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 java.util.regex.Matcher
13 import groovy.transform.ExternalizeMethods
14 import groovy.util.XmlParser
15 import groovy.xml.XmlUtil
16 import groovy.json.JsonBuilder
17 import com.vladsch.flexmark.util.ast.Node
18 import com.vladsch.flexmark.html.HtmlRenderer
19 import com.vladsch.flexmark.parser.Parser
20 import com.vladsch.flexmark.util.data.MutableDataSet
21 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
22 import com.vladsch.flexmark.ext.tables.TablesExtension
23 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
24 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
25 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
26 import com.vladsch.flexmark.ext.toc.TocExtension
27 import com.google.common.hash.HashCode
28 import com.google.common.hash.Hashing
29 import com.google.common.io.Files
30 import org.jsoup.Jsoup
31 import org.jsoup.nodes.Element
39 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
40 classpath "org.jsoup:jsoup:1.14.3"
41 classpath "com.eowise:gradle-imagemagick:0.5.1"
50 id "com.diffplug.gradle.spotless" version "3.28.0"
51 id 'com.github.johnrengelman.shadow' version '4.0.3'
52 id 'com.install4j.gradle' version '10.0.3'
53 id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
54 id 'com.palantir.git-version' version '0.13.0' apply false
65 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
66 def string(Object o) {
67 return o == null ? "" : o.toString()
70 def overrideProperties(String propsFileName, boolean output = false) {
71 if (propsFileName == null) {
74 def propsFile = file(propsFileName)
75 if (propsFile != null && propsFile.exists()) {
76 println("Using properties from file '${propsFileName}'")
78 def p = new Properties()
79 def localPropsFIS = new FileInputStream(propsFile)
85 if (project.hasProperty(key)) {
86 oldval = project.findProperty(key)
87 project.setProperty(key, val)
89 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
92 ext.setProperty(key, val)
94 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
98 } catch (Exception e) {
99 println("Exception reading local.properties")
106 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
107 jalviewDirRelativePath = jalviewDir
110 getdownChannelName = CHANNEL.toLowerCase()
111 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
112 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
113 channelDirName = propertiesChannelName
114 // Import channel_properties
115 if (getdownChannelName.startsWith("develop-")) {
116 channelDirName = "develop-SUFFIX"
118 channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
119 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
120 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
121 overrideProperties(channelGradleProperties, false)
122 // local build environment properties
123 // can be "projectDir/local.properties"
124 overrideProperties("${projectDir}/local.properties", true)
125 // or "../projectDir_local.properties"
126 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
129 // Import releaseProps from the RELEASE file
130 // or a file specified via JALVIEW_RELEASE_FILE if defined
131 // Expect jalview.version and target release branch in jalview.release
132 releaseProps = new Properties();
133 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
134 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
136 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
137 releaseProps.load(it)
139 } catch (Exception fileLoadError) {
140 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
143 // Set JALVIEW_VERSION if it is not already set
144 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
145 JALVIEW_VERSION = releaseProps.get("jalview.version")
147 println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
149 // this property set when running Eclipse headlessly
150 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
151 // this property set by Eclipse
152 eclipseApplicationProperty = string("eclipse.application")
153 // CHECK IF RUNNING FROM WITHIN ECLIPSE
154 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
155 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
156 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
157 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
158 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
162 println("WITHIN ECLIPSE IDE")
164 println("HEADLESS BUILD")
167 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
169 println("J2S ENABLED")
172 System.properties.sort { it.key }.each {
173 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
176 if (false && IN_ECLIPSE) {
177 jalviewDir = jalviewDirAbsolutePath
182 buildDate = new Date().format("yyyyMMdd")
185 bareSourceDir = string(source_dir)
186 sourceDir = string("${jalviewDir}/${bareSourceDir}")
187 resourceDir = string("${jalviewDir}/${resource_dir}")
188 bareTestSourceDir = string(test_source_dir)
189 testDir = string("${jalviewDir}/${bareTestSourceDir}")
191 classesDir = string("${jalviewDir}/${classes_dir}")
194 useClover = clover.equals("true")
195 cloverBuildDir = "${buildDir}/clover"
