1 /* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
2 * For properties set within build.gradle, use camelCaseNoSpace.
4 import org.apache.tools.ant.filters.ReplaceTokens
5 import org.gradle.internal.os.OperatingSystem
6 import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
7 import org.gradle.api.internal.PropertiesTransformer
8 import org.gradle.util.ConfigureUtil
9 import org.gradle.plugins.ide.eclipse.model.Output
10 import org.gradle.plugins.ide.eclipse.model.Library
11 import java.security.MessageDigest
12 import groovy.transform.ExternalizeMethods
13 import groovy.util.XmlParser
14 import groovy.xml.XmlUtil
15 import com.vladsch.flexmark.util.ast.Node
16 import com.vladsch.flexmark.html.HtmlRenderer
17 import com.vladsch.flexmark.parser.Parser
18 import com.vladsch.flexmark.util.data.MutableDataSet
19 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
20 import com.vladsch.flexmark.ext.tables.TablesExtension
21 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
22 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
23 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
24 import com.vladsch.flexmark.ext.toc.TocExtension
32 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
41 id "com.diffplug.gradle.spotless" version "3.28.0"
42 id 'com.github.johnrengelman.shadow' version '4.0.3'
43 id 'com.install4j.gradle' version '9.0.6'
44 id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
45 id 'com.palantir.git-version' version '0.13.0' apply false
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 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
390 apply plugin: "com.palantir.git-version"
391 def details = versionDetails()
392 gitHash = details.gitHash
393 gitBranch = details.branchName
394 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
395 println("Not in a git repository. Using git values from RELEASE properties file.")
396 gitHash = releaseProps.getProperty("git.hash")
397 gitBranch = releaseProps.getProperty("git.branch")
398 } catch(java.lang.RuntimeException e1) {
399 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
402 println("Using a ${CHANNEL} profile.")
404 additional_compiler_args = []
405 // configure classpath/args for j8/j11 compilation
406 if (JAVA_VERSION.equals("1.8")) {
407 JAVA_INTEGER_VERSION = string("8")
410 libDistDir = j8libDir
411 compile_source_compatibility = 1.8
412 compile_target_compatibility = 1.8
413 // these are getdown.txt properties defined dependent on the JAVA_VERSION
414 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
415 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
416 // this property is assigned below and expanded to multiple lines in the getdown task
417 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
418 // this property is for the Java library used in eclipse
419 eclipseJavaRuntimeName = string("JavaSE-1.8")
420 } else if (JAVA_VERSION.equals("11")) {
421 JAVA_INTEGER_VERSION = string("11")
423 libDistDir = j11libDir
424 compile_source_compatibility = 11
425 compile_target_compatibility = 11
426 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
427 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
428 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
429 eclipseJavaRuntimeName = string("JavaSE-11")
430 /* compile without modules -- using classpath libraries
431 additional_compiler_args += [
432 '--module-path', modules_compileClasspath.asPath,
433 '--add-modules', j11modules
436 } else if (JAVA_VERSION.equals("17")) {
437 JAVA_INTEGER_VERSION = string("17")
439 libDistDir = j17libDir
440 compile_source_compatibility = 17
441 compile_target_compatibility = 17
442 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
443 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
444 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
445 eclipseJavaRuntimeName = string("JavaSE-17")
446 /* compile without modules -- using classpath libraries
447 additional_compiler_args += [
448 '--module-path', modules_compileClasspath.asPath,
449 '--add-modules', j11modules
453 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
458 JAVA_MIN_VERSION = JAVA_VERSION
459 JAVA_MAX_VERSION = JAVA_VERSION
460 def jreInstallsDir = string(jre_installs_dir)
461 if (jreInstallsDir.startsWith("~/")) {
462 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
464 macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
465 windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
466 linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
467 macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz")
468 windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz")
469 linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz")
470 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
471 install4jConfFileName = string("jalview-install4j-conf.install4j")
472 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
473 install4jHomeDir = install4j_home_dir
474 if (install4jHomeDir.startsWith("~/")) {
475 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
478 resourceBuildDir = string("${buildDir}/resources")
479 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
480 helpBuildDir = string("${resourceBuildDir}/help_build")
481 docBuildDir = string("${resourceBuildDir}/doc_build")
483 if (buildProperties == null) {
484 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
486 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
487 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
488 helpSourceDir = string("${helpParentDir}/${help_dir}")
489 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
492 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
493 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
494 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
496 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
498 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
500 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
501 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
502 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
503 jalviewjsJalviewCoreHtmlFile = string("")
504 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
505 jalviewjsCoreClasslists = []
506 jalviewjsJalviewTemplateName = string(jalviewjs_name)
507 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
508 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
509 jalviewjsJ2sProps = null
510 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
512 eclipseWorkspace = null
513 eclipseBinary = string("")
514 eclipseVersion = string("")
524 outputDir = file(classesDir)
528 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
531 compileClasspath = files(sourceSets.main.java.outputDir)
532 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
534 runtimeClasspath = compileClasspath
535 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
540 srcDirs cloverInstrDir
541 outputDir = cloverClassesDir
545 srcDirs = sourceSets.main.resources.srcDirs
548 compileClasspath = files( sourceSets.clover.java.outputDir )
549 //compileClasspath += files( testClassesDir )
550 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
551 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
552 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
554 runtimeClasspath = compileClasspath
559 srcDirs testSourceDir
560 outputDir = file(testClassesDir)
564 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
567 compileClasspath = files( sourceSets.test.java.outputDir )
568 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
569 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
571 runtimeClasspath = compileClasspath
572 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
578 // eclipse project and settings files creation, also used by buildship
581 name = eclipse_project_name
583 natures 'org.eclipse.jdt.core.javanature',
584 'org.eclipse.jdt.groovy.core.groovyNature',
585 'org.eclipse.buildship.core.gradleprojectnature'
587 buildCommand 'org.eclipse.jdt.core.javabuilder'
588 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
592 //defaultOutputDir = sourceSets.main.java.outputDir
593 configurations.each{ c->
594 if (c.isCanBeResolved()) {
595 minusConfigurations += [c]
599 plusConfigurations = [ ]
603 def removeTheseToo = []
604 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
605 cp.entries.each { entry ->
606 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
607 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
608 // we add the resources and help/help dirs in as libs afterwards (see below)
609 if (entry.kind == 'src') {
610 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
611 removeTheseToo += entry
613 alreadyAddedSrcPath.putAt(entry.path, true)
618 cp.entries.removeAll(removeTheseToo)
620 //cp.entries += new Output("${eclipse_bin_dir}/main")
621 if (file(helpParentDir).isDirectory()) {
622 cp.entries += new Library(fileReference(helpParentDir))
624 if (file(resourceDir).isDirectory()) {
625 cp.entries += new Library(fileReference(resourceDir))
628 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
630 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
631 //don't want to add outputDir as eclipse is using its own output dir in bin/main
632 if (it.isDirectory() || ! it.exists()) {
633 // don't add dirs to classpath, especially if they don't exist
634 return false // groovy "continue" in .any closure
636 def itPath = it.toString()
637 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
638 // make relative path
639 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
641 if (alreadyAddedLibPath.get(itPath)) {
642 //println("Not adding duplicate entry "+itPath)
644 //println("Adding entry "+itPath)
645 cp.entries += new Library(fileReference(itPath))
646 alreadyAddedLibPath.put(itPath, true)
650 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
651 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
652 if (it.isDirectory() || ! it.exists()) {
653 // don't add dirs to classpath
654 return false // groovy "continue" in .any closure
657 def itPath = it.toString()
658 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
659 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
661 if (alreadyAddedLibPath.get(itPath)) {
664 def lib = new Library(fileReference(itPath))
665 lib.entryAttributes["test"] = "true"
667 alreadyAddedLibPath.put(itPath, true)
675 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
680 // for the IDE, use java 11 compatibility
681 sourceCompatibility = compile_source_compatibility
682 targetCompatibility = compile_target_compatibility
683 javaRuntimeName = eclipseJavaRuntimeName
685 // add in jalview project specific properties/preferences into eclipse core preferences
687 withProperties { props ->
688 def jalview_prefs = new Properties()
689 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
690 jalview_prefs.load(ins)
692 jalview_prefs.forEach { t, v ->
693 if (props.getAt(t) == null) {
697 // codestyle file -- overrides previous formatter prefs
698 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
699 if (csFile.exists()) {
700 XmlParser parser = new XmlParser()
701 def profiles = parser.parse(csFile)
702 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
703 if (profile != null) {
704 profile.'setting'.each { s ->
706 def value = s.'@value'
707 if (id != null && value != null) {
708 props.putAt(id, value)
719 // Don't want these to be activated if in headless build
720 synchronizationTasks "eclipseSynchronizationTask"
721 //autoBuildTasks "eclipseAutoBuildTask"
727 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
728 // Class to allow updating arbitrary properties files
729 class PropertiesFile extends PropertiesPersistableConfigurationObject {
730 public PropertiesFile(PropertiesTransformer t) { super(t); }
731 @Override protected void load(Properties properties) { }
732 @Override protected void store(Properties properties) { }
733 @Override protected String getDefaultResourceName() { return ""; }
734 // This is necessary, because PropertiesPersistableConfigurationObject fails
735 // if no default properties file exists.
