurations.cloverRuntime
1029 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1030 sourceCompatibility = compile_source_compatibility
1031 targetCompatibility = compile_target_compatibility
1032 options.compilerArgs = additional_compiler_args
1033 options.encoding = "UTF-8"
1035 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1042 sourceCompatibility = compile_source_compatibility
1043 targetCompatibility = compile_target_compatibility
1044 options.compilerArgs = additional_compiler_args
1046 print ("Setting target compatibility to "+targetCompatibility+"\n")
1053 delete sourceSets.main.java.outputDir
1059 dependsOn cleanClover
1061 delete sourceSets.test.java.outputDir
1066 // format is a string like date.format("dd MMMM yyyy")
1067 def getDate(format) {
1068 return date.format(format)
1072 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1073 MutableDataSet options = new MutableDataSet()
1075 def extensions = new ArrayList<>()
1076 extensions.add(AnchorLinkExtension.create())
1077 extensions.add(AutolinkExtension.create())
1078 extensions.add(StrikethroughExtension.create())
1079 extensions.add(TaskListExtension.create())
1080 extensions.add(TablesExtension.create())
1081 extensions.add(TocExtension.create())
1083 options.set(Parser.EXTENSIONS, extensions)
1085 // set GFM table parsing options
1086 options.set(TablesExtension.WITH_CAPTION, false)
1087 options.set(TablesExtension.COLUMN_SPANS, false)
1088 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1089 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1090 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1091 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1092 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1094 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1095 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1096 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1097 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1099 Parser parser = Parser.builder(options).build()
1100 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1102 mdFiles.each { mdFile ->
1103 // add table of contents
1104 def mdText = "[TOC]\n"+mdFile.text
1106 // grab the first top-level title
1108 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1109 def matcher = mdText =~ titleRegex
1110 if (matcher.size() > 0) {
1111 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1112 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1114 // or use the filename if none found
1115 if (title == null) {
1116 title = mdFile.getName()
1119 Node document = parser.parse(mdText)
1120 String htmlBody = renderer.render(document)
1121 def htmlText = '''<html>
1122 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1123 <html xmlns="http://www.w3.org/1999/xhtml">
1125 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1126 <meta http-equiv="Content-Style-Type" content="text/css" />
1127 <meta name="generator" content="flexmark" />
1129 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1131 <style type="text/css">code{white-space: pre;}</style>
1133 htmlText += ((cssFile != null) ? cssFile.text : '')
1134 htmlText += '''</head>
1137 htmlText += htmlBody
1143 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1144 def htmlFile = file(htmlFilePath)
1145 println("Creating ${htmlFilePath}")
1146 htmlFile.text = htmlText
1151 task copyDocs(type: Copy) {
1152 def inputDir = "${jalviewDir}/${doc_dir}"
1153 def outputDir = "${docBuildDir}/${doc_dir}"
1157 include('**/*.html')
1159 filter(ReplaceTokens,
1163 'Version-Rel': JALVIEW_VERSION,
1164 'Year-Rel': getDate("yyyy")
1171 exclude('**/*.html')
1176 inputs.dir(inputDir)
1177 outputs.dir(outputDir)
1181 task convertMdFiles {
1183 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1184 def cssFile = file("${jalviewDir}/${flexmark_css}")
1187 convertMdToHtml(mdFiles, cssFile)
1190 inputs.files(mdFiles)
1191 inputs.file(cssFile)
1194 mdFiles.each { mdFile ->
1195 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1196 htmlFiles.add(file(htmlFilePath))
1198 outputs.files(htmlFiles)
1202 task copyHelp(type: Copy) {
1203 def inputDir = helpSourceDir
1204 def outputDir = "${helpBuildDir}/${help_dir}"
1208 include('**/*.html')
1212 filter(ReplaceTokens,
1216 'Version-Rel': JALVIEW_VERSION,
1217 'Year-Rel': getDate("yyyy")
1224 exclude('**/*.html')
1231 inputs.dir(inputDir)
1232 outputs.files(helpFile)
1233 outputs.dir(outputDir)
1237 task copyResources(type: Copy) {
1239 description = "Copy (and make text substitutions in) the resources dir to the build area"
1241 def inputDir = resourceDir
1242 def outputDir = resourcesBuildDir
1246 include('**/*.html')
1248 filter(ReplaceTokens,
1252 'Version-Rel': JALVIEW_VERSION,
1253 'Year-Rel': getDate("yyyy")
1260 exclude('**/*.html')
1265 inputs.dir(inputDir)
1266 outputs.dir(outputDir)
1269 task copyChannelResources(type: Copy) {
1270 dependsOn copyResources
1272 description = "Copy the channel resources dir to the build resources area"
1274 def inputDir = "${channelDir}/${resource_dir}"
1275 def outputDir = resourcesBuildDir
1279 inputs.dir(inputDir)
1280 outputs.dir(outputDir)
1283 task createBuildProperties(type: WriteProperties) {
1284 dependsOn copyResources
1286 description = "Create the ${buildProperties} file"
1288 inputs.dir(sourceDir)
1289 inputs.dir(resourcesBuildDir)
1290 outputFile (buildProperties)
1291 // taking time specific comment out to allow better incremental builds
1292 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1293 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1294 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1295 property "VERSION", JALVIEW_VERSION
1296 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1297 if (getdownSetAppBaseProperty) {
1298 property "GETDOWNAPPBASE", getdownAppBase
1299 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1301 outputs.file(outputFile)
1305 task buildIndices(type: JavaExec) {
1307 classpath = sourceSets.main.compileClasspath
1308 main = "com.sun.java.help.search.Indexer"
1309 workingDir = "${helpBuildDir}/${help_dir}"
1312 inputs.dir("${workingDir}/${argDir}")
1314 outputs.dir("${classesDir}/doc")
1315 outputs.dir("${classesDir}/help")
1316 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1317 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1318 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1319 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1320 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1321 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1324 task buildResources {
1325 dependsOn copyResources
1326 dependsOn copyChannelResources
1327 dependsOn createBuildProperties
1331 dependsOn buildResources
1334 dependsOn convertMdFiles
1335 dependsOn buildIndices
1339 compileJava.dependsOn prepare
1340 run.dependsOn compileJava
1341 //run.dependsOn prepare
1344 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1349 dependsOn cloverClasses
1351 dependsOn compileJava //?
