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 codeFiles.sort().each{f ->
1611 def name = f.getName()
1612 def line = "code = ${getdownAppDistDir}/${name}\n"
1613 getdownTextString += line
1620 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1622 if (JAVA_VERSION.equals("11")) {
1623 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1624 j11libFiles.sort().each{f ->
1625 def name = f.getName()
1626 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1627 getdownTextString += line
1630 into getdownJ11libDir
1636 // 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.
1637 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1638 getdownTextString += "resource = ${getdown_launcher_new}\n"
1639 getdownTextString += "class = ${main_class}\n"
1640 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
1641 if (getdownSetAppBaseProperty) {
1642 getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
1643 getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
1646 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1647 getdown_txt.write(getdownTextString)
1649 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1650 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1651 launchJvl.write("appbase=${getdownAppBase}")
1653 // files going into the getdown website dir: getdown-launcher.jar
1655 from getdownLauncher
1656 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1657 into getdownWebsiteDir
1660 // files going into the getdown website dir: getdown-launcher(-local).jar
1662 from getdownLauncher
1663 if (file(getdownLauncher).getName() != getdown_launcher) {
1664 rename(file(getdownLauncher).getName(), getdown_launcher)
1666 into getdownWebsiteDir
1669 // files going into the getdown website dir: ./install dir and files
1670 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1673 from getdownLauncher
1674 from "${getdownAppDir}/${getdown_build_properties}"
1675 if (file(getdownLauncher).getName() != getdown_launcher) {
1676 rename(file(getdownLauncher).getName(), getdown_launcher)
1678 into getdownInstallDir
1681 // and make a copy in the getdown files dir (these are not downloaded by getdown)
1683 from getdownInstallDir
1684 into getdownFilesInstallDir
1688 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
1692 from getdownLauncher
1693 from "${getdownWebsiteDir}/${getdown_build_properties}"
1694 from "${getdownWebsiteDir}/${channel_props}"
1695 if (file(getdownLauncher).getName() != getdown_launcher) {
1696 rename(file(getdownLauncher).getName(), getdown_launcher)
1698 into getdownFilesDir
1701 // and ./resources (not all downloaded by getdown)
1703 from getdownResourceDir
1704 into "${getdownFilesDir}/${getdown_resource_dir}"
1709 inputs.dir("${jalviewDir}/${package_dir}")
1711 outputs.dir(getdownWebsiteDir)
1712 outputs.dir(getdownFilesDir)
1716 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1717 task getdownDigestDir(type: JavaExec) {
1719 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1721 def digestDirPropertyName = "DIGESTDIR"
1723 classpath = files(getdownLauncher)
1724 def digestDir = findProperty(digestDirPropertyName)
1725 if (digestDir == null) {
1726 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1730 main = "com.threerings.getdown.tools.Digester"
1734 task getdownDigest(type: JavaExec) {
1735 group = "distribution"
1736 description = "Digest the getdown website folder"
1737 dependsOn getdownWebsite
1739 classpath = files(getdownLauncher)
1741 main = "com.threerings.getdown.tools.Digester"
1742 args getdownWebsiteDir
1743 inputs.dir(getdownWebsiteDir)
1744 outputs.file("${getdownWebsiteDir}/digest2.txt")
1749 group = "distribution"
1750 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1751 dependsOn getdownDigest
1753 if (reportRsyncCommand) {
1754 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1755 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1756 println "LIKELY RSYNC COMMAND:"
1757 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1758 if (RUNRSYNC == "true") {
1760 commandLine "mkdir", "-p", toDir
1763 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1771 tasks.withType(JavaCompile) {
1772 options.encoding = 'UTF-8'
1778 delete getdownWebsiteDir
1779 delete getdownFilesDir
1785 if (file(install4jHomeDir).exists()) {
1787 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1788 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1789 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1790 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1792 installDir(file(install4jHomeDir))
1794 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1798 task copyInstall4jTemplate {
1799 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1800 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1801 inputs.file(install4jTemplateFile)
1802 inputs.file(install4jFileAssociationsFile)
1803 inputs.property("CHANNEL", { CHANNEL })
1804 outputs.file(install4jConfFile)
1807 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1809 // turn off code signing if no OSX_KEYPASS
1810 if (OSX_KEYPASS == "") {
1811 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1812 codeSigning.'@macEnabled' = "false"
1814 install4jConfigXml.'**'.windows.each { windows ->
1815 windows.'@runPostProcessor' = "false"
1819 // disable install screen for OSX dmg (for 2.11.2.0)
1820 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
1821 macosArchive.attributes().remove('executeSetupApp')
1822 macosArchive.attributes().remove('setupAppId')
1825 // turn off checksum creation for LOCAL channel
1826 def e = install4jConfigXml.application[0]
1827 if (CHANNEL == "LOCAL") {
1828 e.'@createChecksums' = "false"
1830 e.'@createChecksums' = "true"
1833 // put file association actions where placeholder action is
1834 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1835 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1836 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1837 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1838 def parent = a.parent()
1840 fileAssociationActions.each { faa ->
1843 // don't need to continue in .any loop once replacements have been made
1848 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1849 // NB we're deleting the /other/ one!
