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 '9.0.6'
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'
56 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
57 def string(Object o) {
58 return o == null ? "" : o.toString()
61 def overrideProperties(String propsFileName, boolean output = false) {
62 if (propsFileName == null) {
65 def propsFile = file(propsFileName)
66 if (propsFile != null && propsFile.exists()) {
67 println("Using properties from file '${propsFileName}'")
69 def p = new Properties()
70 def localPropsFIS = new FileInputStream(propsFile)
76 if (project.hasProperty(key)) {
77 oldval = project.findProperty(key)
78 project.setProperty(key, val)
80 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
83 ext.setProperty(key, val)
85 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
89 } catch (Exception e) {
90 println("Exception reading local.properties")
97 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
98 jalviewDirRelativePath = jalviewDir
100 getdownChannelName = CHANNEL.toLowerCase()
101 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
102 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
103 // Import channel_properties
104 channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
105 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
106 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
107 overrideProperties(channelGradleProperties, false)
108 // local build environment properties
109 // can be "projectDir/local.properties"
110 overrideProperties("${projectDir}/local.properties", true)
111 // or "../projectDir_local.properties"
112 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
115 // Import releaseProps from the RELEASE file
116 // or a file specified via JALVIEW_RELEASE_FILE if defined
117 // Expect jalview.version and target release branch in jalview.release
118 def releaseProps = new Properties();
119 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
120 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
122 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
123 releaseProps.load(it)
125 } catch (Exception fileLoadError) {
126 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
129 // Set JALVIEW_VERSION if it is not already set
130 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
131 JALVIEW_VERSION = releaseProps.get("jalview.version")
134 // this property set when running Eclipse headlessly
135 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
136 // this property set by Eclipse
137 eclipseApplicationProperty = string("eclipse.application")
138 // CHECK IF RUNNING FROM WITHIN ECLIPSE
139 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
140 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
141 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
142 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
143 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
147 println("WITHIN ECLIPSE IDE")
149 println("HEADLESS BUILD")
152 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
154 println("J2S ENABLED")
157 System.properties.sort { it.key }.each {
158 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
161 if (false && IN_ECLIPSE) {
162 jalviewDir = jalviewDirAbsolutePath
167 buildDate = new Date().format("yyyyMMdd")
170 bareSourceDir = string(source_dir)
171 sourceDir = string("${jalviewDir}/${bareSourceDir}")
172 resourceDir = string("${jalviewDir}/${resource_dir}")
173 bareTestSourceDir = string(test_source_dir)
174 testDir = string("${jalviewDir}/${bareTestSourceDir}")
176 classesDir = string("${jalviewDir}/${classes_dir}")
179 useClover = clover.equals("true")
180 cloverBuildDir = "${buildDir}/clover"
181 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
182 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
183 cloverReportDir = file("${buildDir}/reports/clover")
184 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
185 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
186 //cloverTestClassesDir = cloverClassesDir
187 cloverDb = string("${cloverBuildDir}/clover.db")
189 testSourceDir = useClover ? cloverTestInstrDir : testDir
190 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
192 getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
194 buildProperties = null
196 // the following values might be overridden by the CHANNEL switch
197 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
198 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
199 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
200 getdownAppDistDir = getdown_app_dir_alt
201 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
202 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
203 reportRsyncCommand = false
204 jvlChannelName = CHANNEL.toLowerCase()
205 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
206 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
207 install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
208 install4jInstallerName = "${jalview_name} Non-Release Installer"
209 install4jExecutableName = install4j_executable_name
210 install4jExtraScheme = "jalviewx"
211 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
212 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
213 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
214 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
218 // TODO: get bamboo build artifact URL for getdown artifacts
219 getdown_channel_base = bamboo_channelbase
220 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
221 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
222 jvlChannelName += "_${getdownChannelName}"
223 // automatically add the test group Not-bamboo for exclusion
224 if ("".equals(testng_excluded_groups)) {
225 testng_excluded_groups = "Not-bamboo"
227 install4jExtraScheme = "jalviewb"
230 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
231 getdownAppDistDir = getdown_app_dir_release
232 reportRsyncCommand = true
234 install4jInstallerName = "${jalview_name} Installer"
238 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
239 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
240 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
241 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
242 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
244 package_dir = string("${ARCHIVEDIR}/${package_dir}")
245 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
248 reportRsyncCommand = true
249 install4jExtraScheme = "jalviewa"
253 getdownChannelName = string("archive/${JALVIEW_VERSION}")
254 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
255 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
256 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
257 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
259 package_dir = string("${ARCHIVEDIR}/${package_dir}")
260 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
263 reportRsyncCommand = true
264 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
265 install4jSuffix = "Archive"
266 install4jExtraScheme = "jalviewa"
270 reportRsyncCommand = true
271 getdownSetAppBaseProperty = true
272 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
273 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
275 install4jSuffix = "Develop"
276 install4jExtraScheme = "jalviewd"
277 install4jInstallerName = "${jalview_name} Develop Installer"
281 reportRsyncCommand = true
282 // Don't ignore transpile errors for release build
283 if (jalviewjs_ignore_transpile_errors.equals("true")) {
284 jalviewjs_ignore_transpile_errors = "false"
285 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
287 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
288 install4jSuffix = "Test"
289 install4jExtraScheme = "jalviewt"
290 install4jInstallerName = "${jalview_name} Test Installer"
293 case ~/^SCRATCH(|-[-\w]*)$/:
294 getdownChannelName = CHANNEL
295 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
297 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
298 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
299 reportRsyncCommand = true
300 install4jSuffix = "Scratch"
304 if (!file("${LOCALDIR}").exists()) {
305 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
307 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
308 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
310 JALVIEW_VERSION = "TEST"
311 install4jSuffix = "Test-Local"
312 install4jExtraScheme = "jalviewt"
313 install4jInstallerName = "${jalview_name} Test Installer"
316 case [ "LOCAL", "JALVIEWJS" ]:
317 JALVIEW_VERSION = "TEST"
318 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
319 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
320 install4jExtraScheme = "jalviewl"
323 default: // something wrong specified
324 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
328 // override getdownAppBase if requested
329 if (findProperty("getdown_appbase_override") != null) {
330 // revert to LOCAL if empty string
331 if (string(getdown_appbase_override) == "") {
332 getdownAppBase = file(getdownWebsiteDir).toURI().toString()
333 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
334 } else if (string(getdown_appbase_override).startsWith("file://")) {
335 getdownAppBase = string(getdown_appbase_override)
336 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
338 getdownAppBase = string(getdown_appbase_override)
340 println("Overriding getdown appbase with '${getdownAppBase}'")
342 // sanitise file name for jalview launcher file for this channel
343 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
344 // install4j application and folder names
345 if (install4jSuffix == "") {
346 install4jApplicationName = "${jalview_name}"
347 install4jBundleId = "${install4j_bundle_id}"
348 install4jWinApplicationId = install4j_release_win_application_id
350 install4jApplicationName = "${jalview_name} ${install4jSuffix}"
351 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
352 // add int hash of install4jSuffix to the last part of the application_id
353 def id = install4j_release_win_application_id
354 def idsplitreverse = id.split("-").reverse()
355 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
356 install4jWinApplicationId = idsplitreverse.reverse().join("-")
358 // sanitise folder and id names
359 // install4jApplicationFolder = e.g. "Jalview Build"
360 install4jApplicationFolder = install4jApplicationName
361 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
362 .replaceAll("_+", "_") // collapse __
363 install4jInternalId = install4jApplicationName
365 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
366 .replaceAll("_+", "") // collapse __
367 //.replaceAll("_*-_*", "-") // collapse _-_
368 install4jUnixApplicationFolder = install4jApplicationName
370 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
371 .replaceAll("_+", "_") // collapse __
372 .replaceAll("_*-_*", "-") // collapse _-_
375 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
376 getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
377 //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
378 getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
379 getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
380 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
381 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
382 /* compile without modules -- using classpath libraries
383 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
384 modules_runtimeClasspath = modules_compileClasspath
386 def details = versionDetails()
387 gitHash = details.gitHash
388 gitBranch = details.branchName
390 println("Using a ${CHANNEL} profile.")
