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.'@executeSetupApp' = "false"
1824 // turn off checksum creation for LOCAL channel
1825 def e = install4jConfigXml.application[0]
1826 if (CHANNEL == "LOCAL") {
1827 e.'@createChecksums' = "false"
1829 e.'@createChecksums' = "true"
1832 // put file association actions where placeholder action is
1833 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1834 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1835 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1836 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1837 def parent = a.parent()
1839 fileAssociationActions.each { faa ->
1842 // don't need to continue in .any loop once replacements have been made
1847 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1848 // NB we're deleting the /other/ one!
1849 // Also remove the examples subdir from non-release versions
1850 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1851 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1852 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1853 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1855 // remove the examples subdir from Full File Set
1856 def files = install4jConfigXml.files[0]
1857 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1858 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1859 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1860 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1861 dirEntry.parent().remove(dirEntry)
1863 install4jConfigXml.'**'.action.any { a ->
1864 if (a.'@customizedId' == customizedIdToDelete) {
1865 def parent = a.parent()
1871 // write install4j file
1872 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1879 delete install4jConfFile
1884 task installers(type: com.install4j.gradle.Install4jTask) {
1885 group = "distribution"
1886 description = "Create the install4j installers"
1888 dependsOn copyInstall4jTemplate
1890 projectFile = install4jConfFile
1892 // create an md5 for the input files to use as version for install4j conf file
1893 def digest = MessageDigest.getInstance("MD5")
1895 (file("${install4jDir}/${install4j_template}").text +
1896 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1897 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1898 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1899 if (filesMd5.length() >= 8) {
1900 filesMd5 = filesMd5.substring(0,8)
1902 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1903 // make install4jBuildDir relative to jalviewDir
1904 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1907 'JALVIEW_NAME': jalview_name,
1908 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1909 'JALVIEW_DIR': "../..",
1910 'OSX_KEYSTORE': OSX_KEYSTORE,
1911 'OSX_APPLEID': OSX_APPLEID,
1912 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
1913 'JSIGN_SH': JSIGN_SH,
1914 'JRE_DIR': getdown_app_dir_java,
1915 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1916 'JALVIEW_VERSION': JALVIEW_VERSION,
1917 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1918 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1919 'JAVA_VERSION': JAVA_VERSION,
1920 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1921 'VERSION': JALVIEW_VERSION,
1922 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1923 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1924 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1925 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1926 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1927 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1928 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1929 'BUNDLE_ID': install4jBundleId,
1930 'INTERNAL_ID': install4jInternalId,
1931 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1932 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
1933 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1934 'WRAPPER_LINK': getdownWrapperLink,
1935 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
1936 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
1937 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
1938 'INSTALLER_NAME': install4jInstallerName,
1939 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1940 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1941 'GETDOWN_FILES_DIR': getdown_files_dir,
1942 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1943 'GETDOWN_DIST_DIR': getdownAppDistDir,
1944 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1945 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1946 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1947 'BUILD_DIR': install4jBuildDir,
1948 'APPLICATION_CATEGORIES': install4j_application_categories,
1949 'APPLICATION_FOLDER': install4jApplicationFolder,
1950 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1951 'EXECUTABLE_NAME': install4jExecutableName,
