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}/${install4jBuildDir}/sha256sums")
2368 if (installersOutputTxt.exists()) {
2369 inputs.file(installersOutputTxt)
2371 if (install4jCheckSums && installersSha256.exists()) {
2372 inputs.file(installersSha256)
2375 shadowJar.archiveFile, // executable JAR
2376 getdownVersionLaunchJvl, // version JVL
2377 sourceDist.archiveFile // source TGZ
2378 ].each { fileName ->
2379 if (file(fileName).exists()) {
2380 inputs.file(fileName)
2384 outputs.file(hugoDataJsonFile)
2387 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
2391 def hugoTemplateSubstitutions(String input) {
2393 output = output.replaceAll("__DATE__", getDate("yyyy-MM-dd"))
2394 output = output.replaceAll("__CHANNEL__", propertiesChannelName)
2395 output = output.replaceAll("__APPLICATION_NAME__", applicationName)
2396 output = output.replaceAll("__GIT_HASH__", gitHash)
2397 output = output.replaceAll("__GIT_BRANCH__", gitBranch)
2398 output = output.replaceAll("__VERSION__", JALVIEW_VERSION)
2399 output = output.replaceAll("__JAVA_VERSION__", JAVA_VERSION)
2400 output = output.replaceAll("__VERSION_UNDERSCORES__", JALVIEW_VERSION_UNDERSCORES)
2404 def ulToList(Element ul, int indent) {
2406 ul.children().each { e ->
2407 if (e.tagName().toLowerCase() == "ul") {
2409 list += ulToList(e, indent+1)
2410 } else if (e.tagName().toLowerCase() == "li") {
2412 def mdItem = " " * indent + "- "
2413 e.childNodes().any {n ->
2414 if (n.nodeName().equals("#comment")) {
2416 issues = n.getData().trim().split(/[,\s]+/)
2420 def issuesLink = (issues.size() > 0) ?
2421 " {{< jal issue=\"${issues.join(",")}\" >}}"
2423 def addedIssues = false
2424 e.childNodes().each { node ->
2425 if (node.nodeName().toLowerCase() == "ul") {
2426 // add issues link before sub list
2427 mdItem += "${issuesLink}\n"
2429 mdItem += ulToList(e, indent+1)
2430 } else if (node.nodeName() == "#text") {
2431 mdItem += node.text()
2435 mdItem += issuesLink
2437 list += "${mdItem}\n"
2443 task hugoTemplates {
2445 description "Create partially populated md pages for hugo website build"
2447 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
2448 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
2449 def templateFiles = fileTree(dir: hugoTemplatesDir)
2452 // specific release template for version archive
2453 def summary = "${applicationName} ${JALVIEW_VERSION}"
2456 if (CHANNEL == "RELEASE") {
2457 def releasesHtmlFile = file("${helpSourceDir}/${releases_html}")
2459 def html = releasesHtmlFile.text
2460 def doc = Jsoup.parse(html)
2461 def table = doc.select("table").first()
2462 def headings = table.select("tr").first().select("th").collect { it.text() }
2463 def releaseRow = null
2464 def trs = table.select("tr")
2466 def tds = tr.select("td")
2467 if (tds.size() == 0)
2469 def releaseTd = tds.first()
2470 if (releaseTd.text().startsWith("${JALVIEW_VERSION} ")) {
2476 if (releaseRow != null && headings != null && headings.size() == 3) {
2477 def releaseTd = releaseRow.select("td").first()
2478 def spaceIndex = releaseTd.text().indexOf(" ")
2479 if (spaceIndex >= 0) {
2480 oldDate = new Date().parse("dd/MM/yyyy", releaseTd.text().substring(spaceIndex+1))
2482 def releaseCells = releaseRow.select("td")
2483 if (releaseCells.size() == 3) {
2484 def title1 = headings[1]
2485 def title2 = headings[2]
2487 def lastDotIndex = JALVIEW_VERSION.lastIndexOf(".")