196 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
197 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
198 cloverReportDir = file("${buildDir}/reports/clover")
199 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
200 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
201 //cloverTestClassesDir = cloverClassesDir
202 cloverDb = string("${cloverBuildDir}/clover.db")
204 testSourceDir = useClover ? cloverTestInstrDir : testDir
205 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
208 backgroundImageText = BACKGROUNDIMAGETEXT
209 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
210 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
211 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
212 getdownFullArchiveDir = null
213 getdownTextLines = []
214 getdownLaunchJvl = null
215 getdownVersionLaunchJvl = null
217 buildProperties = null
219 // the following values might be overridden by the CHANNEL switch
220 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
221 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
222 getdownArchiveAppBase = getdown_archive_base
223 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
224 getdownAppDistDir = getdown_app_dir_alt
225 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
226 getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
227 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
228 reportRsyncCommand = false
229 jvlChannelName = CHANNEL.toLowerCase()
230 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
231 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
232 install4jDMGBackgroundImageDir = "${install4j_images_dir}"
233 install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
234 install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
235 install4jInstallerName = "${jalview_name} Non-Release Installer"
236 install4jExecutableName = install4j_executable_name
237 install4jExtraScheme = "jalviewx"
238 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
239 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
240 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
241 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
242 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
243 install4jCheckSums = true
245 applicationName = "${jalview_name}"
249 // TODO: get bamboo build artifact URL for getdown artifacts
250 getdown_channel_base = bamboo_channelbase
251 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
252 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
253 jvlChannelName += "_${getdownChannelName}"
254 // automatically add the test group Not-bamboo for exclusion
255 if ("".equals(testng_excluded_groups)) {
256 testng_excluded_groups = "Not-bamboo"
258 install4jExtraScheme = "jalviewb"
259 backgroundImageText = true
262 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
263 getdownAppDistDir = getdown_app_dir_release
264 getdownSetAppBaseProperty = true
265 reportRsyncCommand = true
267 install4jInstallerName = "${jalview_name} Installer"
271 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
272 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
273 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
274 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
275 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
277 package_dir = string("${ARCHIVEDIR}/${package_dir}")
278 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
281 reportRsyncCommand = true
282 install4jExtraScheme = "jalviewa"
286 getdownChannelName = string("archive/${JALVIEW_VERSION}")
287 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
288 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
289 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
290 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
292 package_dir = string("${ARCHIVEDIR}/${package_dir}")
293 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
296 reportRsyncCommand = true
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
298 install4jSuffix = "Archive"
299 install4jExtraScheme = "jalviewa"
302 case ~/^DEVELOP-([\.\-\w]*)$/:
303 def suffix = Matcher.lastMatcher[0][1]
304 reportRsyncCommand = true
305 getdownSetAppBaseProperty = true
306 JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
307 install4jSuffix = "Develop ${suffix}"
308 install4jExtraScheme = "jalviewd"
309 install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
310 getdownChannelName = string("develop-${suffix}")
311 getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
312 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
313 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
314 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
315 channelSuffix = string(suffix)
316 backgroundImageText = true
320 reportRsyncCommand = true
321 getdownSetAppBaseProperty = true
322 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
323 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
325 install4jSuffix = "Develop"
326 install4jExtraScheme = "jalviewd"
327 install4jInstallerName = "${jalview_name} Develop Installer"
328 backgroundImageText = true
332 reportRsyncCommand = true
333 getdownSetAppBaseProperty = true