1850 // Also remove the examples subdir from non-release versions
1851 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1852 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1853 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1854 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1856 // remove the examples subdir from Full File Set
1857 def files = install4jConfigXml.files[0]
1858 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1859 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1860 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1861 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1862 dirEntry.parent().remove(dirEntry)
1864 install4jConfigXml.'**'.action.any { a ->
1865 if (a.'@customizedId' == customizedIdToDelete) {
1866 def parent = a.parent()
1872 // write install4j file
1873 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1880 delete install4jConfFile
1885 task installers(type: com.install4j.gradle.Install4jTask) {
1886 group = "distribution"
1887 description = "Create the install4j installers"
1889 dependsOn copyInstall4jTemplate
1891 projectFile = install4jConfFile
1893 // create an md5 for the input files to use as version for install4j conf file
1894 def digest = MessageDigest.getInstance("MD5")
1896 (file("${install4jDir}/${install4j_template}").text +
1897 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1898 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1899 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1900 if (filesMd5.length() >= 8) {
1901 filesMd5 = filesMd5.substring(0,8)
1903 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1904 // make install4jBuildDir relative to jalviewDir
1905 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1908 'JALVIEW_NAME': jalview_name,
1909 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1910 'JALVIEW_DIR': "../..",
1911 'OSX_KEYSTORE': OSX_KEYSTORE,
1912 'OSX_APPLEID': OSX_APPLEID,
1913 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
1914 'JSIGN_SH': JSIGN_SH,
1915 'JRE_DIR': getdown_app_dir_java,
1916 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1917 'JALVIEW_VERSION': JALVIEW_VERSION,
1918 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1919 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1920 'JAVA_VERSION': JAVA_VERSION,
1921 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1922 'VERSION': JALVIEW_VERSION,
1923 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1924 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1925 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1926 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1927 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1928 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1929 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1930 'BUNDLE_ID': install4jBundleId,
1931 'INTERNAL_ID': install4jInternalId,
1932 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1933 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
1934 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1935 'WRAPPER_LINK': getdownWrapperLink,
1936 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
1937 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
1938 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
1939 'INSTALLER_NAME': install4jInstallerName,
1940 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1941 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1942 'GETDOWN_FILES_DIR': getdown_files_dir,
1943 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1944 'GETDOWN_DIST_DIR': getdownAppDistDir,
1945 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1946 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1947 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1948 'BUILD_DIR': install4jBuildDir,
1949 'APPLICATION_CATEGORIES': install4j_application_categories,
1950 'APPLICATION_FOLDER': install4jApplicationFolder,
1951 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1952 'EXECUTABLE_NAME': install4jExecutableName,
1953 'EXTRA_SCHEME': install4jExtraScheme,
1954 'MAC_ICONS_FILE': install4jMacIconsFile,
1955 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
1956 'PNG_ICON_FILE': install4jPngIconFile,
1957 'BACKGROUND': install4jBackground,
1961 //println("INSTALL4J VARIABLES:")
1962 //variables.each{k,v->println("${k}=${v}")}
1964 destination = "${jalviewDir}/${install4jBuildDir}"
1965 buildSelected = true
1967 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1969 disableSigning = true
1970 disableNotarization = true
1974 macKeystorePassword = OSX_KEYPASS