392 additional_compiler_args = []
393 // configure classpath/args for j8/j11 compilation
394 if (JAVA_VERSION.equals("1.8")) {
395 JAVA_INTEGER_VERSION = string("8")
398 libDistDir = j8libDir
399 compile_source_compatibility = 1.8
400 compile_target_compatibility = 1.8
401 // these are getdown.txt properties defined dependent on the JAVA_VERSION
402 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
403 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
404 // this property is assigned below and expanded to multiple lines in the getdown task
405 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
406 // this property is for the Java library used in eclipse
407 eclipseJavaRuntimeName = string("JavaSE-1.8")
408 } else if (JAVA_VERSION.equals("11")) {
409 JAVA_INTEGER_VERSION = string("11")
411 libDistDir = j11libDir
412 compile_source_compatibility = 11
413 compile_target_compatibility = 11
414 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
415 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
416 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
417 eclipseJavaRuntimeName = string("JavaSE-11")
418 /* compile without modules -- using classpath libraries
419 additional_compiler_args += [
420 '--module-path', modules_compileClasspath.asPath,
421 '--add-modules', j11modules
424 } else if (JAVA_VERSION.equals("17")) {
425 JAVA_INTEGER_VERSION = string("17")
427 libDistDir = j17libDir
428 compile_source_compatibility = 17
429 compile_target_compatibility = 17
430 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
431 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
432 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
433 eclipseJavaRuntimeName = string("JavaSE-17")
434 /* compile without modules -- using classpath libraries
435 additional_compiler_args += [
436 '--module-path', modules_compileClasspath.asPath,
437 '--add-modules', j11modules
441 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
446 JAVA_MIN_VERSION = JAVA_VERSION
447 JAVA_MAX_VERSION = JAVA_VERSION
448 def jreInstallsDir = string(jre_installs_dir)
449 if (jreInstallsDir.startsWith("~/")) {
450 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
452 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
453 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
454 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
455 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz")
456 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz")
457 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz")
458 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
459 install4jConfFileName = string("jalview-install4j-conf.install4j")
460 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
461 install4jHomeDir = install4j_home_dir
462 if (install4jHomeDir.startsWith("~/")) {
463 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
466 resourceBuildDir = string("${buildDir}/resources")
467 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
468 helpBuildDir = string("${resourceBuildDir}/help_build")
469 docBuildDir = string("${resourceBuildDir}/doc_build")
471 if (buildProperties == null) {
472 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
474 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
475 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
476 helpSourceDir = string("${helpParentDir}/${help_dir}")
477 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
480 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
481 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
482 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
484 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
486 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
488 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
489 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
490 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
491 jalviewjsJalviewCoreHtmlFile = string("")
492 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
493 jalviewjsCoreClasslists = []
494 jalviewjsJalviewTemplateName = string(jalviewjs_name)
495 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
496 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
497 jalviewjsJ2sProps = null
498 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
500 eclipseWorkspace = null
501 eclipseBinary = string("")
502 eclipseVersion = string("")
512 outputDir = file(classesDir)
516 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
519 compileClasspath = files(sourceSets.main.java.outputDir)
520 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
522 runtimeClasspath = compileClasspath
523 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
528 srcDirs cloverInstrDir
529 outputDir = cloverClassesDir
533 srcDirs = sourceSets.main.resources.srcDirs
536 compileClasspath = files( sourceSets.clover.java.outputDir )
537 //compileClasspath += files( testClassesDir )
538 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
539 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
540 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
542 runtimeClasspath = compileClasspath
547 srcDirs testSourceDir
548 outputDir = file(testClassesDir)
552 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
555 compileClasspath = files( sourceSets.test.java.outputDir )
556 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
557 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
559 runtimeClasspath = compileClasspath
560 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
566 // eclipse project and settings files creation, also used by buildship
569 name = eclipse_project_name
571 natures 'org.eclipse.jdt.core.javanature',
572 'org.eclipse.jdt.groovy.core.groovyNature',
573 'org.eclipse.buildship.core.gradleprojectnature'
575 buildCommand 'org.eclipse.jdt.core.javabuilder'
576 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
580 //defaultOutputDir = sourceSets.main.java.outputDir
581 configurations.each{ c->
582 if (c.isCanBeResolved()) {
583 minusConfigurations += [c]
587 plusConfigurations = [ ]
591 def removeTheseToo = []
592 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
593 cp.entries.each { entry ->
594 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
595 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
596 // we add the resources and help/help dirs in as libs afterwards (see below)
597 if (entry.kind == 'src') {
598 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
599 removeTheseToo += entry
601 alreadyAddedSrcPath.putAt(entry.path, true)
606 cp.entries.removeAll(removeTheseToo)
608 //cp.entries += new Output("${eclipse_bin_dir}/main")
609 if (file(helpParentDir).isDirectory()) {
610 cp.entries += new Library(fileReference(helpParentDir))
612 if (file(resourceDir).isDirectory()) {
613 cp.entries += new Library(fileReference(resourceDir))
616 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
618 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
619 //don't want to add outputDir as eclipse is using its own output dir in bin/main
620 if (it.isDirectory() || ! it.exists()) {
621 // don't add dirs to classpath, especially if they don't exist
622 return false // groovy "continue" in .any closure
624 def itPath = it.toString()
625 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
626 // make relative path
627 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
629 if (alreadyAddedLibPath.get(itPath)) {
630 //println("Not adding duplicate entry "+itPath)
632 //println("Adding entry "+itPath)
633 cp.entries += new Library(fileReference(itPath))
634 alreadyAddedLibPath.put(itPath, true)
638 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
639 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
640 if (it.isDirectory() || ! it.exists()) {
641 // don't add dirs to classpath
642 return false // groovy "continue" in .any closure
645 def itPath = it.toString()
646 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
647 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
649 if (alreadyAddedLibPath.get(itPath)) {
652 def lib = new Library(fileReference(itPath))
653 lib.entryAttributes["test"] = "true"
655 alreadyAddedLibPath.put(itPath, true)
663 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
668 // for the IDE, use java 11 compatibility
669 sourceCompatibility = compile_source_compatibility
670 targetCompatibility = compile_target_compatibility
671 javaRuntimeName = eclipseJavaRuntimeName
673 // add in jalview project specific properties/preferences into eclipse core preferences
675 withProperties { props ->
676 def jalview_prefs = new Properties()
677 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
678 jalview_prefs.load(ins)
680 jalview_prefs.forEach { t, v ->
681 if (props.getAt(t) == null) {
685 // codestyle file -- overrides previous formatter prefs
686 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
687 if (csFile.exists()) {
688 XmlParser parser = new XmlParser()
689 def profiles = parser.parse(csFile)
690 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
691 if (profile != null) {
692 profile.'setting'.each { s ->
694 def value = s.'@value'
695 if (id != null && value != null) {
696 props.putAt(id, value)
707 // Don't want these to be activated if in headless build
708 synchronizationTasks "eclipseSynchronizationTask"
709 //autoBuildTasks "eclipseAutoBuildTask"
715 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
716 // Class to allow updating arbitrary properties files
717 class PropertiesFile extends PropertiesPersistableConfigurationObject {
718 public PropertiesFile(PropertiesTransformer t) { super(t); }
719 @Override protected void load(Properties properties) { }
720 @Override protected void store(Properties properties) { }
721 @Override protected String getDefaultResourceName() { return ""; }
722 // This is necessary, because PropertiesPersistableConfigurationObject fails
723 // if no default properties file exists.