736 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
739 // Task to update arbitrary properties files (set outputFile)
740 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
741 private final PropertiesFileContentMerger file;
742 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
743 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
744 protected void configure(PropertiesFile props) {
745 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
747 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
750 task eclipseUIPreferences(type: PropertiesFileTask) {
751 description = "Generate Eclipse additional settings"
752 def filename = "org.eclipse.jdt.ui.prefs"
753 outputFile = "$projectDir/.settings/${filename}" as File
756 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
761 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
762 description = "Generate Eclipse additional settings"
763 def filename = "org.eclipse.jdt.groovy.core.prefs"
764 outputFile = "$projectDir/.settings/${filename}" as File
767 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
772 task eclipseAllPreferences {
774 dependsOn eclipseUIPreferences
775 dependsOn eclipseGroovyCorePreferences
778 eclipseUIPreferences.mustRunAfter eclipseJdt
779 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
781 /* end of eclipse preferences hack */
789 delete cloverBuildDir
790 delete cloverReportDir
795 task cloverInstrJava(type: JavaExec) {
796 group = "Verification"
797 description = "Create clover instrumented source java files"
799 dependsOn cleanClover
801 inputs.files(sourceSets.main.allJava)
802 outputs.dir(cloverInstrDir)
804 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
805 classpath = sourceSets.clover.compileClasspath
806 main = "com.atlassian.clover.CloverInstr"
814 cloverInstrDir.getPath(),
816 def srcFiles = sourceSets.main.allJava.files
819 { file -> file.absolutePath }
822 args argsList.toArray()
825 delete cloverInstrDir
826 println("Clover: About to instrument "+srcFiles.size() +" files")
831 task cloverInstrTests(type: JavaExec) {
832 group = "Verification"
833 description = "Create clover instrumented source test files"
835 dependsOn cleanClover
837 inputs.files(testDir)
838 outputs.dir(cloverTestInstrDir)
840 classpath = sourceSets.clover.compileClasspath
841 main = "com.atlassian.clover.CloverInstr"
851 cloverTestInstrDir.getPath(),
853 args argsList.toArray()
856 delete cloverTestInstrDir
857 println("Clover: About to instrument test files")
863 group = "Verification"
864 description = "Create clover instrumented all source files"
866 dependsOn cloverInstrJava
867 dependsOn cloverInstrTests
871 cloverClasses.dependsOn cloverInstr
874 task cloverConsoleReport(type: JavaExec) {
875 group = "Verification"
876 description = "Creates clover console report"
879 file(cloverDb).exists()
882 inputs.dir cloverClassesDir
884 classpath = sourceSets.clover.runtimeClasspath
885 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
887 if (cloverreport_mem.length() > 0) {
888 maxHeapSize = cloverreport_mem
890 if (cloverreport_jvmargs.length() > 0) {
891 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
901 args argsList.toArray()
905 task cloverHtmlReport(type: JavaExec) {
906 group = "Verification"
907 description = "Creates clover HTML report"
910 file(cloverDb).exists()
913 def cloverHtmlDir = cloverReportDir
914 inputs.dir cloverClassesDir
915 outputs.dir cloverHtmlDir
917 classpath = sourceSets.clover.runtimeClasspath
918 main = "com.atlassian.clover.reporters.html.HtmlReporter"
920 if (cloverreport_mem.length() > 0) {
921 maxHeapSize = cloverreport_mem
923 if (cloverreport_jvmargs.length() > 0) {
924 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
935 if (cloverreport_html_options.length() > 0) {
936 argsList += cloverreport_html_options.split(" ")
939 args argsList.toArray()
943 task cloverXmlReport(type: JavaExec) {
944 group = "Verification"
945 description = "Creates clover XML report"
948 file(cloverDb).exists()
951 def cloverXmlFile = "${cloverReportDir}/clover.xml"
952 inputs.dir cloverClassesDir
953 outputs.file cloverXmlFile
955 classpath = sourceSets.clover.runtimeClasspath
956 main = "com.atlassian.clover.reporters.xml.XMLReporter"
958 if (cloverreport_mem.length() > 0) {
959 maxHeapSize = cloverreport_mem
961 if (cloverreport_jvmargs.length() > 0) {
962 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
973 if (cloverreport_xml_options.length() > 0) {
974 argsList += cloverreport_xml_options.split(" ")
977 args argsList.toArray()
982 group = "Verification"
983 description = "Creates clover reports"
985 dependsOn cloverXmlReport
986 dependsOn cloverHtmlReport
993 sourceCompatibility = compile_source_compatibility
994 targetCompatibility = compile_target_compatibility
995 options.compilerArgs += additional_compiler_args
996 print ("Setting target compatibility to "+targetCompatibility+"\n")
998 //classpath += configurations.cloverRuntime
1004 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1005 sourceCompatibility = compile_source_compatibility
1006 targetCompatibility = compile_target_compatibility
1007 options.compilerArgs = additional_compiler_args
1008 options.encoding = "UTF-8"
1010 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1017 sourceCompatibility = compile_source_compatibility
1018 targetCompatibility = compile_target_compatibility
1019 options.compilerArgs = additional_compiler_args
1021 print ("Setting target compatibility to "+targetCompatibility+"\n")
1028 delete sourceSets.main.java.outputDir
1034 dependsOn cleanClover
1036 delete sourceSets.test.java.outputDir
1041 // format is a string like date.format("dd MMMM yyyy")
1042 def getDate(format) {
1043 def date = new Date()
1044 return date.format(format)
1048 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1049 MutableDataSet options = new MutableDataSet()
1051 def extensions = new ArrayList<>()
1052 extensions.add(AnchorLinkExtension.create())
1053 extensions.add(AutolinkExtension.create())
1054 extensions.add(StrikethroughExtension.create())
1055 extensions.add(TaskListExtension.create())
1056 extensions.add(TablesExtension.create())
1057 extensions.add(TocExtension.create())
1059 options.set(Parser.EXTENSIONS, extensions)
1061 // set GFM table parsing options
1062 options.set(TablesExtension.WITH_CAPTION, false)
1063 options.set(TablesExtension.COLUMN_SPANS, false)
1064 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1065 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1066 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1067 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1068 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1070 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1071 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1072 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1073 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1075 Parser parser = Parser.builder(options).build()
1076 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1078 mdFiles.each { mdFile ->
1079 // add table of contents
1080 def mdText = "[TOC]\n"+mdFile.text
1082 // grab the first top-level title
1084 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1085 def matcher = mdText =~ titleRegex
1086 if (matcher.size() > 0) {
1087 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1088 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1090 // or use the filename if none found
1091 if (title == null) {
1092 title = mdFile.getName()
1095 Node document = parser.parse(mdText)