2488 if (lastDotIndex > 0) {
2489 def patchRelease = JALVIEW_VERSION.substring(lastDotIndex+1) as Integer
2490 def patchReleaseString = null
2491 if (patchRelease == 0) {
2492 patchReleaseString = "first minor"
2493 } else if (patchRelease == 1) {
2494 patchReleaseString = "first patch"
2495 } else if (patchRelease == 2) {
2496 patchReleaseString = "second patch"
2497 } else if (patchRelease == 3) {
2498 patchReleaseString = "third patch"
2499 } else if (patchRelease == 4) {
2500 patchReleaseString = "fourth patch"
2501 } else if (patchRelease == 5) {
2502 patchReleaseString = "fifth patch"
2503 } else if (patchRelease == 6) {
2504 patchReleaseString = "sixth patch"
2505 } else if (patchRelease == 7) {
2506 patchReleaseString = "seventh patch"
2507 } else if (patchRelease > 13 && (patchRelease % 10 == 1)) {
2508 patchReleaseString += "st"
2509 } else if (patchRelease > 13 && (patchRelease % 10 == 2)) {
2510 patchReleaseString += "nd"
2511 } else if (patchRelease > 13 && (patchRelease % 10 == 3)) {
2512 patchReleaseString += "rd"
2513 } else if (patchRelease != null) {
2514 patchReleaseString += "th"
2516 summary += (patchReleaseString != null) ? " is the ${patchReleaseString} release in the ${JALVIEW_VERSION.substring(0,lastDotIndex)} series." : ""
2520 if (headings[col] != null && headings[col].size() > 0) {
2521 def noheadings = true
2522 releaseCells[col].children().each { e ->
2523 if (e.tagName().toLowerCase() == "ul") {
2524 def list = ulToList(e, 0)
2525 if (noheadings && list != "") {
2526 changes += "\n### ${headings[col]}\n\n"
2530 } else if (e.tagName().toLowerCase() == "em") {
2531 changes += "\n#### ${e.text()}\n\n"
2543 templateFiles.each{ templateFile ->
2544 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
2545 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
2546 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
2548 def outPathName = string("${hugoBuildDir}/$newRelPathName")
2552 rename(templateFile.getName(), newFileName)
2556 def newFile = file("${outPathName}/${newFileName}".toString())
2557 def content = newFile.text
2558 content = content.replaceAll("__SUMMARY__", summary)
2559 content = content.replaceAll("__CHANGES__", changes)
2560 if (oldDate != null) {
2561 content = content.replaceAll("__DATE__", oldDate.format("yyyy-MM-dd"))
2563 newFile.text = hugoTemplateSubstitutions(content)
2567 inputs.dir(hugoTemplatesDir)
2568 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
2569 inputs.property("CHANNEL", { CHANNEL })
2575 dependsOn pubhtmlhelp
2577 inputs.dir("${helpBuildDir}/${help_dir}")
2578 outputs.dir("${buildDir}/distributions/${help_dir}")
2582 task j2sSetHeadlessBuild {
2589 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2591 description "Enable the alternative J2S Config file for headless build"
2593 outputFile = jalviewjsJ2sSettingsFileName
2594 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2595 def j2sProps = new Properties()
2596 if (j2sPropsFile.exists()) {
2598 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2599 j2sProps.load(j2sPropsFileFIS)
2600 j2sPropsFileFIS.close()
2602 j2sProps.each { prop, val ->
2605 } catch (Exception e) {
2606 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2610 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2611 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2616 task jalviewjsSetEclipseWorkspace {
2617 def propKey = "jalviewjs_eclipse_workspace"
2619 if (project.hasProperty(propKey)) {
2620 propVal = project.getProperty(propKey)
2621 if (propVal.startsWith("~/")) {
2622 propVal = System.getProperty("user.home") + propVal.substring(1)
2625 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2626 def propsFile = file(propsFileName)
2627 def eclipseWsDir = propVal
2628 def props = new Properties()
2630 def writeProps = true
2631 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2632 def ins = new FileInputStream(propsFileName)
2635 if (props.getProperty(propKey, null) != null) {
2636 eclipseWsDir = props.getProperty(propKey)
2641 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2642 def tempDir = File.createTempDir()
2643 eclipseWsDir = tempDir.getAbsolutePath()
2646 eclipseWorkspace = file(eclipseWsDir)
2649 // do not run a headless transpile when we claim to be in Eclipse
2651 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2652 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2654 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2658 props.setProperty(propKey, eclipseWsDir)
2659 propsFile.parentFile.mkdirs()
2660 def bytes = new ByteArrayOutputStream()
2661 props.store(bytes, null)
2662 def propertiesString = bytes.toString()
2663 propsFile.text = propertiesString
2669 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2672 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2673 outputs.file(propsFileName)