724 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
727 // Task to update arbitrary properties files (set outputFile)
728 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
729 private final PropertiesFileContentMerger file;
730 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
731 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
732 protected void configure(PropertiesFile props) {
733 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
735 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
738 task eclipseUIPreferences(type: PropertiesFileTask) {
739 description = "Generate Eclipse additional settings"
740 def filename = "org.eclipse.jdt.ui.prefs"
741 outputFile = "$projectDir/.settings/${filename}" as File
744 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
749 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
750 description = "Generate Eclipse additional settings"
751 def filename = "org.eclipse.jdt.groovy.core.prefs"
752 outputFile = "$projectDir/.settings/${filename}" as File
755 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
760 task eclipseAllPreferences {
762 dependsOn eclipseUIPreferences
763 dependsOn eclipseGroovyCorePreferences
766 eclipseUIPreferences.mustRunAfter eclipseJdt
767 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
769 /* end of eclipse preferences hack */
777 delete cloverBuildDir
778 delete cloverReportDir
783 task cloverInstrJava(type: JavaExec) {
784 group = "Verification"
785 description = "Create clover instrumented source java files"
787 dependsOn cleanClover
789 inputs.files(sourceSets.main.allJava)
790 outputs.dir(cloverInstrDir)
792 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
793 classpath = sourceSets.clover.compileClasspath
794 main = "com.atlassian.clover.CloverInstr"
802 cloverInstrDir.getPath(),
804 def srcFiles = sourceSets.main.allJava.files
807 { file -> file.absolutePath }
810 args argsList.toArray()
813 delete cloverInstrDir
814 println("Clover: About to instrument "+srcFiles.size() +" files")
819 task cloverInstrTests(type: JavaExec) {
820 group = "Verification"
821 description = "Create clover instrumented source test files"
823 dependsOn cleanClover
825 inputs.files(testDir)
826 outputs.dir(cloverTestInstrDir)
828 classpath = sourceSets.clover.compileClasspath
829 main = "com.atlassian.clover.CloverInstr"
839 cloverTestInstrDir.getPath(),
841 args argsList.toArray()
844 delete cloverTestInstrDir
845 println("Clover: About to instrument test files")
851 group = "Verification"
852 description = "Create clover instrumented all source files"
854 dependsOn cloverInstrJava
855 dependsOn cloverInstrTests
859 cloverClasses.dependsOn cloverInstr
862 task cloverConsoleReport(type: JavaExec) {
863 group = "Verification"
864 description = "Creates clover console report"
867 file(cloverDb).exists()
870 inputs.dir cloverClassesDir
872 classpath = sourceSets.clover.runtimeClasspath
873 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
875 if (cloverreport_mem.length() > 0) {
876 maxHeapSize = cloverreport_mem
878 if (cloverreport_jvmargs.length() > 0) {
879 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
889 args argsList.toArray()
893 task cloverHtmlReport(type: JavaExec) {
894 group = "Verification"
895 description = "Creates clover HTML report"
898 file(cloverDb).exists()
901 def cloverHtmlDir = cloverReportDir
902 inputs.dir cloverClassesDir
903 outputs.dir cloverHtmlDir
905 classpath = sourceSets.clover.runtimeClasspath
906 main = "com.atlassian.clover.reporters.html.HtmlReporter"
908 if (cloverreport_mem.length() > 0) {
909 maxHeapSize = cloverreport_mem
911 if (cloverreport_jvmargs.length() > 0) {
912 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
923 if (cloverreport_html_options.length() > 0) {
924 argsList += cloverreport_html_options.split(" ")
927 args argsList.toArray()
931 task cloverXmlReport(type: JavaExec) {
932 group = "Verification"
933 description = "Creates clover XML report"
936 file(cloverDb).exists()
939 def cloverXmlFile = "${cloverReportDir}/clover.xml"
940 inputs.dir cloverClassesDir
941 outputs.file cloverXmlFile
943 classpath = sourceSets.clover.runtimeClasspath
944 main = "com.atlassian.clover.reporters.xml.XMLReporter"
946 if (cloverreport_mem.length() > 0) {
947 maxHeapSize = cloverreport_mem
949 if (cloverreport_jvmargs.length() > 0) {
950 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
961 if (cloverreport_xml_options.length() > 0) {
962 argsList += cloverreport_xml_options.split(" ")
965 args argsList.toArray()
970 group = "Verification"
971 description = "Creates clover reports"
973 dependsOn cloverXmlReport
974 dependsOn cloverHtmlReport
981 sourceCompatibility = compile_source_compatibility
982 targetCompatibility = compile_target_compatibility
983 options.compilerArgs += additional_compiler_args
984 print ("Setting target compatibility to "+targetCompatibility+"\n")
986 //classpath += configurations.cloverRuntime
992 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
993 sourceCompatibility = compile_source_compatibility
994 targetCompatibility = compile_target_compatibility
995 options.compilerArgs = additional_compiler_args
996 options.encoding = "UTF-8"
998 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1005 sourceCompatibility = compile_source_compatibility
1006 targetCompatibility = compile_target_compatibility
1007 options.compilerArgs = additional_compiler_args
1009 print ("Setting target compatibility to "+targetCompatibility+"\n")
1016 delete sourceSets.main.java.outputDir
1022 dependsOn cleanClover
1024 delete sourceSets.test.java.outputDir
1029 // format is a string like date.format("dd MMMM yyyy")
1030 def getDate(format) {
1031 def date = new Date()
1032 return date.format(format)
1036 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1037 MutableDataSet options = new MutableDataSet()
1039 def extensions = new ArrayList<>()
1040 extensions.add(AnchorLinkExtension.create())
1041 extensions.add(AutolinkExtension.create())
1042 extensions.add(StrikethroughExtension.create())
1043 extensions.add(TaskListExtension.create())
1044 extensions.add(TablesExtension.create())
1045 extensions.add(TocExtension.create())
1047 options.set(Parser.EXTENSIONS, extensions)
1049 // set GFM table parsing options
1050 options.set(TablesExtension.WITH_CAPTION, false)
1051 options.set(TablesExtension.COLUMN_SPANS, false)
1052 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1053 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1054 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1055 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1056 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1058 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1059 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1060 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1061 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1063 Parser parser = Parser.builder(options).build()
1064 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1066 mdFiles.each { mdFile ->
1067 // add table of contents
1068 def mdText = "[TOC]\n"+mdFile.text
1070 // grab the first top-level title
1072 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1073 def matcher = mdText =~ titleRegex
1074 if (matcher.size() > 0) {
1075 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1076 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1078 // or use the filename if none found
1079 if (title == null) {
1080 title = mdFile.getName()
1083 Node document = parser.parse(mdText)
1084 String htmlBody = renderer.render(document)
1085 def htmlText = '''<html>
1086 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1087 <html xmlns="http://www.w3.org/1999/xhtml">
1089 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1090 <meta http-equiv="Content-Style-Type" content="text/css" />
1091 <meta name="generator" content="flexmark" />
1093 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1095 <style type="text/css">code{white-space: pre;}</style>
1097 htmlText += ((cssFile != null) ? cssFile.text : '')
1098 htmlText += '''</head>
1101 htmlText += htmlBody
1107 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1108 def htmlFile = file(htmlFilePath)
1109 println("Creating ${htmlFilePath}")
1110 htmlFile.text = htmlText
1115 task copyDocs(type: Copy) {
1116 def inputDir = "${jalviewDir}/${doc_dir}"
1117 def outputDir = "${docBuildDir}/${doc_dir}"
1121 include('**/*.html')
1123 filter(ReplaceTokens,
1127 'Version-Rel': JALVIEW_VERSION,
1128 'Year-Rel': getDate("yyyy")
1135 exclude('**/*.html')
1140 inputs.dir(inputDir)
1141 outputs.dir(outputDir)
1145 task convertMdFiles {
1147 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1148 def cssFile = file("${jalviewDir}/${flexmark_css}")
1151 convertMdToHtml(mdFiles, cssFile)
1154 inputs.files(mdFiles)
1155 inputs.file(cssFile)
1158 mdFiles.each { mdFile ->
1159 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1160 htmlFiles.add(file(htmlFilePath))
1162 outputs.files(htmlFiles)
1166 task copyHelp(type: Copy) {
1167 def inputDir = helpSourceDir
1168 def outputDir = "${helpBuildDir}/${help_dir}"
1172 include('**/*.html')
1176 filter(ReplaceTokens,
1180 'Version-Rel': JALVIEW_VERSION,
1181 'Year-Rel': getDate("yyyy")
1188 exclude('**/*.html')
1195 inputs.dir(inputDir)
1196 outputs.files(helpFile)
1197 outputs.dir(outputDir)
1201 task copyResources(type: Copy) {
1203 description = "Copy (and make text substitutions in) the resources dir to the build area"
1205 def inputDir = resourceDir
1206 def outputDir = resourcesBuildDir
1210 include('**/*.html')
1212 filter(ReplaceTokens,
1216 'Version-Rel': JALVIEW_VERSION,
1217 'Year-Rel': getDate("yyyy")
1224 exclude('**/*.html')
1229 inputs.dir(inputDir)