334 // Don't ignore transpile errors for release build
335 if (jalviewjs_ignore_transpile_errors.equals("true")) {
336 jalviewjs_ignore_transpile_errors = "false"
337 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
339 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
340 install4jSuffix = "Test"
341 install4jExtraScheme = "jalviewt"
342 install4jInstallerName = "${jalview_name} Test Installer"
343 backgroundImageText = true
346 case ~/^SCRATCH(|-[-\w]*)$/:
347 getdownChannelName = CHANNEL
348 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
350 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
351 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
352 reportRsyncCommand = true
353 install4jSuffix = "Scratch"
357 if (!file("${LOCALDIR}").exists()) {
358 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
360 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
361 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
363 JALVIEW_VERSION = "TEST"
364 install4jSuffix = "Test-Local"
365 install4jExtraScheme = "jalviewt"
366 install4jInstallerName = "${jalview_name} Test Installer"
367 backgroundImageText = true
370 case [ "LOCAL", "JALVIEWJS" ]:
371 JALVIEW_VERSION = "TEST"
372 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
373 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
374 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
375 install4jExtraScheme = "jalviewl"
376 install4jCheckSums = false
379 default: // something wrong specified
380 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
384 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
385 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
386 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
387 // override getdownAppBase if requested
388 if (findProperty("getdown_appbase_override") != null) {
389 // revert to LOCAL if empty string
390 if (string(getdown_appbase_override) == "") {
391 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
392 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
393 } else if (string(getdown_appbase_override).startsWith("file://")) {
394 getdownAppBase = string(getdown_appbase_override)
395 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
397 getdownAppBase = string(getdown_appbase_override)
399 println("Overriding getdown appbase with '${getdownAppBase}'")
401 // sanitise file name for jalview launcher file for this channel
402 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
403 // install4j application and folder names
404 if (install4jSuffix == "") {
405 install4jBundleId = "${install4j_bundle_id}"
406 install4jWinApplicationId = install4j_release_win_application_id
408 applicationName = "${jalview_name} ${install4jSuffix}"
409 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
410 // add int hash of install4jSuffix to the last part of the application_id
411 def id = install4j_release_win_application_id
412 def idsplitreverse = id.split("-").reverse()
413 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
414 install4jWinApplicationId = idsplitreverse.reverse().join("-")
416 // sanitise folder and id names
417 // install4jApplicationFolder = e.g. "Jalview Build"
418 install4jApplicationFolder = applicationName
419 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
420 .replaceAll("_+", "_") // collapse __
421 install4jInternalId = applicationName
423 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
424 .replaceAll("_+", "") // collapse __
425 //.replaceAll("_*-_*", "-") // collapse _-_
426 install4jUnixApplicationFolder = applicationName
428 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
429 .replaceAll("_+", "_") // collapse __
430 .replaceAll("_*-_*", "-") // collapse _-_
433 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
434 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
435 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
436 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
437 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
438 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
439 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
440 /* compile without modules -- using classpath libraries
441 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
442 modules_runtimeClasspath = modules_compileClasspath
448 apply plugin: "com.palantir.git-version"
449 def details = versionDetails()
450 gitHash = details.gitHash
451 gitBranch = details.branchName
452 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
453 println("Not in a git repository. Using git values from RELEASE properties file.")
454 gitHash = releaseProps.getProperty("git.hash")
455 gitBranch = releaseProps.getProperty("git.branch")
456 } catch(java.lang.RuntimeException e1) {
457 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
460 println("Using a ${CHANNEL} profile.")
462 additional_compiler_args = []
463 // configure classpath/args for j8/j11 compilation
464 if (JAVA_VERSION.equals("1.8")) {
465 JAVA_INTEGER_VERSION = string("8")
468 libDistDir = j8libDir
469 compile_source_compatibility = 1.8
470 compile_target_compatibility = 1.8
