1 /* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
2 * For properties set within build.gradle, use camelCaseNoSpace.
4 import org.apache.tools.ant.filters.ReplaceTokens
5 import org.gradle.internal.os.OperatingSystem
6 import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
7 import org.gradle.api.internal.PropertiesTransformer
8 import org.gradle.util.ConfigureUtil
9 import org.gradle.plugins.ide.eclipse.model.Output
10 import org.gradle.plugins.ide.eclipse.model.Library
11 import java.security.MessageDigest
12 import groovy.transform.ExternalizeMethods
13 import groovy.util.XmlParser
14 import groovy.xml.XmlUtil
15 import com.vladsch.flexmark.util.ast.Node
16 import com.vladsch.flexmark.html.HtmlRenderer
17 import com.vladsch.flexmark.parser.Parser
18 import com.vladsch.flexmark.util.data.MutableDataSet
19 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
20 import com.vladsch.flexmark.ext.tables.TablesExtension
21 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
22 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
23 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
24 import com.vladsch.flexmark.ext.toc.TocExtension
32 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
41 id "com.diffplug.gradle.spotless" version "3.28.0"
42 id 'com.github.johnrengelman.shadow' version '4.0.3'
43 id 'com.install4j.gradle' version '8.0.10'
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 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
454 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
455 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
456 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
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 // turn off checksum creation for LOCAL channel
1820 def e = install4jConfigXml.application[0]
1821 if (CHANNEL == "LOCAL") {
1822 e.'@createChecksums' = "false"
1824 e.'@createChecksums' = "true"
1827 // put file association actions where placeholder action is
1828 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1829 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1830 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1831 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1832 def parent = a.parent()
1834 fileAssociationActions.each { faa ->
1837 // don't need to continue in .any loop once replacements have been made
1842 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1843 // NB we're deleting the /other/ one!
1844 // Also remove the examples subdir from non-release versions
1845 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1846 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1847 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1848 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1850 // remove the examples subdir from Full File Set
1851 def files = install4jConfigXml.files[0]
1852 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1853 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1854 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1855 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1856 dirEntry.parent().remove(dirEntry)
1858 install4jConfigXml.'**'.action.any { a ->
1859 if (a.'@customizedId' == customizedIdToDelete) {
1860 def parent = a.parent()
1866 // write install4j file
1867 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1874 delete install4jConfFile
1879 task installers(type: com.install4j.gradle.Install4jTask) {
1880 group = "distribution"
1881 description = "Create the install4j installers"
1883 dependsOn copyInstall4jTemplate
1885 projectFile = install4jConfFile
1887 // create an md5 for the input files to use as version for install4j conf file
1888 def digest = MessageDigest.getInstance("MD5")
1890 (file("${install4jDir}/${install4j_template}").text +
1891 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1892 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1893 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1894 if (filesMd5.length() >= 8) {
1895 filesMd5 = filesMd5.substring(0,8)
1897 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1898 // make install4jBuildDir relative to jalviewDir
1899 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1902 'JALVIEW_NAME': jalview_name,
1903 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1904 'JALVIEW_DIR': "../..",
1905 'OSX_KEYSTORE': OSX_KEYSTORE,
1906 'OSX_APPLEID': OSX_APPLEID,