1355 includeGroups testng_groups
1356 excludeGroups testng_excluded_groups
1358 useDefaultListeners=true
1361 maxHeapSize = "1024m"
1363 workingDir = jalviewDir
1364 def testLaf = project.findProperty("test_laf")
1365 if (testLaf != null) {
1366 println("Setting Test LaF to '${testLaf}'")
1367 systemProperty "laf", testLaf
1369 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1370 if (testHiDPIScale != null) {
1371 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1372 systemProperty "sun.java2d.uiScale", testHiDPIScale
1374 sourceCompatibility = compile_source_compatibility
1375 targetCompatibility = compile_target_compatibility
1376 jvmArgs += additional_compiler_args
1380 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1386 task compileLinkCheck(type: JavaCompile) {
1388 classpath = files("${jalviewDir}/${utils_dir}")
1389 destinationDir = file("${jalviewDir}/${utils_dir}")
1390 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1392 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1393 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1394 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1395 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1399 task linkCheck(type: JavaExec) {
1401 dependsOn compileLinkCheck
1403 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1404 classpath = files("${jalviewDir}/${utils_dir}")
1405 main = "HelpLinksChecker"
1406 workingDir = jalviewDir
1407 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1409 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1410 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1413 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1417 inputs.dir(helpBuildDir)
1418 outputs.file(helpLinksCheckerOutFile)
1422 // import the pubhtmlhelp target
1423 ant.properties.basedir = "${jalviewDir}"
1424 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1425 ant.importBuild "${utils_dir}/publishHelp.xml"
1428 task cleanPackageDir(type: Delete) {
1430 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1440 attributes "Main-Class": main_class,
1441 "Permissions": "all-permissions",
1442 "Application-Name": applicationName,
1443 "Codebase": application_codebase,
1444 "Implementation-Version": JALVIEW_VERSION
1447 def outputDir = "${jalviewDir}/${package_dir}"
1448 destinationDirectory = file(outputDir)
1449 archiveFileName = rootProject.name+".jar"
1450 duplicatesStrategy "EXCLUDE"
1457 exclude "**/*.jar.*"
1459 inputs.dir(sourceSets.main.java.outputDir)
1460 sourceSets.main.resources.srcDirs.each{ dir ->
1463 outputs.file("${outputDir}/${archiveFileName}")
1467 task copyJars(type: Copy) {
1468 from fileTree(dir: classesDir, include: "**/*.jar").files
1469 into "${jalviewDir}/${package_dir}"
1473 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1474 task syncJars(type: Sync) {
1476 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1477 into "${jalviewDir}/${package_dir}"
1479 include jar.archiveFileName.getOrNull()
1486 description = "Put all required libraries in dist"
1487 // order of "cleanPackageDir", "copyJars", "jar" important!
1488 jar.mustRunAfter cleanPackageDir
1489 syncJars.mustRunAfter cleanPackageDir
1490 dependsOn cleanPackageDir
1493 outputs.dir("${jalviewDir}/${package_dir}")
1498 dependsOn cleanPackageDir
1505 group = "distribution"
1506 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1510 from ("${jalviewDir}/${libDistDir}") {
1514 attributes "Implementation-Version": JALVIEW_VERSION,
1515 "Application-Name": applicationName
1518 duplicatesStrategy "INCLUDE"
1520 mainClassName = shadow_jar_main_class
1522 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1527 task getdownWebsite() {
1528 group = "distribution"
1529 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1534 def getdownWebsiteResourceFilenames = []
1535 def getdownResourceDir = getdownResourceDir
1536 def getdownResourceFilenames = []
1539 // clean the getdown website and files dir before creating getdown folders
1540 delete getdownAppBaseDir
1541 delete getdownFilesDir
1544 from buildProperties
1545 rename(file(buildProperties).getName(), getdown_build_properties)
1548 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1551 from channelPropsFile
1552 into getdownAppBaseDir
1554 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
1556 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
1557 def props = project.properties.sort { it.key }
1558 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1559 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1561 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1562 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1564 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1565 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1567 if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
1568 props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
1569 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
1570 props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
1571 props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
1572 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
1573 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
1576 props.put("getdown_txt_title", jalview_name)
1577 props.put("getdown_txt_ui.name", applicationName)
1579 // start with appbase
1580 getdownTextLines += "appbase = ${getdownAppBase}"
1581 props.each{ prop, val ->
1582 if (prop.startsWith("getdown_txt_") && val != null) {
1583 if (prop.startsWith("getdown_txt_multi_")) {
1584 def key = prop.substring(18)
1585 val.split(",").each{ v ->
1586 def line = "${key} = ${v}"
1587 getdownTextLines += line
1590 // file values rationalised
1591 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1593 if (val.indexOf('/') == 0) {
1596 } else if (val.indexOf('/') > 0) {
1597 // relative path (relative to jalviewDir)
1598 r = file( "${jalviewDir}/${val}" )
1601 val = "${getdown_resource_dir}/" + r.getName()
1602 getdownWebsiteResourceFilenames += val
1603 getdownResourceFilenames += r.getPath()
1606 if (! prop.startsWith("getdown_txt_resource")) {
1607 def line = prop.substring(12) + " = ${val}"
1608 getdownTextLines += line
1614 getdownWebsiteResourceFilenames.each{ filename ->
1615 getdownTextLines += "resource = ${filename}"
1617 getdownResourceFilenames.each{ filename ->
1620 into getdownResourceDir
1624 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
1625 getdownWrapperScripts.each{ script ->
1626 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
1630 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
1632 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
1637 fileTree(file(package_dir)).each{ f ->
1638 if (f.isDirectory()) {
1639 def files = fileTree(dir: f, include: ["*"]).getFiles()
1641 } else if (f.exists()) {
1645 def jalviewJar = jar.archiveFileName.getOrNull()
1646 // put jalview.jar first for CLASSPATH and .properties files reasons
1647 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
1648 def name = f.getName()
1649 def line = "code = ${getdownAppDistDir}/${name}"
1650 getdownTextLines += line
1657 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1659 if (JAVA_VERSION.equals("11")) {
1660 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1661 j11libFiles.sort().each{f ->
1662 def name = f.getName()
1663 def line = "code = ${getdown_j11lib_dir}/${name}"
1664 getdownTextLines += line
1667 into getdownJ11libDir
1673 // 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.
