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 com.vladsch.flexmark.util.ast.Node
16 import com.vladsch.flexmark.html.HtmlRenderer
17 import com.vladsch.flexmark.parser.Parser
18 import com.vladsch.flexmark.util.data.MutableDataSet
19 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
20 import com.vladsch.flexmark.ext.tables.TablesExtension
21 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
22 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
23 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
24 import com.vladsch.flexmark.ext.toc.TocExtension
32 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
41 id "com.diffplug.gradle.spotless" version "3.28.0"
42 id 'com.github.johnrengelman.shadow' version '4.0.3'
43 id 'com.install4j.gradle' version '8.0.4'
44 id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
45 id 'com.palantir.git-version' version '0.12.3'
55 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
56 def string(Object o) {
57 return o == null ? "" : o.toString()
62 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
63 jalviewDirRelativePath = jalviewDir
65 // local build environment properties
66 // can be "projectDir/local.properties"
67 def localProps = "${projectDir}/local.properties"
69 if (file(localProps).exists()) {
70 propsFile = localProps
72 // or "../projectDir_local.properties"
73 def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
74 if (file(dirLocalProps).exists()) {
75 propsFile = dirLocalProps
77 if (propsFile != null) {
79 def p = new Properties()
80 def localPropsFIS = new FileInputStream(propsFile)
85 def oldval = findProperty(key)
88 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
90 println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
93 } catch (Exception e) {
94 System.out.println("Exception reading local.properties")
99 // Import releaseProps from the RELEASE file
100 // or a file specified via JALVIEW_RELEASE_FILE if defined
101 // Expect jalview.version and target release branch in jalview.release
102 def releaseProps = new Properties();
103 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
104 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
106 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
107 releaseProps.load(it)
109 } catch (Exception fileLoadError) {
110 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
113 // Set JALVIEW_VERSION if it is not already set
114 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
115 JALVIEW_VERSION = releaseProps.get("jalview.version")
118 // this property set when running Eclipse headlessly
119 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
120 // this property set by Eclipse
121 eclipseApplicationProperty = string("eclipse.application")
122 // CHECK IF RUNNING FROM WITHIN ECLIPSE
123 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
124 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
125 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
126 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
127 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
131 println("WITHIN ECLIPSE IDE")
133 println("HEADLESS BUILD")
136 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
138 println("J2S ENABLED")
141 System.properties.sort { it.key }.each {
142 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
145 if (false && IN_ECLIPSE) {
146 jalviewDir = jalviewDirAbsolutePath
151 bareSourceDir = string(source_dir)
152 sourceDir = string("${jalviewDir}/${bareSourceDir}")
153 resourceDir = string("${jalviewDir}/${resource_dir}")
154 bareTestSourceDir = string(test_source_dir)
155 testDir = string("${jalviewDir}/${bareTestSourceDir}")
157 classesDir = string("${jalviewDir}/${classes_dir}")
160 useClover = clover.equals("true")
161 cloverBuildDir = "${buildDir}/clover"
162 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
163 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
164 cloverReportDir = file("${buildDir}/reports/clover")
165 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
166 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
167 //cloverTestClassesDir = cloverClassesDir
168 cloverDb = string("${cloverBuildDir}/clover.db")
170 testSourceDir = useClover ? cloverTestInstrDir : testDir
171 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
173 getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
176 // the following values might be overridden by the CHANNEL switch
177 getdownChannelName = CHANNEL.toLowerCase()
178 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
179 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
180 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
181 getdownAppDistDir = getdown_app_dir_alt
182 reportRsyncCommand = false
183 jvlChannelName = CHANNEL.toLowerCase()
184 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
185 install4jDSStore = "DS_Store-NON-RELEASE"
186 install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
187 install4jInstallerName = "${jalview_name} Non-Release Installer"
188 install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
189 install4jExtraScheme = "jalviewx"
193 // TODO: get bamboo build artifact URL for getdown artifacts
194 getdown_channel_base = bamboo_channelbase
195 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
196 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
197 jvlChannelName += "_${getdownChannelName}"
198 // automatically add the test group Not-bamboo for exclusion
199 if ("".equals(testng_excluded_groups)) {
200 testng_excluded_groups = "Not-bamboo"
202 install4jExtraScheme = "jalviewb"
206 getdownAppDistDir = getdown_app_dir_release
207 reportRsyncCommand = true
209 install4jDSStore = "DS_Store"
210 install4jDMGBackgroundImage = "jalview_dmg_background.png"
211 install4jInstallerName = "${jalview_name} Installer"
215 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
216 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
217 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
218 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
219 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
221 package_dir = string("${ARCHIVEDIR}/${package_dir}")
222 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
225 reportRsyncCommand = true
226 install4jExtraScheme = "jalviewa"
230 getdownChannelName = string("archive/${JALVIEW_VERSION}")
231 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
232 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
233 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
234 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
236 package_dir = string("${ARCHIVEDIR}/${package_dir}")
237 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
240 reportRsyncCommand = true
241 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
242 install4jSuffix = "Archive"
243 install4jExtraScheme = "jalviewa"
247 reportRsyncCommand = true
249 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
250 JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
252 channelPropertiesFile = string("${channel_properties_dir}/develop_properties")
253 getdownImagesDir = "${getdown_images_dir}/develop"
254 getdownBgColour = "000000"
255 getdownFgColour = "FFFFFF"
256 getdownLightFgColour = "CCCCFF"
257 install4jSuffix = "Develop"
258 install4jDSStore = "DS_Store-DEVELOP"
259 install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
260 install4jExtraScheme = "jalviewd"
261 install4jInstallerName = "${jalview_name} Develop Installer"
262 install4jMacIconsFile = string("${install4j_utils_dir}/develop/${install4j_mac_icons_file}")
263 install4jWindowsIconsFile = string("${install4j_utils_dir}/develop/${install4j_windows_icons_file}")
264 install4jPngIconFile = string("${install4j_utils_dir}/develop/${install4j_png_icon_file}")
268 reportRsyncCommand = true
269 // Don't ignore transpile errors for release build
270 if (jalviewjs_ignore_transpile_errors.equals("true")) {
271 jalviewjs_ignore_transpile_errors = "false"
272 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
274 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
275 install4jSuffix = "Test"
276 install4jDSStore = "DS_Store-TEST-RELEASE"
277 install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
278 install4jExtraScheme = "jalviewt"
279 install4jInstallerName = "${jalview_name} Test Installer"
282 case ~/^SCRATCH(|-[-\w]*)$/:
283 getdownChannelName = CHANNEL
284 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
286 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
287 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
288 reportRsyncCommand = true
289 install4jSuffix = "Scratch"
293 if (!file("${LOCALDIR}").exists()) {
294 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
296 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
299 JALVIEW_VERSION = "TEST"
300 install4jSuffix = "Test-Local"
301 install4jDSStore = "DS_Store-TEST-RELEASE"
302 install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
303 install4jExtraScheme = "jalviewt"
304 install4jInstallerName = "${jalview_name} Test Installer"
308 JALVIEW_VERSION = "TEST"
309 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
310 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
311 install4jExtraScheme = "jalviewl"
314 default: // something wrong specified
315 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
319 // override getdownAppBase if requested
320 if (findProperty("getdown_appbase_override") != null) {
321 getdownAppBase = string(getProperty("getdown_appbase_override"))
322 println("Overriding getdown appbase with '${getdownAppBase}'")
324 // sanitise file name for jalview launcher file for this channel
325 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
326 // install4j application and folder names
327 if (install4jSuffix == "") {
328 install4jApplicationName = "${jalview_name}"
329 install4jBundleId = "${install4j_bundle_id}"
330 install4jWinApplicationId = install4j_release_win_application_id
332 install4jApplicationName = "${jalview_name} ${install4jSuffix}"
333 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
334 // add int hash of install4jSuffix to the last part of the application_id
335 def id = install4j_release_win_application_id
336 def idsplitreverse = id.split("-").reverse()
337 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
338 install4jWinApplicationId = idsplitreverse.reverse().join("-")
340 // sanitise folder and id names
341 // install4jApplicationFolder = e.g. "Jalview Build"
342 install4jApplicationFolder = install4jApplicationName
343 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
344 .replaceAll("_+", "_") // collapse __
345 install4jInternalId = install4jApplicationName
347 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
348 .replaceAll("_+", "") // collapse __
349 //.replaceAll("_*-_*", "-") // collapse _-_
350 install4jUnixApplicationFolder = install4jApplicationName
352 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
353 .replaceAll("_+", "_") // collapse __
354 .replaceAll("_*-_*", "-") // collapse _-_
357 getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
358 //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
359 getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
360 getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
361 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
362 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
363 /* compile without modules -- using classpath libraries
364 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
365 modules_runtimeClasspath = modules_compileClasspath
367 def details = versionDetails()
368 gitHash = details.gitHash
369 gitBranch = details.branchName
371 println("Using a ${CHANNEL} profile.")