1977 if (OSX_ALTOOLPASS) {
1978 appleIdPassword = OSX_ALTOOLPASS
1979 disableNotarization = false
1981 disableNotarization = true
1985 println("Using projectFile "+projectFile)
1986 if (!disableNotarization) { println("Will notarize OSX App DMG") }
1990 inputs.dir(getdownWebsiteDir)
1991 inputs.file(install4jConfFile)
1992 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1993 inputs.dir(macosJavaVMDir)
1994 inputs.dir(windowsJavaVMDir)
1995 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2001 eclipse().configFile(eclipse_codestyle_file)
2006 task sourceDist(type: Tar) {
2007 group "distribution"
2008 description "Create a source .tar.gz file for distribution"
2010 dependsOn createBuildProperties
2011 dependsOn convertMdFiles
2013 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
2014 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
2015 archiveFileName = outputFileName
2017 compression Compression.GZIP
2032 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2034 "utils/InstallAnywhere",
2049 "gradle.properties",
2060 ".settings/org.eclipse.jdt.core.jalview.prefs",
2064 exclude (EXCLUDE_FILES)
2065 include (PROCESS_FILES)
2066 filter(ReplaceTokens,
2070 'Version-Rel': JALVIEW_VERSION,
2071 'Year-Rel': getDate("yyyy")
2076 exclude (EXCLUDE_FILES)
2077 exclude (PROCESS_FILES)
2078 exclude ("appletlib")
2079 exclude ("**/*locales")
2080 exclude ("*locales/**")
2081 exclude ("utils/InstallAnywhere")
2083 exclude (getdown_files_dir)
2084 exclude (getdown_website_dir)
2086 // exluding these as not using jars as modules yet
2087 exclude ("${j11modDir}/**/*.jar")
2090 include(INCLUDE_FILES)
2092 // from (jalviewDir) {
2093 // // explicit includes for stuff that seemed to not get included
2094 // include(fileTree("test/**/*."))
2095 // exclude(EXCLUDE_FILES)
2096 // exclude(PROCESS_FILES)
2099 from(file(buildProperties).getParent()) {
2100 include(file(buildProperties).getName())
2101 rename(file(buildProperties).getName(), "build_properties")
2103 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2112 dependsOn pubhtmlhelp
2114 inputs.dir("${helpBuildDir}/${help_dir}")
2115 outputs.dir("${buildDir}/distributions/${help_dir}")
2119 task j2sSetHeadlessBuild {
2126 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2128 description "Enable the alternative J2S Config file for headless build"
2130 outputFile = jalviewjsJ2sSettingsFileName
2131 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2132 def j2sProps = new Properties()
2133 if (j2sPropsFile.exists()) {
2135 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2136 j2sProps.load(j2sPropsFileFIS)
2137 j2sPropsFileFIS.close()
2139 j2sProps.each { prop, val ->
2142 } catch (Exception e) {
2143 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2147 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2148 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2153 task jalviewjsSetEclipseWorkspace {
2154 def propKey = "jalviewjs_eclipse_workspace"
2156 if (project.hasProperty(propKey)) {
2157 propVal = project.getProperty(propKey)
2158 if (propVal.startsWith("~/")) {
2159 propVal = System.getProperty("user.home") + propVal.substring(1)
2162 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2163 def propsFile = file(propsFileName)
2164 def eclipseWsDir = propVal
2165 def props = new Properties()
2167 def writeProps = true
2168 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2169 def ins = new FileInputStream(propsFileName)
2172 if (props.getProperty(propKey, null) != null) {
2173 eclipseWsDir = props.getProperty(propKey)
2178 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2179 def tempDir = File.createTempDir()
2180 eclipseWsDir = tempDir.getAbsolutePath()
2183 eclipseWorkspace = file(eclipseWsDir)
2186 // do not run a headless transpile when we claim to be in Eclipse
2188 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2189 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2191 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2195 props.setProperty(propKey, eclipseWsDir)
2196 propsFile.parentFile.mkdirs()
2197 def bytes = new ByteArrayOutputStream()
2198 props.store(bytes, null)
2199 def propertiesString = bytes.toString()
2200 propsFile.text = propertiesString
2206 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2209 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2210 outputs.file(propsFileName)
2211 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2215 task jalviewjsEclipsePaths {
2218 def eclipseRoot = jalviewjs_eclipse_root
2219 if (eclipseRoot.startsWith("~/")) {