1230 outputs.dir(outputDir)
1233 task copyChannelResources(type: Copy) {
1234 dependsOn copyResources
1236 description = "Copy the channel resources dir to the build resources area"
1238 def inputDir = "${channelDir}/${resource_dir}"
1239 def outputDir = resourcesBuildDir
1243 inputs.dir(inputDir)
1244 outputs.dir(outputDir)
1247 task createBuildProperties(type: WriteProperties) {
1248 dependsOn copyResources
1250 description = "Create the ${buildProperties} file"
1252 inputs.dir(sourceDir)
1253 inputs.dir(resourcesBuildDir)
1254 outputFile (buildProperties)
1255 // taking time specific comment out to allow better incremental builds
1256 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1257 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1258 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1259 property "VERSION", JALVIEW_VERSION
1260 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1261 if (getdownSetAppBaseProperty) {
1262 property "GETDOWNAPPBASE", getdownAppBase
1263 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1265 outputs.file(outputFile)
1269 task buildIndices(type: JavaExec) {
1271 classpath = sourceSets.main.compileClasspath
1272 main = "com.sun.java.help.search.Indexer"
1273 workingDir = "${helpBuildDir}/${help_dir}"
1276 inputs.dir("${workingDir}/${argDir}")
1278 outputs.dir("${classesDir}/doc")
1279 outputs.dir("${classesDir}/help")
1280 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1281 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1282 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1283 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1284 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1285 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1288 task buildResources {
1289 dependsOn copyResources
1290 dependsOn copyChannelResources
1291 dependsOn createBuildProperties
1295 dependsOn buildResources
1298 dependsOn convertMdFiles
1299 dependsOn buildIndices
1303 compileJava.dependsOn prepare
1304 run.dependsOn compileJava
1305 //run.dependsOn prepare
1308 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1313 dependsOn cloverClasses
1315 dependsOn compileJava //?
1319 includeGroups testng_groups
1320 excludeGroups testng_excluded_groups
1322 useDefaultListeners=true
1325 maxHeapSize = "1024m"
1327 workingDir = jalviewDir
1328 def testLaf = project.findProperty("test_laf")
1329 if (testLaf != null) {
1330 println("Setting Test LaF to '${testLaf}'")
1331 systemProperty "laf", testLaf
1333 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1334 if (testHiDPIScale != null) {
1335 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1336 systemProperty "sun.java2d.uiScale", testHiDPIScale
1338 sourceCompatibility = compile_source_compatibility
1339 targetCompatibility = compile_target_compatibility
1340 jvmArgs += additional_compiler_args
1344 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1350 task compileLinkCheck(type: JavaCompile) {
1352 classpath = files("${jalviewDir}/${utils_dir}")
1353 destinationDir = file("${jalviewDir}/${utils_dir}")
1354 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1356 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1357 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1358 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1359 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1363 task linkCheck(type: JavaExec) {
1365 dependsOn compileLinkCheck
1367 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1368 classpath = files("${jalviewDir}/${utils_dir}")
1369 main = "HelpLinksChecker"
1370 workingDir = jalviewDir
1371 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1373 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1374 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1377 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1381 inputs.dir(helpBuildDir)
1382 outputs.file(helpLinksCheckerOutFile)
1386 // import the pubhtmlhelp target
1387 ant.properties.basedir = "${jalviewDir}"
1388 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1389 ant.importBuild "${utils_dir}/publishHelp.xml"
1392 task cleanPackageDir(type: Delete) {
1394 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1404 attributes "Main-Class": main_class,
1405 "Permissions": "all-permissions",
1406 "Application-Name": install4jApplicationName,
1407 "Codebase": application_codebase,
1408 "Implementation-Version": JALVIEW_VERSION
1411 def outputDir = "${jalviewDir}/${package_dir}"
1412 destinationDirectory = file(outputDir)
1413 archiveFileName = rootProject.name+".jar"
1414 duplicatesStrategy "EXCLUDE"
1421 exclude "**/*.jar.*"
1423 inputs.dir(sourceSets.main.java.outputDir)
1424 sourceSets.main.resources.srcDirs.each{ dir ->
1427 outputs.file("${outputDir}/${archiveFileName}")
1431 task copyJars(type: Copy) {
1432 from fileTree(dir: classesDir, include: "**/*.jar").files
1433 into "${jalviewDir}/${package_dir}"
1437 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1438 task syncJars(type: Sync) {
1440 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1441 into "${jalviewDir}/${package_dir}"
1443 include jar.archiveFileName.getOrNull()
1450 description = "Put all required libraries in dist"
1451 // order of "cleanPackageDir", "copyJars", "jar" important!
1452 jar.mustRunAfter cleanPackageDir
1453 syncJars.mustRunAfter cleanPackageDir
1454 dependsOn cleanPackageDir
1457 outputs.dir("${jalviewDir}/${package_dir}")
1462 dependsOn cleanPackageDir
1469 group = "distribution"
1470 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1474 from ("${jalviewDir}/${libDistDir}") {
1478 attributes "Implementation-Version": JALVIEW_VERSION,
1479 "Application-Name": install4jApplicationName
1482 duplicatesStrategy "INCLUDE"
1484 mainClassName = shadow_jar_main_class
1486 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1491 task getdownWebsite() {
1492 group = "distribution"
1493 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1498 def getdownWebsiteResourceFilenames = []
1499 def getdownTextString = ""
1500 def getdownResourceDir = getdownResourceDir
1501 def getdownResourceFilenames = []
1504 // clean the getdown website and files dir before creating getdown folders
1505 delete getdownWebsiteDir
1506 delete getdownFilesDir
1509 from buildProperties
1510 rename(file(buildProperties).getName(), getdown_build_properties)
1513 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1516 from channelPropsFile
1517 into getdownWebsiteDir
1519 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
1521 // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
1522 def props = project.properties.sort { it.key }
1523 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1524 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1526 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1527 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1529 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1530 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1532 if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
1533 props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
1534 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
1535 props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
1536 props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
1537 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
1538 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
1541 props.put("getdown_txt_title", jalview_name)
1542 props.put("getdown_txt_ui.name", install4jApplicationName)
1544 // start with appbase
1545 getdownTextString += "appbase = ${getdownAppBase}\n"
1546 props.each{ prop, val ->
1547 if (prop.startsWith("getdown_txt_") && val != null) {
1548 if (prop.startsWith("getdown_txt_multi_")) {
1549 def key = prop.substring(18)
1550 val.split(",").each{ v ->
1551 def line = "${key} = ${v}\n"
1552 getdownTextString += line
1555 // file values rationalised
1556 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1558 if (val.indexOf('/') == 0) {
1561 } else if (val.indexOf('/') > 0) {
1562 // relative path (relative to jalviewDir)
1563 r = file( "${jalviewDir}/${val}" )
1566 val = "${getdown_resource_dir}/" + r.getName()
1567 getdownWebsiteResourceFilenames += val
1568 getdownResourceFilenames += r.getPath()
1571 if (! prop.startsWith("getdown_txt_resource")) {
1572 def line = prop.substring(12) + " = ${val}\n"
1573 getdownTextString += line
1579 getdownWebsiteResourceFilenames.each{ filename ->
1580 getdownTextString += "resource = ${filename}\n"
1582 getdownResourceFilenames.each{ filename ->
1585 into getdownResourceDir
1589 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
1590 getdownWrapperScripts.each{ script ->
1591 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
1595 into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
1597 getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
1602 fileTree(file(package_dir)).each{ f ->
1603 if (f.isDirectory()) {
1604 def files = fileTree(dir: f, include: ["*"]).getFiles()
1606 } else if (f.exists()) {
1610 def jalviewJar = jar.archiveFileName.getOrNull()
1611 // put jalview.jar first for CLASSPATH and .properties files reasons
1612 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
1613 def name = f.getName()
1614 def line = "code = ${getdownAppDistDir}/${name}\n"
1615 getdownTextString += line
1622 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1624 if (JAVA_VERSION.equals("11")) {
1625 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1626 j11libFiles.sort().each{f ->
1627 def name = f.getName()
1628 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1629 getdownTextString += line
1632 into getdownJ11libDir
1638 // 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.