373 additional_compiler_args = []
374 // configure classpath/args for j8/j11 compilation
375 if (JAVA_VERSION.equals("1.8")) {
376 JAVA_INTEGER_VERSION = string("8")
379 libDistDir = j8libDir
380 compile_source_compatibility = 1.8
381 compile_target_compatibility = 1.8
382 // these are getdown.txt properties defined dependent on the JAVA_VERSION
383 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
384 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
385 // this property is assigned below and expanded to multiple lines in the getdown task
386 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
387 // this property is for the Java library used in eclipse
388 eclipseJavaRuntimeName = string("JavaSE-1.8")
389 } else if (JAVA_VERSION.equals("11")) {
390 JAVA_INTEGER_VERSION = string("11")
392 libDistDir = j11libDir
393 compile_source_compatibility = 11
394 compile_target_compatibility = 11
395 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
396 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
397 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
398 eclipseJavaRuntimeName = string("JavaSE-11")
399 /* compile without modules -- using classpath libraries
400 additional_compiler_args += [
401 '--module-path', modules_compileClasspath.asPath,
402 '--add-modules', j11modules
405 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
406 JAVA_INTEGER_VERSION = JAVA_VERSION
408 libDistDir = j11libDir
409 compile_source_compatibility = JAVA_VERSION
410 compile_target_compatibility = JAVA_VERSION
411 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
412 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
413 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
414 eclipseJavaRuntimeName = string("JavaSE-11")
415 /* compile without modules -- using classpath libraries
416 additional_compiler_args += [
417 '--module-path', modules_compileClasspath.asPath,
418 '--add-modules', j11modules
422 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
427 JAVA_MIN_VERSION = JAVA_VERSION
428 JAVA_MAX_VERSION = JAVA_VERSION
429 def jreInstallsDir = string(jre_installs_dir)
430 if (jreInstallsDir.startsWith("~/")) {
431 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
433 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
434 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
435 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
436 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
437 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
438 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
439 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
440 install4jConfFileName = string("jalview-install4j-conf.install4j")
441 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
442 install4jHomeDir = install4j_home_dir
443 if (install4jHomeDir.startsWith("~/")) {
444 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
447 resourceBuildDir = string("${buildDir}/resources")
448 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
449 helpBuildDir = string("${resourceBuildDir}/help_build")
450 docBuildDir = string("${resourceBuildDir}/doc_build")
452 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
453 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
454 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
455 helpSourceDir = string("${helpParentDir}/${help_dir}")
456 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
459 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
460 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
461 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
463 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
465 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
467 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
468 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
469 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
470 jalviewjsJalviewCoreHtmlFile = string("")
471 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
472 jalviewjsCoreClasslists = []
473 jalviewjsJalviewTemplateName = string(jalviewjs_name)
474 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
475 jalviewjsJ2sProps = null
476 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
478 eclipseWorkspace = null
479 eclipseBinary = string("")
480 eclipseVersion = string("")
490 outputDir = file(classesDir)
494 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
497 compileClasspath = files(sourceSets.main.java.outputDir)
498 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
500 runtimeClasspath = compileClasspath
501 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
506 srcDirs cloverInstrDir
507 outputDir = cloverClassesDir
511 srcDirs = sourceSets.main.resources.srcDirs
514 compileClasspath = files( sourceSets.clover.java.outputDir )
515 //compileClasspath += files( testClassesDir )
516 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
517 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
518 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
520 runtimeClasspath = compileClasspath
525 srcDirs testSourceDir
526 outputDir = file(testClassesDir)
530 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
533 compileClasspath = files( sourceSets.test.java.outputDir )
534 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
535 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
537 runtimeClasspath = compileClasspath
538 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
544 // eclipse project and settings files creation, also used by buildship
547 name = eclipse_project_name
549 natures 'org.eclipse.jdt.core.javanature',
550 'org.eclipse.jdt.groovy.core.groovyNature',
551 'org.eclipse.buildship.core.gradleprojectnature'
553 buildCommand 'org.eclipse.jdt.core.javabuilder'
554 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
558 //defaultOutputDir = sourceSets.main.java.outputDir
559 configurations.each{ c->
560 if (c.isCanBeResolved()) {
561 minusConfigurations += [c]
565 plusConfigurations = [ ]
569 def removeTheseToo = []
570 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
571 cp.entries.each { entry ->
572 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
573 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
574 // we add the resources and help/help dirs in as libs afterwards (see below)
575 if (entry.kind == 'src') {
576 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
577 removeTheseToo += entry
579 alreadyAddedSrcPath.putAt(entry.path, true)
584 cp.entries.removeAll(removeTheseToo)
586 //cp.entries += new Output("${eclipse_bin_dir}/main")
587 if (file(helpParentDir).isDirectory()) {
588 cp.entries += new Library(fileReference(helpParentDir))
590 if (file(resourceDir).isDirectory()) {
591 cp.entries += new Library(fileReference(resourceDir))
594 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
596 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
597 //don't want to add outputDir as eclipse is using its own output dir in bin/main
598 if (it.isDirectory() || ! it.exists()) {
599 // don't add dirs to classpath, especially if they don't exist
600 return false // groovy "continue" in .any closure
602 def itPath = it.toString()
603 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
604 // make relative path
605 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
607 if (alreadyAddedLibPath.get(itPath)) {
608 //println("Not adding duplicate entry "+itPath)
610 //println("Adding entry "+itPath)
611 cp.entries += new Library(fileReference(itPath))
612 alreadyAddedLibPath.put(itPath, true)
616 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
617 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
618 if (it.isDirectory() || ! it.exists()) {
619 // don't add dirs to classpath
620 return false // groovy "continue" in .any closure
623 def itPath = it.toString()
624 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
625 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
627 if (alreadyAddedLibPath.get(itPath)) {
630 def lib = new Library(fileReference(itPath))
631 lib.entryAttributes["test"] = "true"
633 alreadyAddedLibPath.put(itPath, true)
641 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
646 // for the IDE, use java 11 compatibility
647 sourceCompatibility = compile_source_compatibility
648 targetCompatibility = compile_target_compatibility
649 javaRuntimeName = eclipseJavaRuntimeName
651 // add in jalview project specific properties/preferences into eclipse core preferences
653 withProperties { props ->
654 def jalview_prefs = new Properties()
655 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
656 jalview_prefs.load(ins)
658 jalview_prefs.forEach { t, v ->
659 if (props.getAt(t) == null) {
663 // codestyle file -- overrides previous formatter prefs
664 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
665 if (csFile.exists()) {
666 XmlParser parser = new XmlParser()
667 def profiles = parser.parse(csFile)
668 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
669 if (profile != null) {
670 profile.'setting'.each { s ->
672 def value = s.'@value'
673 if (id != null && value != null) {
674 props.putAt(id, value)
685 // Don't want these to be activated if in headless build
686 synchronizationTasks "eclipseSynchronizationTask"
687 //autoBuildTasks "eclipseAutoBuildTask"
693 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
694 // Class to allow updating arbitrary properties files
695 class PropertiesFile extends PropertiesPersistableConfigurationObject {
696 public PropertiesFile(PropertiesTransformer t) { super(t); }
697 @Override protected void load(Properties properties) { }
698 @Override protected void store(Properties properties) { }
699 @Override protected String getDefaultResourceName() { return ""; }
700 // This is necessary, because PropertiesPersistableConfigurationObject fails
701 // if no default properties file exists.