1096 String htmlBody = renderer.render(document)
1097 def htmlText = '''<html>
1098 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1099 <html xmlns="http://www.w3.org/1999/xhtml">
1101 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1102 <meta http-equiv="Content-Style-Type" content="text/css" />
1103 <meta name="generator" content="flexmark" />
1105 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1107 <style type="text/css">code{white-space: pre;}</style>
1109 htmlText += ((cssFile != null) ? cssFile.text : '')
1110 htmlText += '''</head>
1113 htmlText += htmlBody
1119 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1120 def htmlFile = file(htmlFilePath)
1121 println("Creating ${htmlFilePath}")
1122 htmlFile.text = htmlText
1127 task copyDocs(type: Copy) {
1128 def inputDir = "${jalviewDir}/${doc_dir}"
1129 def outputDir = "${docBuildDir}/${doc_dir}"
1133 include('**/*.html')
1135 filter(ReplaceTokens,
1139 'Version-Rel': JALVIEW_VERSION,
1140 'Year-Rel': getDate("yyyy")
1147 exclude('**/*.html')
1152 inputs.dir(inputDir)
1153 outputs.dir(outputDir)
1157 task convertMdFiles {
1159 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1160 def cssFile = file("${jalviewDir}/${flexmark_css}")
1163 convertMdToHtml(mdFiles, cssFile)
1166 inputs.files(mdFiles)
1167 inputs.file(cssFile)
1170 mdFiles.each { mdFile ->
1171 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1172 htmlFiles.add(file(htmlFilePath))
1174 outputs.files(htmlFiles)
1178 task copyHelp(type: Copy) {
1179 def inputDir = helpSourceDir
1180 def outputDir = "${helpBuildDir}/${help_dir}"
1184 include('**/*.html')
1188 filter(ReplaceTokens,
1192 'Version-Rel': JALVIEW_VERSION,
1193 'Year-Rel': getDate("yyyy")
1200 exclude('**/*.html')
1207 inputs.dir(inputDir)
1208 outputs.files(helpFile)
1209 outputs.dir(outputDir)
1213 task copyResources(type: Copy) {
1215 description = "Copy (and make text substitutions in) the resources dir to the build area"
1217 def inputDir = resourceDir
1218 def outputDir = resourcesBuildDir
1222 include('**/*.html')
1224 filter(ReplaceTokens,
1228 'Version-Rel': JALVIEW_VERSION,
1229 'Year-Rel': getDate("yyyy")
1236 exclude('**/*.html')
1241 inputs.dir(inputDir)
1242 outputs.dir(outputDir)
1245 task copyChannelResources(type: Copy) {
1246 dependsOn copyResources
1248 description = "Copy the channel resources dir to the build resources area"
1250 def inputDir = "${channelDir}/${resource_dir}"
1251 def outputDir = resourcesBuildDir
1255 inputs.dir(inputDir)
1256 outputs.dir(outputDir)
1259 task createBuildProperties(type: WriteProperties) {
1260 dependsOn copyResources
1262 description = "Create the ${buildProperties} file"
1264 inputs.dir(sourceDir)
1265 inputs.dir(resourcesBuildDir)
1266 outputFile (buildProperties)
1267 // taking time specific comment out to allow better incremental builds
1268 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1269 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1270 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1271 property "VERSION", JALVIEW_VERSION
1272 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1273 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1274 if (getdownSetAppBaseProperty) {
1275 property "GETDOWNAPPBASE", getdownAppBase
1276 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1278 outputs.file(outputFile)
1282 task buildIndices(type: JavaExec) {
1284 classpath = sourceSets.main.compileClasspath
1285 main = "com.sun.java.help.search.Indexer"
1286 workingDir = "${helpBuildDir}/${help_dir}"
1289 inputs.dir("${workingDir}/${argDir}")
1291 outputs.dir("${classesDir}/doc")
1292 outputs.dir("${classesDir}/help")
1293 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1294 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1295 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1296 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1297 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1298 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1301 task buildResources {
1302 dependsOn copyResources
1303 dependsOn copyChannelResources
1304 dependsOn createBuildProperties
1308 dependsOn buildResources
1311 dependsOn convertMdFiles
1312 dependsOn buildIndices
1316 compileJava.dependsOn prepare
1317 run.dependsOn compileJava
1318 //run.dependsOn prepare
1321 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1326 dependsOn cloverClasses
1328 dependsOn compileJava //?
1332 includeGroups testng_groups
1333 excludeGroups testng_excluded_groups
1335 useDefaultListeners=true
1338 maxHeapSize = "1024m"
1340 workingDir = jalviewDir
1341 def testLaf = project.findProperty("test_laf")
1342 if (testLaf != null) {
1343 println("Setting Test LaF to '${testLaf}'")
1344 systemProperty "laf", testLaf
1346 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1347 if (testHiDPIScale != null) {
1348 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1349 systemProperty "sun.java2d.uiScale", testHiDPIScale
1351 sourceCompatibility = compile_source_compatibility
1352 targetCompatibility = compile_target_compatibility
1353 jvmArgs += additional_compiler_args
1357 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1363 task compileLinkCheck(type: JavaCompile) {
1365 classpath = files("${jalviewDir}/${utils_dir}")
1366 destinationDir = file("${jalviewDir}/${utils_dir}")
1367 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1369 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1370 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1371 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1372 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1376 task linkCheck(type: JavaExec) {
1378 dependsOn compileLinkCheck
1380 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1381 classpath = files("${jalviewDir}/${utils_dir}")
1382 main = "HelpLinksChecker"
1383 workingDir = jalviewDir
1384 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1386 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1387 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1390 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1394 inputs.dir(helpBuildDir)
1395 outputs.file(helpLinksCheckerOutFile)
1399 // import the pubhtmlhelp target
1400 ant.properties.basedir = "${jalviewDir}"
1401 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1402 ant.importBuild "${utils_dir}/publishHelp.xml"
1405 task cleanPackageDir(type: Delete) {
1407 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1417 attributes "Main-Class": main_class,
1418 "Permissions": "all-permissions",
1419 "Application-Name": install4jApplicationName,
1420 "Codebase": application_codebase,
1421 "Implementation-Version": JALVIEW_VERSION
1424 def outputDir = "${jalviewDir}/${package_dir}"
1425 destinationDirectory = file(outputDir)
1426 archiveFileName = rootProject.name+".jar"
1427 duplicatesStrategy "EXCLUDE"
1434 exclude "**/*.jar.*"
1436 inputs.dir(sourceSets.main.java.outputDir)
1437 sourceSets.main.resources.srcDirs.each{ dir ->
1440 outputs.file("${outputDir}/${archiveFileName}")
1444 task copyJars(type: Copy) {
1445 from fileTree(dir: classesDir, include: "**/*.jar").files
1446 into "${jalviewDir}/${package_dir}"
1450 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1451 task syncJars(type: Sync) {
1453 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1454 into "${jalviewDir}/${package_dir}"
1456 include jar.archiveFileName.getOrNull()
1463 description = "Put all required libraries in dist"
1464 // order of "cleanPackageDir", "copyJars", "jar" important!