1952 'EXTRA_SCHEME': install4jExtraScheme,
1953 'MAC_ICONS_FILE': install4jMacIconsFile,
1954 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
1955 'PNG_ICON_FILE': install4jPngIconFile,
1956 'BACKGROUND': install4jBackground,
1960 //println("INSTALL4J VARIABLES:")
1961 //variables.each{k,v->println("${k}=${v}")}
1963 destination = "${jalviewDir}/${install4jBuildDir}"
1964 buildSelected = true
1966 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1968 disableSigning = true
1969 disableNotarization = true
1973 macKeystorePassword = OSX_KEYPASS
1976 if (OSX_ALTOOLPASS) {
1977 appleIdPassword = OSX_ALTOOLPASS
1978 disableNotarization = false
1980 disableNotarization = true
1984 println("Using projectFile "+projectFile)
1985 if (!disableNotarization) { println("Will notarize OSX App DMG") }
1989 inputs.dir(getdownWebsiteDir)
1990 inputs.file(install4jConfFile)
1991 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1992 inputs.dir(macosJavaVMDir)
1993 inputs.dir(windowsJavaVMDir)
1994 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2000 eclipse().configFile(eclipse_codestyle_file)
2005 task sourceDist(type: Tar) {
2006 group "distribution"
2007 description "Create a source .tar.gz file for distribution"
2009 dependsOn createBuildProperties
2010 dependsOn convertMdFiles
2012 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
2013 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
2014 archiveFileName = outputFileName
2016 compression Compression.GZIP
2031 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2033 "utils/InstallAnywhere",
2048 "gradle.properties",
2059 ".settings/org.eclipse.jdt.core.jalview.prefs",
2063 exclude (EXCLUDE_FILES)
2064 include (PROCESS_FILES)
2065 filter(ReplaceTokens,
2069 'Version-Rel': JALVIEW_VERSION,
2070 'Year-Rel': getDate("yyyy")
2075 exclude (EXCLUDE_FILES)
2076 exclude (PROCESS_FILES)
2077 exclude ("appletlib")
2078 exclude ("**/*locales")
2079 exclude ("*locales/**")
2080 exclude ("utils/InstallAnywhere")
2082 exclude (getdown_files_dir)
2083 exclude (getdown_website_dir)
2085 // exluding these as not using jars as modules yet
2086 exclude ("${j11modDir}/**/*.jar")
2089 include(INCLUDE_FILES)
2091 // from (jalviewDir) {
2092 // // explicit includes for stuff that seemed to not get included
2093 // include(fileTree("test/**/*."))
2094 // exclude(EXCLUDE_FILES)
2095 // exclude(PROCESS_FILES)
2098 from(file(buildProperties).getParent()) {
2099 include(file(buildProperties).getName())
2100 rename(file(buildProperties).getName(), "build_properties")
2102 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2111 dependsOn pubhtmlhelp
2113 inputs.dir("${helpBuildDir}/${help_dir}")
2114 outputs.dir("${buildDir}/distributions/${help_dir}")
2118 task j2sSetHeadlessBuild {
2125 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2127 description "Enable the alternative J2S Config file for headless build"
2129 outputFile = jalviewjsJ2sSettingsFileName
2130 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2131 def j2sProps = new Properties()
2132 if (j2sPropsFile.exists()) {
2134 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2135 j2sProps.load(j2sPropsFileFIS)
2136 j2sPropsFileFIS.close()
2138 j2sProps.each { prop, val ->
2141 } catch (Exception e) {
2142 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2146 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2147 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2152 task jalviewjsSetEclipseWorkspace {
2153 def propKey = "jalviewjs_eclipse_workspace"
2155 if (project.hasProperty(propKey)) {
2156 propVal = project.getProperty(propKey)
2157 if (propVal.startsWith("~/")) {
2158 propVal = System.getProperty("user.home") + propVal.substring(1)
2161 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2162 def propsFile = file(propsFileName)
2163 def eclipseWsDir = propVal
2164 def props = new Properties()
2166 def writeProps = true
2167 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2168 def ins = new FileInputStream(propsFileName)
2171 if (props.getProperty(propKey, null) != null) {
2172 eclipseWsDir = props.getProperty(propKey)
2177 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2178 def tempDir = File.createTempDir()
2179 eclipseWsDir = tempDir.getAbsolutePath()
2182 eclipseWorkspace = file(eclipseWsDir)
2185 // do not run a headless transpile when we claim to be in Eclipse
2187 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2188 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2190 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2194 props.setProperty(propKey, eclipseWsDir)
2195 propsFile.parentFile.mkdirs()
2196 def bytes = new ByteArrayOutputStream()
2197 props.store(bytes, null)
2198 def propertiesString = bytes.toString()
2199 propsFile.text = propertiesString