1907 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
1908 'JSIGN_SH': JSIGN_SH,
1909 'JRE_DIR': getdown_app_dir_java,
1910 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1911 'JALVIEW_VERSION': JALVIEW_VERSION,
1912 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1913 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1914 'JAVA_VERSION': JAVA_VERSION,
1915 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1916 'VERSION': JALVIEW_VERSION,
1917 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1918 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1919 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1920 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1921 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1922 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1923 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1924 'BUNDLE_ID': install4jBundleId,
1925 'INTERNAL_ID': install4jInternalId,
1926 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1927 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
1928 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1929 'WRAPPER_LINK': getdownWrapperLink,
1930 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
1931 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
1932 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
1933 'INSTALLER_NAME': install4jInstallerName,
1934 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1935 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1936 'GETDOWN_FILES_DIR': getdown_files_dir,
1937 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1938 'GETDOWN_DIST_DIR': getdownAppDistDir,
1939 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1940 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1941 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1942 'BUILD_DIR': install4jBuildDir,
1943 'APPLICATION_CATEGORIES': install4j_application_categories,
1944 'APPLICATION_FOLDER': install4jApplicationFolder,
1945 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1946 'EXECUTABLE_NAME': install4jExecutableName,
1947 'EXTRA_SCHEME': install4jExtraScheme,
1948 'MAC_ICONS_FILE': install4jMacIconsFile,
1949 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
1950 'PNG_ICON_FILE': install4jPngIconFile,
1951 'BACKGROUND': install4jBackground,
1955 //println("INSTALL4J VARIABLES:")
1956 //variables.each{k,v->println("${k}=${v}")}
1958 destination = "${jalviewDir}/${install4jBuildDir}"
1959 buildSelected = true
1961 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1963 disableSigning = true
1964 disableNotarization = true
1968 macKeystorePassword = OSX_KEYPASS
1971 if (OSX_ALTOOLPASS) {
1972 appleIdPassword = OSX_ALTOOLPASS
1973 disableNotarization = false
1975 disableNotarization = true
1979 println("Using projectFile "+projectFile)
1980 if (!disableNotarization) { println("Will notarize OSX App DMG") }
1984 inputs.dir(getdownWebsiteDir)
1985 inputs.file(install4jConfFile)
1986 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
1987 inputs.dir(macosJavaVMDir)
1988 inputs.dir(windowsJavaVMDir)
1989 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
1995 eclipse().configFile(eclipse_codestyle_file)
2000 task sourceDist(type: Tar) {
2001 group "distribution"
2002 description "Create a source .tar.gz file for distribution"
2004 dependsOn createBuildProperties
2005 dependsOn convertMdFiles
2007 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
2008 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
2009 archiveFileName = outputFileName
2011 compression Compression.GZIP
2026 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2028 "utils/InstallAnywhere",
2043 "gradle.properties",
2054 ".settings/org.eclipse.jdt.core.jalview.prefs",
2058 exclude (EXCLUDE_FILES)
2059 include (PROCESS_FILES)
2060 filter(ReplaceTokens,
2064 'Version-Rel': JALVIEW_VERSION,
2065 'Year-Rel': getDate("yyyy")
2070 exclude (EXCLUDE_FILES)
2071 exclude (PROCESS_FILES)
2072 exclude ("appletlib")
2073 exclude ("**/*locales")
2074 exclude ("*locales/**")
2075 exclude ("utils/InstallAnywhere")
2077 exclude (getdown_files_dir)
2078 exclude (getdown_website_dir)
2080 // exluding these as not using jars as modules yet
2081 exclude ("${j11modDir}/**/*.jar")
2084 include(INCLUDE_FILES)
2086 // from (jalviewDir) {
2087 // // explicit includes for stuff that seemed to not get included
2088 // include(fileTree("test/**/*."))