702 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
705 // Task to update arbitrary properties files (set outputFile)
706 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
707 private final PropertiesFileContentMerger file;
708 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
709 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
710 protected void configure(PropertiesFile props) {
711 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
713 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
716 task eclipseUIPreferences(type: PropertiesFileTask) {
717 description = "Generate Eclipse additional settings"
718 def filename = "org.eclipse.jdt.ui.prefs"
719 outputFile = "$projectDir/.settings/${filename}" as File
722 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
727 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
728 description = "Generate Eclipse additional settings"
729 def filename = "org.eclipse.jdt.groovy.core.prefs"
730 outputFile = "$projectDir/.settings/${filename}" as File
733 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
738 task eclipseAllPreferences {
740 dependsOn eclipseUIPreferences
741 dependsOn eclipseGroovyCorePreferences
744 eclipseUIPreferences.mustRunAfter eclipseJdt
745 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
747 /* end of eclipse preferences hack */
755 delete cloverBuildDir
756 delete cloverReportDir
761 task cloverInstrJava(type: JavaExec) {
762 group = "Verification"
763 description = "Create clover instrumented source java files"
765 dependsOn cleanClover
767 inputs.files(sourceSets.main.allJava)
768 outputs.dir(cloverInstrDir)
770 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
771 classpath = sourceSets.clover.compileClasspath
772 main = "com.atlassian.clover.CloverInstr"
780 cloverInstrDir.getPath(),
782 def srcFiles = sourceSets.main.allJava.files
785 { file -> file.absolutePath }
788 args argsList.toArray()
791 delete cloverInstrDir
792 println("Clover: About to instrument "+srcFiles.size() +" files")
797 task cloverInstrTests(type: JavaExec) {
798 group = "Verification"
799 description = "Create clover instrumented source test files"
801 dependsOn cleanClover
803 inputs.files(testDir)
804 outputs.dir(cloverTestInstrDir)
806 classpath = sourceSets.clover.compileClasspath
807 main = "com.atlassian.clover.CloverInstr"
817 cloverTestInstrDir.getPath(),
819 args argsList.toArray()
822 delete cloverTestInstrDir
823 println("Clover: About to instrument test files")
829 group = "Verification"
830 description = "Create clover instrumented all source files"
832 dependsOn cloverInstrJava
833 dependsOn cloverInstrTests
837 cloverClasses.dependsOn cloverInstr
840 task cloverConsoleReport(type: JavaExec) {
841 group = "Verification"
842 description = "Creates clover console report"
845 file(cloverDb).exists()
848 inputs.dir cloverClassesDir
850 classpath = sourceSets.clover.runtimeClasspath
851 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
853 if (cloverreport_mem.length() > 0) {
854 maxHeapSize = cloverreport_mem
856 if (cloverreport_jvmargs.length() > 0) {
857 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
867 args argsList.toArray()
871 task cloverHtmlReport(type: JavaExec) {
872 group = "Verification"
873 description = "Creates clover HTML report"
876 file(cloverDb).exists()
879 def cloverHtmlDir = cloverReportDir
880 inputs.dir cloverClassesDir
881 outputs.dir cloverHtmlDir
883 classpath = sourceSets.clover.runtimeClasspath
884 main = "com.atlassian.clover.reporters.html.HtmlReporter"
886 if (cloverreport_mem.length() > 0) {
887 maxHeapSize = cloverreport_mem
889 if (cloverreport_jvmargs.length() > 0) {
890 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
901 if (cloverreport_html_options.length() > 0) {
902 argsList += cloverreport_html_options.split(" ")
905 args argsList.toArray()
909 task cloverXmlReport(type: JavaExec) {
910 group = "Verification"
911 description = "Creates clover XML report"
914 file(cloverDb).exists()
917 def cloverXmlFile = "${cloverReportDir}/clover.xml"
918 inputs.dir cloverClassesDir
919 outputs.file cloverXmlFile
921 classpath = sourceSets.clover.runtimeClasspath
922 main = "com.atlassian.clover.reporters.xml.XMLReporter"
924 if (cloverreport_mem.length() > 0) {
925 maxHeapSize = cloverreport_mem
927 if (cloverreport_jvmargs.length() > 0) {
928 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
939 if (cloverreport_xml_options.length() > 0) {
940 argsList += cloverreport_xml_options.split(" ")
943 args argsList.toArray()
948 group = "Verification"
949 description = "Creates clover reports"
951 dependsOn cloverXmlReport
952 dependsOn cloverHtmlReport
959 sourceCompatibility = compile_source_compatibility
960 targetCompatibility = compile_target_compatibility
961 options.compilerArgs += additional_compiler_args
962 print ("Setting target compatibility to "+targetCompatibility+"\n")
964 //classpath += configurations.cloverRuntime
970 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
971 sourceCompatibility = compile_source_compatibility
972 targetCompatibility = compile_target_compatibility
973 options.compilerArgs = additional_compiler_args
974 options.encoding = "UTF-8"
976 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
983 sourceCompatibility = compile_source_compatibility
984 targetCompatibility = compile_target_compatibility
985 options.compilerArgs = additional_compiler_args
987 print ("Setting target compatibility to "+targetCompatibility+"\n")
994 delete sourceSets.main.java.outputDir
1000 dependsOn cleanClover
1002 delete sourceSets.test.java.outputDir
1007 // format is a string like date.format("dd MMMM yyyy")
1008 def getDate(format) {
1009 def date = new Date()
1010 return date.format(format)
1014 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1015 MutableDataSet options = new MutableDataSet()
1017 def extensions = new ArrayList<>()
1018 extensions.add(AnchorLinkExtension.create())
1019 extensions.add(AutolinkExtension.create())
1020 extensions.add(StrikethroughExtension.create())
1021 extensions.add(TaskListExtension.create())
1022 extensions.add(TablesExtension.create())
1023 extensions.add(TocExtension.create())
1025 options.set(Parser.EXTENSIONS, extensions)
1027 // set GFM table parsing options
1028 options.set(TablesExtension.WITH_CAPTION, false)
1029 options.set(TablesExtension.COLUMN_SPANS, false)
1030 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1031 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1032 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1033 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1034 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1036 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1037 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1038 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1039 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1041 Parser parser = Parser.builder(options).build()
1042 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1044 mdFiles.each { mdFile ->
1045 // add table of contents