2205 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2208 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2209 outputs.file(propsFileName)
2210 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2214 task jalviewjsEclipsePaths {
2217 def eclipseRoot = jalviewjs_eclipse_root
2218 if (eclipseRoot.startsWith("~/")) {
2219 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2221 if (OperatingSystem.current().isMacOsX()) {
2222 eclipseRoot += "/Eclipse.app"
2223 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2224 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2225 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2226 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2227 eclipseRoot += "/eclipse"
2229 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2230 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2231 } else { // linux or unix
2232 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2233 eclipseRoot += "/eclipse"
2234 println("eclipseDir exists")
2236 eclipseBinary = "${eclipseRoot}/eclipse"
2237 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2240 eclipseVersion = "4.13" // default
2241 def assumedVersion = true
2242 if (file(eclipseProduct).exists()) {
2243 def fis = new FileInputStream(eclipseProduct)
2244 def props = new Properties()
2246 eclipseVersion = props.getProperty("version")
2248 assumedVersion = false
2251 def propKey = "eclipse_debug"
2252 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2255 // do not run a headless transpile when we claim to be in Eclipse
2257 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2258 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2260 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2263 if (!assumedVersion) {
2264 println("ECLIPSE VERSION=${eclipseVersion}")
2270 task printProperties {
2272 description "Output to console all System.properties"
2274 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2280 dependsOn eclipseProject
2281 dependsOn eclipseClasspath
2282 dependsOn eclipseJdt
2286 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2287 task jalviewjsEclipseCopyDropins(type: Copy) {
2288 dependsOn jalviewjsEclipsePaths
2290 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2291 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2292 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2299 // this eclipse -clean doesn't actually work
2300 task jalviewjsCleanEclipse(type: Exec) {
2301 dependsOn eclipseSetup
2302 dependsOn jalviewjsEclipsePaths
2303 dependsOn jalviewjsEclipseCopyDropins
2305 executable(eclipseBinary)
2306 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2312 def inputString = """exit
2315 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2316 standardInput = inputByteStream
2319 /* not really working yet
2320 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2324 task jalviewjsTransferUnzipSwingJs {
2325 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2329 from zipTree(file_zip)
2330 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2334 inputs.file file_zip
2335 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2339 task jalviewjsTransferUnzipLib {
2340 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2343 zipFiles.each { file_zip ->
2345 from zipTree(file_zip)
2346 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2351 inputs.files zipFiles
2352 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2356 task jalviewjsTransferUnzipAllLibs {
2357 dependsOn jalviewjsTransferUnzipSwingJs
2358 dependsOn jalviewjsTransferUnzipLib
2362 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2364 description "Create the alternative j2s file from the j2s.* properties"
2366 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2367 def siteDirProperty = "j2s.site.directory"
2368 def setSiteDir = false
2369 jalviewjsJ2sProps.each { prop, val ->
2371 if (prop == siteDirProperty) {
2372 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2373 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2379 if (!setSiteDir) { // default site location, don't override specifically set property
2380 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2383 outputFile = jalviewjsJ2sAltSettingsFileName
2386 inputs.properties(jalviewjsJ2sProps)
2387 outputs.file(jalviewjsJ2sAltSettingsFileName)
2392 task jalviewjsEclipseSetup {
2393 dependsOn jalviewjsEclipseCopyDropins
2394 dependsOn jalviewjsSetEclipseWorkspace
2395 dependsOn jalviewjsCreateJ2sSettings
2399 task jalviewjsSyncAllLibs (type: Sync) {
2400 dependsOn jalviewjsTransferUnzipAllLibs
2401 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2402 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2403 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2407 def outputFiles = []
2408 rename { filename ->
2409 outputFiles += "${outputDir}/${filename}"
2416 // should this be exclude really ?