2089 // exclude(EXCLUDE_FILES)
2090 // exclude(PROCESS_FILES)
2093 from(file(buildProperties).getParent()) {
2094 include(file(buildProperties).getName())
2095 rename(file(buildProperties).getName(), "build_properties")
2097 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2106 dependsOn pubhtmlhelp
2108 inputs.dir("${helpBuildDir}/${help_dir}")
2109 outputs.dir("${buildDir}/distributions/${help_dir}")
2113 task j2sSetHeadlessBuild {
2120 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2122 description "Enable the alternative J2S Config file for headless build"
2124 outputFile = jalviewjsJ2sSettingsFileName
2125 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2126 def j2sProps = new Properties()
2127 if (j2sPropsFile.exists()) {
2129 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2130 j2sProps.load(j2sPropsFileFIS)
2131 j2sPropsFileFIS.close()
2133 j2sProps.each { prop, val ->
2136 } catch (Exception e) {
2137 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2141 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2142 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2147 task jalviewjsSetEclipseWorkspace {
2148 def propKey = "jalviewjs_eclipse_workspace"
2150 if (project.hasProperty(propKey)) {
2151 propVal = project.getProperty(propKey)
2152 if (propVal.startsWith("~/")) {
2153 propVal = System.getProperty("user.home") + propVal.substring(1)
2156 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2157 def propsFile = file(propsFileName)
2158 def eclipseWsDir = propVal
2159 def props = new Properties()
2161 def writeProps = true
2162 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2163 def ins = new FileInputStream(propsFileName)
2166 if (props.getProperty(propKey, null) != null) {
2167 eclipseWsDir = props.getProperty(propKey)
2172 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2173 def tempDir = File.createTempDir()
2174 eclipseWsDir = tempDir.getAbsolutePath()
2177 eclipseWorkspace = file(eclipseWsDir)
2180 // do not run a headless transpile when we claim to be in Eclipse
2182 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2183 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2185 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2189 props.setProperty(propKey, eclipseWsDir)
2190 propsFile.parentFile.mkdirs()
2191 def bytes = new ByteArrayOutputStream()
2192 props.store(bytes, null)
2193 def propertiesString = bytes.toString()
2194 propsFile.text = propertiesString
2200 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2203 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2204 outputs.file(propsFileName)
2205 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2209 task jalviewjsEclipsePaths {
2212 def eclipseRoot = jalviewjs_eclipse_root
2213 if (eclipseRoot.startsWith("~/")) {
2214 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2216 if (OperatingSystem.current().isMacOsX()) {
2217 eclipseRoot += "/Eclipse.app"
2218 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2219 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2220 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2221 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2222 eclipseRoot += "/eclipse"
2224 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2225 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2226 } else { // linux or unix
2227 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2228 eclipseRoot += "/eclipse"
2229 println("eclipseDir exists")
2231 eclipseBinary = "${eclipseRoot}/eclipse"
2232 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2235 eclipseVersion = "4.13" // default
2236 def assumedVersion = true
2237 if (file(eclipseProduct).exists()) {
2238 def fis = new FileInputStream(eclipseProduct)
2239 def props = new Properties()
2241 eclipseVersion = props.getProperty("version")
2243 assumedVersion = false
2246 def propKey = "eclipse_debug"
2247 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2250 // do not run a headless transpile when we claim to be in Eclipse
2252 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2253 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2255 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2258 if (!assumedVersion) {
2259 println("ECLIPSE VERSION=${eclipseVersion}")
2265 task printProperties {
2267 description "Output to console all System.properties"
2269 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2275 dependsOn eclipseProject
2276 dependsOn eclipseClasspath
2277 dependsOn eclipseJdt
2281 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2282 task jalviewjsEclipseCopyDropins(type: Copy) {
2283 dependsOn jalviewjsEclipsePaths
2285 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2286 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2287 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2294 // this eclipse -clean doesn't actually work
2295 task jalviewjsCleanEclipse(type: Exec) {
2296 dependsOn eclipseSetup
2297 dependsOn jalviewjsEclipsePaths
2298 dependsOn jalviewjsEclipseCopyDropins
2300 executable(eclipseBinary)
2301 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2307 def inputString = """exit
2310 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2311 standardInput = inputByteStream
2314 /* not really working yet
2315 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2319 task jalviewjsTransferUnzipSwingJs {
2320 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2324 from zipTree(file_zip)
2325 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2329 inputs.file file_zip
2330 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2334 task jalviewjsTransferUnzipLib {
2335 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2338 zipFiles.each { file_zip ->
2340 from zipTree(file_zip)
2341 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2346 inputs.files zipFiles
2347 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2351 task jalviewjsTransferUnzipAllLibs {
2352 dependsOn jalviewjsTransferUnzipSwingJs
2353 dependsOn jalviewjsTransferUnzipLib
2357 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2359 description "Create the alternative j2s file from the j2s.* properties"
2361 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2362 def siteDirProperty = "j2s.site.directory"
2363 def setSiteDir = false
2364 jalviewjsJ2sProps.each { prop, val ->
2366 if (prop == siteDirProperty) {
2367 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2368 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2374 if (!setSiteDir) { // default site location, don't override specifically set property
2375 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2378 outputFile = jalviewjsJ2sAltSettingsFileName
2381 inputs.properties(jalviewjsJ2sProps)
2382 outputs.file(jalviewjsJ2sAltSettingsFileName)
2387 task jalviewjsEclipseSetup {
2388 dependsOn jalviewjsEclipseCopyDropins
2389 dependsOn jalviewjsSetEclipseWorkspace
2390 dependsOn jalviewjsCreateJ2sSettings
2394 task jalviewjsSyncAllLibs (type: Sync) {
2395 dependsOn jalviewjsTransferUnzipAllLibs
2396 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2397 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2398 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2402 def outputFiles = []
2403 rename { filename ->
2404 outputFiles += "${outputDir}/${filename}"
2411 // should this be exclude really ?