2674 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2678 task jalviewjsEclipsePaths {
2681 def eclipseRoot = jalviewjs_eclipse_root
2682 if (eclipseRoot.startsWith("~/")) {
2683 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2685 if (OperatingSystem.current().isMacOsX()) {
2686 eclipseRoot += "/Eclipse.app"
2687 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2688 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2689 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2690 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2691 eclipseRoot += "/eclipse"
2693 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2694 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2695 } else { // linux or unix
2696 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2697 eclipseRoot += "/eclipse"
2698 println("eclipseDir exists")
2700 eclipseBinary = "${eclipseRoot}/eclipse"
2701 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2704 eclipseVersion = "4.13" // default
2705 def assumedVersion = true
2706 if (file(eclipseProduct).exists()) {
2707 def fis = new FileInputStream(eclipseProduct)
2708 def props = new Properties()
2710 eclipseVersion = props.getProperty("version")
2712 assumedVersion = false
2715 def propKey = "eclipse_debug"
2716 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2719 // do not run a headless transpile when we claim to be in Eclipse
2721 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2722 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2724 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2727 if (!assumedVersion) {
2728 println("ECLIPSE VERSION=${eclipseVersion}")
2734 task printProperties {
2736 description "Output to console all System.properties"
2738 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2744 dependsOn eclipseProject
2745 dependsOn eclipseClasspath
2746 dependsOn eclipseJdt
2750 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2751 task jalviewjsEclipseCopyDropins(type: Copy) {
2752 dependsOn jalviewjsEclipsePaths
2754 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2755 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2756 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2763 // this eclipse -clean doesn't actually work
2764 task jalviewjsCleanEclipse(type: Exec) {
2765 dependsOn eclipseSetup
2766 dependsOn jalviewjsEclipsePaths
2767 dependsOn jalviewjsEclipseCopyDropins
2769 executable(eclipseBinary)
2770 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2776 def inputString = """exit
2779 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2780 standardInput = inputByteStream
2783 /* not really working yet
2784 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2788 task jalviewjsTransferUnzipSwingJs {
2789 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2793 from zipTree(file_zip)
2794 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2798 inputs.file file_zip
2799 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2803 task jalviewjsTransferUnzipLib {
2804 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2807 zipFiles.each { file_zip ->
2809 from zipTree(file_zip)
2810 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2815 inputs.files zipFiles
2816 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2820 task jalviewjsTransferUnzipAllLibs {
2821 dependsOn jalviewjsTransferUnzipSwingJs
2822 dependsOn jalviewjsTransferUnzipLib
2826 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2828 description "Create the alternative j2s file from the j2s.* properties"
2830 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2831 def siteDirProperty = "j2s.site.directory"
2832 def setSiteDir = false
2833 jalviewjsJ2sProps.each { prop, val ->
2835 if (prop == siteDirProperty) {
2836 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2837 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2843 if (!setSiteDir) { // default site location, don't override specifically set property
2844 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2847 outputFile = jalviewjsJ2sAltSettingsFileName
2850 inputs.properties(jalviewjsJ2sProps)
2851 outputs.file(jalviewjsJ2sAltSettingsFileName)
2856 task jalviewjsEclipseSetup {
2857 dependsOn jalviewjsEclipseCopyDropins
2858 dependsOn jalviewjsSetEclipseWorkspace
2859 dependsOn jalviewjsCreateJ2sSettings
2863 task jalviewjsSyncAllLibs (type: Sync) {
2864 dependsOn jalviewjsTransferUnzipAllLibs
2865 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2866 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2867 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2871 def outputFiles = []
2872 rename { filename ->
2873 outputFiles += "${outputDir}/${filename}"
2880 // should this be exclude really ?