2417 duplicatesStrategy "INCLUDE"
2419 outputs.files outputFiles
2420 inputs.files inputFiles
2424 task jalviewjsSyncResources (type: Sync) {
2425 dependsOn buildResources
2427 def inputFiles = fileTree(dir: resourcesBuildDir)
2428 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2432 def outputFiles = []
2433 rename { filename ->
2434 outputFiles += "${outputDir}/${filename}"
2440 outputs.files outputFiles
2441 inputs.files inputFiles
2445 task jalviewjsSyncSiteResources (type: Sync) {
2446 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2447 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2451 def outputFiles = []
2452 rename { filename ->
2453 outputFiles += "${outputDir}/${filename}"
2459 outputs.files outputFiles
2460 inputs.files inputFiles
2464 task jalviewjsSyncBuildProperties (type: Sync) {
2465 dependsOn createBuildProperties
2466 def inputFiles = [file(buildProperties)]
2467 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2471 def outputFiles = []
2472 rename { filename ->
2473 outputFiles += "${outputDir}/${filename}"
2479 outputs.files outputFiles
2480 inputs.files inputFiles
2484 task jalviewjsProjectImport(type: Exec) {
2485 dependsOn eclipseSetup
2486 dependsOn jalviewjsEclipsePaths
2487 dependsOn jalviewjsEclipseSetup
2490 // do not run a headless import when we claim to be in Eclipse
2492 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2493 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2495 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2499 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2500 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2501 executable(eclipseBinary)
2502 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2506 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2508 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2509 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2512 inputs.file("${jalviewDir}/.project")
2513 outputs.upToDateWhen {
2514 file(projdir).exists()
2519 task jalviewjsTranspile(type: Exec) {
2520 dependsOn jalviewjsEclipseSetup
2521 dependsOn jalviewjsProjectImport
2522 dependsOn jalviewjsEclipsePaths
2524 dependsOn jalviewjsEnableAltFileProperty
2528 // do not run a headless transpile when we claim to be in Eclipse
2530 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2531 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2533 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2537 executable(eclipseBinary)
2538 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2542 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2544 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2545 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2551 stdout = new ByteArrayOutputStream()
2552 stderr = new ByteArrayOutputStream()
2554 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2555 def logOutFile = file(logOutFileName)
2556 logOutFile.createNewFile()
2557 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2558 BINARY: ${eclipseBinary}
2559 VERSION: ${eclipseVersion}
2560 WORKSPACE: ${eclipseWorkspace}
2561 DEBUG: ${eclipseDebug}
2564 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2565 // combine stdout and stderr
2566 def logErrFOS = logOutFOS
2568 if (jalviewjs_j2s_to_console.equals("true")) {
2569 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2570 new org.apache.tools.ant.util.TeeOutputStream(
2574 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2575 new org.apache.tools.ant.util.TeeOutputStream(
2580 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2583 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2590 if (stdout.toString().contains("Error processing ")) {
2591 // j2s did not complete transpile
2592 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2593 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2594 println("IGNORING TRANSPILE ERRORS")
2595 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2597 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2602 inputs.dir("${jalviewDir}/${sourceDir}")
2603 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2604 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2608 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2610 def stdout = new ByteArrayOutputStream()
2611 def stderr = new ByteArrayOutputStream()
2613 def coreFile = file(jsfile)
2615 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2617 logOutFile.createNewFile()
2618 logOutFile.append(msg+"\n")
2620 def coreTop = file(prefixFile)