2412 duplicatesStrategy "INCLUDE"
2414 outputs.files outputFiles
2415 inputs.files inputFiles
2419 task jalviewjsSyncResources (type: Sync) {
2420 dependsOn buildResources
2422 def inputFiles = fileTree(dir: resourcesBuildDir)
2423 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2427 def outputFiles = []
2428 rename { filename ->
2429 outputFiles += "${outputDir}/${filename}"
2435 outputs.files outputFiles
2436 inputs.files inputFiles
2440 task jalviewjsSyncSiteResources (type: Sync) {
2441 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2442 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2446 def outputFiles = []
2447 rename { filename ->
2448 outputFiles += "${outputDir}/${filename}"
2454 outputs.files outputFiles
2455 inputs.files inputFiles
2459 task jalviewjsSyncBuildProperties (type: Sync) {
2460 dependsOn createBuildProperties
2461 def inputFiles = [file(buildProperties)]
2462 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2466 def outputFiles = []
2467 rename { filename ->
2468 outputFiles += "${outputDir}/${filename}"
2474 outputs.files outputFiles
2475 inputs.files inputFiles
2479 task jalviewjsProjectImport(type: Exec) {
2480 dependsOn eclipseSetup
2481 dependsOn jalviewjsEclipsePaths
2482 dependsOn jalviewjsEclipseSetup
2485 // do not run a headless import when we claim to be in Eclipse
2487 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2488 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2490 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2494 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2495 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2496 executable(eclipseBinary)
2497 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2501 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2503 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2504 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2507 inputs.file("${jalviewDir}/.project")
2508 outputs.upToDateWhen {
2509 file(projdir).exists()
2514 task jalviewjsTranspile(type: Exec) {
2515 dependsOn jalviewjsEclipseSetup
2516 dependsOn jalviewjsProjectImport
2517 dependsOn jalviewjsEclipsePaths
2519 dependsOn jalviewjsEnableAltFileProperty
2523 // do not run a headless transpile when we claim to be in Eclipse
2525 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2526 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2528 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2532 executable(eclipseBinary)
2533 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2537 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2539 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2540 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2546 stdout = new ByteArrayOutputStream()
2547 stderr = new ByteArrayOutputStream()
2549 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2550 def logOutFile = file(logOutFileName)
2551 logOutFile.createNewFile()
2552 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2553 BINARY: ${eclipseBinary}
2554 VERSION: ${eclipseVersion}
2555 WORKSPACE: ${eclipseWorkspace}
2556 DEBUG: ${eclipseDebug}
2559 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2560 // combine stdout and stderr
2561 def logErrFOS = logOutFOS
2563 if (jalviewjs_j2s_to_console.equals("true")) {
2564 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2565 new org.apache.tools.ant.util.TeeOutputStream(
2569 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2570 new org.apache.tools.ant.util.TeeOutputStream(
2575 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2578 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2585 if (stdout.toString().contains("Error processing ")) {
2586 // j2s did not complete transpile
2587 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2588 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2589 println("IGNORING TRANSPILE ERRORS")
2590 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2592 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2597 inputs.dir("${jalviewDir}/${sourceDir}")
2598 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2599 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2603 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2605 def stdout = new ByteArrayOutputStream()
2606 def stderr = new ByteArrayOutputStream()
2608 def coreFile = file(jsfile)
2610 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2612 logOutFile.createNewFile()
2613 logOutFile.append(msg+"\n")
2615 def coreTop = file(prefixFile)