1674 //getdownTextLines += "class = " + file(getdownLauncher).getName()
1675 getdownTextLines += "resource = ${getdown_launcher_new}"
1676 getdownTextLines += "class = ${main_class}"
1677 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
1678 if (getdownSetAppBaseProperty) {
1679 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
1680 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
1683 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
1684 getdownTxt.write(getdownTextLines.join("\n"))
1686 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1687 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
1688 launchJvl.write("appbase=${getdownAppBase}")
1690 // files going into the getdown website dir: getdown-launcher.jar
1692 from getdownLauncher
1693 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1694 into getdownAppBaseDir
1697 // files going into the getdown website dir: getdown-launcher(-local).jar
1699 from getdownLauncher
1700 if (file(getdownLauncher).getName() != getdown_launcher) {
1701 rename(file(getdownLauncher).getName(), getdown_launcher)
1703 into getdownAppBaseDir
1706 // files going into the getdown website dir: ./install dir and files
1707 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1710 from getdownLauncher
1711 from "${getdownAppDir}/${getdown_build_properties}"
1712 if (file(getdownLauncher).getName() != getdown_launcher) {
1713 rename(file(getdownLauncher).getName(), getdown_launcher)
1715 into getdownInstallDir
1718 // and make a copy in the getdown files dir (these are not downloaded by getdown)
1720 from getdownInstallDir
1721 into getdownFilesInstallDir
1725 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
1729 from getdownLauncher
1730 from "${getdownAppBaseDir}/${getdown_build_properties}"
1731 from "${getdownAppBaseDir}/${channel_props}"
1732 if (file(getdownLauncher).getName() != getdown_launcher) {
1733 rename(file(getdownLauncher).getName(), getdown_launcher)
1735 into getdownFilesDir
1738 // and ./resource (not all downloaded by getdown)
1740 from getdownResourceDir
1741 into "${getdownFilesDir}/${getdown_resource_dir}"
1746 inputs.dir("${jalviewDir}/${package_dir}")
1748 outputs.dir(getdownAppBaseDir)
1749 outputs.dir(getdownFilesDir)
1753 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1754 task getdownDigestDir(type: JavaExec) {
1756 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1758 def digestDirPropertyName = "DIGESTDIR"
1760 classpath = files(getdownLauncher)
1761 def digestDir = findProperty(digestDirPropertyName)
1762 if (digestDir == null) {
1763 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1767 main = "com.threerings.getdown.tools.Digester"
1771 task getdownDigest(type: JavaExec) {
1772 group = "distribution"
1773 description = "Digest the getdown website folder"
1774 dependsOn getdownWebsite
1776 classpath = files(getdownLauncher)
1778 main = "com.threerings.getdown.tools.Digester"
1779 args getdownAppBaseDir
1780 inputs.dir(getdownAppBaseDir)
1781 outputs.file("${getdownAppBaseDir}/digest2.txt")
1786 group = "distribution"
1787 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1788 dependsOn getdownDigest
1790 if (reportRsyncCommand) {
1791 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
1792 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1793 println "LIKELY RSYNC COMMAND:"
1794 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1795 if (RUNRSYNC == "true") {
1797 commandLine "mkdir", "-p", toDir
1800 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1808 task getdownArchiveBuild() {
1809 group = "distribution"
1810 description = "Put files in the archive dir to go on the website"
1812 dependsOn getdownWebsite
1814 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
1815 def vDir = "${getdownArchiveDir}/${v}"
1816 getdownFullArchiveDir = "${vDir}/getdown"
1817 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
1819 def vAltDir = "alt_${v}"
1820 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
1823 // cleanup old "old" dir
1824 delete getdownArchiveDir
1826 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
1827 getdownArchiveTxt.getParentFile().mkdirs()
1828 def getdownArchiveTextLines = []
1829 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
1833 from "${getdownAppBaseDir}/${getdownAppDistDir}"
1834 into "${getdownFullArchiveDir}/${vAltDir}"
1837 getdownTextLines.each { line ->
1838 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
1839 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
1840 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
1841 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
1842 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
1843 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
1844 // remove the existing resource = resource/ or bin/ lines
1845 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
1846 getdownArchiveTextLines += line
1850 // the resource dir -- add these files as resource lines in getdown.txt
1852 from "${archiveImagesDir}"
1853 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
1855 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
1859 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
1861 def vLaunchJvl = file(getdownVersionLaunchJvl)
1862 vLaunchJvl.getParentFile().mkdirs()
1863 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
1864 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
1865 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
1866 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
1867 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
1868 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
1870 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
1872 from getdownLauncher
1873 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
1874 from "${getdownAppBaseDir}/${getdown_launcher_new}"
1875 from "${getdownAppBaseDir}/${channel_props}"
1876 if (file(getdownLauncher).getName() != getdown_launcher) {
1877 rename(file(getdownLauncher).getName(), getdown_launcher)
1879 into getdownFullArchiveDir
1885 task getdownArchiveDigest(type: JavaExec) {
1886 group = "distribution"
1887 description = "Digest the getdown archive folder"
1889 dependsOn getdownArchiveBuild
1892 classpath = files(getdownLauncher)
1893 args getdownFullArchiveDir
1895 main = "com.threerings.getdown.tools.Digester"
1896 inputs.dir(getdownFullArchiveDir)
1897 outputs.file("${getdownFullArchiveDir}/digest2.txt")
1900 task getdownArchive() {
1901 group = "distribution"
1902 description = "Build the website archive dir with getdown digest"
1904 dependsOn getdownArchiveBuild
1905 dependsOn getdownArchiveDigest
1908 tasks.withType(JavaCompile) {
1909 options.encoding = 'UTF-8'
1915 delete getdownAppBaseDir
1916 delete getdownFilesDir
1917 delete getdownArchiveDir
1923 if (file(install4jHomeDir).exists()) {
1925 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1926 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1927 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1928 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1930 installDir(file(install4jHomeDir))
1932 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1936 task copyInstall4jTemplate {
1937 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1938 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1939 inputs.file(install4jTemplateFile)
1940 inputs.file(install4jFileAssociationsFile)
1941 inputs.property("CHANNEL", { CHANNEL })
1942 outputs.file(install4jConfFile)
1945 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1947 // turn off code signing if no OSX_KEYPASS
1948 if (OSX_KEYPASS == "") {
1949 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1950 codeSigning.'@macEnabled' = "false"
1952 install4jConfigXml.'**'.windows.each { windows ->
1953 windows.'@runPostProcessor' = "false"
1957 // disable install screen for OSX dmg (for 2.11.2.0)
1958 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
1959 macosArchive.attributes().remove('executeSetupApp')
1960 macosArchive.attributes().remove('setupAppId')
1963 // turn off checksum creation for LOCAL channel
1964 def e = install4jConfigXml.application[0]
1965 e.'@createChecksums' = string(install4jCheckSums)
1967 // put file association actions where placeholder action is
1968 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1969 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1970 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1971 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1972 def parent = a.parent()
1974 fileAssociationActions.each { faa ->
1977 // don't need to continue in .any loop once replacements have been made
1982 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1983 // NB we're deleting the /other/ one!
1984 // Also remove the examples subdir from non-release versions
1985 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1986 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1987 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1988 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1990 // remove the examples subdir from Full File Set
1991 def files = install4jConfigXml.files[0]
1992 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1993 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1994 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1995 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1996 dirEntry.parent().remove(dirEntry)
1998 install4jConfigXml.'**'.action.any { a ->
1999 if (a.'@customizedId' == customizedIdToDelete) {
2000 def parent = a.parent()
2006 // write install4j file
2007 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2014 delete install4jConfFile
2018 task cleanInstallersDataFiles {
2019 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2020 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2021 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2023 delete installersOutputTxt
2024 delete installersSha256
2025 delete hugoDataJsonFile
2029 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2030 group = "distribution"
2031 description = "Create the install4j installers"
2033 dependsOn copyInstall4jTemplate
2034 dependsOn cleanInstallersDataFiles
2036 projectFile = install4jConfFile