1639 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1640 getdownTextString += "resource = ${getdown_launcher_new}\n"
1641 getdownTextString += "class = ${main_class}\n"
1642 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
1643 if (getdownSetAppBaseProperty) {
1644 getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
1645 getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
1648 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1649 getdown_txt.write(getdownTextString)
1651 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1652 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1653 launchJvl.write("appbase=${getdownAppBase}")
1655 // files going into the getdown website dir: getdown-launcher.jar
1657 from getdownLauncher
1658 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1659 into getdownWebsiteDir
1662 // files going into the getdown website dir: getdown-launcher(-local).jar
1664 from getdownLauncher
1665 if (file(getdownLauncher).getName() != getdown_launcher) {
1666 rename(file(getdownLauncher).getName(), getdown_launcher)
1668 into getdownWebsiteDir
1671 // files going into the getdown website dir: ./install dir and files
1672 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1675 from getdownLauncher
1676 from "${getdownAppDir}/${getdown_build_properties}"
1677 if (file(getdownLauncher).getName() != getdown_launcher) {
1678 rename(file(getdownLauncher).getName(), getdown_launcher)
1680 into getdownInstallDir
1683 // and make a copy in the getdown files dir (these are not downloaded by getdown)
1685 from getdownInstallDir
1686 into getdownFilesInstallDir
1690 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
1694 from getdownLauncher
1695 from "${getdownWebsiteDir}/${getdown_build_properties}"
1696 from "${getdownWebsiteDir}/${channel_props}"
1697 if (file(getdownLauncher).getName() != getdown_launcher) {
1698 rename(file(getdownLauncher).getName(), getdown_launcher)
1700 into getdownFilesDir
1703 // and ./resources (not all downloaded by getdown)
1705 from getdownResourceDir
1706 into "${getdownFilesDir}/${getdown_resource_dir}"
1711 inputs.dir("${jalviewDir}/${package_dir}")
1713 outputs.dir(getdownWebsiteDir)
1714 outputs.dir(getdownFilesDir)
1718 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1719 task getdownDigestDir(type: JavaExec) {
1721 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1723 def digestDirPropertyName = "DIGESTDIR"
1725 classpath = files(getdownLauncher)
1726 def digestDir = findProperty(digestDirPropertyName)
1727 if (digestDir == null) {
1728 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1732 main = "com.threerings.getdown.tools.Digester"
1736 task getdownDigest(type: JavaExec) {
1737 group = "distribution"
1738 description = "Digest the getdown website folder"
1739 dependsOn getdownWebsite
1741 classpath = files(getdownLauncher)
1743 main = "com.threerings.getdown.tools.Digester"
1744 args getdownWebsiteDir
1745 inputs.dir(getdownWebsiteDir)
1746 outputs.file("${getdownWebsiteDir}/digest2.txt")
1751 group = "distribution"
1752 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1753 dependsOn getdownDigest
1755 if (reportRsyncCommand) {
1756 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1757 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1758 println "LIKELY RSYNC COMMAND:"
1759 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1760 if (RUNRSYNC == "true") {
1762 commandLine "mkdir", "-p", toDir
1765 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1773 tasks.withType(JavaCompile) {
1774 options.encoding = 'UTF-8'
1780 delete getdownWebsiteDir
1781 delete getdownFilesDir
1787 if (file(install4jHomeDir).exists()) {
1789 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1790 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1791 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1792 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1794 installDir(file(install4jHomeDir))
1796 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1800 task copyInstall4jTemplate {
1801 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1802 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1803 inputs.file(install4jTemplateFile)
1804 inputs.file(install4jFileAssociationsFile)
1805 inputs.property("CHANNEL", { CHANNEL })
1806 outputs.file(install4jConfFile)
1809 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1811 // turn off code signing if no OSX_KEYPASS
1812 if (OSX_KEYPASS == "") {
1813 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1814 codeSigning.'@macEnabled' = "false"
1816 install4jConfigXml.'**'.windows.each { windows ->
1817 windows.'@runPostProcessor' = "false"
1821 // disable install screen for OSX dmg (for 2.11.2.0)
1822 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
1823 macosArchive.attributes().remove('executeSetupApp')
1824 macosArchive.attributes().remove('setupAppId')
1827 // turn off checksum creation for LOCAL channel
1828 def e = install4jConfigXml.application[0]
1829 if (CHANNEL == "LOCAL") {
1830 e.'@createChecksums' = "false"
1832 e.'@createChecksums' = "true"
1835 // put file association actions where placeholder action is
1836 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1837 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1838 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1839 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1840 def parent = a.parent()
1842 fileAssociationActions.each { faa ->
1845 // don't need to continue in .any loop once replacements have been made
1850 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1851 // NB we're deleting the /other/ one!
1852 // Also remove the examples subdir from non-release versions
1853 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1854 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1855 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1856 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1858 // remove the examples subdir from Full File Set
1859 def files = install4jConfigXml.files[0]
1860 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1861 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1862 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1863 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1864 dirEntry.parent().remove(dirEntry)
1866 install4jConfigXml.'**'.action.any { a ->
1867 if (a.'@customizedId' == customizedIdToDelete) {
1868 def parent = a.parent()
1874 // write install4j file
1875 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1882 delete install4jConfFile
1887 task installers(type: com.install4j.gradle.Install4jTask) {
1888 group = "distribution"
1889 description = "Create the install4j installers"
1891 dependsOn copyInstall4jTemplate
1893 projectFile = install4jConfFile
1895 // create an md5 for the input files to use as version for install4j conf file
1896 def digest = MessageDigest.getInstance("MD5")
1898 (file("${install4jDir}/${install4j_template}").text +
1899 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1900 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1901 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1902 if (filesMd5.length() >= 8) {
1903 filesMd5 = filesMd5.substring(0,8)
1905 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1906 // make install4jBuildDir relative to jalviewDir
1907 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1910 'JALVIEW_NAME': jalview_name,
1911 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1912 'JALVIEW_DIR': "../..",
1913 'OSX_KEYSTORE': OSX_KEYSTORE,
1914 'OSX_APPLEID': OSX_APPLEID,
1915 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
1916 'JSIGN_SH': JSIGN_SH,
1917 'JRE_DIR': getdown_app_dir_java,
1918 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1919 'JALVIEW_VERSION': JALVIEW_VERSION,
1920 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1921 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1922 'JAVA_VERSION': JAVA_VERSION,
1923 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1924 'VERSION': JALVIEW_VERSION,
1925 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1926 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1927 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1928 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1929 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1930 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1931 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1932 'BUNDLE_ID': install4jBundleId,
1933 'INTERNAL_ID': install4jInternalId,
1934 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1935 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
1936 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1937 'WRAPPER_LINK': getdownWrapperLink,
1938 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
1939 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
1940 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
1941 'INSTALLER_NAME': install4jInstallerName,
1942 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1943 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1944 'GETDOWN_FILES_DIR': getdown_files_dir,
1945 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1946 'GETDOWN_DIST_DIR': getdownAppDistDir,
1947 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1948 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1949 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1950 'BUILD_DIR': install4jBuildDir,
1951 'APPLICATION_CATEGORIES': install4j_application_categories,
1952 'APPLICATION_FOLDER': install4jApplicationFolder,
1953 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1954 'EXECUTABLE_NAME': install4jExecutableName,