2616 def coreBottom = file(suffixFile)
2617 coreFile.getParentFile().mkdirs()
2618 coreFile.createNewFile()
2619 coreFile.write( coreTop.getText("UTF-8") )
2623 def t = f.getText("UTF-8")
2624 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2625 coreFile.append( t )
2627 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2629 logOutFile.append(msg+"\n")
2632 coreFile.append( coreBottom.getText("UTF-8") )
2634 msg = "Generating ${zjsfile}"
2636 logOutFile.append(msg+"\n")
2637 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2638 def logErrFOS = logOutFOS
2641 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2642 main = "com.google.javascript.jscomp.CommandLineRunner"
2643 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2644 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2647 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2649 logOutFile.append(msg+"\n")
2651 if (logOutConsole) {
2652 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2653 new org.apache.tools.ant.util.TeeOutputStream(
2657 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2658 new org.apache.tools.ant.util.TeeOutputStream(
2663 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2666 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2673 logOutFile.append(msg+"\n")
2677 task jalviewjsBuildAllCores {
2679 description "Build the core js lib closures listed in the classlists dir"
2680 dependsOn jalviewjsTranspile
2681 dependsOn jalviewjsTransferUnzipSwingJs
2683 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2684 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2685 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2686 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2687 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2688 def prefixFile = "${jsDir}/core/coretop2.js"
2689 def suffixFile = "${jsDir}/core/corebottom2.js"
2691 inputs.file prefixFile
2692 inputs.file suffixFile
2694 def classlistFiles = []
2695 // add the classlists found int the jalviewjs_classlists_dir
2696 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2698 def name = file.getName() - ".txt"
2705 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2706 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2707 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2709 jalviewjsCoreClasslists = []
2711 classlistFiles.each {
2714 def file = hash['file']
2715 if (! file.exists()) {
2716 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2717 return false // this is a "continue" in groovy .each closure
2719 def name = hash['name']
2721 name = file.getName() - ".txt"
2729 def list = fileTree(dir: j2sDir, includes: filelist)
2731 def jsfile = "${outputDir}/core${name}.js"
2732 def zjsfile = "${outputDir}/core${name}.z.js"
2734 jalviewjsCoreClasslists += [
2743 outputs.file(jsfile)
2744 outputs.file(zjsfile)
2747 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2748 def stevesoftClasslistName = "_stevesoft"
2749 def stevesoftClasslist = [
2750 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2751 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2752 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2753 'name': stevesoftClasslistName
2755 jalviewjsCoreClasslists += stevesoftClasslist
2756 inputs.files(stevesoftClasslist['list'])
2757 outputs.file(stevesoftClasslist['jsfile'])
2758 outputs.file(stevesoftClasslist['zjsfile'])
2761 def allClasslistName = "_all"
2762 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2763 allJsFiles += fileTree(
2767 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2768 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2769 "**/org/jmol/export/JSExporter.js"
2772 allJsFiles += fileTree(
2776 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2777 "**/sun/misc/Unsafe.js",
2778 "**/swingjs/jquery/jquery-editable-select.js",
2779 "**/swingjs/jquery/j2sComboBox.js",
2780 "**/sun/misc/FloatingDecimal.js"
2783 def allClasslist = [
2784 'jsfile': "${outputDir}/core${allClasslistName}.js",
2785 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2787 'name': allClasslistName
2789 // not including this version of "all" core at the moment
2790 //jalviewjsCoreClasslists += allClasslist
2791 inputs.files(allClasslist['list'])
2792 outputs.file(allClasslist['jsfile'])
2793 outputs.file(allClasslist['zjsfile'])
2796 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2797 logOutFile.getParentFile().mkdirs()
2798 logOutFile.createNewFile()