2621 def coreBottom = file(suffixFile)
2622 coreFile.getParentFile().mkdirs()
2623 coreFile.createNewFile()
2624 coreFile.write( coreTop.getText("UTF-8") )
2628 def t = f.getText("UTF-8")
2629 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2630 coreFile.append( t )
2632 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2634 logOutFile.append(msg+"\n")
2637 coreFile.append( coreBottom.getText("UTF-8") )
2639 msg = "Generating ${zjsfile}"
2641 logOutFile.append(msg+"\n")
2642 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2643 def logErrFOS = logOutFOS
2646 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2647 main = "com.google.javascript.jscomp.CommandLineRunner"
2648 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2649 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2652 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2654 logOutFile.append(msg+"\n")
2656 if (logOutConsole) {
2657 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2658 new org.apache.tools.ant.util.TeeOutputStream(
2662 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2663 new org.apache.tools.ant.util.TeeOutputStream(
2668 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2671 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2678 logOutFile.append(msg+"\n")
2682 task jalviewjsBuildAllCores {
2684 description "Build the core js lib closures listed in the classlists dir"
2685 dependsOn jalviewjsTranspile
2686 dependsOn jalviewjsTransferUnzipSwingJs
2688 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2689 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2690 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2691 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2692 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2693 def prefixFile = "${jsDir}/core/coretop2.js"
2694 def suffixFile = "${jsDir}/core/corebottom2.js"
2696 inputs.file prefixFile
2697 inputs.file suffixFile
2699 def classlistFiles = []
2700 // add the classlists found int the jalviewjs_classlists_dir
2701 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2703 def name = file.getName() - ".txt"
2710 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2711 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2712 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2714 jalviewjsCoreClasslists = []
2716 classlistFiles.each {
2719 def file = hash['file']
2720 if (! file.exists()) {
2721 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2722 return false // this is a "continue" in groovy .each closure
2724 def name = hash['name']
2726 name = file.getName() - ".txt"
2734 def list = fileTree(dir: j2sDir, includes: filelist)
2736 def jsfile = "${outputDir}/core${name}.js"
2737 def zjsfile = "${outputDir}/core${name}.z.js"
2739 jalviewjsCoreClasslists += [
2748 outputs.file(jsfile)
2749 outputs.file(zjsfile)
2752 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2753 def stevesoftClasslistName = "_stevesoft"
2754 def stevesoftClasslist = [
2755 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2756 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2757 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2758 'name': stevesoftClasslistName
2760 jalviewjsCoreClasslists += stevesoftClasslist
2761 inputs.files(stevesoftClasslist['list'])
2762 outputs.file(stevesoftClasslist['jsfile'])
2763 outputs.file(stevesoftClasslist['zjsfile'])
2766 def allClasslistName = "_all"
2767 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2768 allJsFiles += fileTree(
2772 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2773 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2774 "**/org/jmol/export/JSExporter.js"
2777 allJsFiles += fileTree(
2781 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2782 "**/sun/misc/Unsafe.js",
2783 "**/swingjs/jquery/jquery-editable-select.js",
2784 "**/swingjs/jquery/j2sComboBox.js",
2785 "**/sun/misc/FloatingDecimal.js"
2788 def allClasslist = [
2789 'jsfile': "${outputDir}/core${allClasslistName}.js",
2790 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2792 'name': allClasslistName
2794 // not including this version of "all" core at the moment
2795 //jalviewjsCoreClasslists += allClasslist
2796 inputs.files(allClasslist['list'])
2797 outputs.file(allClasslist['jsfile'])
2798 outputs.file(allClasslist['zjsfile'])
2801 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2802 logOutFile.getParentFile().mkdirs()
2803 logOutFile.createNewFile()