471 // these are getdown.txt properties defined dependent on the JAVA_VERSION
472 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
473 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
474 // this property is assigned below and expanded to multiple lines in the getdown task
475 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
476 // this property is for the Java library used in eclipse
477 eclipseJavaRuntimeName = string("JavaSE-1.8")
478 } else if (JAVA_VERSION.equals("11")) {
479 JAVA_INTEGER_VERSION = string("11")
481 libDistDir = j11libDir
482 compile_source_compatibility = 11
483 compile_target_compatibility = 11
484 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
485 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
486 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
487 eclipseJavaRuntimeName = string("JavaSE-11")
488 /* compile without modules -- using classpath libraries
489 additional_compiler_args += [
490 '--module-path', modules_compileClasspath.asPath,
491 '--add-modules', j11modules
494 } else if (JAVA_VERSION.equals("17")) {
495 JAVA_INTEGER_VERSION = string("17")
497 libDistDir = j17libDir
498 compile_source_compatibility = 17
499 compile_target_compatibility = 17
500 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
501 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
502 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
503 eclipseJavaRuntimeName = string("JavaSE-17")
504 /* compile without modules -- using classpath libraries
505 additional_compiler_args += [
506 '--module-path', modules_compileClasspath.asPath,
507 '--add-modules', j11modules
511 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
516 JAVA_MIN_VERSION = JAVA_VERSION
517 JAVA_MAX_VERSION = JAVA_VERSION
518 jreInstallsDir = string(jre_installs_dir)
519 if (jreInstallsDir.startsWith("~/")) {
520 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
522 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
523 install4jConfFileName = string("jalview-install4j-conf.install4j")
524 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
525 install4jHomeDir = install4j_home_dir
526 if (install4jHomeDir.startsWith("~/")) {
527 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
530 resourceBuildDir = string("${buildDir}/resources")
531 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
532 helpBuildDir = string("${resourceBuildDir}/help_build")
533 docBuildDir = string("${resourceBuildDir}/doc_build")
535 if (buildProperties == null) {
536 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
538 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
539 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
540 helpSourceDir = string("${helpParentDir}/${help_dir}")
541 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
544 convertBinaryExpectedLocation = imagemagick_convert
545 if (convertBinaryExpectedLocation.startsWith("~/")) {
546 convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
548 if (file(convertBinaryExpectedLocation).exists()) {
549 convertBinary = convertBinaryExpectedLocation
552 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
553 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
554 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
556 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
558 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
560 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
561 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
562 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
563 jalviewjsJalviewCoreHtmlFile = string("")
564 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
565 jalviewjsCoreClasslists = []
566 jalviewjsJalviewTemplateName = string(jalviewjs_name)
567 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
568 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
569 jalviewjsJ2sProps = null
570 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
572 eclipseWorkspace = null
573 eclipseBinary = string("")
574 eclipseVersion = string("")
584 outputDir = file(classesDir)
588 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
591 compileClasspath = files(sourceSets.main.java.outputDir)
592 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
594 runtimeClasspath = compileClasspath
595 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
600 srcDirs cloverInstrDir
601 outputDir = cloverClassesDir
605 srcDirs = sourceSets.main.resources.srcDirs
608 compileClasspath = files( sourceSets.clover.java.outputDir )
609 //compileClasspath += files( testClassesDir )
610 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
611 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
612 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
614 runtimeClasspath = compileClasspath
619 srcDirs testSourceDir
620 outputDir = file(testClassesDir)
624 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
627 compileClasspath = files( sourceSets.test.java.outputDir )
628 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
629 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
631 runtimeClasspath = compileClasspath
632 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