2038 // create an md5 for the input files to use as version for install4j conf file
2039 def digest = MessageDigest.getInstance("MD5")
2041 (file("${install4jDir}/${install4j_template}").text +
2042 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2043 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2044 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2045 if (filesMd5.length() >= 8) {
2046 filesMd5 = filesMd5.substring(0,8)
2048 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2051 'JALVIEW_NAME': jalview_name,
2052 'JALVIEW_APPLICATION_NAME': applicationName,
2053 'JALVIEW_DIR': "../..",
2054 'OSX_KEYSTORE': OSX_KEYSTORE,
2055 'OSX_APPLEID': OSX_APPLEID,
2056 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2057 'JSIGN_SH': JSIGN_SH,
2058 'JRE_DIR': getdown_app_dir_java,
2059 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2060 'JALVIEW_VERSION': JALVIEW_VERSION,
2061 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2062 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2063 'JAVA_VERSION': JAVA_VERSION,
2064 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2065 'VERSION': JALVIEW_VERSION,
2066 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
2067 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
2068 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
2069 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
2070 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
2071 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
2072 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2073 'BUNDLE_ID': install4jBundleId,
2074 'INTERNAL_ID': install4jInternalId,
2075 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2076 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2077 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
2078 'WRAPPER_LINK': getdownWrapperLink,
2079 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2080 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2081 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2082 'INSTALLER_NAME': install4jInstallerName,
2083 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2084 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2085 'GETDOWN_FILES_DIR': getdown_files_dir,
2086 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2087 'GETDOWN_DIST_DIR': getdownAppDistDir,
2088 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2089 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2090 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2091 'BUILD_DIR': install4jBuildDir,
2092 'APPLICATION_CATEGORIES': install4j_application_categories,
2093 'APPLICATION_FOLDER': install4jApplicationFolder,
2094 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2095 'EXECUTABLE_NAME': install4jExecutableName,
2096 'EXTRA_SCHEME': install4jExtraScheme,
2097 'MAC_ICONS_FILE': install4jMacIconsFile,
2098 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2099 'PNG_ICON_FILE': install4jPngIconFile,
2100 'BACKGROUND': install4jBackground,
2104 //println("INSTALL4J VARIABLES:")
2105 //variables.each{k,v->println("${k}=${v}")}
2107 destination = "${jalviewDir}/${install4jBuildDir}"
2108 buildSelected = true
2110 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2112 disableSigning = true
2113 disableNotarization = true
2117 macKeystorePassword = OSX_KEYPASS
2120 if (OSX_ALTOOLPASS) {
2121 appleIdPassword = OSX_ALTOOLPASS
2122 disableNotarization = false
2124 disableNotarization = true
2128 println("Using projectFile "+projectFile)
2129 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2133 inputs.dir(getdownAppBaseDir)
2134 inputs.file(install4jConfFile)
2135 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2136 inputs.dir(macosJavaVMDir)
2137 inputs.dir(windowsJavaVMDir)
2138 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2141 def getDataHash(File myFile) {
2142 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2143 return myFile.exists()
2145 "file" : myFile.getName(),
2146 "filesize" : myFile.length(),
2147 "sha256" : hash.toString()
2152 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2154 "channel" : getdownChannelName,
2155 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2156 "git-commit" : "${gitHash} [${gitBranch}]",
2157 "version" : JALVIEW_VERSION
2159 // install4j installer files
2160 if (installersOutputTxt.exists()) {
2162 installersOutputTxt.readLines().each { def line ->
2163 if (line.startsWith("#")) {
2166 line.replaceAll("\n","")
2167 def vals = line.split("\t")
2168 def filename = vals[3]
2169 def filesize = file(filename).length()
2170 filename = filename.replaceAll(/^.*\//, "")
2171 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2172 idHash."${filename}" = vals[0]
2174 if (install4jCheckSums && installersSha256.exists()) {
2175 installersSha256.readLines().each { def line ->
2176 if (line.startsWith("#")) {
2179 line.replaceAll("\n","")
2180 def vals = line.split(/\s+\*?/)
2181 def filename = vals[1]
2182 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2188 "JAR": shadowJar.archiveFile, // executable JAR
2189 "JVL": getdownVersionLaunchJvl, // version JVL
2190 "SOURCE": sourceDist.archiveFile // source TGZ
2191 ].each { key, value ->
2192 def file = file(value)
2193 if (file.exists()) {
2194 def fileHash = getDataHash(file)
2195 if (fileHash != null) {
2196 hash."${key}" = fileHash;
2200 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2203 task staticMakeInstallersJsonFile {
2205 def output = findProperty("i4j_output")
2206 def sha256 = findProperty("i4j_sha256")
2207 def json = findProperty("i4j_json")
2208 if (output == null || sha256 == null || json == null) {
2209 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2211 writeDataJsonFile(file(output), file(sha256), file(json))
2216 dependsOn installerFiles
2222 eclipse().configFile(eclipse_codestyle_file)
2226 task createSourceReleaseProperties(type: WriteProperties) {
2227 group = "distribution"
2228 description = "Create the source RELEASE properties file"
2230 def sourceTarBuildDir = "${buildDir}/sourceTar"
2231 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2232 outputFile (sourceReleasePropertiesFile)
2235 releaseProps.each{ key, val -> property key, val }
2236 property "git.branch", gitBranch
2237 property "git.hash", gitHash
2240 outputs.file(outputFile)
2243 task sourceDist(type: Tar) {
2244 group "distribution"
2245 description "Create a source .tar.gz file for distribution"
2247 dependsOn createBuildProperties
2248 dependsOn convertMdFiles
2249 dependsOn eclipseAllPreferences
2250 dependsOn createSourceReleaseProperties
2253 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2254 archiveFileName = outputFileName
2256 compression Compression.GZIP
2271 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2273 "utils/InstallAnywhere",
2288 "gradle.properties",
2300 ".settings/org.eclipse.buildship.core.prefs",
2301 ".settings/org.eclipse.jdt.core.prefs"
2305 exclude (EXCLUDE_FILES)
2306 include (PROCESS_FILES)
2307 filter(ReplaceTokens,
2311 'Version-Rel': JALVIEW_VERSION,
2312 'Year-Rel': getDate("yyyy")
2317 exclude (EXCLUDE_FILES)
2318 exclude (PROCESS_FILES)
2319 exclude ("appletlib")
2320 exclude ("**/*locales")
2321 exclude ("*locales/**")
2322 exclude ("utils/InstallAnywhere")
2324 exclude (getdown_files_dir)
2325 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2326 //exclude (getdown_website_dir)
2327 //exclude (getdown_archive_dir)
2329 // exluding these as not using jars as modules yet
2330 exclude ("${j11modDir}/**/*.jar")
2333 include(INCLUDE_FILES)
2335 // from (jalviewDir) {
2336 // // explicit includes for stuff that seemed to not get included
2337 // include(fileTree("test/**/*."))
2338 // exclude(EXCLUDE_FILES)
2339 // exclude(PROCESS_FILES)
2342 from(file(buildProperties).getParent()) {
2343 include(file(buildProperties).getName())
2344 rename(file(buildProperties).getName(), "build_properties")
2346 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2350 def sourceTarBuildDir = "${buildDir}/sourceTar"
2351 from(sourceTarBuildDir) {
2352 // this includes the appended RELEASE properties file
2356 task dataInstallersJson {
2358 description "Create the installers-VERSION.json data file for installer files created"
2360 mustRunAfter installers
2361 mustRunAfter shadowJar
2362 mustRunAfter sourceDist
2363 mustRunAfter getdownArchive
2365 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2366 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2368 if (installersOutputTxt.exists()) {
2369 inputs.file(installersOutputTxt)
2371 if (install4jCheckSums && installersSha256.exists()) {
2372 inputs.file(installersSha256)
2375 shadowJar.archiveFile, // executable JAR
2376 getdownVersionLaunchJvl, // version JVL
2377 sourceDist.archiveFile // source TGZ
2378 ].each { fileName ->
2379 if (file(fileName).exists()) {
2380 inputs.file(fileName)
2384 outputs.file(hugoDataJsonFile)
2387 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
2391 def hugoTemplateSubstitutions(String input) {
2393 output = output.replaceAll("__DATE__", getDate("yyyy-MM-dd"))
2394 output = output.replaceAll("__CHANNEL__", propertiesChannelName)
2395 output = output.replaceAll("__APPLICATION_NAME__", applicationName)
2396 output = output.replaceAll("__GIT_HASH__", gitHash)
2397 output = output.replaceAll("__GIT_BRANCH__", gitBranch)
2398 output = output.replaceAll("__VERSION__", JALVIEW_VERSION)
2399 output = output.replaceAll("__JAVA_VERSION__", JAVA_VERSION)
2400 output = output.replaceAll("__VERSION_UNDERSCORES__", JALVIEW_VERSION_UNDERSCORES)
2404 def ulToList(Element ul, int indent) {
2406 ul.children().each { e ->
2407 if (e.tagName().toLowerCase() == "ul") {
2408 list = list.stripTrailing() + "\n"
2409 list += ulToList(e, indent+1)
2410 } else if (e.tagName().toLowerCase() == "li") {
2413 def mdItem = " " * indent + "- "
2414 e.childNodes().any {n ->
2415 if (n.nodeName().equals("#comment")) {
2416 mdItem += "{{<comment>}}${n.getData()}{{</comment>}} "
2417 issuesText = n.getData().trim()
2418 issues = n.getData().trim().split(/[,\s]+/).findAll { it.startsWith("JAL-") }
2422 def safeText = issuesText.replaceAll('"', '\"')
2423 def joinedIssues = issues.join(",")
2424 def issuesLink = (issues.size() > 0) ?