1046 def mdText = "[TOC]\n"+mdFile.text
1048 // grab the first top-level title
1050 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1051 def matcher = mdText =~ titleRegex
1052 if (matcher.size() > 0) {
1053 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1054 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1056 // or use the filename if none found
1057 if (title == null) {
1058 title = mdFile.getName()
1061 Node document = parser.parse(mdText)
1062 String htmlBody = renderer.render(document)
1063 def htmlText = '''<html>
1064 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1065 <html xmlns="http://www.w3.org/1999/xhtml">
1067 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1068 <meta http-equiv="Content-Style-Type" content="text/css" />
1069 <meta name="generator" content="flexmark" />
1071 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1073 <style type="text/css">code{white-space: pre;}</style>
1075 htmlText += ((cssFile != null) ? cssFile.text : '')
1076 htmlText += '''</head>
1079 htmlText += htmlBody
1085 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1086 def htmlFile = file(htmlFilePath)
1087 println("Creating ${htmlFilePath}")
1088 htmlFile.text = htmlText
1093 task copyDocs(type: Copy) {
1094 def inputDir = "${jalviewDir}/${doc_dir}"
1095 def outputDir = "${docBuildDir}/${doc_dir}"
1099 include('**/*.html')
1101 filter(ReplaceTokens,
1105 'Version-Rel': JALVIEW_VERSION,
1106 'Year-Rel': getDate("yyyy")
1113 exclude('**/*.html')
1118 inputs.dir(inputDir)
1119 outputs.dir(outputDir)
1123 task convertMdFiles {
1125 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1126 def cssFile = file("${jalviewDir}/${flexmark_css}")
1129 convertMdToHtml(mdFiles, cssFile)
1132 inputs.files(mdFiles)
1133 inputs.file(cssFile)
1136 mdFiles.each { mdFile ->
1137 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1138 htmlFiles.add(file(htmlFilePath))
1140 outputs.files(htmlFiles)
1144 task copyHelp(type: Copy) {
1145 def inputDir = helpSourceDir
1146 def outputDir = "${helpBuildDir}/${help_dir}"
1150 include('**/*.html')
1154 filter(ReplaceTokens,
1158 'Version-Rel': JALVIEW_VERSION,
1159 'Year-Rel': getDate("yyyy")
1166 exclude('**/*.html')
1173 inputs.dir(inputDir)
1174 outputs.files(helpFile)
1175 outputs.dir(outputDir)
1179 task copyResources(type: Copy) {
1180 def inputDir = resourceDir
1181 def outputDir = resourcesBuildDir
1185 include('**/*.html')
1187 filter(ReplaceTokens,
1191 'Version-Rel': JALVIEW_VERSION,
1192 'Year-Rel': getDate("yyyy")
1199 exclude('**/*.html')
1204 inputs.dir(inputDir)
1205 outputs.dir(outputDir)
1209 task createBuildProperties(type: WriteProperties) {
1210 dependsOn copyResources
1212 description = "Create the ${buildProperties} file"
1214 inputs.dir(sourceDir)
1215 inputs.dir(resourcesBuildDir)
1216 outputFile (buildProperties)
1217 // taking time specific comment out to allow better incremental builds
1218 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1219 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1220 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1221 property "VERSION", JALVIEW_VERSION
1222 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1223 outputs.file(outputFile)
1227 task buildIndices(type: JavaExec) {
1229 classpath = sourceSets.main.compileClasspath
1230 main = "com.sun.java.help.search.Indexer"
1231 workingDir = "${helpBuildDir}/${help_dir}"
1234 inputs.dir("${workingDir}/${argDir}")
1236 outputs.dir("${classesDir}/doc")
1237 outputs.dir("${classesDir}/help")
1238 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1239 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1240 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1241 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1242 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1243 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1248 dependsOn copyResources
1251 dependsOn createBuildProperties
1252 dependsOn convertMdFiles
1253 dependsOn buildIndices
1257 compileJava.dependsOn prepare
1258 run.dependsOn compileJava
1259 //run.dependsOn prepare
1262 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1267 dependsOn cloverClasses
1269 dependsOn compileJava //?
1273 includeGroups testng_groups
1274 excludeGroups testng_excluded_groups
1276 useDefaultListeners=true
1279 maxHeapSize = "1024m"
1281 workingDir = jalviewDir
1282 def testLaf = project.findProperty("test_laf")
1283 if (testLaf != null) {
1284 println("Setting Test LaF to '${testLaf}'")
1285 systemProperty "laf", testLaf
1287 sourceCompatibility = compile_source_compatibility
1288 targetCompatibility = compile_target_compatibility
1289 jvmArgs += additional_compiler_args
1293 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1299 task compileLinkCheck(type: JavaCompile) {
1301 classpath = files("${jalviewDir}/${utils_dir}")
1302 destinationDir = file("${jalviewDir}/${utils_dir}")
1303 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1305 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1306 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1307 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1308 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1312 task linkCheck(type: JavaExec) {
1314 dependsOn compileLinkCheck
1316 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1317 classpath = files("${jalviewDir}/${utils_dir}")
1318 main = "HelpLinksChecker"
1319 workingDir = jalviewDir
1320 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1322 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1324 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1327 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1331 inputs.dir(helpBuildDir)
1332 outputs.file(helpLinksCheckerOutFile)
1336 // import the pubhtmlhelp target
1337 ant.properties.basedir = "${jalviewDir}"
1338 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1339 ant.importBuild "${utils_dir}/publishHelp.xml"
1342 task cleanPackageDir(type: Delete) {
1344 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1354 attributes "Main-Class": main_class,
1355 "Permissions": "all-permissions",
1356 "Application-Name": install4jApplicationName,
1357 "Codebase": application_codebase,
1358 "Implementation-Version": JALVIEW_VERSION
1361 destinationDirectory = file("${jalviewDir}/${package_dir}")
1362 archiveFileName = rootProject.name+".jar"
1368 exclude "**/*.jar.*"
1370 inputs.dir(sourceSets.main.java.outputDir)
1371 sourceSets.main.resources.srcDirs.each{ dir ->
1374 outputs.file("${destinationDirectory}/${archiveFileName}")
1378 task copyJars(type: Copy) {
1379 from fileTree(dir: classesDir, include: "**/*.jar").files
1380 into "${jalviewDir}/${package_dir}"
1384 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1385 task syncJars(type: Sync) {
1387 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1388 into "${jalviewDir}/${package_dir}"
1390 include jar.archiveFileName.getOrNull()
1397 description = "Put all required libraries in dist"
1398 // order of "cleanPackageDir", "copyJars", "jar" important!