638 // eclipse project and settings files creation, also used by buildship
641 name = eclipse_project_name
643 natures 'org.eclipse.jdt.core.javanature',
644 'org.eclipse.jdt.groovy.core.groovyNature',
645 'org.eclipse.buildship.core.gradleprojectnature'
647 buildCommand 'org.eclipse.jdt.core.javabuilder'
648 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
652 //defaultOutputDir = sourceSets.main.java.outputDir
653 configurations.each{ c->
654 if (c.isCanBeResolved()) {
655 minusConfigurations += [c]
659 plusConfigurations = [ ]
663 def removeTheseToo = []
664 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
665 cp.entries.each { entry ->
666 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
667 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
668 // we add the resources and help/help dirs in as libs afterwards (see below)
669 if (entry.kind == 'src') {
670 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
671 removeTheseToo += entry
673 alreadyAddedSrcPath.putAt(entry.path, true)
678 cp.entries.removeAll(removeTheseToo)
680 //cp.entries += new Output("${eclipse_bin_dir}/main")
681 if (file(helpParentDir).isDirectory()) {
682 cp.entries += new Library(fileReference(helpParentDir))
684 if (file(resourceDir).isDirectory()) {
685 cp.entries += new Library(fileReference(resourceDir))
688 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
690 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
691 //don't want to add outputDir as eclipse is using its own output dir in bin/main
692 if (it.isDirectory() || ! it.exists()) {
693 // don't add dirs to classpath, especially if they don't exist
694 return false // groovy "continue" in .any closure
696 def itPath = it.toString()
697 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
698 // make relative path
699 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
701 if (alreadyAddedLibPath.get(itPath)) {
702 //println("Not adding duplicate entry "+itPath)
704 //println("Adding entry "+itPath)
705 cp.entries += new Library(fileReference(itPath))
706 alreadyAddedLibPath.put(itPath, true)
710 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
711 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
712 if (it.isDirectory() || ! it.exists()) {
713 // don't add dirs to classpath
714 return false // groovy "continue" in .any closure
717 def itPath = it.toString()
718 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
719 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
721 if (alreadyAddedLibPath.get(itPath)) {
724 def lib = new Library(fileReference(itPath))
725 lib.entryAttributes["test"] = "true"
727 alreadyAddedLibPath.put(itPath, true)
735 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
740 // for the IDE, use java 11 compatibility
741 sourceCompatibility = compile_source_compatibility
742 targetCompatibility = compile_target_compatibility
743 javaRuntimeName = eclipseJavaRuntimeName
745 // add in jalview project specific properties/preferences into eclipse core preferences
747 withProperties { props ->
748 def jalview_prefs = new Properties()
749 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
750 jalview_prefs.load(ins)
752 jalview_prefs.forEach { t, v ->
753 if (props.getAt(t) == null) {
757 // codestyle file -- overrides previous formatter prefs
758 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
759 if (csFile.exists()) {
760 XmlParser parser = new XmlParser()
761 def profiles = parser.parse(csFile)
762 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
763 if (profile != null) {
764 profile.'setting'.each { s ->
766 def value = s.'@value'
767 if (id != null && value != null) {
768 props.putAt(id, value)
779 // Don't want these to be activated if in headless build
780 synchronizationTasks "eclipseSynchronizationTask"
781 //autoBuildTasks "eclipseAutoBuildTask"
787 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
788 // Class to allow updating arbitrary properties files
789 class PropertiesFile extends PropertiesPersistableConfigurationObject {
790 public PropertiesFile(PropertiesTransformer t) { super(t); }
791 @Override protected void load(Properties properties) { }
792 @Override protected void store(Properties properties) { }
793 @Override protected String getDefaultResourceName() { return ""; }
794 // This is necessary, because PropertiesPersistableConfigurationObject fails
795 // if no default properties file exists.
796 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
799 // Task to update arbitrary properties files (set outputFile)
800 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
801 private final PropertiesFileContentMerger file;
802 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
803 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
804 protected void configure(PropertiesFile props) {
805 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
807 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
810 task eclipseUIPreferences(type: PropertiesFileTask) {
811 description = "Generate Eclipse additional settings"
812 def filename = "org.eclipse.jdt.ui.prefs"