2804 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2806 jalviewjsCoreClasslists.each {
2807 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2814 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2817 into file(outputFile).getParentFile()
2818 rename { filename ->
2819 if (filename.equals(inputFile.getName())) {
2820 return file(outputFile).getName()
2824 filter(ReplaceTokens,
2828 'MAIN': '"'+main_class+'"',
2830 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2831 'COREKEY': jalviewjs_core_key,
2832 'CORENAME': coreName
2839 task jalviewjsPublishCoreTemplates {
2840 dependsOn jalviewjsBuildAllCores
2841 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2842 def inputFile = file(inputFileName)
2843 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2845 def outputFiles = []
2846 jalviewjsCoreClasslists.each { cl ->
2847 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2848 cl['outputfile'] = outputFile
2849 outputFiles += outputFile
2853 jalviewjsCoreClasslists.each { cl ->
2854 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2857 inputs.file(inputFile)
2858 outputs.files(outputFiles)
2862 task jalviewjsSyncCore (type: Sync) {
2863 dependsOn jalviewjsBuildAllCores
2864 dependsOn jalviewjsPublishCoreTemplates
2865 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2866 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2870 def outputFiles = []
2871 rename { filename ->
2872 outputFiles += "${outputDir}/${filename}"
2878 outputs.files outputFiles
2879 inputs.files inputFiles
2883 // this Copy version of TransferSiteJs will delete anything else in the target dir
2884 task jalviewjsCopyTransferSiteJs(type: Copy) {
2885 dependsOn jalviewjsTranspile
2886 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2887 into "${jalviewDir}/${jalviewjsSiteDir}"
2891 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2892 task jalviewjsSyncTransferSiteJs(type: Sync) {
2893 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2895 into "${jalviewDir}/${jalviewjsSiteDir}"
2902 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2903 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2904 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2905 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2907 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2908 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2909 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2910 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2913 task jalviewjsPrepareSite {
2915 description "Prepares the website folder including unzipping files and copying resources"
2916 dependsOn jalviewjsSyncAllLibs
2917 dependsOn jalviewjsSyncResources
2918 dependsOn jalviewjsSyncSiteResources
2919 dependsOn jalviewjsSyncBuildProperties
2920 dependsOn jalviewjsSyncCore
2924 task jalviewjsBuildSite {
2926 description "Builds the whole website including transpiled code"
2927 dependsOn jalviewjsCopyTransferSiteJs
2928 dependsOn jalviewjsPrepareSite
2932 task cleanJalviewjsTransferSite {
2934 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2935 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2936 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2937 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2942 task cleanJalviewjsSite {
2943 dependsOn cleanJalviewjsTransferSite
2945 delete "${jalviewDir}/${jalviewjsSiteDir}"
2950 task jalviewjsSiteTar(type: Tar) {
2952 description "Creates a tar.gz file for the website"
2953 dependsOn jalviewjsBuildSite
2954 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2955 archiveFileName = outputFilename
2957 compression Compression.GZIP
2959 from "${jalviewDir}/${jalviewjsSiteDir}"
2960 into jalviewjs_site_dir // this is inside the tar file
2962 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
2966 task jalviewjsServer {
2968 def filename = "jalviewjsTest.html"
2969 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
2970 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
2975 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
2976 factory = f.newInstance()
2977 } catch (ClassNotFoundException e) {
2978 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
2980 def port = Integer.valueOf(jalviewjs_server_port)
2985 while(port < start+1000 && !running) {
2987 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
2988 jalviewjsServer = factory.start(doc_root, port)
2990 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
2991 println("SERVER STARTED with document root ${doc_root}.")