1399 jar.mustRunAfter cleanPackageDir
1400 syncJars.mustRunAfter cleanPackageDir
1401 dependsOn cleanPackageDir
1404 outputs.dir("${jalviewDir}/${package_dir}")
1409 dependsOn cleanPackageDir
1416 group = "distribution"
1417 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1421 from ("${jalviewDir}/${libDistDir}") {
1425 attributes "Implementation-Version": JALVIEW_VERSION,
1426 "Application-Name": install4jApplicationName
1428 mainClassName = shadow_jar_main_class
1430 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1435 task getdownWebsite() {
1436 group = "distribution"
1437 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1442 def getdownWebsiteResourceFilenames = []
1443 def getdownTextString = ""
1444 def getdownResourceDir = getdownResourceDir
1445 def getdownResourceFilenames = []
1448 // clean the getdown website and files dir before creating getdown folders
1449 delete getdownWebsiteDir
1450 delete getdownFilesDir
1453 from buildProperties
1454 rename(build_properties_file, getdown_build_properties)
1457 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1459 // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
1460 def props = project.properties.sort { it.key }
1461 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1462 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1464 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1465 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1467 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1468 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1471 props.put("getdown_txt_title", jalview_name)
1472 props.put("getdown_txt_ui.name", install4jApplicationName)
1474 // start with appbase
1475 getdownTextString += "appbase = ${getdownAppBase}\n"
1476 props.each{ prop, val ->
1477 if (prop.startsWith("getdown_txt_") && val != null) {
1478 if (prop.startsWith("getdown_txt_multi_")) {
1479 def key = prop.substring(18)
1480 val.split(",").each{ v ->
1481 def line = "${key} = ${v}\n"
1482 getdownTextString += line
1485 // file values rationalised
1486 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1488 if (val.indexOf('/') == 0) {
1491 } else if (val.indexOf('/') > 0) {
1492 // relative path (relative to jalviewDir)
1493 r = file( "${jalviewDir}/${val}" )
1496 val = "${getdown_resource_dir}/" + r.getName()
1497 getdownWebsiteResourceFilenames += val
1498 getdownResourceFilenames += r.getPath()
1501 if (! prop.startsWith("getdown_txt_resource")) {
1502 def line = prop.substring(12) + " = ${val}\n"
1503 getdownTextString += line
1509 getdownWebsiteResourceFilenames.each{ filename ->
1510 getdownTextString += "resource = ${filename}\n"
1512 getdownResourceFilenames.each{ filename ->
1515 into getdownResourceDir
1520 fileTree(file(package_dir)).each{ f ->
1521 if (f.isDirectory()) {
1522 def files = fileTree(dir: f, include: ["*"]).getFiles()
1524 } else if (f.exists()) {
1528 codeFiles.sort().each{f ->
1529 def name = f.getName()
1530 def line = "code = ${getdownAppDistDir}/${name}\n"
1531 getdownTextString += line
1538 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1540 if (JAVA_VERSION.equals("11")) {
1541 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1542 j11libFiles.sort().each{f ->
1543 def name = f.getName()
1544 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1545 getdownTextString += line
1548 into getdownJ11libDir
1554 // 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.
1555 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1556 getdownTextString += "resource = ${getdown_launcher_new}\n"
1557 getdownTextString += "class = ${main_class}\n"
1559 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1560 getdown_txt.write(getdownTextString)
1562 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1563 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1564 launchJvl.write("appbase=${getdownAppBase}")
1567 from getdownLauncher
1568 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1569 into getdownWebsiteDir
1573 from getdownLauncher
1574 if (file(getdownLauncher).getName() != getdown_launcher) {
1575 rename(file(getdownLauncher).getName(), getdown_launcher)
1577 into getdownWebsiteDir
1580 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1583 from getdownLauncher
1584 from "${getdownWebsiteDir}/${getdown_build_properties}"
1585 if (file(getdownLauncher).getName() != getdown_launcher) {
1586 rename(file(getdownLauncher).getName(), getdown_launcher)
1588 into getdownInstallDir
1592 from getdownInstallDir
1593 into getdownFilesInstallDir
1600 from getdownLauncher
1601 from "${getdownWebsiteDir}/${getdown_build_properties}"
1602 if (file(getdownLauncher).getName() != getdown_launcher) {
1603 rename(file(getdownLauncher).getName(), getdown_launcher)
1605 into getdownFilesDir
1609 from getdownResourceDir
1610 into "${getdownFilesDir}/${getdown_resource_dir}"
1615 inputs.dir("${jalviewDir}/${package_dir}")
1617 outputs.dir(getdownWebsiteDir)
1618 outputs.dir(getdownFilesDir)
1622 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1623 task getdownDigestDir(type: JavaExec) {
1625 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1627 def digestDirPropertyName = "DIGESTDIR"
1629 classpath = files(getdownLauncher)
1630 def digestDir = findProperty(digestDirPropertyName)
1631 if (digestDir == null) {
1632 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1636 main = "com.threerings.getdown.tools.Digester"
1640 task getdownDigest(type: JavaExec) {
1641 group = "distribution"
1642 description = "Digest the getdown website folder"
1643 dependsOn getdownWebsite
1645 classpath = files(getdownLauncher)
1647 main = "com.threerings.getdown.tools.Digester"
1648 args getdownWebsiteDir
1649 inputs.dir(getdownWebsiteDir)
1650 outputs.file("${getdownWebsiteDir}/digest2.txt")
1655 group = "distribution"
1656 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1657 dependsOn getdownDigest
1659 if (reportRsyncCommand) {
1660 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1661 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1662 println "LIKELY RSYNC COMMAND:"
1663 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1664 if (RUNRSYNC == "true") {
1666 commandLine "mkdir", "-p", toDir
1669 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1677 tasks.withType(JavaCompile) {
1678 options.encoding = 'UTF-8'
1684 delete getdownWebsiteDir
1685 delete getdownFilesDir
1691 if (file(install4jHomeDir).exists()) {
1693 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1694 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1695 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1696 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1698 installDir(file(install4jHomeDir))
1700 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1704 task copyInstall4jTemplate {
1705 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1706 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1707 inputs.file(install4jTemplateFile)
1708 inputs.file(install4jFileAssociationsFile)
1709 inputs.property("CHANNEL", { CHANNEL })
1710 outputs.file(install4jConfFile)
1713 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1715 // turn off code signing if no OSX_KEYPASS
1716 if (OSX_KEYPASS == "") {
1717 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1718 codeSigning.'@macEnabled' = "false"
1720 install4jConfigXml.'**'.windows.each { windows ->
1721 windows.'@runPostProcessor' = "false"
1725 // turn off checksum creation for LOCAL channel
1726 def e = install4jConfigXml.application[0]
1727 if (CHANNEL == "LOCAL") {
1728 e.'@createChecksums' = "false"
1730 e.'@createChecksums' = "true"
1733 // put file association actions where placeholder action is
1734 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1735 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1736 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1737 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1738 def parent = a.parent()
1740 fileAssociationActions.each { faa ->
1743 // don't need to continue in .any loop once replacements have been made
1748 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1749 // NB we're deleting the /other/ one!