2881 duplicatesStrategy "INCLUDE"
2883 outputs.files outputFiles
2884 inputs.files inputFiles
2888 task jalviewjsSyncResources (type: Sync) {
2889 dependsOn buildResources
2891 def inputFiles = fileTree(dir: resourcesBuildDir)
2892 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2896 def outputFiles = []
2897 rename { filename ->
2898 outputFiles += "${outputDir}/${filename}"
2904 outputs.files outputFiles
2905 inputs.files inputFiles
2909 task jalviewjsSyncSiteResources (type: Sync) {
2910 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2911 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2915 def outputFiles = []
2916 rename { filename ->
2917 outputFiles += "${outputDir}/${filename}"
2923 outputs.files outputFiles
2924 inputs.files inputFiles
2928 task jalviewjsSyncBuildProperties (type: Sync) {
2929 dependsOn createBuildProperties
2930 def inputFiles = [file(buildProperties)]
2931 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2935 def outputFiles = []
2936 rename { filename ->
2937 outputFiles += "${outputDir}/${filename}"
2943 outputs.files outputFiles
2944 inputs.files inputFiles
2948 task jalviewjsProjectImport(type: Exec) {
2949 dependsOn eclipseSetup
2950 dependsOn jalviewjsEclipsePaths
2951 dependsOn jalviewjsEclipseSetup
2954 // do not run a headless import when we claim to be in Eclipse
2956 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2957 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2959 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2963 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2964 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2965 executable(eclipseBinary)
2966 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2970 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2972 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2973 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2976 inputs.file("${jalviewDir}/.project")
2977 outputs.upToDateWhen {
2978 file(projdir).exists()
2983 task jalviewjsTranspile(type: Exec) {
2984 dependsOn jalviewjsEclipseSetup
2985 dependsOn jalviewjsProjectImport
2986 dependsOn jalviewjsEclipsePaths
2988 dependsOn jalviewjsEnableAltFileProperty
2992 // do not run a headless transpile when we claim to be in Eclipse
2994 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2995 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2997 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3001 executable(eclipseBinary)
3002 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3006 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3008 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3009 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3015 stdout = new ByteArrayOutputStream()
3016 stderr = new ByteArrayOutputStream()
3018 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3019 def logOutFile = file(logOutFileName)
3020 logOutFile.createNewFile()
3021 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3022 BINARY: ${eclipseBinary}
3023 VERSION: ${eclipseVersion}
3024 WORKSPACE: ${eclipseWorkspace}
3025 DEBUG: ${eclipseDebug}
3028 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3029 // combine stdout and stderr
3030 def logErrFOS = logOutFOS
3032 if (jalviewjs_j2s_to_console.equals("true")) {
3033 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3034 new org.apache.tools.ant.util.TeeOutputStream(
3038 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3039 new org.apache.tools.ant.util.TeeOutputStream(
3044 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3047 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3054 if (stdout.toString().contains("Error processing ")) {
3055 // j2s did not complete transpile
3056 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3057 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3058 println("IGNORING TRANSPILE ERRORS")
3059 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3061 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3066 inputs.dir("${jalviewDir}/${sourceDir}")
3067 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3068 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3072 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3074 def stdout = new ByteArrayOutputStream()
3075 def stderr = new ByteArrayOutputStream()
3077 def coreFile = file(jsfile)
3079 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3081 logOutFile.createNewFile()
3082 logOutFile.append(msg+"\n")
3084 def coreTop = file(prefixFile)