1465 jar.mustRunAfter cleanPackageDir
1466 syncJars.mustRunAfter cleanPackageDir
1467 dependsOn cleanPackageDir
1470 outputs.dir("${jalviewDir}/${package_dir}")
1475 dependsOn cleanPackageDir
1482 group = "distribution"
1483 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1487 from ("${jalviewDir}/${libDistDir}") {
1491 attributes "Implementation-Version": JALVIEW_VERSION,
1492 "Application-Name": install4jApplicationName
1495 duplicatesStrategy "INCLUDE"
1497 mainClassName = shadow_jar_main_class
1499 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1504 task getdownWebsite() {
1505 group = "distribution"
1506 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1511 def getdownWebsiteResourceFilenames = []
1512 def getdownTextString = ""
1513 def getdownResourceDir = getdownResourceDir
1514 def getdownResourceFilenames = []
1517 // clean the getdown website and files dir before creating getdown folders
1518 delete getdownWebsiteDir
1519 delete getdownFilesDir
1522 from buildProperties
1523 rename(file(buildProperties).getName(), getdown_build_properties)
1526 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1529 from channelPropsFile
1530 into getdownWebsiteDir
1532 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
1534 // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
1535 def props = project.properties.sort { it.key }
1536 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
1537 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
1539 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
1540 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
1542 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
1543 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
1545 if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
1546 props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
1547 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
1548 props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
1549 props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
1550 props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
1551 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
1554 props.put("getdown_txt_title", jalview_name)
1555 props.put("getdown_txt_ui.name", install4jApplicationName)
1557 // start with appbase
1558 getdownTextString += "appbase = ${getdownAppBase}\n"
1559 props.each{ prop, val ->
1560 if (prop.startsWith("getdown_txt_") && val != null) {
1561 if (prop.startsWith("getdown_txt_multi_")) {
1562 def key = prop.substring(18)
1563 val.split(",").each{ v ->
1564 def line = "${key} = ${v}\n"
1565 getdownTextString += line
1568 // file values rationalised
1569 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
1571 if (val.indexOf('/') == 0) {
1574 } else if (val.indexOf('/') > 0) {
1575 // relative path (relative to jalviewDir)
1576 r = file( "${jalviewDir}/${val}" )
1579 val = "${getdown_resource_dir}/" + r.getName()
1580 getdownWebsiteResourceFilenames += val
1581 getdownResourceFilenames += r.getPath()
1584 if (! prop.startsWith("getdown_txt_resource")) {
1585 def line = prop.substring(12) + " = ${val}\n"
1586 getdownTextString += line
1592 getdownWebsiteResourceFilenames.each{ filename ->
1593 getdownTextString += "resource = ${filename}\n"
1595 getdownResourceFilenames.each{ filename ->
1598 into getdownResourceDir
1602 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
1603 getdownWrapperScripts.each{ script ->
1604 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
1608 into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
1610 getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
1615 fileTree(file(package_dir)).each{ f ->
1616 if (f.isDirectory()) {
1617 def files = fileTree(dir: f, include: ["*"]).getFiles()
1619 } else if (f.exists()) {
1623 def jalviewJar = jar.archiveFileName.getOrNull()
1624 // put jalview.jar first for CLASSPATH and .properties files reasons
1625 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
1626 def name = f.getName()
1627 def line = "code = ${getdownAppDistDir}/${name}\n"
1628 getdownTextString += line
1635 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
1637 if (JAVA_VERSION.equals("11")) {
1638 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
1639 j11libFiles.sort().each{f ->
1640 def name = f.getName()
1641 def line = "code = ${getdown_j11lib_dir}/${name}\n"
1642 getdownTextString += line
1645 into getdownJ11libDir
1651 // 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.
1652 //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
1653 getdownTextString += "resource = ${getdown_launcher_new}\n"
1654 getdownTextString += "class = ${main_class}\n"
1655 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
1656 if (getdownSetAppBaseProperty) {
1657 getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
1658 getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
1661 def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
1662 getdown_txt.write(getdownTextString)
1664 def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
1665 def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
1666 launchJvl.write("appbase=${getdownAppBase}")
1668 // files going into the getdown website dir: getdown-launcher.jar
1670 from getdownLauncher
1671 rename(file(getdownLauncher).getName(), getdown_launcher_new)
1672 into getdownWebsiteDir
1675 // files going into the getdown website dir: getdown-launcher(-local).jar
1677 from getdownLauncher
1678 if (file(getdownLauncher).getName() != getdown_launcher) {
1679 rename(file(getdownLauncher).getName(), getdown_launcher)
1681 into getdownWebsiteDir
1684 // files going into the getdown website dir: ./install dir and files
1685 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
1688 from getdownLauncher
1689 from "${getdownAppDir}/${getdown_build_properties}"
1690 if (file(getdownLauncher).getName() != getdown_launcher) {
1691 rename(file(getdownLauncher).getName(), getdown_launcher)
1693 into getdownInstallDir
1696 // and make a copy in the getdown files dir (these are not downloaded by getdown)
1698 from getdownInstallDir
1699 into getdownFilesInstallDir
1703 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
1707 from getdownLauncher
1708 from "${getdownWebsiteDir}/${getdown_build_properties}"
1709 from "${getdownWebsiteDir}/${channel_props}"
1710 if (file(getdownLauncher).getName() != getdown_launcher) {
1711 rename(file(getdownLauncher).getName(), getdown_launcher)
1713 into getdownFilesDir
1716 // and ./resources (not all downloaded by getdown)
1718 from getdownResourceDir
1719 into "${getdownFilesDir}/${getdown_resource_dir}"
1724 inputs.dir("${jalviewDir}/${package_dir}")
1726 outputs.dir(getdownWebsiteDir)
1727 outputs.dir(getdownFilesDir)
1731 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
1732 task getdownDigestDir(type: JavaExec) {
1734 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
1736 def digestDirPropertyName = "DIGESTDIR"
1738 classpath = files(getdownLauncher)
1739 def digestDir = findProperty(digestDirPropertyName)
1740 if (digestDir == null) {
1741 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
1745 main = "com.threerings.getdown.tools.Digester"
1749 task getdownDigest(type: JavaExec) {
1750 group = "distribution"
1751 description = "Digest the getdown website folder"
1752 dependsOn getdownWebsite
1754 classpath = files(getdownLauncher)
1756 main = "com.threerings.getdown.tools.Digester"
1757 args getdownWebsiteDir
1758 inputs.dir(getdownWebsiteDir)
1759 outputs.file("${getdownWebsiteDir}/digest2.txt")
1764 group = "distribution"
1765 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1766 dependsOn getdownDigest
1768 if (reportRsyncCommand) {
1769 def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1770 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1771 println "LIKELY RSYNC COMMAND:"
1772 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1773 if (RUNRSYNC == "true") {
1775 commandLine "mkdir", "-p", toDir
1778 commandLine "rsync", "-avh", "--delete", fromDir, toDir
1786 tasks.withType(JavaCompile) {
1787 options.encoding = 'UTF-8'
1793 delete getdownWebsiteDir
1794 delete getdownFilesDir
1800 if (file(install4jHomeDir).exists()) {
1802 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
1803 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1804 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
1805 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
1807 installDir(file(install4jHomeDir))
1809 mediaTypes = Arrays.asList(install4j_media_types.split(","))
1813 task copyInstall4jTemplate {
1814 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
1815 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
1816 inputs.file(install4jTemplateFile)
1817 inputs.file(install4jFileAssociationsFile)
1818 inputs.property("CHANNEL", { CHANNEL })
1819 outputs.file(install4jConfFile)
1822 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
1824 // turn off code signing if no OSX_KEYPASS
1825 if (OSX_KEYPASS == "") {
1826 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
1827 codeSigning.'@macEnabled' = "false"
1829 install4jConfigXml.'**'.windows.each { windows ->
1830 windows.'@runPostProcessor' = "false"
1834 // disable install screen for OSX dmg (for 2.11.2.0)
1835 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
1836 macosArchive.attributes().remove('executeSetupApp')
1837 macosArchive.attributes().remove('setupAppId')
1840 // turn off checksum creation for LOCAL channel
1841 def e = install4jConfigXml.application[0]
1842 if (CHANNEL == "LOCAL") {
1843 e.'@createChecksums' = "false"
1845 e.'@createChecksums' = "true"
1848 // put file association actions where placeholder action is
1849 def install4jFileAssociationsText = install4jFileAssociationsFile.text
1850 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
1851 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
1852 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
1853 def parent = a.parent()
1855 fileAssociationActions.each { faa ->
1858 // don't need to continue in .any loop once replacements have been made
1863 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
1864 // NB we're deleting the /other/ one!