2799 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2801 jalviewjsCoreClasslists.each {
2802 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2809 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2812 into file(outputFile).getParentFile()
2813 rename { filename ->
2814 if (filename.equals(inputFile.getName())) {
2815 return file(outputFile).getName()
2819 filter(ReplaceTokens,
2823 'MAIN': '"'+main_class+'"',
2825 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2826 'COREKEY': jalviewjs_core_key,
2827 'CORENAME': coreName
2834 task jalviewjsPublishCoreTemplates {
2835 dependsOn jalviewjsBuildAllCores
2836 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2837 def inputFile = file(inputFileName)
2838 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2840 def outputFiles = []
2841 jalviewjsCoreClasslists.each { cl ->
2842 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2843 cl['outputfile'] = outputFile
2844 outputFiles += outputFile
2848 jalviewjsCoreClasslists.each { cl ->
2849 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2852 inputs.file(inputFile)
2853 outputs.files(outputFiles)
2857 task jalviewjsSyncCore (type: Sync) {
2858 dependsOn jalviewjsBuildAllCores
2859 dependsOn jalviewjsPublishCoreTemplates
2860 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2861 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2865 def outputFiles = []
2866 rename { filename ->
2867 outputFiles += "${outputDir}/${filename}"
2873 outputs.files outputFiles
2874 inputs.files inputFiles
2878 // this Copy version of TransferSiteJs will delete anything else in the target dir
2879 task jalviewjsCopyTransferSiteJs(type: Copy) {
2880 dependsOn jalviewjsTranspile
2881 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2882 into "${jalviewDir}/${jalviewjsSiteDir}"
2886 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2887 task jalviewjsSyncTransferSiteJs(type: Sync) {
2888 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2890 into "${jalviewDir}/${jalviewjsSiteDir}"
2897 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2898 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2899 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2900 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2902 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2903 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2904 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2905 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2908 task jalviewjsPrepareSite {
2910 description "Prepares the website folder including unzipping files and copying resources"
2911 dependsOn jalviewjsSyncAllLibs
2912 dependsOn jalviewjsSyncResources
2913 dependsOn jalviewjsSyncSiteResources
2914 dependsOn jalviewjsSyncBuildProperties
2915 dependsOn jalviewjsSyncCore
2919 task jalviewjsBuildSite {
2921 description "Builds the whole website including transpiled code"
2922 dependsOn jalviewjsCopyTransferSiteJs
2923 dependsOn jalviewjsPrepareSite
2927 task cleanJalviewjsTransferSite {
2929 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2930 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2931 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2932 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2937 task cleanJalviewjsSite {
2938 dependsOn cleanJalviewjsTransferSite
2940 delete "${jalviewDir}/${jalviewjsSiteDir}"
2945 task jalviewjsSiteTar(type: Tar) {
2947 description "Creates a tar.gz file for the website"
2948 dependsOn jalviewjsBuildSite
2949 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2950 archiveFileName = outputFilename
2952 compression Compression.GZIP
2954 from "${jalviewDir}/${jalviewjsSiteDir}"
2955 into jalviewjs_site_dir // this is inside the tar file
2957 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
2961 task jalviewjsServer {
2963 def filename = "jalviewjsTest.html"
2964 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
2965 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
2970 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
2971 factory = f.newInstance()
2972 } catch (ClassNotFoundException e) {
2973 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
2975 def port = Integer.valueOf(jalviewjs_server_port)
2980 while(port < start+1000 && !running) {
2982 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
2983 jalviewjsServer = factory.start(doc_root, port)
2985 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
2986 println("SERVER STARTED with document root ${doc_root}.")