2220 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2222 if (OperatingSystem.current().isMacOsX()) {
2223 eclipseRoot += "/Eclipse.app"
2224 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2225 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2226 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2227 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2228 eclipseRoot += "/eclipse"
2230 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2231 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2232 } else { // linux or unix
2233 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2234 eclipseRoot += "/eclipse"
2235 println("eclipseDir exists")
2237 eclipseBinary = "${eclipseRoot}/eclipse"
2238 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2241 eclipseVersion = "4.13" // default
2242 def assumedVersion = true
2243 if (file(eclipseProduct).exists()) {
2244 def fis = new FileInputStream(eclipseProduct)
2245 def props = new Properties()
2247 eclipseVersion = props.getProperty("version")
2249 assumedVersion = false
2252 def propKey = "eclipse_debug"
2253 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2256 // do not run a headless transpile when we claim to be in Eclipse
2258 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2259 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2261 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2264 if (!assumedVersion) {
2265 println("ECLIPSE VERSION=${eclipseVersion}")
2271 task printProperties {
2273 description "Output to console all System.properties"
2275 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2281 dependsOn eclipseProject
2282 dependsOn eclipseClasspath
2283 dependsOn eclipseJdt
2287 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2288 task jalviewjsEclipseCopyDropins(type: Copy) {
2289 dependsOn jalviewjsEclipsePaths
2291 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2292 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2293 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2300 // this eclipse -clean doesn't actually work
2301 task jalviewjsCleanEclipse(type: Exec) {
2302 dependsOn eclipseSetup
2303 dependsOn jalviewjsEclipsePaths
2304 dependsOn jalviewjsEclipseCopyDropins
2306 executable(eclipseBinary)
2307 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2313 def inputString = """exit
2316 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2317 standardInput = inputByteStream
2320 /* not really working yet
2321 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2325 task jalviewjsTransferUnzipSwingJs {
2326 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2330 from zipTree(file_zip)
2331 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2335 inputs.file file_zip
2336 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2340 task jalviewjsTransferUnzipLib {
2341 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2344 zipFiles.each { file_zip ->
2346 from zipTree(file_zip)
2347 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2352 inputs.files zipFiles
2353 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2357 task jalviewjsTransferUnzipAllLibs {
2358 dependsOn jalviewjsTransferUnzipSwingJs
2359 dependsOn jalviewjsTransferUnzipLib
2363 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2365 description "Create the alternative j2s file from the j2s.* properties"
2367 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2368 def siteDirProperty = "j2s.site.directory"
2369 def setSiteDir = false
2370 jalviewjsJ2sProps.each { prop, val ->
2372 if (prop == siteDirProperty) {
2373 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2374 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2380 if (!setSiteDir) { // default site location, don't override specifically set property
2381 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2384 outputFile = jalviewjsJ2sAltSettingsFileName
2387 inputs.properties(jalviewjsJ2sProps)
2388 outputs.file(jalviewjsJ2sAltSettingsFileName)
2393 task jalviewjsEclipseSetup {
2394 dependsOn jalviewjsEclipseCopyDropins
2395 dependsOn jalviewjsSetEclipseWorkspace
2396 dependsOn jalviewjsCreateJ2sSettings
2400 task jalviewjsSyncAllLibs (type: Sync) {
2401 dependsOn jalviewjsTransferUnzipAllLibs
2402 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2403 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2404 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2408 def outputFiles = []
2409 rename { filename ->
2410 outputFiles += "${outputDir}/${filename}"
2417 // should this be exclude really ?