1865 // Also remove the examples subdir from non-release versions
1866 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
1867 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
1868 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
1869 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
1871 // remove the examples subdir from Full File Set
1872 def files = install4jConfigXml.files[0]
1873 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
1874 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
1875 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
1876 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
1877 dirEntry.parent().remove(dirEntry)
1879 install4jConfigXml.'**'.action.any { a ->
1880 if (a.'@customizedId' == customizedIdToDelete) {
1881 def parent = a.parent()
1887 // write install4j file
1888 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
1895 delete install4jConfFile
1900 task installers(type: com.install4j.gradle.Install4jTask) {
1901 group = "distribution"
1902 description = "Create the install4j installers"
1904 dependsOn copyInstall4jTemplate
1906 projectFile = install4jConfFile
1908 // create an md5 for the input files to use as version for install4j conf file
1909 def digest = MessageDigest.getInstance("MD5")
1911 (file("${install4jDir}/${install4j_template}").text +
1912 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
1913 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
1914 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
1915 if (filesMd5.length() >= 8) {
1916 filesMd5 = filesMd5.substring(0,8)
1918 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
1919 // make install4jBuildDir relative to jalviewDir
1920 def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
1923 'JALVIEW_NAME': jalview_name,
1924 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
1925 'JALVIEW_DIR': "../..",
1926 'OSX_KEYSTORE': OSX_KEYSTORE,
1927 'OSX_APPLEID': OSX_APPLEID,
1928 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
1929 'JSIGN_SH': JSIGN_SH,
1930 'JRE_DIR': getdown_app_dir_java,
1931 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
1932 'JALVIEW_VERSION': JALVIEW_VERSION,
1933 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
1934 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
1935 'JAVA_VERSION': JAVA_VERSION,
1936 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1937 'VERSION': JALVIEW_VERSION,
1938 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1939 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1940 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
1941 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1942 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1943 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
1944 'COPYRIGHT_MESSAGE': install4j_copyright_message,
1945 'BUNDLE_ID': install4jBundleId,
1946 'INTERNAL_ID': install4jInternalId,
1947 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
1948 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
1949 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
1950 'WRAPPER_LINK': getdownWrapperLink,
1951 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
1952 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
1953 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
1954 'INSTALLER_NAME': install4jInstallerName,
1955 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
1956 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
1957 'GETDOWN_FILES_DIR': getdown_files_dir,
1958 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1959 'GETDOWN_DIST_DIR': getdownAppDistDir,
1960 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1961 'GETDOWN_INSTALL_DIR': getdown_install_dir,
1962 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
1963 'BUILD_DIR': install4jBuildDir,
1964 'APPLICATION_CATEGORIES': install4j_application_categories,
1965 'APPLICATION_FOLDER': install4jApplicationFolder,
1966 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
1967 'EXECUTABLE_NAME': install4jExecutableName,
1968 'EXTRA_SCHEME': install4jExtraScheme,
1969 'MAC_ICONS_FILE': install4jMacIconsFile,
1970 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
1971 'PNG_ICON_FILE': install4jPngIconFile,
1972 'BACKGROUND': install4jBackground,
1976 //println("INSTALL4J VARIABLES:")
1977 //variables.each{k,v->println("${k}=${v}")}
1979 destination = "${jalviewDir}/${install4jBuildDir}"
1980 buildSelected = true
1982 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
1984 disableSigning = true
1985 disableNotarization = true
1989 macKeystorePassword = OSX_KEYPASS
1992 if (OSX_ALTOOLPASS) {
1993 appleIdPassword = OSX_ALTOOLPASS
1994 disableNotarization = false
1996 disableNotarization = true
2000 println("Using projectFile "+projectFile)
2001 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2005 inputs.dir(getdownWebsiteDir)
2006 inputs.file(install4jConfFile)
2007 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2008 inputs.dir(macosJavaVMDir)
2009 inputs.dir(windowsJavaVMDir)
2010 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2016 eclipse().configFile(eclipse_codestyle_file)
2020 task createSourceReleaseProperties(type: WriteProperties) {
2021 group = "distribution"
2022 description = "Create the source RELEASE properties file"
2024 def sourceTarBuildDir = "${buildDir}/sourceTar"
2025 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2026 outputFile (sourceReleasePropertiesFile)
2029 releaseProps.each{ key, val -> property key, val }
2030 property "git.branch", gitBranch
2031 property "git.hash", gitHash
2034 outputs.file(outputFile)
2037 task sourceDist(type: Tar) {
2038 group "distribution"
2039 description "Create a source .tar.gz file for distribution"
2041 dependsOn createBuildProperties
2042 dependsOn convertMdFiles
2043 dependsOn eclipseAllPreferences
2044 dependsOn createSourceReleaseProperties
2047 def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
2048 def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
2049 archiveFileName = outputFileName
2051 compression Compression.GZIP
2066 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2068 "utils/InstallAnywhere",
2083 "gradle.properties",
2095 ".settings/org.eclipse.buildship.core.prefs",
2096 ".settings/org.eclipse.jdt.core.prefs"
2100 exclude (EXCLUDE_FILES)
2101 include (PROCESS_FILES)
2102 filter(ReplaceTokens,
2106 'Version-Rel': JALVIEW_VERSION,
2107 'Year-Rel': getDate("yyyy")
2112 exclude (EXCLUDE_FILES)
2113 exclude (PROCESS_FILES)
2114 exclude ("appletlib")
2115 exclude ("**/*locales")
2116 exclude ("*locales/**")
2117 exclude ("utils/InstallAnywhere")
2119 exclude (getdown_files_dir)
2120 exclude (getdown_website_dir)
2122 // exluding these as not using jars as modules yet
2123 exclude ("${j11modDir}/**/*.jar")
2126 include(INCLUDE_FILES)
2128 // from (jalviewDir) {
2129 // // explicit includes for stuff that seemed to not get included
2130 // include(fileTree("test/**/*."))