2425 " {{< jal issue=\"${joinedIssues}\" alt=\"${safeText}\" >}}"
2427 def addedIssues = false
2428 e.childNodes().each { node ->
2429 if (node.nodeName().toLowerCase() == "ul") {
2430 // add issues link before sub list if it's last
2431 if (node.nextSibling() == null) {
2432 mdItem += "${issuesLink}"
2435 mdItem = mdItem.stripTrailing() + "\n"
2436 mdItem += ulToList(node, indent+1)
2437 } else if (node.nodeName() == "#text") {
2438 mdItem += node.text()
2439 } else if (node.nodeName().toLowerCase() == "strong") {
2440 mdItem += "**${node.text()}**"
2441 } else if (node.nodeName().toLowerCase() == "em") {
2442 // if (true || (node.text().length() > 50 && node.text().count(" ") > 10) || (!node.nextSibling().text().startsWith("\\s*\\n"))) {
2443 mdItem += "*${node.text()}*"
2445 // mdItem += "### "+node.text()
2447 } else if (node.nodeName().toLowerCase() == "br") {
2449 } else if (node.nodeName().toLowerCase() == "a") {
2450 mdItem += "[${node.text()}](${node.attr('href')})"
2454 mdItem += issuesLink
2456 list += mdItem.stripTrailing()+"\n"
2457 } else if (e.tagName().toLowerCase() == "div") {
2458 e.children().each { eee ->
2459 list += ulToList(eee, indent)
2461 } else if (e.tagName().toLowerCase() == "strong") {
2462 list += "**${e.text()}**"
2463 } else if (e.tagName().toLowerCase() == "em") {
2464 if (e.text().length() > 50 && e.text().count(" ") > 20) {
2465 list += "*${e.text()}*"
2467 list += "\n\n### ${e.text()}\n\n"
2474 task hugoTemplates {
2476 description "Create partially populated md pages for hugo website build"
2478 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
2479 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
2480 def templateFiles = fileTree(dir: hugoTemplatesDir)
2483 // specific release template for version archive
2484 def summary = "${applicationName} ${JALVIEW_VERSION}"
2487 if (CHANNEL == "RELEASE") {
2488 def releasesHtmlFile = file("${helpSourceDir}/${releases_html}")
2490 def html = releasesHtmlFile.text
2491 def doc = Jsoup.parse(html)
2492 def table = doc.select("table").first()
2493 def headings = table.select("tr").first().select("th").collect { it.text() }
2494 def releaseRow = null
2495 def trs = table.select("tr")
2497 def tds = tr.select("td")
2498 if (tds.size() == 0)
2500 def releaseTd = tds.first()
2501 if (releaseTd.text().startsWith("${JALVIEW_VERSION} ")) {
2507 if (releaseRow != null && headings != null && headings.size() == 3) {
2508 def releaseTd = releaseRow.select("td").first()
2509 def spaceIndex = releaseTd.text().indexOf(" ")
2510 if (spaceIndex >= 0) {
2511 oldDate = new Date().parse("dd/MM/yyyy", releaseTd.text().substring(spaceIndex+1))
2513 def releaseCells = releaseRow.select("td")
2514 if (releaseCells.size() == 3) {
2515 def title1 = headings[1]
2516 def title2 = headings[2]
2518 def lastDotIndex = JALVIEW_VERSION.lastIndexOf(".")
2519 if (lastDotIndex > 0) {
2521 def patchRelease = JALVIEW_VERSION.substring(lastDotIndex+1) as Integer
2522 def patchReleaseString = null
2523 if (patchRelease == 0) {
2524 patchReleaseString = "first minor"
2525 } else if (patchRelease == 1) {
2526 patchReleaseString = "first patch"
2527 } else if (patchRelease == 2) {
2528 patchReleaseString = "second patch"
2529 } else if (patchRelease == 3) {
2530 patchReleaseString = "third patch"
2531 } else if (patchRelease == 4) {
2532 patchReleaseString = "fourth patch"
2533 } else if (patchRelease == 5) {
2534 patchReleaseString = "fifth patch"
2535 } else if (patchRelease == 6) {
2536 patchReleaseString = "sixth patch"
2537 } else if (patchRelease == 7) {
2538 patchReleaseString = "seventh patch"
2539 } else if (patchRelease > 13 && (patchRelease % 10 == 1)) {
2540 patchReleaseString += "st"
2541 } else if (patchRelease > 13 && (patchRelease % 10 == 2)) {
2542 patchReleaseString += "nd"
2543 } else if (patchRelease > 13 && (patchRelease % 10 == 3)) {
2544 patchReleaseString += "rd"
2545 } else if (patchRelease != null) {
2546 patchReleaseString += "th"
2548 summary += (patchReleaseString != null) ? " is the ${patchReleaseString} release in the ${JALVIEW_VERSION.substring(0,lastDotIndex)} series." : ""
2549 } catch(Exception e) {
2556 if (headings[col] != null && headings[col].size() > 0) {
2557 releaseCells[col].children().each { e ->
2558 if (e.tagName().toLowerCase() == "ul" || e.tagName().toLowerCase() == "div") {
2559 if (colChanges != "") {
2560 colChanges = colChanges.stripTrailing() + "\n"
2562 colChanges += ulToList(e, 0)
2563 } else if (e.tagName().toLowerCase() == "em") {
2564 colChanges += "\n\n### ${e.text()}\n\n"
2568 if (colChanges != "") {
2569 def className = headings[col].replaceAll(" ","_").toLowerCase().replaceAll("[^_a-z]","")
2570 changes += "<div class=\"${className}\">\n\n## ${headings[col]}\n\n${colChanges}\n</div>\n\n"
2574 if (changes != "") {
2575 changes = "<div class=\"release_notes\">\n\n${changes}\n\n</div>"
2581 templateFiles.each{ templateFile ->
2582 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
2583 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
2584 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
2586 def outPathName = string("${hugoBuildDir}/$newRelPathName")
2590 rename(templateFile.getName(), newFileName)
2594 def newFile = file("${outPathName}/${newFileName}".toString())
2595 def content = newFile.text
2596 // summary in version archive release pages only appears from 2.10.2b2 onwards
2597 if (oldDate.format("yyyy") as Integer >= 2019 || JALVIEW_VERSION.startsWith("2.10")) {
2598 def summaryFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
2599 if (summaryFile.exists()) {
2600 summary = summaryFile.text
2604 content = content.replaceAll("__SUMMARY__", summary)
2606 content = content.replaceAll("__SUMMARY__", "")
2608 content = content.replaceAll("__CHANGES__", changes)
2609 if (oldDate != null) {
2610 if (oldDate[java.util.Calendar.YEAR] < 90) {
2611 oldDate[java.util.Calendar.YEAR] += 2000
2613 content = content.replaceAll("__DATE__", oldDate.format("yyyy-MM-dd"))
2615 newFile.text = hugoTemplateSubstitutions(content)
2619 inputs.dir(hugoTemplatesDir)
2620 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
2621 inputs.property("CHANNEL", { CHANNEL })
2627 dependsOn pubhtmlhelp
2629 inputs.dir("${helpBuildDir}/${help_dir}")
2630 outputs.dir("${buildDir}/distributions/${help_dir}")
2634 task j2sSetHeadlessBuild {
2641 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2643 description "Enable the alternative J2S Config file for headless build"
2645 outputFile = jalviewjsJ2sSettingsFileName
2646 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2647 def j2sProps = new Properties()