1955 'EXTRA_SCHEME': install4jExtraScheme,
1956 'MAC_ICONS_FILE': install4jMacIconsFile,
1957 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
1958 'PNG_ICON_FILE': install4jPngIconFile,
1959 'BACKGROUND': install4jBackground,
1963 //println("INSTALL4J VARIABLES:")
1964 //variables.each{k,v->println("${k}=${v}")}
1966 destination = "${jalviewDir}/${install4jBuildDir}"
1967 buildSelected = true
1969 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1971 disableSigning = true
1972 disableNotarization = true
1976 macKeystorePassword = OSX_KEYPASS
1979 if (OSX_ALTOOLPASS) {
1980 appleIdPassword = OSX_ALTOOLPASS
1981 disableNotarization = false
1983 disableNotarization = true
1987 println("Using projectFile "+projectFile)
1988 if (!disableNotarization) { println("Will notarize OSX App DMG") }
1992 inputs.dir(getdownWebsiteDir)
1993 inputs.file(install4jConfFile)
1994 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1995 inputs.dir(macosJavaVMDir)
1996 inputs.dir(windowsJavaVMDir)
1997 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2003 eclipse().configFile(eclipse_codestyle_file)
2008 task sourceDist(type: Tar) {
2009 group "distribution"
2010 description "Create a source .tar.gz file for distribution"
2012 dependsOn createBuildProperties
2013 dependsOn convertMdFiles
2015 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
2016 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
2017 archiveFileName = outputFileName
2019 compression Compression.GZIP
2034 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2036 "utils/InstallAnywhere",
2051 "gradle.properties",
2062 ".settings/org.eclipse.jdt.core.jalview.prefs",
2066 exclude (EXCLUDE_FILES)
2067 include (PROCESS_FILES)
2068 filter(ReplaceTokens,
2072 'Version-Rel': JALVIEW_VERSION,
2073 'Year-Rel': getDate("yyyy")
2078 exclude (EXCLUDE_FILES)
2079 exclude (PROCESS_FILES)
2080 exclude ("appletlib")
2081 exclude ("**/*locales")
2082 exclude ("*locales/**")
2083 exclude ("utils/InstallAnywhere")
2085 exclude (getdown_files_dir)
2086 exclude (getdown_website_dir)
2088 // exluding these as not using jars as modules yet
2089 exclude ("${j11modDir}/**/*.jar")
2092 include(INCLUDE_FILES)
2094 // from (jalviewDir) {
2095 // // explicit includes for stuff that seemed to not get included
2096 // include(fileTree("test/**/*."))
2097 // exclude(EXCLUDE_FILES)
2098 // exclude(PROCESS_FILES)
2101 from(file(buildProperties).getParent()) {
2102 include(file(buildProperties).getName())
2103 rename(file(buildProperties).getName(), "build_properties")
2105 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2114 dependsOn pubhtmlhelp
2116 inputs.dir("${helpBuildDir}/${help_dir}")
2117 outputs.dir("${buildDir}/distributions/${help_dir}")
2121 task j2sSetHeadlessBuild {
2128 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2130 description "Enable the alternative J2S Config file for headless build"
2132 outputFile = jalviewjsJ2sSettingsFileName
2133 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2134 def j2sProps = new Properties()
2135 if (j2sPropsFile.exists()) {
2137 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2138 j2sProps.load(j2sPropsFileFIS)
2139 j2sPropsFileFIS.close()
2141 j2sProps.each { prop, val ->
2144 } catch (Exception e) {
2145 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2149 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2150 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2155 task jalviewjsSetEclipseWorkspace {
2156 def propKey = "jalviewjs_eclipse_workspace"
2158 if (project.hasProperty(propKey)) {
2159 propVal = project.getProperty(propKey)
2160 if (propVal.startsWith("~/")) {
2161 propVal = System.getProperty("user.home") + propVal.substring(1)
2164 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2165 def propsFile = file(propsFileName)
2166 def eclipseWsDir = propVal
2167 def props = new Properties()
2169 def writeProps = true
2170 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2171 def ins = new FileInputStream(propsFileName)
2174 if (props.getProperty(propKey, null) != null) {
2175 eclipseWsDir = props.getProperty(propKey)
2180 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2181 def tempDir = File.createTempDir()
2182 eclipseWsDir = tempDir.getAbsolutePath()
2185 eclipseWorkspace = file(eclipseWsDir)
2188 // do not run a headless transpile when we claim to be in Eclipse
2190 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2191 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2193 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2197 props.setProperty(propKey, eclipseWsDir)
2198 propsFile.parentFile.mkdirs()
2199 def bytes = new ByteArrayOutputStream()
2200 props.store(bytes, null)
2201 def propertiesString = bytes.toString()
2202 propsFile.text = propertiesString
2208 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2211 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2212 outputs.file(propsFileName)
2213 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2217 task jalviewjsEclipsePaths {
2220 def eclipseRoot = jalviewjs_eclipse_root
2221 if (eclipseRoot.startsWith("~/")) {
2222 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2224 if (OperatingSystem.current().isMacOsX()) {
2225 eclipseRoot += "/Eclipse.app"
2226 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2227 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2228 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2229 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2230 eclipseRoot += "/eclipse"
2232 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2233 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2234 } else { // linux or unix
2235 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2236 eclipseRoot += "/eclipse"
2237 println("eclipseDir exists")
2239 eclipseBinary = "${eclipseRoot}/eclipse"
2240 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2243 eclipseVersion = "4.13" // default
2244 def assumedVersion = true
2245 if (file(eclipseProduct).exists()) {
2246 def fis = new FileInputStream(eclipseProduct)
2247 def props = new Properties()
2249 eclipseVersion = props.getProperty("version")
2251 assumedVersion = false
2254 def propKey = "eclipse_debug"
2255 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2258 // do not run a headless transpile when we claim to be in Eclipse
2260 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2261 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2263 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2266 if (!assumedVersion) {
2267 println("ECLIPSE VERSION=${eclipseVersion}")
2273 task printProperties {
2275 description "Output to console all System.properties"
2277 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2283 dependsOn eclipseProject
2284 dependsOn eclipseClasspath
2285 dependsOn eclipseJdt
2289 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2290 task jalviewjsEclipseCopyDropins(type: Copy) {
2291 dependsOn jalviewjsEclipsePaths
2293 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2294 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2295 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2302 // this eclipse -clean doesn't actually work
2303 task jalviewjsCleanEclipse(type: Exec) {
2304 dependsOn eclipseSetup
2305 dependsOn jalviewjsEclipsePaths
2306 dependsOn jalviewjsEclipseCopyDropins
2308 executable(eclipseBinary)
2309 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2315 def inputString = """exit
2318 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2319 standardInput = inputByteStream
2322 /* not really working yet
2323 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2327 task jalviewjsTransferUnzipSwingJs {
2328 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2332 from zipTree(file_zip)
2333 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2337 inputs.file file_zip
2338 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2342 task jalviewjsTransferUnzipLib {
2343 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2346 zipFiles.each { file_zip ->
2348 from zipTree(file_zip)
2349 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2354 inputs.files zipFiles
2355 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2359 task jalviewjsTransferUnzipAllLibs {
2360 dependsOn jalviewjsTransferUnzipSwingJs
2361 dependsOn jalviewjsTransferUnzipLib
2365 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2367 description "Create the alternative j2s file from the j2s.* properties"
2369 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2370 def siteDirProperty = "j2s.site.directory"
2371 def setSiteDir = false
2372 jalviewjsJ2sProps.each { prop, val ->
2374 if (prop == siteDirProperty) {
2375 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2376 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2382 if (!setSiteDir) { // default site location, don't override specifically set property
2383 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2386 outputFile = jalviewjsJ2sAltSettingsFileName
2389 inputs.properties(jalviewjsJ2sProps)
2390 outputs.file(jalviewjsJ2sAltSettingsFileName)
2395 task jalviewjsEclipseSetup {
2396 dependsOn jalviewjsEclipseCopyDropins
2397 dependsOn jalviewjsSetEclipseWorkspace
2398 dependsOn jalviewjsCreateJ2sSettings
2402 task jalviewjsSyncAllLibs (type: Sync) {
2403 dependsOn jalviewjsTransferUnzipAllLibs
2404 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2405 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2406 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2410 def outputFiles = []
2411 rename { filename ->
2412 outputFiles += "${outputDir}/${filename}"
2419 // should this be exclude really ?