2131 // exclude(EXCLUDE_FILES)
2132 // exclude(PROCESS_FILES)
2135 from(file(buildProperties).getParent()) {
2136 include(file(buildProperties).getName())
2137 rename(file(buildProperties).getName(), "build_properties")
2139 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2143 def sourceTarBuildDir = "${buildDir}/sourceTar"
2144 from(sourceTarBuildDir) {
2145 // this includes the appended RELEASE properties file
2152 dependsOn pubhtmlhelp
2154 inputs.dir("${helpBuildDir}/${help_dir}")
2155 outputs.dir("${buildDir}/distributions/${help_dir}")
2159 task j2sSetHeadlessBuild {
2166 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2168 description "Enable the alternative J2S Config file for headless build"
2170 outputFile = jalviewjsJ2sSettingsFileName
2171 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2172 def j2sProps = new Properties()
2173 if (j2sPropsFile.exists()) {
2175 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2176 j2sProps.load(j2sPropsFileFIS)
2177 j2sPropsFileFIS.close()
2179 j2sProps.each { prop, val ->
2182 } catch (Exception e) {
2183 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2187 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2188 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2193 task jalviewjsSetEclipseWorkspace {
2194 def propKey = "jalviewjs_eclipse_workspace"
2196 if (project.hasProperty(propKey)) {
2197 propVal = project.getProperty(propKey)
2198 if (propVal.startsWith("~/")) {
2199 propVal = System.getProperty("user.home") + propVal.substring(1)
2202 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2203 def propsFile = file(propsFileName)
2204 def eclipseWsDir = propVal
2205 def props = new Properties()
2207 def writeProps = true
2208 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2209 def ins = new FileInputStream(propsFileName)
2212 if (props.getProperty(propKey, null) != null) {
2213 eclipseWsDir = props.getProperty(propKey)
2218 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2219 def tempDir = File.createTempDir()
2220 eclipseWsDir = tempDir.getAbsolutePath()
2223 eclipseWorkspace = file(eclipseWsDir)
2226 // do not run a headless transpile when we claim to be in Eclipse
2228 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2229 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2231 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2235 props.setProperty(propKey, eclipseWsDir)
2236 propsFile.parentFile.mkdirs()
2237 def bytes = new ByteArrayOutputStream()
2238 props.store(bytes, null)
2239 def propertiesString = bytes.toString()
2240 propsFile.text = propertiesString
2246 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
2249 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
2250 outputs.file(propsFileName)
2251 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
2255 task jalviewjsEclipsePaths {
2258 def eclipseRoot = jalviewjs_eclipse_root
2259 if (eclipseRoot.startsWith("~/")) {
2260 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
2262 if (OperatingSystem.current().isMacOsX()) {
2263 eclipseRoot += "/Eclipse.app"
2264 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
2265 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
2266 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
2267 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2268 eclipseRoot += "/eclipse"
2270 eclipseBinary = "${eclipseRoot}/eclipse.exe"
2271 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2272 } else { // linux or unix
2273 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
2274 eclipseRoot += "/eclipse"
2275 println("eclipseDir exists")
2277 eclipseBinary = "${eclipseRoot}/eclipse"
2278 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
2281 eclipseVersion = "4.13" // default
2282 def assumedVersion = true
2283 if (file(eclipseProduct).exists()) {
2284 def fis = new FileInputStream(eclipseProduct)
2285 def props = new Properties()
2287 eclipseVersion = props.getProperty("version")
2289 assumedVersion = false
2292 def propKey = "eclipse_debug"
2293 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
2296 // do not run a headless transpile when we claim to be in Eclipse
2298 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2299 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2301 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2304 if (!assumedVersion) {
2305 println("ECLIPSE VERSION=${eclipseVersion}")
2311 task printProperties {
2313 description "Output to console all System.properties"
2315 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
2321 dependsOn eclipseProject
2322 dependsOn eclipseClasspath
2323 dependsOn eclipseJdt
2327 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
2328 task jalviewjsEclipseCopyDropins(type: Copy) {
2329 dependsOn jalviewjsEclipsePaths
2331 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
2332 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
2333 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
2340 // this eclipse -clean doesn't actually work
2341 task jalviewjsCleanEclipse(type: Exec) {
2342 dependsOn eclipseSetup
2343 dependsOn jalviewjsEclipsePaths
2344 dependsOn jalviewjsEclipseCopyDropins
2346 executable(eclipseBinary)
2347 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
2353 def inputString = """exit
2356 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
2357 standardInput = inputByteStream
2360 /* not really working yet
2361 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
2365 task jalviewjsTransferUnzipSwingJs {
2366 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
2370 from zipTree(file_zip)
2371 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2375 inputs.file file_zip
2376 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2380 task jalviewjsTransferUnzipLib {
2381 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
2384 zipFiles.each { file_zip ->
2386 from zipTree(file_zip)
2387 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2392 inputs.files zipFiles
2393 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2397 task jalviewjsTransferUnzipAllLibs {
2398 dependsOn jalviewjsTransferUnzipSwingJs
2399 dependsOn jalviewjsTransferUnzipLib
2403 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
2405 description "Create the alternative j2s file from the j2s.* properties"
2407 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
2408 def siteDirProperty = "j2s.site.directory"
2409 def setSiteDir = false
2410 jalviewjsJ2sProps.each { prop, val ->
2412 if (prop == siteDirProperty) {
2413 if (!(val.startsWith('/') || val.startsWith("file://") )) {
2414 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
2420 if (!setSiteDir) { // default site location, don't override specifically set property
2421 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
2424 outputFile = jalviewjsJ2sAltSettingsFileName
2427 inputs.properties(jalviewjsJ2sProps)
2428 outputs.file(jalviewjsJ2sAltSettingsFileName)
2433 task jalviewjsEclipseSetup {
2434 dependsOn jalviewjsEclipseCopyDropins
2435 dependsOn jalviewjsSetEclipseWorkspace
2436 dependsOn jalviewjsCreateJ2sSettings
2440 task jalviewjsSyncAllLibs (type: Sync) {
2441 dependsOn jalviewjsTransferUnzipAllLibs
2442 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
2443 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
2444 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2448 def outputFiles = []
2449 rename { filename ->
2450 outputFiles += "${outputDir}/${filename}"
2457 // should this be exclude really ?