2648 if (j2sPropsFile.exists()) {
2650 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2651 j2sProps.load(j2sPropsFileFIS)
2652 j2sPropsFileFIS.close()
2654 j2sProps.each { prop, val ->
2657 } catch (Exception e) {
2658 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2662 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2663 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2668 task jalviewjsSetEclipseWorkspace {
2669 def propKey = "jalviewjs_eclipse_workspace"
2671 if (project.hasProperty(propKey)) {
2672 propVal = project.getProperty(propKey)
2673 if (propVal.startsWith("~/")) {
2674 propVal = System.getProperty("user.home") + propVal.substring(1)
2677 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2678 def propsFile = file(propsFileName)
2679 def eclipseWsDir = propVal
2680 def props = new Properties()
2682 def writeProps = true
2683 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2684 def ins = new FileInputStream(propsFileName)
2687 if (props.getProperty(propKey, null) != null) {
2688 eclipseWsDir = props.getProperty(propKey)
2693 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2694 def tempDir = File.createTempDir()
2695 eclipseWsDir = tempDir.getAbsolutePath()
2698 eclipseWorkspace = file(eclipseWsDir)
2701 // do not run a headless transpile when we claim to be in Eclipse
2703 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2704 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2706 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2710 props.setProperty(propKey, eclipseWsDir)
2711 propsFile.parentFile.mkdirs()
2712 def bytes = new ByteArrayOutputStream()
2713 props.store(bytes, null)
2714 def propertiesString = bytes.toString()
2715 propsFile.text = propertiesString
2721 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2724 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2725 outputs.file(propsFileName)
2726 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2730 task jalviewjsEclipsePaths {
2733 def eclipseRoot = jalviewjs_eclipse_root
2734 if (eclipseRoot.startsWith("~/")) {
2735 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2737 if (OperatingSystem.current().isMacOsX()) {
2738 eclipseRoot += "/Eclipse.app"
2739 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2740 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2741 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2742 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2743 eclipseRoot += "/eclipse"
2745 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2746 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2747 } else { // linux or unix
2748 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2749 eclipseRoot += "/eclipse"
2750 println("eclipseDir exists")
2752 eclipseBinary = "${eclipseRoot}/eclipse"
2753 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2756 eclipseVersion = "4.13" // default
2757 def assumedVersion = true
2758 if (file(eclipseProduct).exists()) {
2759 def fis = new FileInputStream(eclipseProduct)
2760 def props = new Properties()
2762 eclipseVersion = props.getProperty("version")
2764 assumedVersion = false
2767 def propKey = "eclipse_debug"
2768 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2771 // do not run a headless transpile when we claim to be in Eclipse
2773 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2774 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2776 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2779 if (!assumedVersion) {
2780 println("ECLIPSE VERSION=${eclipseVersion}")
2786 task printProperties {
2788 description "Output to console all System.properties"
2790 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2796 dependsOn eclipseProject
2797 dependsOn eclipseClasspath
2798 dependsOn eclipseJdt
2802 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2803 task jalviewjsEclipseCopyDropins(type: Copy) {
2804 dependsOn jalviewjsEclipsePaths
2806 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2807 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2808 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2815 // this eclipse -clean doesn't actually work
2816 task jalviewjsCleanEclipse(type: Exec) {
2817 dependsOn eclipseSetup
2818 dependsOn jalviewjsEclipsePaths
2819 dependsOn jalviewjsEclipseCopyDropins
2821 executable(eclipseBinary)
2822 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2828 def inputString = """exit
2831 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2832 standardInput = inputByteStream
2835 /* not really working yet
2836 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2840 task jalviewjsTransferUnzipSwingJs {
2841 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2845 from zipTree(file_zip)
2846 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2850 inputs.file file_zip
2851 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2855 task jalviewjsTransferUnzipLib {
2856 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2859 zipFiles.each { file_zip ->
2861 from zipTree(file_zip)
2862 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2867 inputs.files zipFiles
2868 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2872 task jalviewjsTransferUnzipAllLibs {
2873 dependsOn jalviewjsTransferUnzipSwingJs
2874 dependsOn jalviewjsTransferUnzipLib
2878 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2880 description "Create the alternative j2s file from the j2s.* properties"
2882 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2883 def siteDirProperty = "j2s.site.directory"
2884 def setSiteDir = false
2885 jalviewjsJ2sProps.each { prop, val ->
2887 if (prop == siteDirProperty) {
2888 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2889 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2895 if (!setSiteDir) { // default site location, don't override specifically set property
2896 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2899 outputFile = jalviewjsJ2sAltSettingsFileName
2902 inputs.properties(jalviewjsJ2sProps)
2903 outputs.file(jalviewjsJ2sAltSettingsFileName)
2908 task jalviewjsEclipseSetup {
2909 dependsOn jalviewjsEclipseCopyDropins
2910 dependsOn jalviewjsSetEclipseWorkspace
2911 dependsOn jalviewjsCreateJ2sSettings
2915 task jalviewjsSyncAllLibs (type: Sync) {
2916 dependsOn jalviewjsTransferUnzipAllLibs
2917 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2918 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2919 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2923 def outputFiles = []
2924 rename { filename ->
2925 outputFiles += "${outputDir}/${filename}"
2932 // should this be exclude really ?