3085 def coreBottom = file(suffixFile)
3086 coreFile.getParentFile().mkdirs()
3087 coreFile.createNewFile()
3088 coreFile.write( coreTop.getText("UTF-8") )
3092 def t = f.getText("UTF-8")
3093 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3094 coreFile.append( t )
3096 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3098 logOutFile.append(msg+"\n")
3101 coreFile.append( coreBottom.getText("UTF-8") )
3103 msg = "Generating ${zjsfile}"
3105 logOutFile.append(msg+"\n")
3106 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3107 def logErrFOS = logOutFOS
3110 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3111 main = "com.google.javascript.jscomp.CommandLineRunner"
3112 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3113 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3116 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3118 logOutFile.append(msg+"\n")
3120 if (logOutConsole) {
3121 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3122 new org.apache.tools.ant.util.TeeOutputStream(
3126 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3127 new org.apache.tools.ant.util.TeeOutputStream(
3132 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3135 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3142 logOutFile.append(msg+"\n")
3146 task jalviewjsBuildAllCores {
3148 description "Build the core js lib closures listed in the classlists dir"
3149 dependsOn jalviewjsTranspile
3150 dependsOn jalviewjsTransferUnzipSwingJs
3152 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3153 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3154 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3155 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3156 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3157 def prefixFile = "${jsDir}/core/coretop2.js"
3158 def suffixFile = "${jsDir}/core/corebottom2.js"
3160 inputs.file prefixFile
3161 inputs.file suffixFile
3163 def classlistFiles = []
3164 // add the classlists found int the jalviewjs_classlists_dir
3165 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3167 def name = file.getName() - ".txt"
3174 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3175 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3176 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3178 jalviewjsCoreClasslists = []
3180 classlistFiles.each {
3183 def file = hash['file']
3184 if (! file.exists()) {
3185 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3186 return false // this is a "continue" in groovy .each closure
3188 def name = hash['name']
3190 name = file.getName() - ".txt"
3198 def list = fileTree(dir: j2sDir, includes: filelist)
3200 def jsfile = "${outputDir}/core${name}.js"
3201 def zjsfile = "${outputDir}/core${name}.z.js"
3203 jalviewjsCoreClasslists += [
3212 outputs.file(jsfile)
3213 outputs.file(zjsfile)
3216 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3217 def stevesoftClasslistName = "_stevesoft"
3218 def stevesoftClasslist = [
3219 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3220 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3221 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3222 'name': stevesoftClasslistName
3224 jalviewjsCoreClasslists += stevesoftClasslist
3225 inputs.files(stevesoftClasslist['list'])
3226 outputs.file(stevesoftClasslist['jsfile'])
3227 outputs.file(stevesoftClasslist['zjsfile'])
3230 def allClasslistName = "_all"
3231 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3232 allJsFiles += fileTree(
3236 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3237 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3238 "**/org/jmol/export/JSExporter.js"
3241 allJsFiles += fileTree(
3245 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3246 "**/sun/misc/Unsafe.js",
3247 "**/swingjs/jquery/jquery-editable-select.js",
3248 "**/swingjs/jquery/j2sComboBox.js",
3249 "**/sun/misc/FloatingDecimal.js"
3252 def allClasslist = [
3253 'jsfile': "${outputDir}/core${allClasslistName}.js",
3254 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3256 'name': allClasslistName
3258 // not including this version of "all" core at the moment
3259 //jalviewjsCoreClasslists += allClasslist
3260 inputs.files(allClasslist['list'])
3261 outputs.file(allClasslist['jsfile'])
3262 outputs.file(allClasslist['zjsfile'])
3265 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3266 logOutFile.getParentFile().mkdirs()
3267 logOutFile.createNewFile()