2418 duplicatesStrategy "INCLUDE"
2420 outputs.files outputFiles
2421 inputs.files inputFiles
2425 task jalviewjsSyncResources (type: Sync) {
2426 dependsOn buildResources
2428 def inputFiles = fileTree(dir: resourcesBuildDir)
2429 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2433 def outputFiles = []
2434 rename { filename ->
2435 outputFiles += "${outputDir}/${filename}"
2441 outputs.files outputFiles
2442 inputs.files inputFiles
2446 task jalviewjsSyncSiteResources (type: Sync) {
2447 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2448 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2452 def outputFiles = []
2453 rename { filename ->
2454 outputFiles += "${outputDir}/${filename}"
2460 outputs.files outputFiles
2461 inputs.files inputFiles
2465 task jalviewjsSyncBuildProperties (type: Sync) {
2466 dependsOn createBuildProperties
2467 def inputFiles = [file(buildProperties)]
2468 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2472 def outputFiles = []
2473 rename { filename ->
2474 outputFiles += "${outputDir}/${filename}"
2480 outputs.files outputFiles
2481 inputs.files inputFiles
2485 task jalviewjsProjectImport(type: Exec) {
2486 dependsOn eclipseSetup
2487 dependsOn jalviewjsEclipsePaths
2488 dependsOn jalviewjsEclipseSetup
2491 // do not run a headless import when we claim to be in Eclipse
2493 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2494 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2496 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2500 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2501 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2502 executable(eclipseBinary)
2503 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2507 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2509 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2510 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2513 inputs.file("${jalviewDir}/.project")
2514 outputs.upToDateWhen {
2515 file(projdir).exists()
2520 task jalviewjsTranspile(type: Exec) {
2521 dependsOn jalviewjsEclipseSetup
2522 dependsOn jalviewjsProjectImport
2523 dependsOn jalviewjsEclipsePaths
2525 dependsOn jalviewjsEnableAltFileProperty
2529 // do not run a headless transpile when we claim to be in Eclipse
2531 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2532 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2534 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2538 executable(eclipseBinary)
2539 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2543 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2545 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2546 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2552 stdout = new ByteArrayOutputStream()
2553 stderr = new ByteArrayOutputStream()
2555 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2556 def logOutFile = file(logOutFileName)
2557 logOutFile.createNewFile()
2558 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2559 BINARY: ${eclipseBinary}
2560 VERSION: ${eclipseVersion}
2561 WORKSPACE: ${eclipseWorkspace}
2562 DEBUG: ${eclipseDebug}
2565 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2566 // combine stdout and stderr
2567 def logErrFOS = logOutFOS
2569 if (jalviewjs_j2s_to_console.equals("true")) {
2570 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2571 new org.apache.tools.ant.util.TeeOutputStream(
2575 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2576 new org.apache.tools.ant.util.TeeOutputStream(
2581 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2584 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2591 if (stdout.toString().contains("Error processing ")) {
2592 // j2s did not complete transpile
2593 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2594 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2595 println("IGNORING TRANSPILE ERRORS")
2596 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2598 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2603 inputs.dir("${jalviewDir}/${sourceDir}")
2604 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2605 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2609 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2611 def stdout = new ByteArrayOutputStream()
2612 def stderr = new ByteArrayOutputStream()
2614 def coreFile = file(jsfile)
2616 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2618 logOutFile.createNewFile()
2619 logOutFile.append(msg+"\n")
2621 def coreTop = file(prefixFile)