1750 // Also remove the examples subdir from non-release versions
1751 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1752 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1753 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1754 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1756 // remove the examples subdir from Full File Set
1757 def files = install4jConfigXml.files[0]
1758 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1759 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1760 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1761 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1762 dirEntry.parent().remove(dirEntry)
1764 install4jConfigXml.'**'.action.any { a ->
1765 if (a.'@customizedId' == customizedIdToDelete) {
1766 def parent = a.parent()
1772 // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
1773 if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
1774 def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
1775 symlink.parent().remove(symlink)
1778 // write install4j file
1779 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1786 delete install4jConfFile
1791 task installers(type: com.install4j.gradle.Install4jTask) {
1792 group = "distribution"
1793 description = "Create the install4j installers"
1795 dependsOn copyInstall4jTemplate
1797 projectFile = install4jConfFile
1799 // create an md5 for the input files to use as version for install4j conf file
1800 def digest = MessageDigest.getInstance("MD5")
1802 (file("${install4jDir}/${install4j_template}").text +
1803 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1804 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1805 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1806 if (filesMd5.length() >= 8) {
1807 filesMd5 = filesMd5.substring(0,8)
1809 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1810 // make install4jBuildDir relative to jalviewDir
1811 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1814 'JALVIEW_NAME': jalview_name,
1815 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1816 'JALVIEW_DIR': "../..",
1817 'OSX_KEYSTORE': OSX_KEYSTORE,
1818 'JSIGN_SH': JSIGN_SH,
1819 'JRE_DIR': getdown_app_dir_java,
1820 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1821 'JALVIEW_VERSION': JALVIEW_VERSION,
1822 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1823 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1824 'JAVA_VERSION': JAVA_VERSION,
1825 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1826 'VERSION': JALVIEW_VERSION,
1827 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1828 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1829 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1830 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1831 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1832 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1833 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1834 'BUNDLE_ID': install4jBundleId,
1835 'INTERNAL_ID': install4jInternalId,
1836 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1837 'MACOS_DS_STORE': install4jDSStore,
1838 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1839 'INSTALLER_NAME': install4jInstallerName,
1840 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1841 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1842 'GETDOWN_FILES_DIR': getdown_files_dir,
1843 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1844 'GETDOWN_DIST_DIR': getdownAppDistDir,
1845 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1846 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1847 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1848 'BUILD_DIR': install4jBuildDir,
1849 'APPLICATION_CATEGORIES': install4j_application_categories,
1850 'APPLICATION_FOLDER': install4jApplicationFolder,
1851 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1852 'EXECUTABLE_NAME': install4jExecutableName,
1853 'EXTRA_SCHEME': install4jExtraScheme,
1856 //println("INSTALL4J VARIABLES:")
1857 //variables.each{k,v->println("${k}=${v}")}
1859 destination = "${jalviewDir}/${install4jBuildDir}"
1860 buildSelected = true
1862 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1864 disableSigning = true
1868 macKeystorePassword = OSX_KEYPASS
1872 println("Using projectFile "+projectFile)
1875 inputs.dir(getdownWebsiteDir)
1876 inputs.file(install4jConfFile)
1877 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1878 inputs.dir(macosJavaVMDir)
1879 inputs.dir(windowsJavaVMDir)
1880 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
1886 eclipse().configFile(eclipse_codestyle_file)
1891 task sourceDist(type: Tar) {
1892 group "distribution"
1893 description "Create a source .tar.gz file for distribution"
1895 dependsOn convertMdFiles
1897 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1898 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1899 archiveFileName = outputFileName
1901 compression Compression.GZIP
1916 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
1918 "utils/InstallAnywhere",
1933 "gradle.properties",
1944 ".settings/org.eclipse.jdt.core.jalview.prefs",
1948 exclude (EXCLUDE_FILES)
1949 include (PROCESS_FILES)
1950 filter(ReplaceTokens,
1954 'Version-Rel': JALVIEW_VERSION,
1955 'Year-Rel': getDate("yyyy")
1960 exclude (EXCLUDE_FILES)
1961 exclude (PROCESS_FILES)
1962 exclude ("appletlib")
1963 exclude ("**/*locales")
1964 exclude ("*locales/**")
1965 exclude ("utils/InstallAnywhere")
1967 exclude (getdown_files_dir)
1968 exclude (getdown_website_dir)
1970 // exluding these as not using jars as modules yet
1971 exclude ("${j11modDir}/**/*.jar")
1974 include(INCLUDE_FILES)
1976 // from (jalviewDir) {
1977 // // explicit includes for stuff that seemed to not get included
1978 // include(fileTree("test/**/*."))
1979 // exclude(EXCLUDE_FILES)
1980 // exclude(PROCESS_FILES)
1987 dependsOn pubhtmlhelp
1989 inputs.dir("${helpBuildDir}/${help_dir}")
1990 outputs.dir("${buildDir}/distributions/${help_dir}")
1994 task j2sSetHeadlessBuild {
2001 task jalviewjsSetEclipseWorkspace {
2002 def propKey = "jalviewjs_eclipse_workspace"
2004 if (project.hasProperty(propKey)) {
2005 propVal = project.getProperty(propKey)
2006 if (propVal.startsWith("~/")) {
2007 propVal = System.getProperty("user.home") + propVal.substring(1)
2010 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2011 def propsFile = file(propsFileName)
2012 def eclipseWsDir = propVal
2013 def props = new Properties()
2015 def writeProps = true
2016 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2017 def ins = new FileInputStream(propsFileName)
2020 if (props.getProperty(propKey, null) != null) {
2021 eclipseWsDir = props.getProperty(propKey)
2026 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2027 def tempDir = File.createTempDir()
2028 eclipseWsDir = tempDir.getAbsolutePath()
2031 eclipseWorkspace = file(eclipseWsDir)
2034 // do not run a headless transpile when we claim to be in Eclipse
2036 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2037 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2039 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2043 props.setProperty(propKey, eclipseWsDir)
2044 propsFile.parentFile.mkdirs()
2045 def bytes = new ByteArrayOutputStream()
2046 props.store(bytes, null)
2047 def propertiesString = bytes.toString()
2048 propsFile.text = propertiesString
2054 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2057 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2058 outputs.file(propsFileName)
2059 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2063 task jalviewjsEclipsePaths {
2066 def eclipseRoot = jalviewjs_eclipse_root
2067 if (eclipseRoot.startsWith("~/")) {
2068 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2070 if (OperatingSystem.current().isMacOsX()) {
2071 eclipseRoot += "/Eclipse.app"
2072 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2073 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2074 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2075 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2076 eclipseRoot += "/eclipse"
2078 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2079 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2080 } else { // linux or unix
2081 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2082 eclipseRoot += "/eclipse"
2083 println("eclipseDir exists")
2085 eclipseBinary = "${eclipseRoot}/eclipse"
2086 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2089 eclipseVersion = "4.13" // default
2090 def assumedVersion = true
2091 if (file(eclipseProduct).exists()) {
2092 def fis = new FileInputStream(eclipseProduct)
2093 def props = new Properties()
2095 eclipseVersion = props.getProperty("version")
2097 assumedVersion = false
2100 def propKey = "eclipse_debug"
2101 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2104 // do not run a headless transpile when we claim to be in Eclipse
2106 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2107 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2109 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2112 if (!assumedVersion) {
2113 println("ECLIPSE VERSION=${eclipseVersion}")
2119 task printProperties {
2121 description "Output to console all System.properties"
2123 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2129 dependsOn eclipseProject
2130 dependsOn eclipseClasspath
2131 dependsOn eclipseJdt
2135 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2136 task jalviewjsEclipseCopyDropins(type: Copy) {
2137 dependsOn jalviewjsEclipsePaths
2139 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2140 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2141 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2148 // this eclipse -clean doesn't actually work
2149 task jalviewjsCleanEclipse(type: Exec) {
2150 dependsOn eclipseSetup
2151 dependsOn jalviewjsEclipsePaths
2152 dependsOn jalviewjsEclipseCopyDropins
2154 executable(eclipseBinary)
2155 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2161 def inputString = """exit
2164 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2165 standardInput = inputByteStream
2168 /* not really working yet