3268 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3270 jalviewjsCoreClasslists.each {
3271 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3278 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3281 into file(outputFile).getParentFile()
3282 rename { filename ->
3283 if (filename.equals(inputFile.getName())) {
3284 return file(outputFile).getName()
3288 filter(ReplaceTokens,
3292 'MAIN': '"'+main_class+'"',
3294 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3295 'COREKEY': jalviewjs_core_key,
3296 'CORENAME': coreName
3303 task jalviewjsPublishCoreTemplates {
3304 dependsOn jalviewjsBuildAllCores
3305 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3306 def inputFile = file(inputFileName)
3307 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3309 def outputFiles = []
3310 jalviewjsCoreClasslists.each { cl ->
3311 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3312 cl['outputfile'] = outputFile
3313 outputFiles += outputFile
3317 jalviewjsCoreClasslists.each { cl ->
3318 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3321 inputs.file(inputFile)
3322 outputs.files(outputFiles)
3326 task jalviewjsSyncCore (type: Sync) {
3327 dependsOn jalviewjsBuildAllCores
3328 dependsOn jalviewjsPublishCoreTemplates
3329 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3330 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3334 def outputFiles = []
3335 rename { filename ->
3336 outputFiles += "${outputDir}/${filename}"
3342 outputs.files outputFiles
3343 inputs.files inputFiles
3347 // this Copy version of TransferSiteJs will delete anything else in the target dir
3348 task jalviewjsCopyTransferSiteJs(type: Copy) {
3349 dependsOn jalviewjsTranspile
3350 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3351 into "${jalviewDir}/${jalviewjsSiteDir}"
3355 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3356 task jalviewjsSyncTransferSiteJs(type: Sync) {
3357 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3359 into "${jalviewDir}/${jalviewjsSiteDir}"
3366 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3367 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3368 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3369 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3371 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3372 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3373 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3374 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3377 task jalviewjsPrepareSite {
3379 description "Prepares the website folder including unzipping files and copying resources"
3380 dependsOn jalviewjsSyncAllLibs
3381 dependsOn jalviewjsSyncResources
3382 dependsOn jalviewjsSyncSiteResources
3383 dependsOn jalviewjsSyncBuildProperties
3384 dependsOn jalviewjsSyncCore
3388 task jalviewjsBuildSite {
3390 description "Builds the whole website including transpiled code"
3391 dependsOn jalviewjsCopyTransferSiteJs
3392 dependsOn jalviewjsPrepareSite
3396 task cleanJalviewjsTransferSite {
3398 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3399 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3400 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3401 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3406 task cleanJalviewjsSite {
3407 dependsOn cleanJalviewjsTransferSite
3409 delete "${jalviewDir}/${jalviewjsSiteDir}"
3414 task jalviewjsSiteTar(type: Tar) {
3416 description "Creates a tar.gz file for the website"
3417 dependsOn jalviewjsBuildSite
3418 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3419 archiveFileName = outputFilename
3421 compression Compression.GZIP
3423 from "${jalviewDir}/${jalviewjsSiteDir}"
3424 into jalviewjs_site_dir // this is inside the tar file
3426 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3430 task jalviewjsServer {
3432 def filename = "jalviewjsTest.html"
3433 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3434 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3439 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3440 factory = f.newInstance()
3441 } catch (ClassNotFoundException e) {
3442 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3444 def port = Integer.valueOf(jalviewjs_server_port)
3449 while(port < start+1000 && !running) {
3451 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3452 jalviewjsServer = factory.start(doc_root, port)
3454 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3455 println("SERVER STARTED with document root ${doc_root}.")