813 outputFile = "$projectDir/.settings/${filename}" as File
816 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
821 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
822 description = "Generate Eclipse additional settings"
823 def filename = "org.eclipse.jdt.groovy.core.prefs"
824 outputFile = "$projectDir/.settings/${filename}" as File
827 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
832 task eclipseAllPreferences {
834 dependsOn eclipseUIPreferences
835 dependsOn eclipseGroovyCorePreferences
838 eclipseUIPreferences.mustRunAfter eclipseJdt
839 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
841 /* end of eclipse preferences hack */
849 delete cloverBuildDir
850 delete cloverReportDir
855 task cloverInstrJava(type: JavaExec) {
856 group = "Verification"
857 description = "Create clover instrumented source java files"
859 dependsOn cleanClover
861 inputs.files(sourceSets.main.allJava)
862 outputs.dir(cloverInstrDir)
864 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
865 classpath = sourceSets.clover.compileClasspath
866 main = "com.atlassian.clover.CloverInstr"
874 cloverInstrDir.getPath(),
876 def srcFiles = sourceSets.main.allJava.files
879 { file -> file.absolutePath }
882 args argsList.toArray()
885 delete cloverInstrDir
886 println("Clover: About to instrument "+srcFiles.size() +" files")
891 task cloverInstrTests(type: JavaExec) {
892 group = "Verification"
893 description = "Create clover instrumented source test files"
895 dependsOn cleanClover
897 inputs.files(testDir)
898 outputs.dir(cloverTestInstrDir)
900 classpath = sourceSets.clover.compileClasspath
901 main = "com.atlassian.clover.CloverInstr"
911 cloverTestInstrDir.getPath(),
913 args argsList.toArray()
916 delete cloverTestInstrDir
917 println("Clover: About to instrument test files")
923 group = "Verification"
924 description = "Create clover instrumented all source files"
926 dependsOn cloverInstrJava
927 dependsOn cloverInstrTests
931 cloverClasses.dependsOn cloverInstr
934 task cloverConsoleReport(type: JavaExec) {
935 group = "Verification"
936 description = "Creates clover console report"
939 file(cloverDb).exists()
942 inputs.dir cloverClassesDir
944 classpath = sourceSets.clover.runtimeClasspath
945 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
947 if (cloverreport_mem.length() > 0) {
948 maxHeapSize = cloverreport_mem
950 if (cloverreport_jvmargs.length() > 0) {
951 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
961 args argsList.toArray()
965 task cloverHtmlReport(type: JavaExec) {
966 group = "Verification"
967 description = "Creates clover HTML report"
970 file(cloverDb).exists()
973 def cloverHtmlDir = cloverReportDir
974 inputs.dir cloverClassesDir
975 outputs.dir cloverHtmlDir
977 classpath = sourceSets.clover.runtimeClasspath
978 main = "com.atlassian.clover.reporters.html.HtmlReporter"
980 if (cloverreport_mem.length() > 0) {
981 maxHeapSize = cloverreport_mem
983 if (cloverreport_jvmargs.length() > 0) {
984 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
995 if (cloverreport_html_options.length() > 0) {
996 argsList += cloverreport_html_options.split(" ")
999 args argsList.toArray()
1003 task cloverXmlReport(type: JavaExec) {
1004 group = "Verification"
1005 description = "Creates clover XML report"
1008 file(cloverDb).exists()
1011 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1012 inputs.dir cloverClassesDir
1013 outputs.file cloverXmlFile
1015 classpath = sourceSets.clover.runtimeClasspath
1016 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1018 if (cloverreport_mem.length() > 0) {
1019 maxHeapSize = cloverreport_mem
1021 if (cloverreport_jvmargs.length() > 0) {
1022 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1033 if (cloverreport_xml_options.length() > 0) {
1034 argsList += cloverreport_xml_options.split(" ")
1037 args argsList.toArray()
1042 group = "Verification"
1043 description = "Creates clover reports"
1045 dependsOn cloverXmlReport
1046 dependsOn cloverHtmlReport
1053 sourceCompatibility = compile_source_compatibility
1054 targetCompatibility = compile_target_compatibility
1055 options.compilerArgs += additional_compiler_args
1056 print ("Setting target compatibility to "+targetCompatibility+"\n")
1058 //classpath += configurations.cloverRuntime
1064 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1065 sourceCompatibility = compile_source_compatibility
1066 targetCompatibility = compile_target_compatibility
1067 options.compilerArgs = additional_compiler_args
1068 options.encoding = "UTF-8"
1070 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1077 sourceCompatibility = compile_source_compatibility
1078 targetCompatibility = compile_target_compatibility
1079 options.compilerArgs = additional_compiler_args
1081 print ("Setting target compatibility to "+targetCompatibility+"\n")
1088 delete sourceSets.main.java.outputDir
1094 dependsOn cleanClover
1096 delete sourceSets.test.java.outputDir
1101 // format is a string like date.format("dd MMMM yyyy")
1102 def getDate(format) {
1103 return date.format(format)
1107 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1108 MutableDataSet options = new MutableDataSet()