2933 duplicatesStrategy "INCLUDE"
2935 outputs.files outputFiles
2936 inputs.files inputFiles
2940 task jalviewjsSyncResources (type: Sync) {
2941 dependsOn buildResources
2943 def inputFiles = fileTree(dir: resourcesBuildDir)
2944 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2948 def outputFiles = []
2949 rename { filename ->
2950 outputFiles += "${outputDir}/${filename}"
2956 outputs.files outputFiles
2957 inputs.files inputFiles
2961 task jalviewjsSyncSiteResources (type: Sync) {
2962 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2963 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2967 def outputFiles = []
2968 rename { filename ->
2969 outputFiles += "${outputDir}/${filename}"
2975 outputs.files outputFiles
2976 inputs.files inputFiles
2980 task jalviewjsSyncBuildProperties (type: Sync) {
2981 dependsOn createBuildProperties
2982 def inputFiles = [file(buildProperties)]
2983 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2987 def outputFiles = []
2988 rename { filename ->
2989 outputFiles += "${outputDir}/${filename}"
2995 outputs.files outputFiles
2996 inputs.files inputFiles
3000 task jalviewjsProjectImport(type: Exec) {
3001 dependsOn eclipseSetup
3002 dependsOn jalviewjsEclipsePaths
3003 dependsOn jalviewjsEclipseSetup
3006 // do not run a headless import when we claim to be in Eclipse
3008 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3009 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3011 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3015 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3016 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3017 executable(eclipseBinary)
3018 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3022 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3024 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3025 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3028 inputs.file("${jalviewDir}/.project")
3029 outputs.upToDateWhen {
3030 file(projdir).exists()
3035 task jalviewjsTranspile(type: Exec) {
3036 dependsOn jalviewjsEclipseSetup
3037 dependsOn jalviewjsProjectImport
3038 dependsOn jalviewjsEclipsePaths
3040 dependsOn jalviewjsEnableAltFileProperty
3044 // do not run a headless transpile when we claim to be in Eclipse
3046 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3047 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3049 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3053 executable(eclipseBinary)
3054 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3058 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3060 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3061 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3067 stdout = new ByteArrayOutputStream()
3068 stderr = new ByteArrayOutputStream()
3070 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3071 def logOutFile = file(logOutFileName)
3072 logOutFile.createNewFile()
3073 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3074 BINARY: ${eclipseBinary}
3075 VERSION: ${eclipseVersion}
3076 WORKSPACE: ${eclipseWorkspace}
3077 DEBUG: ${eclipseDebug}
3080 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3081 // combine stdout and stderr
3082 def logErrFOS = logOutFOS
3084 if (jalviewjs_j2s_to_console.equals("true")) {
3085 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3086 new org.apache.tools.ant.util.TeeOutputStream(
3090 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3091 new org.apache.tools.ant.util.TeeOutputStream(
3096 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3099 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3106 if (stdout.toString().contains("Error processing ")) {
3107 // j2s did not complete transpile
3108 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3109 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3110 println("IGNORING TRANSPILE ERRORS")
3111 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3113 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3118 inputs.dir("${jalviewDir}/${sourceDir}")
3119 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3120 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3124 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3126 def stdout = new ByteArrayOutputStream()
3127 def stderr = new ByteArrayOutputStream()
3129 def coreFile = file(jsfile)
3131 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3133 logOutFile.createNewFile()
3134 logOutFile.append(msg+"\n")
3136 def coreTop = file(prefixFile)
3137 def coreBottom = file(suffixFile)
3138 coreFile.getParentFile().mkdirs()
3139 coreFile.createNewFile()
3140 coreFile.write( coreTop.getText("UTF-8") )
3144 def t = f.getText("UTF-8")
3145 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3146 coreFile.append( t )
3148 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3150 logOutFile.append(msg+"\n")
3153 coreFile.append( coreBottom.getText("UTF-8") )
3155 msg = "Generating ${zjsfile}"
3157 logOutFile.append(msg+"\n")
3158 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3159 def logErrFOS = logOutFOS
3162 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3163 main = "com.google.javascript.jscomp.CommandLineRunner"
3164 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3165 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3168 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3170 logOutFile.append(msg+"\n")
3172 if (logOutConsole) {
3173 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3174 new org.apache.tools.ant.util.TeeOutputStream(
3178 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3179 new org.apache.tools.ant.util.TeeOutputStream(
3184 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3187 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3194 logOutFile.append(msg+"\n")
3198 task jalviewjsBuildAllCores {
3200 description "Build the core js lib closures listed in the classlists dir"
3201 dependsOn jalviewjsTranspile
3202 dependsOn jalviewjsTransferUnzipSwingJs
3204 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3205 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3206 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3207 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3208 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3209 def prefixFile = "${jsDir}/core/coretop2.js"
3210 def suffixFile = "${jsDir}/core/corebottom2.js"
3212 inputs.file prefixFile
3213 inputs.file suffixFile
3215 def classlistFiles = []
3216 // add the classlists found int the jalviewjs_classlists_dir
3217 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3219 def name = file.getName() - ".txt"
3226 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3227 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3228 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3230 jalviewjsCoreClasslists = []
3232 classlistFiles.each {
3235 def file = hash['file']
3236 if (! file.exists()) {
3237 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3238 return false // this is a "continue" in groovy .each closure
3240 def name = hash['name']
3242 name = file.getName() - ".txt"
3250 def list = fileTree(dir: j2sDir, includes: filelist)
3252 def jsfile = "${outputDir}/core${name}.js"
3253 def zjsfile = "${outputDir}/core${name}.z.js"
3255 jalviewjsCoreClasslists += [
3264 outputs.file(jsfile)
3265 outputs.file(zjsfile)
3268 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3269 def stevesoftClasslistName = "_stevesoft"
3270 def stevesoftClasslist = [
3271 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3272 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3273 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3274 'name': stevesoftClasslistName
3276 jalviewjsCoreClasslists += stevesoftClasslist
3277 inputs.files(stevesoftClasslist['list'])
3278 outputs.file(stevesoftClasslist['jsfile'])
3279 outputs.file(stevesoftClasslist['zjsfile'])
3282 def allClasslistName = "_all"
3283 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3284 allJsFiles += fileTree(
3288 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3289 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3290 "**/org/jmol/export/JSExporter.js"
3293 allJsFiles += fileTree(
3297 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3298 "**/sun/misc/Unsafe.js",
3299 "**/swingjs/jquery/jquery-editable-select.js",
3300 "**/swingjs/jquery/j2sComboBox.js",
3301 "**/sun/misc/FloatingDecimal.js"
3304 def allClasslist = [
3305 'jsfile': "${outputDir}/core${allClasslistName}.js",
3306 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3308 'name': allClasslistName
3310 // not including this version of "all" core at the moment
3311 //jalviewjsCoreClasslists += allClasslist
3312 inputs.files(allClasslist['list'])
3313 outputs.file(allClasslist['jsfile'])
3314 outputs.file(allClasslist['zjsfile'])
3317 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3318 logOutFile.getParentFile().mkdirs()
3319 logOutFile.createNewFile()
3320 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3322 jalviewjsCoreClasslists.each {
3323 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3330 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3333 into file(outputFile).getParentFile()
3334 rename { filename ->
3335 if (filename.equals(inputFile.getName())) {
3336 return file(outputFile).getName()
3340 filter(ReplaceTokens,
3344 'MAIN': '"'+main_class+'"',