2458 duplicatesStrategy "INCLUDE"
2460 outputs.files outputFiles
2461 inputs.files inputFiles
2465 task jalviewjsSyncResources (type: Sync) {
2466 dependsOn buildResources
2468 def inputFiles = fileTree(dir: resourcesBuildDir)
2469 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2473 def outputFiles = []
2474 rename { filename ->
2475 outputFiles += "${outputDir}/${filename}"
2481 outputs.files outputFiles
2482 inputs.files inputFiles
2486 task jalviewjsSyncSiteResources (type: Sync) {
2487 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
2488 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2492 def outputFiles = []
2493 rename { filename ->
2494 outputFiles += "${outputDir}/${filename}"
2500 outputs.files outputFiles
2501 inputs.files inputFiles
2505 task jalviewjsSyncBuildProperties (type: Sync) {
2506 dependsOn createBuildProperties
2507 def inputFiles = [file(buildProperties)]
2508 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
2512 def outputFiles = []
2513 rename { filename ->
2514 outputFiles += "${outputDir}/${filename}"
2520 outputs.files outputFiles
2521 inputs.files inputFiles
2525 task jalviewjsProjectImport(type: Exec) {
2526 dependsOn eclipseSetup
2527 dependsOn jalviewjsEclipsePaths
2528 dependsOn jalviewjsEclipseSetup
2531 // do not run a headless import when we claim to be in Eclipse
2533 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2534 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2536 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2540 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
2541 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
2542 executable(eclipseBinary)
2543 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
2547 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2549 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2550 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2553 inputs.file("${jalviewDir}/.project")
2554 outputs.upToDateWhen {
2555 file(projdir).exists()
2560 task jalviewjsTranspile(type: Exec) {
2561 dependsOn jalviewjsEclipseSetup
2562 dependsOn jalviewjsProjectImport
2563 dependsOn jalviewjsEclipsePaths
2565 dependsOn jalviewjsEnableAltFileProperty
2569 // do not run a headless transpile when we claim to be in Eclipse
2571 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2572 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2574 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2578 executable(eclipseBinary)
2579 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
2583 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
2585 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
2586 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
2592 stdout = new ByteArrayOutputStream()
2593 stderr = new ByteArrayOutputStream()
2595 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
2596 def logOutFile = file(logOutFileName)
2597 logOutFile.createNewFile()
2598 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
2599 BINARY: ${eclipseBinary}
2600 VERSION: ${eclipseVersion}
2601 WORKSPACE: ${eclipseWorkspace}
2602 DEBUG: ${eclipseDebug}
2605 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2606 // combine stdout and stderr
2607 def logErrFOS = logOutFOS
2609 if (jalviewjs_j2s_to_console.equals("true")) {
2610 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2611 new org.apache.tools.ant.util.TeeOutputStream(
2615 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2616 new org.apache.tools.ant.util.TeeOutputStream(
2621 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2624 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2631 if (stdout.toString().contains("Error processing ")) {
2632 // j2s did not complete transpile
2633 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2634 if (jalviewjs_ignore_transpile_errors.equals("true")) {
2635 println("IGNORING TRANSPILE ERRORS")
2636 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2638 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
2643 inputs.dir("${jalviewDir}/${sourceDir}")
2644 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
2645 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
2649 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
2651 def stdout = new ByteArrayOutputStream()
2652 def stderr = new ByteArrayOutputStream()
2654 def coreFile = file(jsfile)
2656 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
2658 logOutFile.createNewFile()
2659 logOutFile.append(msg+"\n")
2661 def coreTop = file(prefixFile)
2662 def coreBottom = file(suffixFile)
2663 coreFile.getParentFile().mkdirs()
2664 coreFile.createNewFile()
2665 coreFile.write( coreTop.getText("UTF-8") )
2669 def t = f.getText("UTF-8")
2670 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
2671 coreFile.append( t )
2673 msg = "...file '"+f.getPath()+"' does not exist, skipping"
2675 logOutFile.append(msg+"\n")
2678 coreFile.append( coreBottom.getText("UTF-8") )
2680 msg = "Generating ${zjsfile}"
2682 logOutFile.append(msg+"\n")
2683 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
2684 def logErrFOS = logOutFOS
2687 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
2688 main = "com.google.javascript.jscomp.CommandLineRunner"
2689 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
2690 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
2693 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
2695 logOutFile.append(msg+"\n")
2697 if (logOutConsole) {
2698 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2699 new org.apache.tools.ant.util.TeeOutputStream(
2703 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2704 new org.apache.tools.ant.util.TeeOutputStream(
2709 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2712 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2719 logOutFile.append(msg+"\n")
2723 task jalviewjsBuildAllCores {
2725 description "Build the core js lib closures listed in the classlists dir"
2726 dependsOn jalviewjsTranspile
2727 dependsOn jalviewjsTransferUnzipSwingJs
2729 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
2730 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
2731 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
2732 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
2733 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
2734 def prefixFile = "${jsDir}/core/coretop2.js"
2735 def suffixFile = "${jsDir}/core/corebottom2.js"
2737 inputs.file prefixFile
2738 inputs.file suffixFile
2740 def classlistFiles = []
2741 // add the classlists found int the jalviewjs_classlists_dir
2742 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
2744 def name = file.getName() - ".txt"
2751 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
2752 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
2753 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
2755 jalviewjsCoreClasslists = []
2757 classlistFiles.each {
2760 def file = hash['file']
2761 if (! file.exists()) {
2762 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
2763 return false // this is a "continue" in groovy .each closure
2765 def name = hash['name']
2767 name = file.getName() - ".txt"
2775 def list = fileTree(dir: j2sDir, includes: filelist)
2777 def jsfile = "${outputDir}/core${name}.js"
2778 def zjsfile = "${outputDir}/core${name}.z.js"
2780 jalviewjsCoreClasslists += [
2789 outputs.file(jsfile)
2790 outputs.file(zjsfile)
2793 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
2794 def stevesoftClasslistName = "_stevesoft"
2795 def stevesoftClasslist = [
2796 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
2797 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
2798 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
2799 'name': stevesoftClasslistName
2801 jalviewjsCoreClasslists += stevesoftClasslist
2802 inputs.files(stevesoftClasslist['list'])
2803 outputs.file(stevesoftClasslist['jsfile'])
2804 outputs.file(stevesoftClasslist['zjsfile'])
2807 def allClasslistName = "_all"
2808 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
2809 allJsFiles += fileTree(
2813 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2814 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
2815 "**/org/jmol/export/JSExporter.js"
2818 allJsFiles += fileTree(
2822 // these exlusions are files that the closure-compiler produces errors for. Should fix them
2823 "**/sun/misc/Unsafe.js",
2824 "**/swingjs/jquery/jquery-editable-select.js",
2825 "**/swingjs/jquery/j2sComboBox.js",
2826 "**/sun/misc/FloatingDecimal.js"
2829 def allClasslist = [
2830 'jsfile': "${outputDir}/core${allClasslistName}.js",
2831 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
2833 'name': allClasslistName
2835 // not including this version of "all" core at the moment
2836 //jalviewjsCoreClasslists += allClasslist
2837 inputs.files(allClasslist['list'])
2838 outputs.file(allClasslist['jsfile'])
2839 outputs.file(allClasslist['zjsfile'])
2842 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
2843 logOutFile.getParentFile().mkdirs()
2844 logOutFile.createNewFile()
2845 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
2847 jalviewjsCoreClasslists.each {
2848 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
2855 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
2858 into file(outputFile).getParentFile()
2859 rename { filename ->
2860 if (filename.equals(inputFile.getName())) {
2861 return file(outputFile).getName()
2865 filter(ReplaceTokens,