3456 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3457 println("For debug: "+url+"?j2sdebug")
3458 println("For verbose: "+url+"?j2sverbose")
3459 } catch (Exception e) {
3464 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3465 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3466 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3468 jalviewjsCoreClasslists.each { cl ->
3469 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3471 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3473 println("For core ${cl.name}: "+urlcore)
3476 file(htmlFile).text = htmlText
3479 outputs.file(htmlFile)
3480 outputs.upToDateWhen({false})
3484 task cleanJalviewjsAll {
3486 description "Delete all configuration and build artifacts to do with JalviewJS build"
3487 dependsOn cleanJalviewjsSite
3488 dependsOn jalviewjsEclipsePaths
3491 delete "${jalviewDir}/${jalviewjsBuildDir}"
3492 delete "${jalviewDir}/${eclipse_bin_dir}"
3493 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3494 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3496 delete jalviewjsJ2sAltSettingsFileName
3499 outputs.upToDateWhen( { false } )
3503 task jalviewjsIDE_checkJ2sPlugin {
3504 group "00 JalviewJS in Eclipse"
3505 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3508 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3509 def j2sPluginFile = file(j2sPlugin)
3510 def eclipseHome = System.properties["eclipse.home.location"]
3511 if (eclipseHome == null || ! IN_ECLIPSE) {
3512 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3514 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3515 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3516 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3517 eclipseJ2sPluginDirs += altPluginsDir
3519 def foundPlugin = false
3520 def j2sPluginFileName = j2sPluginFile.getName()
3521 def eclipseJ2sPlugin
3522 def eclipseJ2sPluginFile
3523 eclipseJ2sPluginDirs.any { dir ->
3524 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3525 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3526 if (eclipseJ2sPluginFile.exists()) {
3532 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3533 System.err.println(msg)
3534 throw new StopExecutionException(msg)
3537 def digest = MessageDigest.getInstance("MD5")
3539 digest.update(j2sPluginFile.text.bytes)
3540 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3542 digest.update(eclipseJ2sPluginFile.text.bytes)
3543 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3545 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3546 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3547 System.err.println(msg)
3548 throw new StopExecutionException(msg)
3550 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3556 task jalviewjsIDE_copyJ2sPlugin {
3557 group "00 JalviewJS in Eclipse"
3558 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3561 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3562 def j2sPluginFile = file(j2sPlugin)
3563 def eclipseHome = System.properties["eclipse.home.location"]
3564 if (eclipseHome == null || ! IN_ECLIPSE) {
3565 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3567 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3568 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3569 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3570 System.err.println(msg)
3573 eclipseJ2sPluginFile.getParentFile().mkdirs()
3574 into eclipseJ2sPluginFile.getParent()
3580 task jalviewjsIDE_j2sFile {
3581 group "00 JalviewJS in Eclipse"
3582 description "Creates the .j2s file"
3583 dependsOn jalviewjsCreateJ2sSettings
3587 task jalviewjsIDE_SyncCore {
3588 group "00 JalviewJS in Eclipse"
3589 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3590 dependsOn jalviewjsSyncCore
3594 task jalviewjsIDE_SyncSiteAll {
3595 dependsOn jalviewjsSyncAllLibs
3596 dependsOn jalviewjsSyncResources
3597 dependsOn jalviewjsSyncSiteResources
3598 dependsOn jalviewjsSyncBuildProperties
3602 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3605 task jalviewjsIDE_PrepareSite {
3606 group "00 JalviewJS in Eclipse"
3607 description "Sync libs and resources to site dir, but not closure cores"
3609 dependsOn jalviewjsIDE_SyncSiteAll
3610 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3614 task jalviewjsIDE_AssembleSite {
3615 group "00 JalviewJS in Eclipse"
3616 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3617 dependsOn jalviewjsPrepareSite
3621 task jalviewjsIDE_SiteClean {
3622 group "00 JalviewJS in Eclipse"
3623 description "Deletes the Eclipse transpiled site"
3624 dependsOn cleanJalviewjsSite
3628 task jalviewjsIDE_Server {
3629 group "00 JalviewJS in Eclipse"
3630 description "Starts a webserver on localhost to test the website"
3631 dependsOn jalviewjsServer
3635 // buildship runs this at import or gradle refresh
3636 task eclipseSynchronizationTask {
3637 //dependsOn eclipseSetup
3638 dependsOn createBuildProperties
3640 dependsOn jalviewjsIDE_j2sFile
3641 dependsOn jalviewjsIDE_checkJ2sPlugin
3642 dependsOn jalviewjsIDE_PrepareSite
3647 // buildship runs this at build time or project refresh
3648 task eclipseAutoBuildTask {
3649 //dependsOn jalviewjsIDE_checkJ2sPlugin
3650 //dependsOn jalviewjsIDE_PrepareSite
3656 description "Build the site"
3657 dependsOn jalviewjsBuildSite