2622 def coreBottom = file(suffixFile)
2623 coreFile.getParentFile().mkdirs()
2624 coreFile.createNewFile()
2625 coreFile.write( coreTop.getText("UTF-8") )
2629 def t = f.getText("UTF-8")
2630 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2631 coreFile.append( t )
2633 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2635 logOutFile.append(msg+"\n")
2638 coreFile.append( coreBottom.getText("UTF-8") )
2640 msg = "Generating ${zjsfile}"
2642 logOutFile.append(msg+"\n")
2643 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2644 def logErrFOS = logOutFOS
2647 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2648 main = "com.google.javascript.jscomp.CommandLineRunner"
2649 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2650 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2653 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2655 logOutFile.append(msg+"\n")
2657 if (logOutConsole) {
2658 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2659 new org.apache.tools.ant.util.TeeOutputStream(
2663 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2664 new org.apache.tools.ant.util.TeeOutputStream(
2669 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2672 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2679 logOutFile.append(msg+"\n")
2683 task jalviewjsBuildAllCores {
2685 description "Build the core js lib closures listed in the classlists dir"
2686 dependsOn jalviewjsTranspile
2687 dependsOn jalviewjsTransferUnzipSwingJs
2689 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2690 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2691 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2692 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2693 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2694 def prefixFile = "${jsDir}/core/coretop2.js"
2695 def suffixFile = "${jsDir}/core/corebottom2.js"
2697 inputs.file prefixFile
2698 inputs.file suffixFile
2700 def classlistFiles = []
2701 // add the classlists found int the jalviewjs_classlists_dir
2702 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2704 def name = file.getName() - ".txt"
2711 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2712 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2713 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2715 jalviewjsCoreClasslists = []
2717 classlistFiles.each {
2720 def file = hash['file']
2721 if (! file.exists()) {
2722 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2723 return false // this is a "continue" in groovy .each closure
2725 def name = hash['name']
2727 name = file.getName() - ".txt"
2735 def list = fileTree(dir: j2sDir, includes: filelist)
2737 def jsfile = "${outputDir}/core${name}.js"
2738 def zjsfile = "${outputDir}/core${name}.z.js"
2740 jalviewjsCoreClasslists += [
2749 outputs.file(jsfile)
2750 outputs.file(zjsfile)
2753 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2754 def stevesoftClasslistName = "_stevesoft"
2755 def stevesoftClasslist = [
2756 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2757 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2758 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2759 'name': stevesoftClasslistName
2761 jalviewjsCoreClasslists += stevesoftClasslist
2762 inputs.files(stevesoftClasslist['list'])
2763 outputs.file(stevesoftClasslist['jsfile'])
2764 outputs.file(stevesoftClasslist['zjsfile'])
2767 def allClasslistName = "_all"
2768 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2769 allJsFiles += fileTree(
2773 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2774 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2775 "**/org/jmol/export/JSExporter.js"
2778 allJsFiles += fileTree(
2782 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2783 "**/sun/misc/Unsafe.js",
2784 "**/swingjs/jquery/jquery-editable-select.js",
2785 "**/swingjs/jquery/j2sComboBox.js",
2786 "**/sun/misc/FloatingDecimal.js"
2789 def allClasslist = [
2790 'jsfile': "${outputDir}/core${allClasslistName}.js",
2791 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2793 'name': allClasslistName
2795 // not including this version of "all" core at the moment
2796 //jalviewjsCoreClasslists += allClasslist
2797 inputs.files(allClasslist['list'])
2798 outputs.file(allClasslist['jsfile'])
2799 outputs.file(allClasslist['zjsfile'])
2802 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2803 logOutFile.getParentFile().mkdirs()
2804 logOutFile.createNewFile()