2169 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2173 task jalviewjsTransferUnzipSwingJs {
2174 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2178 from zipTree(file_zip)
2179 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2183 inputs.file file_zip
2184 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2188 task jalviewjsTransferUnzipLib {
2189 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2192 zipFiles.each { file_zip ->
2194 from zipTree(file_zip)
2195 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2200 inputs.files zipFiles
2201 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2205 task jalviewjsTransferUnzipAllLibs {
2206 dependsOn jalviewjsTransferUnzipSwingJs
2207 dependsOn jalviewjsTransferUnzipLib
2211 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2213 description "Create the .j2s file from the j2s.* properties"
2215 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2216 def siteDirProperty = "j2s.site.directory"
2217 def setSiteDir = false
2218 jalviewjsJ2sProps.each { prop, val ->
2220 if (prop == siteDirProperty) {
2221 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2222 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2228 if (!setSiteDir) { // default site location, don't override specifically set property
2229 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2232 outputFile = jalviewjsJ2sSettingsFileName
2235 inputs.properties(jalviewjsJ2sProps)
2236 outputs.file(jalviewjsJ2sSettingsFileName)
2241 task jalviewjsEclipseSetup {
2242 dependsOn jalviewjsEclipseCopyDropins
2243 dependsOn jalviewjsSetEclipseWorkspace
2244 dependsOn jalviewjsCreateJ2sSettings
2248 task jalviewjsSyncAllLibs (type: Sync) {
2249 dependsOn jalviewjsTransferUnzipAllLibs
2250 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2251 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2252 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2256 def outputFiles = []
2257 rename { filename ->
2258 outputFiles += "${outputDir}/${filename}"
2264 outputs.files outputFiles
2265 inputs.files inputFiles
2269 task jalviewjsSyncResources (type: Sync) {
2270 def inputFiles = fileTree(dir: resourceDir)
2271 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2275 def outputFiles = []
2276 rename { filename ->
2277 outputFiles += "${outputDir}/${filename}"
2283 outputs.files outputFiles
2284 inputs.files inputFiles
2288 task jalviewjsSyncSiteResources (type: Sync) {
2289 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2290 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2294 def outputFiles = []
2295 rename { filename ->
2296 outputFiles += "${outputDir}/${filename}"
2302 outputs.files outputFiles
2303 inputs.files inputFiles
2307 task jalviewjsSyncBuildProperties (type: Sync) {
2308 dependsOn createBuildProperties
2309 def inputFiles = [file(buildProperties)]
2310 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2314 def outputFiles = []
2315 rename { filename ->
2316 outputFiles += "${outputDir}/${filename}"
2322 outputs.files outputFiles
2323 inputs.files inputFiles
2327 task jalviewjsProjectImport(type: Exec) {
2328 dependsOn eclipseSetup
2329 dependsOn jalviewjsEclipsePaths
2330 dependsOn jalviewjsEclipseSetup
2333 // do not run a headless import when we claim to be in Eclipse
2335 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2336 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2338 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2342 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2343 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2344 executable(eclipseBinary)
2345 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2349 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2351 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2354 inputs.file("${jalviewDir}/.project")
2355 outputs.upToDateWhen {
2356 file(projdir).exists()
2361 task jalviewjsTranspile(type: Exec) {
2362 dependsOn jalviewjsEclipseSetup
2363 dependsOn jalviewjsProjectImport
2364 dependsOn jalviewjsEclipsePaths
2367 // do not run a headless transpile when we claim to be in Eclipse
2369 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2370 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2372 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2376 executable(eclipseBinary)
2377 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2381 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2383 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2389 stdout = new ByteArrayOutputStream()
2390 stderr = new ByteArrayOutputStream()
2392 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2393 def logOutFile = file(logOutFileName)
2394 logOutFile.createNewFile()
2395 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2396 BINARY: ${eclipseBinary}
2397 VERSION: ${eclipseVersion}
2398 WORKSPACE: ${eclipseWorkspace}
2399 DEBUG: ${eclipseDebug}
2402 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2403 // combine stdout and stderr
2404 def logErrFOS = logOutFOS
2406 if (jalviewjs_j2s_to_console.equals("true")) {
2407 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2408 new org.apache.tools.ant.util.TeeOutputStream(
2412 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2413 new org.apache.tools.ant.util.TeeOutputStream(
2418 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2421 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2428 if (stdout.toString().contains("Error processing ")) {
2429 // j2s did not complete transpile
2430 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2431 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2432 println("IGNORING TRANSPILE ERRORS")
2433 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2435 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2440 inputs.dir("${jalviewDir}/${sourceDir}")
2441 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2442 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2446 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2448 def stdout = new ByteArrayOutputStream()
2449 def stderr = new ByteArrayOutputStream()
2451 def coreFile = file(jsfile)
2453 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2455 logOutFile.createNewFile()
2456 logOutFile.append(msg+"\n")
2458 def coreTop = file(prefixFile)
2459 def coreBottom = file(suffixFile)
2460 coreFile.getParentFile().mkdirs()
2461 coreFile.createNewFile()
2462 coreFile.write( coreTop.getText("UTF-8") )
2466 def t = f.getText("UTF-8")
2467 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2468 coreFile.append( t )
2470 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2472 logOutFile.append(msg+"\n")
2475 coreFile.append( coreBottom.getText("UTF-8") )
2477 msg = "Generating ${zjsfile}"
2479 logOutFile.append(msg+"\n")
2480 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2481 def logErrFOS = logOutFOS
2484 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2485 main = "com.google.javascript.jscomp.CommandLineRunner"
2486 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2487 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2490 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2492 logOutFile.append(msg+"\n")
2494 if (logOutConsole) {
2495 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2496 new org.apache.tools.ant.util.TeeOutputStream(
2500 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2501 new org.apache.tools.ant.util.TeeOutputStream(
2506 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2509 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2516 logOutFile.append(msg+"\n")
2520 task jalviewjsBuildAllCores {
2522 description "Build the core js lib closures listed in the classlists dir"
2523 dependsOn jalviewjsTranspile
2524 dependsOn jalviewjsTransferUnzipSwingJs
2526 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2527 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2528 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2529 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2530 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2531 def prefixFile = "${jsDir}/core/coretop2.js"
2532 def suffixFile = "${jsDir}/core/corebottom2.js"
2534 inputs.file prefixFile
2535 inputs.file suffixFile
2537 def classlistFiles = []
2538 // add the classlists found int the jalviewjs_classlists_dir
2539 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2541 def name = file.getName() - ".txt"
2548 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2549 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2550 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2552 jalviewjsCoreClasslists = []
2554 classlistFiles.each {
2557 def file = hash['file']
2558 if (! file.exists()) {
2559 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2560 return false // this is a "continue" in groovy .each closure
2562 def name = hash['name']
2564 name = file.getName() - ".txt"
2572 def list = fileTree(dir: j2sDir, includes: filelist)
2574 def jsfile = "${outputDir}/core${name}.js"
2575 def zjsfile = "${outputDir}/core${name}.z.js"
2577 jalviewjsCoreClasslists += [
2586 outputs.file(jsfile)
2587 outputs.file(zjsfile)
2590 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2591 def stevesoftClasslistName = "_stevesoft"
2592 def stevesoftClasslist = [
2593 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2594 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2595 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2596 'name': stevesoftClasslistName
2598 jalviewjsCoreClasslists += stevesoftClasslist
2599 inputs.files(stevesoftClasslist['list'])
2600 outputs.file(stevesoftClasslist['jsfile'])
2601 outputs.file(stevesoftClasslist['zjsfile'])
2604 def allClasslistName = "_all"
2605 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2606 allJsFiles += fileTree(
2610 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2611 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2612 "**/org/jmol/export/JSExporter.js"
2615 allJsFiles += fileTree(
2619 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2620 "**/sun/misc/Unsafe.js",
2621 "**/swingjs/jquery/jquery-editable-select.js",
2622 "**/swingjs/jquery/j2sComboBox.js",
2623 "**/sun/misc/FloatingDecimal.js"
2626 def allClasslist = [
2627 'jsfile': "${outputDir}/core${allClasslistName}.js",