2869 'MAIN': '"'+main_class+'"',
2871 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
2872 'COREKEY': jalviewjs_core_key,
2873 'CORENAME': coreName
2880 task jalviewjsPublishCoreTemplates {
2881 dependsOn jalviewjsBuildAllCores
2882 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
2883 def inputFile = file(inputFileName)
2884 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2886 def outputFiles = []
2887 jalviewjsCoreClasslists.each { cl ->
2888 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
2889 cl['outputfile'] = outputFile
2890 outputFiles += outputFile
2894 jalviewjsCoreClasslists.each { cl ->
2895 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
2898 inputs.file(inputFile)
2899 outputs.files(outputFiles)
2903 task jalviewjsSyncCore (type: Sync) {
2904 dependsOn jalviewjsBuildAllCores
2905 dependsOn jalviewjsPublishCoreTemplates
2906 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
2907 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
2911 def outputFiles = []
2912 rename { filename ->
2913 outputFiles += "${outputDir}/${filename}"
2919 outputs.files outputFiles
2920 inputs.files inputFiles
2924 // this Copy version of TransferSiteJs will delete anything else in the target dir
2925 task jalviewjsCopyTransferSiteJs(type: Copy) {
2926 dependsOn jalviewjsTranspile
2927 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2928 into "${jalviewDir}/${jalviewjsSiteDir}"
2932 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
2933 task jalviewjsSyncTransferSiteJs(type: Sync) {
2934 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2936 into "${jalviewDir}/${jalviewjsSiteDir}"
2943 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
2944 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
2945 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
2946 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
2948 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
2949 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
2950 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
2951 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
2954 task jalviewjsPrepareSite {
2956 description "Prepares the website folder including unzipping files and copying resources"
2957 dependsOn jalviewjsSyncAllLibs
2958 dependsOn jalviewjsSyncResources
2959 dependsOn jalviewjsSyncSiteResources
2960 dependsOn jalviewjsSyncBuildProperties
2961 dependsOn jalviewjsSyncCore
2965 task jalviewjsBuildSite {
2967 description "Builds the whole website including transpiled code"
2968 dependsOn jalviewjsCopyTransferSiteJs
2969 dependsOn jalviewjsPrepareSite
2973 task cleanJalviewjsTransferSite {
2975 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
2976 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
2977 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
2978 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
2983 task cleanJalviewjsSite {
2984 dependsOn cleanJalviewjsTransferSite
2986 delete "${jalviewDir}/${jalviewjsSiteDir}"
2991 task jalviewjsSiteTar(type: Tar) {
2993 description "Creates a tar.gz file for the website"
2994 dependsOn jalviewjsBuildSite
2995 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
2996 archiveFileName = outputFilename
2998 compression Compression.GZIP
3000 from "${jalviewDir}/${jalviewjsSiteDir}"
3001 into jalviewjs_site_dir // this is inside the tar file
3003 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3007 task jalviewjsServer {
3009 def filename = "jalviewjsTest.html"
3010 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3011 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3016 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3017 factory = f.newInstance()
3018 } catch (ClassNotFoundException e) {
3019 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3021 def port = Integer.valueOf(jalviewjs_server_port)
3026 while(port < start+1000 && !running) {
3028 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3029 jalviewjsServer = factory.start(doc_root, port)
3031 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3032 println("SERVER STARTED with document root ${doc_root}.")
3033 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3034 println("For debug: "+url+"?j2sdebug")
3035 println("For verbose: "+url+"?j2sverbose")
3036 } catch (Exception e) {
3041 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3042 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3043 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3045 jalviewjsCoreClasslists.each { cl ->
3046 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3048 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3050 println("For core ${cl.name}: "+urlcore)
3053 file(htmlFile).text = htmlText
3056 outputs.file(htmlFile)
3057 outputs.upToDateWhen({false})
3061 task cleanJalviewjsAll {
3063 description "Delete all configuration and build artifacts to do with JalviewJS build"
3064 dependsOn cleanJalviewjsSite
3065 dependsOn jalviewjsEclipsePaths
3068 delete "${jalviewDir}/${jalviewjsBuildDir}"
3069 delete "${jalviewDir}/${eclipse_bin_dir}"
3070 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3071 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3073 delete jalviewjsJ2sAltSettingsFileName
3076 outputs.upToDateWhen( { false } )
3080 task jalviewjsIDE_checkJ2sPlugin {
3081 group "00 JalviewJS in Eclipse"
3082 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3085 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3086 def j2sPluginFile = file(j2sPlugin)
3087 def eclipseHome = System.properties["eclipse.home.location"]
3088 if (eclipseHome == null || ! IN_ECLIPSE) {
3089 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3091 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3092 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3093 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3094 eclipseJ2sPluginDirs += altPluginsDir
3096 def foundPlugin = false
3097 def j2sPluginFileName = j2sPluginFile.getName()
3098 def eclipseJ2sPlugin
3099 def eclipseJ2sPluginFile
3100 eclipseJ2sPluginDirs.any { dir ->
3101 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3102 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3103 if (eclipseJ2sPluginFile.exists()) {
3109 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3110 System.err.println(msg)
3111 throw new StopExecutionException(msg)
3114 def digest = MessageDigest.getInstance("MD5")
3116 digest.update(j2sPluginFile.text.bytes)
3117 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3119 digest.update(eclipseJ2sPluginFile.text.bytes)
3120 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3122 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3123 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3124 System.err.println(msg)
3125 throw new StopExecutionException(msg)
3127 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3133 task jalviewjsIDE_copyJ2sPlugin {
3134 group "00 JalviewJS in Eclipse"
3135 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3138 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3139 def j2sPluginFile = file(j2sPlugin)
3140 def eclipseHome = System.properties["eclipse.home.location"]
3141 if (eclipseHome == null || ! IN_ECLIPSE) {
3142 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3144 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3145 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3146 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3147 System.err.println(msg)
3150 eclipseJ2sPluginFile.getParentFile().mkdirs()
3151 into eclipseJ2sPluginFile.getParent()
3157 task jalviewjsIDE_j2sFile {
3158 group "00 JalviewJS in Eclipse"
3159 description "Creates the .j2s file"
3160 dependsOn jalviewjsCreateJ2sSettings
3164 task jalviewjsIDE_SyncCore {
3165 group "00 JalviewJS in Eclipse"
3166 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3167 dependsOn jalviewjsSyncCore
3171 task jalviewjsIDE_SyncSiteAll {
3172 dependsOn jalviewjsSyncAllLibs
3173 dependsOn jalviewjsSyncResources
3174 dependsOn jalviewjsSyncSiteResources
3175 dependsOn jalviewjsSyncBuildProperties
3179 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3182 task jalviewjsIDE_PrepareSite {
3183 group "00 JalviewJS in Eclipse"
3184 description "Sync libs and resources to site dir, but not closure cores"
3186 dependsOn jalviewjsIDE_SyncSiteAll
3187 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3191 task jalviewjsIDE_AssembleSite {
3192 group "00 JalviewJS in Eclipse"
3193 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3194 dependsOn jalviewjsPrepareSite
3198 task jalviewjsIDE_SiteClean {
3199 group "00 JalviewJS in Eclipse"
3200 description "Deletes the Eclipse transpiled site"
3201 dependsOn cleanJalviewjsSite
3205 task jalviewjsIDE_Server {
3206 group "00 JalviewJS in Eclipse"
3207 description "Starts a webserver on localhost to test the website"
3208 dependsOn jalviewjsServer
3212 // buildship runs this at import or gradle refresh
3213 task eclipseSynchronizationTask {
3214 //dependsOn eclipseSetup
3215 dependsOn createBuildProperties
3217 dependsOn jalviewjsIDE_j2sFile
3218 dependsOn jalviewjsIDE_checkJ2sPlugin
3219 dependsOn jalviewjsIDE_PrepareSite
3224 // buildship runs this at build time or project refresh
3225 task eclipseAutoBuildTask {
3226 //dependsOn jalviewjsIDE_checkJ2sPlugin
3227 //dependsOn jalviewjsIDE_PrepareSite
3233 description "Build the site"
3234 dependsOn jalviewjsBuildSite