2805 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2807 jalviewjsCoreClasslists.each {
2808 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2815 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2818 into file(outputFile).getParentFile()
2819 rename { filename ->
2820 if (filename.equals(inputFile.getName())) {
2821 return file(outputFile).getName()
2825 filter(ReplaceTokens,
2829 'MAIN': '"'+main_class+'"',
2831 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2832 'COREKEY': jalviewjs_core_key,
2833 'CORENAME': coreName
2840 task jalviewjsPublishCoreTemplates {
2841 dependsOn jalviewjsBuildAllCores
2842 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2843 def inputFile = file(inputFileName)
2844 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2846 def outputFiles = []
2847 jalviewjsCoreClasslists.each { cl ->
2848 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2849 cl['outputfile'] = outputFile
2850 outputFiles += outputFile
2854 jalviewjsCoreClasslists.each { cl ->
2855 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2858 inputs.file(inputFile)
2859 outputs.files(outputFiles)
2863 task jalviewjsSyncCore (type: Sync) {
2864 dependsOn jalviewjsBuildAllCores
2865 dependsOn jalviewjsPublishCoreTemplates
2866 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2867 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2871 def outputFiles = []
2872 rename { filename ->
2873 outputFiles += "${outputDir}/${filename}"
2879 outputs.files outputFiles
2880 inputs.files inputFiles
2884 // this Copy version of TransferSiteJs will delete anything else in the target dir
2885 task jalviewjsCopyTransferSiteJs(type: Copy) {
2886 dependsOn jalviewjsTranspile
2887 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2888 into "${jalviewDir}/${jalviewjsSiteDir}"
2892 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2893 task jalviewjsSyncTransferSiteJs(type: Sync) {
2894 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2896 into "${jalviewDir}/${jalviewjsSiteDir}"
2903 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2904 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2905 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2906 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2908 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2909 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2910 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2911 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2914 task jalviewjsPrepareSite {
2916 description "Prepares the website folder including unzipping files and copying resources"
2917 dependsOn jalviewjsSyncAllLibs
2918 dependsOn jalviewjsSyncResources
2919 dependsOn jalviewjsSyncSiteResources
2920 dependsOn jalviewjsSyncBuildProperties
2921 dependsOn jalviewjsSyncCore
2925 task jalviewjsBuildSite {
2927 description "Builds the whole website including transpiled code"
2928 dependsOn jalviewjsCopyTransferSiteJs
2929 dependsOn jalviewjsPrepareSite
2933 task cleanJalviewjsTransferSite {
2935 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2936 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2937 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2938 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2943 task cleanJalviewjsSite {
2944 dependsOn cleanJalviewjsTransferSite
2946 delete "${jalviewDir}/${jalviewjsSiteDir}"
2951 task jalviewjsSiteTar(type: Tar) {
2953 description "Creates a tar.gz file for the website"
2954 dependsOn jalviewjsBuildSite
2955 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2956 archiveFileName = outputFilename
2958 compression Compression.GZIP
2960 from "${jalviewDir}/${jalviewjsSiteDir}"
2961 into jalviewjs_site_dir // this is inside the tar file
2963 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
2967 task jalviewjsServer {
2969 def filename = "jalviewjsTest.html"
2970 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
2971 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
2976 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
2977 factory = f.newInstance()
2978 } catch (ClassNotFoundException e) {
2979 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
2981 def port = Integer.valueOf(jalviewjs_server_port)
2986 while(port < start+1000 && !running) {
2988 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
2989 jalviewjsServer = factory.start(doc_root, port)
2991 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
2992 println("SERVER STARTED with document root ${doc_root}.")