2420 duplicatesStrategy "INCLUDE"
2422 outputs.files outputFiles
2423 inputs.files inputFiles
2427 task jalviewjsSyncResources (type: Sync) {
2428 dependsOn buildResources
2430 def inputFiles = fileTree(dir: resourcesBuildDir)
2431 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2435 def outputFiles = []
2436 rename { filename ->
2437 outputFiles += "${outputDir}/${filename}"
2443 outputs.files outputFiles
2444 inputs.files inputFiles
2448 task jalviewjsSyncSiteResources (type: Sync) {
2449 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2450 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2454 def outputFiles = []
2455 rename { filename ->
2456 outputFiles += "${outputDir}/${filename}"
2462 outputs.files outputFiles
2463 inputs.files inputFiles
2467 task jalviewjsSyncBuildProperties (type: Sync) {
2468 dependsOn createBuildProperties
2469 def inputFiles = [file(buildProperties)]
2470 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2474 def outputFiles = []
2475 rename { filename ->
2476 outputFiles += "${outputDir}/${filename}"
2482 outputs.files outputFiles
2483 inputs.files inputFiles
2487 task jalviewjsProjectImport(type: Exec) {
2488 dependsOn eclipseSetup
2489 dependsOn jalviewjsEclipsePaths
2490 dependsOn jalviewjsEclipseSetup
2493 // do not run a headless import when we claim to be in Eclipse
2495 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2496 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2498 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2502 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2503 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2504 executable(eclipseBinary)
2505 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2509 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2511 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2512 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2515 inputs.file("${jalviewDir}/.project")
2516 outputs.upToDateWhen {
2517 file(projdir).exists()
2522 task jalviewjsTranspile(type: Exec) {
2523 dependsOn jalviewjsEclipseSetup
2524 dependsOn jalviewjsProjectImport
2525 dependsOn jalviewjsEclipsePaths
2527 dependsOn jalviewjsEnableAltFileProperty
2531 // do not run a headless transpile when we claim to be in Eclipse
2533 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2534 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2536 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2540 executable(eclipseBinary)
2541 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2545 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2547 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2548 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2554 stdout = new ByteArrayOutputStream()
2555 stderr = new ByteArrayOutputStream()
2557 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2558 def logOutFile = file(logOutFileName)
2559 logOutFile.createNewFile()
2560 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2561 BINARY: ${eclipseBinary}
2562 VERSION: ${eclipseVersion}
2563 WORKSPACE: ${eclipseWorkspace}
2564 DEBUG: ${eclipseDebug}
2567 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2568 // combine stdout and stderr
2569 def logErrFOS = logOutFOS
2571 if (jalviewjs_j2s_to_console.equals("true")) {
2572 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2573 new org.apache.tools.ant.util.TeeOutputStream(
2577 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2578 new org.apache.tools.ant.util.TeeOutputStream(
2583 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2586 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2593 if (stdout.toString().contains("Error processing ")) {
2594 // j2s did not complete transpile
2595 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2596 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2597 println("IGNORING TRANSPILE ERRORS")
2598 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2600 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2605 inputs.dir("${jalviewDir}/${sourceDir}")
2606 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2607 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2611 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2613 def stdout = new ByteArrayOutputStream()
2614 def stderr = new ByteArrayOutputStream()
2616 def coreFile = file(jsfile)
2618 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2620 logOutFile.createNewFile()
2621 logOutFile.append(msg+"\n")
2623 def coreTop = file(prefixFile)
2624 def coreBottom = file(suffixFile)
2625 coreFile.getParentFile().mkdirs()
2626 coreFile.createNewFile()
2627 coreFile.write( coreTop.getText("UTF-8") )
2631 def t = f.getText("UTF-8")
2632 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2633 coreFile.append( t )
2635 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2637 logOutFile.append(msg+"\n")
2640 coreFile.append( coreBottom.getText("UTF-8") )
2642 msg = "Generating ${zjsfile}"
2644 logOutFile.append(msg+"\n")
2645 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2646 def logErrFOS = logOutFOS
2649 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2650 main = "com.google.javascript.jscomp.CommandLineRunner"
2651 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2652 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2655 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2657 logOutFile.append(msg+"\n")
2659 if (logOutConsole) {
2660 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2661 new org.apache.tools.ant.util.TeeOutputStream(
2665 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2666 new org.apache.tools.ant.util.TeeOutputStream(
2671 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2674 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2681 logOutFile.append(msg+"\n")
2685 task jalviewjsBuildAllCores {
2687 description "Build the core js lib closures listed in the classlists dir"
2688 dependsOn jalviewjsTranspile
2689 dependsOn jalviewjsTransferUnzipSwingJs
2691 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2692 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2693 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2694 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2695 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2696 def prefixFile = "${jsDir}/core/coretop2.js"
2697 def suffixFile = "${jsDir}/core/corebottom2.js"
2699 inputs.file prefixFile
2700 inputs.file suffixFile
2702 def classlistFiles = []
2703 // add the classlists found int the jalviewjs_classlists_dir
2704 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2706 def name = file.getName() - ".txt"
2713 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2714 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2715 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2717 jalviewjsCoreClasslists = []
2719 classlistFiles.each {
2722 def file = hash['file']
2723 if (! file.exists()) {
2724 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2725 return false // this is a "continue" in groovy .each closure
2727 def name = hash['name']
2729 name = file.getName() - ".txt"
2737 def list = fileTree(dir: j2sDir, includes: filelist)
2739 def jsfile = "${outputDir}/core${name}.js"
2740 def zjsfile = "${outputDir}/core${name}.z.js"
2742 jalviewjsCoreClasslists += [
2751 outputs.file(jsfile)
2752 outputs.file(zjsfile)
2755 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2756 def stevesoftClasslistName = "_stevesoft"
2757 def stevesoftClasslist = [
2758 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2759 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2760 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2761 'name': stevesoftClasslistName
2763 jalviewjsCoreClasslists += stevesoftClasslist
2764 inputs.files(stevesoftClasslist['list'])
2765 outputs.file(stevesoftClasslist['jsfile'])
2766 outputs.file(stevesoftClasslist['zjsfile'])
2769 def allClasslistName = "_all"
2770 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2771 allJsFiles += fileTree(
2775 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2776 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2777 "**/org/jmol/export/JSExporter.js"
2780 allJsFiles += fileTree(
2784 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2785 "**/sun/misc/Unsafe.js",
2786 "**/swingjs/jquery/jquery-editable-select.js",
2787 "**/swingjs/jquery/j2sComboBox.js",
2788 "**/sun/misc/FloatingDecimal.js"
2791 def allClasslist = [
2792 'jsfile': "${outputDir}/core${allClasslistName}.js",
2793 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2795 'name': allClasslistName
2797 // not including this version of "all" core at the moment
2798 //jalviewjsCoreClasslists += allClasslist
2799 inputs.files(allClasslist['list'])
2800 outputs.file(allClasslist['jsfile'])
2801 outputs.file(allClasslist['zjsfile'])
2804 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2805 logOutFile.getParentFile().mkdirs()
2806 logOutFile.createNewFile()
2807 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2809 jalviewjsCoreClasslists.each {
2810 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2817 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2820 into file(outputFile).getParentFile()
2821 rename { filename ->
2822 if (filename.equals(inputFile.getName())) {
2823 return file(outputFile).getName()
2827 filter(ReplaceTokens,
2831 'MAIN': '"'+main_class+'"',