2628 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2630 'name': allClasslistName
2632 // not including this version of "all" core at the moment
2633 //jalviewjsCoreClasslists += allClasslist
2634 inputs.files(allClasslist['list'])
2635 outputs.file(allClasslist['jsfile'])
2636 outputs.file(allClasslist['zjsfile'])
2639 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2640 logOutFile.getParentFile().mkdirs()
2641 logOutFile.createNewFile()
2642 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2644 jalviewjsCoreClasslists.each {
2645 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2652 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2655 into file(outputFile).getParentFile()
2656 rename { filename ->
2657 if (filename.equals(inputFile.getName())) {
2658 return file(outputFile).getName()
2662 filter(ReplaceTokens,
2666 'MAIN': '"'+main_class+'"',
2668 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2669 'COREKEY': jalviewjs_core_key,
2670 'CORENAME': coreName
2677 task jalviewjsPublishCoreTemplates {
2678 dependsOn jalviewjsBuildAllCores
2679 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2680 def inputFile = file(inputFileName)
2681 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2683 def outputFiles = []
2684 jalviewjsCoreClasslists.each { cl ->
2685 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2686 cl['outputfile'] = outputFile
2687 outputFiles += outputFile
2691 jalviewjsCoreClasslists.each { cl ->
2692 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2695 inputs.file(inputFile)
2696 outputs.files(outputFiles)
2700 task jalviewjsSyncCore (type: Sync) {
2701 dependsOn jalviewjsBuildAllCores
2702 dependsOn jalviewjsPublishCoreTemplates
2703 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2704 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2708 def outputFiles = []
2709 rename { filename ->
2710 outputFiles += "${outputDir}/${filename}"
2716 outputs.files outputFiles
2717 inputs.files inputFiles
2721 // this Copy version of TransferSiteJs will delete anything else in the target dir
2722 task jalviewjsCopyTransferSiteJs(type: Copy) {
2723 dependsOn jalviewjsTranspile
2724 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2725 into "${jalviewDir}/${jalviewjsSiteDir}"
2729 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2730 task jalviewjsSyncTransferSiteJs(type: Sync) {
2731 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2733 into "${jalviewDir}/${jalviewjsSiteDir}"
2740 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2741 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2742 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2743 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2745 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2746 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2747 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2748 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2751 task jalviewjsPrepareSite {
2753 description "Prepares the website folder including unzipping files and copying resources"
2754 dependsOn jalviewjsSyncAllLibs
2755 dependsOn jalviewjsSyncResources
2756 dependsOn jalviewjsSyncSiteResources
2757 dependsOn jalviewjsSyncBuildProperties
2758 dependsOn jalviewjsSyncCore
2762 task jalviewjsBuildSite {
2764 description "Builds the whole website including transpiled code"
2765 dependsOn jalviewjsCopyTransferSiteJs
2766 dependsOn jalviewjsPrepareSite
2770 task cleanJalviewjsTransferSite {
2772 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2773 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2774 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2775 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2780 task cleanJalviewjsSite {
2781 dependsOn cleanJalviewjsTransferSite
2783 delete "${jalviewDir}/${jalviewjsSiteDir}"
2788 task jalviewjsSiteTar(type: Tar) {
2790 description "Creates a tar.gz file for the website"
2791 dependsOn jalviewjsBuildSite
2792 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2793 archiveFileName = outputFilename
2795 compression Compression.GZIP
2797 from "${jalviewDir}/${jalviewjsSiteDir}"
2798 into jalviewjs_site_dir // this is inside the tar file
2800 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
2804 task jalviewjsServer {
2806 def filename = "jalviewjsTest.html"
2807 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
2808 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
2811 SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
2812 def port = Integer.valueOf(jalviewjs_server_port)
2817 while(port < start+1000 && !running) {
2819 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
2820 jalviewjsServer = factory.start(doc_root, port)
2822 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
2823 println("SERVER STARTED with document root ${doc_root}.")
2824 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
2825 println("For debug: "+url+"?j2sdebug")
2826 println("For verbose: "+url+"?j2sverbose")
2827 } catch (Exception e) {
2832 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
2833 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
2834 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
2836 jalviewjsCoreClasslists.each { cl ->
2837 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
2839 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
2841 println("For core ${cl.name}: "+urlcore)
2844 file(htmlFile).text = htmlText
2847 outputs.file(htmlFile)
2848 outputs.upToDateWhen({false})
2852 task cleanJalviewjsAll {
2854 description "Delete all configuration and build artifacts to do with JalviewJS build"
2855 dependsOn cleanJalviewjsSite
2856 dependsOn jalviewjsEclipsePaths
2859 delete "${jalviewDir}/${jalviewjsBuildDir}"
2860 delete "${jalviewDir}/${eclipse_bin_dir}"
2861 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
2862 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
2864 delete "${jalviewDir}/${jalviewjs_j2s_settings}"
2867 outputs.upToDateWhen( { false } )
2871 task jalviewjsIDE_checkJ2sPlugin {
2872 group "00 JalviewJS in Eclipse"
2873 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
2876 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
2877 def j2sPluginFile = file(j2sPlugin)
2878 def eclipseHome = System.properties["eclipse.home.location"]
2879 if (eclipseHome == null || ! IN_ECLIPSE) {
2880 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
2882 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
2883 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
2884 if (altPluginsDir != null && file(altPluginsDir).exists()) {
2885 eclipseJ2sPluginDirs += altPluginsDir
2887 def foundPlugin = false
2888 def j2sPluginFileName = j2sPluginFile.getName()
2889 def eclipseJ2sPlugin
2890 def eclipseJ2sPluginFile
2891 eclipseJ2sPluginDirs.any { dir ->
2892 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
2893 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
2894 if (eclipseJ2sPluginFile.exists()) {
2900 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
2901 System.err.println(msg)
2902 throw new StopExecutionException(msg)
2905 def digest = MessageDigest.getInstance("MD5")
2907 digest.update(j2sPluginFile.text.bytes)
2908 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
2910 digest.update(eclipseJ2sPluginFile.text.bytes)
2911 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
2913 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
2914 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
2915 System.err.println(msg)
2916 throw new StopExecutionException(msg)
2918 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
2924 task jalviewjsIDE_copyJ2sPlugin {
2925 group "00 JalviewJS in Eclipse"
2926 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
2929 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
2930 def j2sPluginFile = file(j2sPlugin)
2931 def eclipseHome = System.properties["eclipse.home.location"]
2932 if (eclipseHome == null || ! IN_ECLIPSE) {
2933 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
2935 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
2936 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
2937 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
2938 System.err.println(msg)
2941 eclipseJ2sPluginFile.getParentFile().mkdirs()
2942 into eclipseJ2sPluginFile.getParent()
2948 task jalviewjsIDE_j2sFile {
2949 group "00 JalviewJS in Eclipse"
2950 description "Creates the .j2s file"
2951 dependsOn jalviewjsCreateJ2sSettings
2955 task jalviewjsIDE_SyncCore {
2956 group "00 JalviewJS in Eclipse"
2957 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
2958 dependsOn jalviewjsSyncCore
2962 task jalviewjsIDE_SyncSiteAll {
2963 dependsOn jalviewjsSyncAllLibs
2964 dependsOn jalviewjsSyncResources
2965 dependsOn jalviewjsSyncSiteResources
2966 dependsOn jalviewjsSyncBuildProperties
2970 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
2973 task jalviewjsIDE_PrepareSite {
2974 group "00 JalviewJS in Eclipse"
2975 description "Sync libs and resources to site dir, but not closure cores"
2977 dependsOn jalviewjsIDE_SyncSiteAll
2978 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
2982 task jalviewjsIDE_AssembleSite {
2983 group "00 JalviewJS in Eclipse"
2984 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
2985 dependsOn jalviewjsPrepareSite
2989 task jalviewjsIDE_SiteClean {
2990 group "00 JalviewJS in Eclipse"
2991 description "Deletes the Eclipse transpiled site"
2992 dependsOn cleanJalviewjsSite
2996 task jalviewjsIDE_Server {
2997 group "00 JalviewJS in Eclipse"
2998 description "Starts a webserver on localhost to test the website"
2999 dependsOn jalviewjsServer
3003 // buildship runs this at import or gradle refresh
3004 task eclipseSynchronizationTask {
3005 //dependsOn eclipseSetup
3006 dependsOn createBuildProperties
3008 dependsOn jalviewjsIDE_j2sFile
3009 dependsOn jalviewjsIDE_checkJ2sPlugin
3010 dependsOn jalviewjsIDE_PrepareSite
3015 // buildship runs this at build time or project refresh
3016 task eclipseAutoBuildTask {
3017 //dependsOn jalviewjsIDE_checkJ2sPlugin
3018 //dependsOn jalviewjsIDE_PrepareSite
3024 description "Build the site"
3025 dependsOn jalviewjsBuildSite