2993 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
2994 println("For debug: "+url+"?j2sdebug")
2995 println("For verbose: "+url+"?j2sverbose")
2996 } catch (Exception e) {
3001 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3002 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3003 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3005 jalviewjsCoreClasslists.each { cl ->
3006 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3008 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3010 println("For core ${cl.name}: "+urlcore)
3013 file(htmlFile).text = htmlText
3016 outputs.file(htmlFile)
3017 outputs.upToDateWhen({false})
3021 task cleanJalviewjsAll {
3023 description "Delete all configuration and build artifacts to do with JalviewJS build"
3024 dependsOn cleanJalviewjsSite
3025 dependsOn jalviewjsEclipsePaths
3028 delete "${jalviewDir}/${jalviewjsBuildDir}"
3029 delete "${jalviewDir}/${eclipse_bin_dir}"
3030 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3031 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3033 delete jalviewjsJ2sAltSettingsFileName
3036 outputs.upToDateWhen( { false } )
3040 task jalviewjsIDE_checkJ2sPlugin {
3041 group "00 JalviewJS in Eclipse"
3042 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3045 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3046 def j2sPluginFile = file(j2sPlugin)
3047 def eclipseHome = System.properties["eclipse.home.location"]
3048 if (eclipseHome == null || ! IN_ECLIPSE) {
3049 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3051 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3052 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3053 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3054 eclipseJ2sPluginDirs += altPluginsDir
3056 def foundPlugin = false
3057 def j2sPluginFileName = j2sPluginFile.getName()
3058 def eclipseJ2sPlugin
3059 def eclipseJ2sPluginFile
3060 eclipseJ2sPluginDirs.any { dir ->
3061 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3062 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3063 if (eclipseJ2sPluginFile.exists()) {
3069 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3070 System.err.println(msg)
3071 throw new StopExecutionException(msg)
3074 def digest = MessageDigest.getInstance("MD5")
3076 digest.update(j2sPluginFile.text.bytes)
3077 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3079 digest.update(eclipseJ2sPluginFile.text.bytes)
3080 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3082 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3083 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3084 System.err.println(msg)
3085 throw new StopExecutionException(msg)
3087 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3093 task jalviewjsIDE_copyJ2sPlugin {
3094 group "00 JalviewJS in Eclipse"
3095 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3098 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3099 def j2sPluginFile = file(j2sPlugin)
3100 def eclipseHome = System.properties["eclipse.home.location"]
3101 if (eclipseHome == null || ! IN_ECLIPSE) {
3102 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3104 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3105 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3106 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3107 System.err.println(msg)
3110 eclipseJ2sPluginFile.getParentFile().mkdirs()
3111 into eclipseJ2sPluginFile.getParent()
3117 task jalviewjsIDE_j2sFile {
3118 group "00 JalviewJS in Eclipse"
3119 description "Creates the .j2s file"
3120 dependsOn jalviewjsCreateJ2sSettings
3124 task jalviewjsIDE_SyncCore {
3125 group "00 JalviewJS in Eclipse"
3126 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3127 dependsOn jalviewjsSyncCore
3131 task jalviewjsIDE_SyncSiteAll {
3132 dependsOn jalviewjsSyncAllLibs
3133 dependsOn jalviewjsSyncResources
3134 dependsOn jalviewjsSyncSiteResources
3135 dependsOn jalviewjsSyncBuildProperties
3139 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3142 task jalviewjsIDE_PrepareSite {
3143 group "00 JalviewJS in Eclipse"
3144 description "Sync libs and resources to site dir, but not closure cores"
3146 dependsOn jalviewjsIDE_SyncSiteAll
3147 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3151 task jalviewjsIDE_AssembleSite {
3152 group "00 JalviewJS in Eclipse"
3153 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3154 dependsOn jalviewjsPrepareSite
3158 task jalviewjsIDE_SiteClean {
3159 group "00 JalviewJS in Eclipse"
3160 description "Deletes the Eclipse transpiled site"
3161 dependsOn cleanJalviewjsSite
3165 task jalviewjsIDE_Server {
3166 group "00 JalviewJS in Eclipse"
3167 description "Starts a webserver on localhost to test the website"
3168 dependsOn jalviewjsServer
3172 // buildship runs this at import or gradle refresh
3173 task eclipseSynchronizationTask {
3174 //dependsOn eclipseSetup
3175 dependsOn createBuildProperties
3177 dependsOn jalviewjsIDE_j2sFile
3178 dependsOn jalviewjsIDE_checkJ2sPlugin
3179 dependsOn jalviewjsIDE_PrepareSite
3184 // buildship runs this at build time or project refresh
3185 task eclipseAutoBuildTask {
3186 //dependsOn jalviewjsIDE_checkJ2sPlugin
3187 //dependsOn jalviewjsIDE_PrepareSite
3193 description "Build the site"
3194 dependsOn jalviewjsBuildSite