2987 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
2988 println("For debug: "+url+"?j2sdebug")
2989 println("For verbose: "+url+"?j2sverbose")
2990 } catch (Exception e) {
2995 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
2996 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
2997 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
2999 jalviewjsCoreClasslists.each { cl ->
3000 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3002 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3004 println("For core ${cl.name}: "+urlcore)
3007 file(htmlFile).text = htmlText
3010 outputs.file(htmlFile)
3011 outputs.upToDateWhen({false})
3015 task cleanJalviewjsAll {
3017 description "Delete all configuration and build artifacts to do with JalviewJS build"
3018 dependsOn cleanJalviewjsSite
3019 dependsOn jalviewjsEclipsePaths
3022 delete "${jalviewDir}/${jalviewjsBuildDir}"
3023 delete "${jalviewDir}/${eclipse_bin_dir}"
3024 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3025 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3027 delete jalviewjsJ2sAltSettingsFileName
3030 outputs.upToDateWhen( { false } )
3034 task jalviewjsIDE_checkJ2sPlugin {
3035 group "00 JalviewJS in Eclipse"
3036 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3039 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3040 def j2sPluginFile = file(j2sPlugin)
3041 def eclipseHome = System.properties["eclipse.home.location"]
3042 if (eclipseHome == null || ! IN_ECLIPSE) {
3043 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3045 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3046 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3047 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3048 eclipseJ2sPluginDirs += altPluginsDir
3050 def foundPlugin = false
3051 def j2sPluginFileName = j2sPluginFile.getName()
3052 def eclipseJ2sPlugin
3053 def eclipseJ2sPluginFile
3054 eclipseJ2sPluginDirs.any { dir ->
3055 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3056 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3057 if (eclipseJ2sPluginFile.exists()) {
3063 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3064 System.err.println(msg)
3065 throw new StopExecutionException(msg)
3068 def digest = MessageDigest.getInstance("MD5")
3070 digest.update(j2sPluginFile.text.bytes)
3071 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3073 digest.update(eclipseJ2sPluginFile.text.bytes)
3074 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3076 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3077 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3078 System.err.println(msg)
3079 throw new StopExecutionException(msg)
3081 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3087 task jalviewjsIDE_copyJ2sPlugin {
3088 group "00 JalviewJS in Eclipse"
3089 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3092 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3093 def j2sPluginFile = file(j2sPlugin)
3094 def eclipseHome = System.properties["eclipse.home.location"]
3095 if (eclipseHome == null || ! IN_ECLIPSE) {
3096 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3098 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3099 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3100 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3101 System.err.println(msg)
3104 eclipseJ2sPluginFile.getParentFile().mkdirs()
3105 into eclipseJ2sPluginFile.getParent()
3111 task jalviewjsIDE_j2sFile {
3112 group "00 JalviewJS in Eclipse"
3113 description "Creates the .j2s file"
3114 dependsOn jalviewjsCreateJ2sSettings
3118 task jalviewjsIDE_SyncCore {
3119 group "00 JalviewJS in Eclipse"
3120 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3121 dependsOn jalviewjsSyncCore
3125 task jalviewjsIDE_SyncSiteAll {
3126 dependsOn jalviewjsSyncAllLibs
3127 dependsOn jalviewjsSyncResources
3128 dependsOn jalviewjsSyncSiteResources
3129 dependsOn jalviewjsSyncBuildProperties
3133 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3136 task jalviewjsIDE_PrepareSite {
3137 group "00 JalviewJS in Eclipse"
3138 description "Sync libs and resources to site dir, but not closure cores"
3140 dependsOn jalviewjsIDE_SyncSiteAll
3141 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3145 task jalviewjsIDE_AssembleSite {
3146 group "00 JalviewJS in Eclipse"
3147 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3148 dependsOn jalviewjsPrepareSite
3152 task jalviewjsIDE_SiteClean {
3153 group "00 JalviewJS in Eclipse"
3154 description "Deletes the Eclipse transpiled site"
3155 dependsOn cleanJalviewjsSite
3159 task jalviewjsIDE_Server {
3160 group "00 JalviewJS in Eclipse"
3161 description "Starts a webserver on localhost to test the website"
3162 dependsOn jalviewjsServer
3166 // buildship runs this at import or gradle refresh
3167 task eclipseSynchronizationTask {
3168 //dependsOn eclipseSetup
3169 dependsOn createBuildProperties
3171 dependsOn jalviewjsIDE_j2sFile
3172 dependsOn jalviewjsIDE_checkJ2sPlugin
3173 dependsOn jalviewjsIDE_PrepareSite
3178 // buildship runs this at build time or project refresh
3179 task eclipseAutoBuildTask {
3180 //dependsOn jalviewjsIDE_checkJ2sPlugin
3181 //dependsOn jalviewjsIDE_PrepareSite
3187 description "Build the site"
3188 dependsOn jalviewjsBuildSite