2833 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2834 'COREKEY': jalviewjs_core_key,
2835 'CORENAME': coreName
2842 task jalviewjsPublishCoreTemplates {
2843 dependsOn jalviewjsBuildAllCores
2844 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2845 def inputFile = file(inputFileName)
2846 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2848 def outputFiles = []
2849 jalviewjsCoreClasslists.each { cl ->
2850 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2851 cl['outputfile'] = outputFile
2852 outputFiles += outputFile
2856 jalviewjsCoreClasslists.each { cl ->
2857 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2860 inputs.file(inputFile)
2861 outputs.files(outputFiles)
2865 task jalviewjsSyncCore (type: Sync) {
2866 dependsOn jalviewjsBuildAllCores
2867 dependsOn jalviewjsPublishCoreTemplates
2868 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2869 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2873 def outputFiles = []
2874 rename { filename ->
2875 outputFiles += "${outputDir}/${filename}"
2881 outputs.files outputFiles
2882 inputs.files inputFiles
2886 // this Copy version of TransferSiteJs will delete anything else in the target dir
2887 task jalviewjsCopyTransferSiteJs(type: Copy) {
2888 dependsOn jalviewjsTranspile
2889 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2890 into "${jalviewDir}/${jalviewjsSiteDir}"
2894 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2895 task jalviewjsSyncTransferSiteJs(type: Sync) {
2896 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2898 into "${jalviewDir}/${jalviewjsSiteDir}"
2905 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2906 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2907 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2908 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2910 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2911 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2912 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2913 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2916 task jalviewjsPrepareSite {
2918 description "Prepares the website folder including unzipping files and copying resources"
2919 dependsOn jalviewjsSyncAllLibs
2920 dependsOn jalviewjsSyncResources
2921 dependsOn jalviewjsSyncSiteResources
2922 dependsOn jalviewjsSyncBuildProperties
2923 dependsOn jalviewjsSyncCore
2927 task jalviewjsBuildSite {
2929 description "Builds the whole website including transpiled code"
2930 dependsOn jalviewjsCopyTransferSiteJs
2931 dependsOn jalviewjsPrepareSite
2935 task cleanJalviewjsTransferSite {
2937 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2938 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2939 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2940 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2945 task cleanJalviewjsSite {
2946 dependsOn cleanJalviewjsTransferSite
2948 delete "${jalviewDir}/${jalviewjsSiteDir}"
2953 task jalviewjsSiteTar(type: Tar) {
2955 description "Creates a tar.gz file for the website"
2956 dependsOn jalviewjsBuildSite
2957 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2958 archiveFileName = outputFilename
2960 compression Compression.GZIP
2962 from "${jalviewDir}/${jalviewjsSiteDir}"
2963 into jalviewjs_site_dir // this is inside the tar file
2965 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
2969 task jalviewjsServer {
2971 def filename = "jalviewjsTest.html"
2972 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
2973 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
2978 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
2979 factory = f.newInstance()
2980 } catch (ClassNotFoundException e) {
2981 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
2983 def port = Integer.valueOf(jalviewjs_server_port)
2988 while(port < start+1000 && !running) {
2990 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
2991 jalviewjsServer = factory.start(doc_root, port)
2993 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
2994 println("SERVER STARTED with document root ${doc_root}.")
2995 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
2996 println("For debug: "+url+"?j2sdebug")
2997 println("For verbose: "+url+"?j2sverbose")
2998 } catch (Exception e) {
3003 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3004 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3005 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3007 jalviewjsCoreClasslists.each { cl ->
3008 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3010 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3012 println("For core ${cl.name}: "+urlcore)
3015 file(htmlFile).text = htmlText
3018 outputs.file(htmlFile)
3019 outputs.upToDateWhen({false})
3023 task cleanJalviewjsAll {
3025 description "Delete all configuration and build artifacts to do with JalviewJS build"
3026 dependsOn cleanJalviewjsSite
3027 dependsOn jalviewjsEclipsePaths
3030 delete "${jalviewDir}/${jalviewjsBuildDir}"
3031 delete "${jalviewDir}/${eclipse_bin_dir}"
3032 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3033 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3035 delete jalviewjsJ2sAltSettingsFileName
3038 outputs.upToDateWhen( { false } )
3042 task jalviewjsIDE_checkJ2sPlugin {
3043 group "00 JalviewJS in Eclipse"
3044 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3047 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3048 def j2sPluginFile = file(j2sPlugin)
3049 def eclipseHome = System.properties["eclipse.home.location"]
3050 if (eclipseHome == null || ! IN_ECLIPSE) {
3051 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3053 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3054 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3055 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3056 eclipseJ2sPluginDirs += altPluginsDir
3058 def foundPlugin = false
3059 def j2sPluginFileName = j2sPluginFile.getName()
3060 def eclipseJ2sPlugin
3061 def eclipseJ2sPluginFile
3062 eclipseJ2sPluginDirs.any { dir ->
3063 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3064 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3065 if (eclipseJ2sPluginFile.exists()) {
3071 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3072 System.err.println(msg)
3073 throw new StopExecutionException(msg)
3076 def digest = MessageDigest.getInstance("MD5")
3078 digest.update(j2sPluginFile.text.bytes)
3079 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3081 digest.update(eclipseJ2sPluginFile.text.bytes)
3082 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3084 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3085 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3086 System.err.println(msg)
3087 throw new StopExecutionException(msg)
3089 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3095 task jalviewjsIDE_copyJ2sPlugin {
3096 group "00 JalviewJS in Eclipse"
3097 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3100 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3101 def j2sPluginFile = file(j2sPlugin)
3102 def eclipseHome = System.properties["eclipse.home.location"]
3103 if (eclipseHome == null || ! IN_ECLIPSE) {
3104 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3106 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3107 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3108 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3109 System.err.println(msg)
3112 eclipseJ2sPluginFile.getParentFile().mkdirs()
3113 into eclipseJ2sPluginFile.getParent()
3119 task jalviewjsIDE_j2sFile {
3120 group "00 JalviewJS in Eclipse"
3121 description "Creates the .j2s file"
3122 dependsOn jalviewjsCreateJ2sSettings
3126 task jalviewjsIDE_SyncCore {
3127 group "00 JalviewJS in Eclipse"
3128 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3129 dependsOn jalviewjsSyncCore
3133 task jalviewjsIDE_SyncSiteAll {
3134 dependsOn jalviewjsSyncAllLibs
3135 dependsOn jalviewjsSyncResources
3136 dependsOn jalviewjsSyncSiteResources
3137 dependsOn jalviewjsSyncBuildProperties
3141 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3144 task jalviewjsIDE_PrepareSite {
3145 group "00 JalviewJS in Eclipse"
3146 description "Sync libs and resources to site dir, but not closure cores"
3148 dependsOn jalviewjsIDE_SyncSiteAll
3149 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3153 task jalviewjsIDE_AssembleSite {
3154 group "00 JalviewJS in Eclipse"
3155 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3156 dependsOn jalviewjsPrepareSite
3160 task jalviewjsIDE_SiteClean {
3161 group "00 JalviewJS in Eclipse"
3162 description "Deletes the Eclipse transpiled site"
3163 dependsOn cleanJalviewjsSite
3167 task jalviewjsIDE_Server {
3168 group "00 JalviewJS in Eclipse"
3169 description "Starts a webserver on localhost to test the website"
3170 dependsOn jalviewjsServer
3174 // buildship runs this at import or gradle refresh
3175 task eclipseSynchronizationTask {
3176 //dependsOn eclipseSetup
3177 dependsOn createBuildProperties
3179 dependsOn jalviewjsIDE_j2sFile
3180 dependsOn jalviewjsIDE_checkJ2sPlugin
3181 dependsOn jalviewjsIDE_PrepareSite
3186 // buildship runs this at build time or project refresh
3187 task eclipseAutoBuildTask {
3188 //dependsOn jalviewjsIDE_checkJ2sPlugin
3189 //dependsOn jalviewjsIDE_PrepareSite
3195 description "Build the site"
3196 dependsOn jalviewjsBuildSite