3346 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3347 'COREKEY': jalviewjs_core_key,
3348 'CORENAME': coreName
3355 task jalviewjsPublishCoreTemplates {
3356 dependsOn jalviewjsBuildAllCores
3357 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3358 def inputFile = file(inputFileName)
3359 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3361 def outputFiles = []
3362 jalviewjsCoreClasslists.each { cl ->
3363 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3364 cl['outputfile'] = outputFile
3365 outputFiles += outputFile
3369 jalviewjsCoreClasslists.each { cl ->
3370 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3373 inputs.file(inputFile)
3374 outputs.files(outputFiles)
3378 task jalviewjsSyncCore (type: Sync) {
3379 dependsOn jalviewjsBuildAllCores
3380 dependsOn jalviewjsPublishCoreTemplates
3381 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3382 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3386 def outputFiles = []
3387 rename { filename ->
3388 outputFiles += "${outputDir}/${filename}"
3394 outputs.files outputFiles
3395 inputs.files inputFiles
3399 // this Copy version of TransferSiteJs will delete anything else in the target dir
3400 task jalviewjsCopyTransferSiteJs(type: Copy) {
3401 dependsOn jalviewjsTranspile
3402 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3403 into "${jalviewDir}/${jalviewjsSiteDir}"
3407 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3408 task jalviewjsSyncTransferSiteJs(type: Sync) {
3409 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3411 into "${jalviewDir}/${jalviewjsSiteDir}"
3418 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3419 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3420 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3421 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3423 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3424 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3425 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3426 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3429 task jalviewjsPrepareSite {
3431 description "Prepares the website folder including unzipping files and copying resources"
3432 dependsOn jalviewjsSyncAllLibs
3433 dependsOn jalviewjsSyncResources
3434 dependsOn jalviewjsSyncSiteResources
3435 dependsOn jalviewjsSyncBuildProperties
3436 dependsOn jalviewjsSyncCore
3440 task jalviewjsBuildSite {
3442 description "Builds the whole website including transpiled code"
3443 dependsOn jalviewjsCopyTransferSiteJs
3444 dependsOn jalviewjsPrepareSite
3448 task cleanJalviewjsTransferSite {
3450 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3451 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3452 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3453 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3458 task cleanJalviewjsSite {
3459 dependsOn cleanJalviewjsTransferSite
3461 delete "${jalviewDir}/${jalviewjsSiteDir}"
3466 task jalviewjsSiteTar(type: Tar) {
3468 description "Creates a tar.gz file for the website"
3469 dependsOn jalviewjsBuildSite
3470 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3471 archiveFileName = outputFilename
3473 compression Compression.GZIP
3475 from "${jalviewDir}/${jalviewjsSiteDir}"
3476 into jalviewjs_site_dir // this is inside the tar file
3478 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3482 task jalviewjsServer {
3484 def filename = "jalviewjsTest.html"
3485 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3486 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3491 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3492 factory = f.newInstance()
3493 } catch (ClassNotFoundException e) {
3494 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3496 def port = Integer.valueOf(jalviewjs_server_port)
3501 while(port < start+1000 && !running) {
3503 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3504 jalviewjsServer = factory.start(doc_root, port)
3506 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3507 println("SERVER STARTED with document root ${doc_root}.")
3508 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3509 println("For debug: "+url+"?j2sdebug")
3510 println("For verbose: "+url+"?j2sverbose")
3511 } catch (Exception e) {
3516 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3517 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3518 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3520 jalviewjsCoreClasslists.each { cl ->
3521 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3523 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3525 println("For core ${cl.name}: "+urlcore)
3528 file(htmlFile).text = htmlText
3531 outputs.file(htmlFile)
3532 outputs.upToDateWhen({false})
3536 task cleanJalviewjsAll {
3538 description "Delete all configuration and build artifacts to do with JalviewJS build"
3539 dependsOn cleanJalviewjsSite
3540 dependsOn jalviewjsEclipsePaths
3543 delete "${jalviewDir}/${jalviewjsBuildDir}"
3544 delete "${jalviewDir}/${eclipse_bin_dir}"
3545 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3546 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3548 delete jalviewjsJ2sAltSettingsFileName
3551 outputs.upToDateWhen( { false } )
3555 task jalviewjsIDE_checkJ2sPlugin {
3556 group "00 JalviewJS in Eclipse"
3557 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3560 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3561 def j2sPluginFile = file(j2sPlugin)
3562 def eclipseHome = System.properties["eclipse.home.location"]
3563 if (eclipseHome == null || ! IN_ECLIPSE) {
3564 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3566 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3567 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3568 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3569 eclipseJ2sPluginDirs += altPluginsDir
3571 def foundPlugin = false
3572 def j2sPluginFileName = j2sPluginFile.getName()
3573 def eclipseJ2sPlugin
3574 def eclipseJ2sPluginFile
3575 eclipseJ2sPluginDirs.any { dir ->
3576 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3577 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3578 if (eclipseJ2sPluginFile.exists()) {
3584 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3585 System.err.println(msg)
3586 throw new StopExecutionException(msg)
3589 def digest = MessageDigest.getInstance("MD5")
3591 digest.update(j2sPluginFile.text.bytes)
3592 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3594 digest.update(eclipseJ2sPluginFile.text.bytes)
3595 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3597 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3598 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3599 System.err.println(msg)
3600 throw new StopExecutionException(msg)
3602 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3608 task jalviewjsIDE_copyJ2sPlugin {
3609 group "00 JalviewJS in Eclipse"
3610 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3613 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3614 def j2sPluginFile = file(j2sPlugin)
3615 def eclipseHome = System.properties["eclipse.home.location"]
3616 if (eclipseHome == null || ! IN_ECLIPSE) {
3617 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3619 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3620 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3621 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3622 System.err.println(msg)
3625 eclipseJ2sPluginFile.getParentFile().mkdirs()
3626 into eclipseJ2sPluginFile.getParent()
3632 task jalviewjsIDE_j2sFile {
3633 group "00 JalviewJS in Eclipse"
3634 description "Creates the .j2s file"
3635 dependsOn jalviewjsCreateJ2sSettings
3639 task jalviewjsIDE_SyncCore {
3640 group "00 JalviewJS in Eclipse"
3641 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3642 dependsOn jalviewjsSyncCore
3646 task jalviewjsIDE_SyncSiteAll {
3647 dependsOn jalviewjsSyncAllLibs
3648 dependsOn jalviewjsSyncResources
3649 dependsOn jalviewjsSyncSiteResources
3650 dependsOn jalviewjsSyncBuildProperties
3654 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3657 task jalviewjsIDE_PrepareSite {
3658 group "00 JalviewJS in Eclipse"
3659 description "Sync libs and resources to site dir, but not closure cores"
3661 dependsOn jalviewjsIDE_SyncSiteAll
3662 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3666 task jalviewjsIDE_AssembleSite {
3667 group "00 JalviewJS in Eclipse"
3668 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3669 dependsOn jalviewjsPrepareSite
3673 task jalviewjsIDE_SiteClean {
3674 group "00 JalviewJS in Eclipse"
3675 description "Deletes the Eclipse transpiled site"
3676 dependsOn cleanJalviewjsSite
3680 task jalviewjsIDE_Server {
3681 group "00 JalviewJS in Eclipse"
3682 description "Starts a webserver on localhost to test the website"
3683 dependsOn jalviewjsServer
3687 // buildship runs this at import or gradle refresh
3688 task eclipseSynchronizationTask {
3689 //dependsOn eclipseSetup
3690 dependsOn createBuildProperties
3692 dependsOn jalviewjsIDE_j2sFile
3693 dependsOn jalviewjsIDE_checkJ2sPlugin
3694 dependsOn jalviewjsIDE_PrepareSite
3699 // buildship runs this at build time or project refresh
3700 task eclipseAutoBuildTask {
3701 //dependsOn jalviewjsIDE_checkJ2sPlugin
3702 //dependsOn jalviewjsIDE_PrepareSite
3708 description "Build the site"
3709 dependsOn jalviewjsBuildSite