2992 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
2993 println("For debug: "+url+"?j2sdebug")
2994 println("For verbose: "+url+"?j2sverbose")
2995 } catch (Exception e) {
3000 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3001 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3002 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3004 jalviewjsCoreClasslists.each { cl ->
3005 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3007 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3009 println("For core ${cl.name}: "+urlcore)
3012 file(htmlFile).text = htmlText
3015 outputs.file(htmlFile)
3016 outputs.upToDateWhen({false})
3020 task cleanJalviewjsAll {
3022 description "Delete all configuration and build artifacts to do with JalviewJS build"
3023 dependsOn cleanJalviewjsSite
3024 dependsOn jalviewjsEclipsePaths
3027 delete "${jalviewDir}/${jalviewjsBuildDir}"
3028 delete "${jalviewDir}/${eclipse_bin_dir}"
3029 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3030 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3032 delete jalviewjsJ2sAltSettingsFileName
3035 outputs.upToDateWhen( { false } )
3039 task jalviewjsIDE_checkJ2sPlugin {
3040 group "00 JalviewJS in Eclipse"
3041 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3044 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3045 def j2sPluginFile = file(j2sPlugin)
3046 def eclipseHome = System.properties["eclipse.home.location"]
3047 if (eclipseHome == null || ! IN_ECLIPSE) {
3048 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3050 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3051 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3052 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3053 eclipseJ2sPluginDirs += altPluginsDir
3055 def foundPlugin = false
3056 def j2sPluginFileName = j2sPluginFile.getName()
3057 def eclipseJ2sPlugin
3058 def eclipseJ2sPluginFile
3059 eclipseJ2sPluginDirs.any { dir ->
3060 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3061 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3062 if (eclipseJ2sPluginFile.exists()) {
3068 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3069 System.err.println(msg)
3070 throw new StopExecutionException(msg)
3073 def digest = MessageDigest.getInstance("MD5")
3075 digest.update(j2sPluginFile.text.bytes)
3076 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3078 digest.update(eclipseJ2sPluginFile.text.bytes)
3079 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3081 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3082 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3083 System.err.println(msg)
3084 throw new StopExecutionException(msg)
3086 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3092 task jalviewjsIDE_copyJ2sPlugin {
3093 group "00 JalviewJS in Eclipse"
3094 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3097 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3098 def j2sPluginFile = file(j2sPlugin)
3099 def eclipseHome = System.properties["eclipse.home.location"]
3100 if (eclipseHome == null || ! IN_ECLIPSE) {
3101 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3103 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3104 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3105 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3106 System.err.println(msg)
3109 eclipseJ2sPluginFile.getParentFile().mkdirs()
3110 into eclipseJ2sPluginFile.getParent()
3116 task jalviewjsIDE_j2sFile {
3117 group "00 JalviewJS in Eclipse"
3118 description "Creates the .j2s file"
3119 dependsOn jalviewjsCreateJ2sSettings
3123 task jalviewjsIDE_SyncCore {
3124 group "00 JalviewJS in Eclipse"
3125 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3126 dependsOn jalviewjsSyncCore
3130 task jalviewjsIDE_SyncSiteAll {
3131 dependsOn jalviewjsSyncAllLibs
3132 dependsOn jalviewjsSyncResources
3133 dependsOn jalviewjsSyncSiteResources
3134 dependsOn jalviewjsSyncBuildProperties
3138 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3141 task jalviewjsIDE_PrepareSite {
3142 group "00 JalviewJS in Eclipse"
3143 description "Sync libs and resources to site dir, but not closure cores"
3145 dependsOn jalviewjsIDE_SyncSiteAll
3146 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3150 task jalviewjsIDE_AssembleSite {
3151 group "00 JalviewJS in Eclipse"
3152 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3153 dependsOn jalviewjsPrepareSite
3157 task jalviewjsIDE_SiteClean {
3158 group "00 JalviewJS in Eclipse"
3159 description "Deletes the Eclipse transpiled site"
3160 dependsOn cleanJalviewjsSite
3164 task jalviewjsIDE_Server {
3165 group "00 JalviewJS in Eclipse"
3166 description "Starts a webserver on localhost to test the website"
3167 dependsOn jalviewjsServer
3171 // buildship runs this at import or gradle refresh
3172 task eclipseSynchronizationTask {
3173 //dependsOn eclipseSetup
3174 dependsOn createBuildProperties
3176 dependsOn jalviewjsIDE_j2sFile
3177 dependsOn jalviewjsIDE_checkJ2sPlugin
3178 dependsOn jalviewjsIDE_PrepareSite
3183 // buildship runs this at build time or project refresh
3184 task eclipseAutoBuildTask {
3185 //dependsOn jalviewjsIDE_checkJ2sPlugin
3186 //dependsOn jalviewjsIDE_PrepareSite
3192 description "Build the site"
3193 dependsOn jalviewjsBuildSite