1110 def extensions = new ArrayList<>()
1111 extensions.add(AnchorLinkExtension.create())
1112 extensions.add(AutolinkExtension.create())
1113 extensions.add(StrikethroughExtension.create())
1114 extensions.add(TaskListExtension.create())
1115 extensions.add(TablesExtension.create())
1116 extensions.add(TocExtension.create())
1118 options.set(Parser.EXTENSIONS, extensions)
1120 // set GFM table parsing options
1121 options.set(TablesExtension.WITH_CAPTION, false)
1122 options.set(TablesExtension.COLUMN_SPANS, false)
1123 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1124 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1125 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1126 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1127 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1129 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1130 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1131 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1132 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1134 Parser parser = Parser.builder(options).build()
1135 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1137 mdFiles.each { mdFile ->
1138 // add table of contents
1139 def mdText = "[TOC]\n"+mdFile.text
1141 // grab the first top-level title
1143 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1144 def matcher = mdText =~ titleRegex
1145 if (matcher.size() > 0) {
1146 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1147 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1149 // or use the filename if none found
1150 if (title == null) {
1151 title = mdFile.getName()
1154 Node document = parser.parse(mdText)
1155 String htmlBody = renderer.render(document)
1156 def htmlText = '''<html>
1157 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1158 <html xmlns="http://www.w3.org/1999/xhtml">
1160 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1161 <meta http-equiv="Content-Style-Type" content="text/css" />
1162 <meta name="generator" content="flexmark" />
1164 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1166 <style type="text/css">code{white-space: pre;}</style>
1168 htmlText += ((cssFile != null) ? cssFile.text : '')
1169 htmlText += '''</head>
1172 htmlText += htmlBody
1178 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1179 def htmlFile = file(htmlFilePath)
1180 println("Creating ${htmlFilePath}")
1181 htmlFile.text = htmlText
1186 task copyDocs(type: Copy) {
1187 def inputDir = "${jalviewDir}/${doc_dir}"
1188 def outputDir = "${docBuildDir}/${doc_dir}"
1192 include('**/*.html')
1194 filter(ReplaceTokens,
1198 'Version-Rel': JALVIEW_VERSION,
1199 'Year-Rel': getDate("yyyy")
1206 exclude('**/*.html')
1211 inputs.dir(inputDir)
1212 outputs.dir(outputDir)
1216 task convertMdFiles {
1218 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1219 def cssFile = file("${jalviewDir}/${flexmark_css}")
1222 convertMdToHtml(mdFiles, cssFile)
1225 inputs.files(mdFiles)
1226 inputs.file(cssFile)
1229 mdFiles.each { mdFile ->
1230 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1231 htmlFiles.add(file(htmlFilePath))
1233 outputs.files(htmlFiles)
1237 def hugoTemplateSubstitutions(String input, Map extras=null) {
1238 def replacements = [
1239 DATE: getDate("yyyy-MM-dd"),
1240 CHANNEL: propertiesChannelName,
1241 APPLICATION_NAME: applicationName,
1243 GIT_BRANCH: gitBranch,
1244 VERSION: JALVIEW_VERSION,
1245 JAVA_VERSION: JAVA_VERSION,
1246 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1251 if (extras != null) {
1252 extras.each{ k, v ->
1253 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1256 replacements.each{ k, v ->
1257 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1262 def mdFileComponents(File mdFile, def dateOnly=false) {
1265 if (mdFile.exists()) {
1266 def inFrontMatter = false
1267 def firstLine = true
1268 mdFile.eachLine { line ->
1269 if (line.matches("---")) {
1270 def prev = inFrontMatter
1271 inFrontMatter = firstLine
1272 if (inFrontMatter != prev)
1275 if (inFrontMatter) {
1277 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1278 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1279 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1280 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1281 } else if (m = line =~ /^channel:\s*(\S+)/) {
1282 map["channel"] = m[0][1]
1283 } else if (m = line =~ /^version:\s*(\S+)/) {
1284 map["version"] = m[0][1]
1285 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1286 map[ m[0][1] ] = m[0][2]
1288 if (dateOnly && map["date"] != null) {
1294 content += line+"\n"
1299 return dateOnly ? map["date"] : [map, content]
1302 task hugoTemplates {
1304 description "Create partially populated md pages for hugo website build"
1306 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1307 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1308 def templateFiles = fileTree(dir: hugoTemplatesDir)
1309 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1310 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1311 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1312 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1315 // specific release template for version archive
1318 def givenDate = null
1319 def givenChannel = null
1320 def givenVersion = null
1321 if (CHANNEL == "RELEASE") {
1322 def (map, content) = mdFileComponents(releaseMdFile)
1323 givenDate = map.date
1324 givenChannel = map.channel
1325 givenVersion = map.version
1327 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1328 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1331 if (whatsnewMdFile.exists())
1332 whatsnew = whatsnewMdFile.text
1335 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1336 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1338 def changesHugo = null
1339 if (changes != null) {
1340 changesHugo = '<div class="release_notes">\n\n'
1341 def inSection = false
1342 changes.eachLine { line ->
1344 if (m = line =~ /^##([^#].*)$/) {
1346 changesHugo += "</div>\n\n"
1348 def section = m[0][1].trim()
1349 section = section.toLowerCase()
1350 section = section.replaceAll(/ +/, "_")
1351 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1352 changesHugo += "<div class=\"${section}\">\n\n"
1354 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1355 def comment = m[0][2].trim()
1356 if (comment != "") {
1357 comment = comment.replaceAll('"', """)
1359 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1360 def newline = m[0][1]
1361 if (comment.trim() != "")
1362 newline += "{{<comment>}}${comment}{{</comment>}} "
1363 newline += m[0][3].trim()
1364 if (issuekeys.size() > 0)
1365 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1366 if (m[0][4] != null)
1371 changesHugo += line+"\n"
1374 changesHugo += "\n</div>\n\n"
1376 changesHugo += '</div>'
1379 templateFiles.each{ templateFile ->
1380 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1381 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1382 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1384 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1388 rename(templateFile.getName(), newFileName)
1392 def newFile = file("${outPathName}/${newFileName}".toString())
1393 def content = newFile.text
1394 newFile.text = hugoTemplateSubstitutions(content,
1397 CHANGES: changesHugo,
1398 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1399 DRAFT: givenDate == null ? "true" : "false",
1400 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1401 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1408 inputs.file(oldJvlFile)
1409 inputs.dir(hugoTemplatesDir)
1410 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1411 inputs.property("CHANNEL", { CHANNEL })
1414 def getMdDate(File mdFile) {
1415 return mdFileComponents(mdFile, true)
1418 def getMdSections(String content) {
1420 def sectionContent = ""
1421 def sectionName = null
1422 content.eachLine { line ->
1424 if (m = line =~ /^##([^#].*)$/) {
1425 if (sectionName != null) {
1426 sections[sectionName] = sectionContent
1430 sectionName = m[0][1].trim()
1431 sectionName = sectionName.toLowerCase()
1432 sectionName = sectionName.replaceAll(/ +/, "_")
1433 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1434 } else if (sectionName != null) {
1435 sectionContent += line+"\n"
1438 if (sectionContent != null) {
1439 sections[sectionName] = sectionContent
1445 task copyHelp(type: Copy) {
1446 def inputDir = helpSourceDir
1447 def outputDir = "${helpBuildDir}/${help_dir}"
1451 include('**/*.html')
1455 filter(ReplaceTokens,
1459 'Version-Rel': JALVIEW_VERSION,
1460 'Year-Rel': getDate("yyyy")
1467 exclude('**/*.html')
1474 inputs.dir(inputDir)
1475 outputs.files(helpFile)
1476 outputs.dir(outputDir)
1480 task releasesTemplates {
1482 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1486 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1487 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1488 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1489 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1490 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1491 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1494 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1495 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1497 if (CHANNEL == "RELEASE") {
1498 if (!releaseMdFile.exists()) {
1499 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1501 if (!whatsnewMdFile.exists()) {
1502 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1506 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1507 def releaseFilesDates = releaseFiles.collectEntries {
1508 [(it): getMdDate(it)]
1510 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1512 def releasesTemplate = releasesTemplateFile.text
1513 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1514 def versionTemplate = m[0][1]
1516 MutableDataSet options = new MutableDataSet()
1518 def extensions = new ArrayList<>()
1519 options.set(Parser.EXTENSIONS, extensions)
1520 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1522 Parser parser = Parser.builder(options).build()
1523 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1525 def actualVersions = releaseFiles.collect { rf ->
1526 def (rfMap, rfContent) = mdFileComponents(rf)
1527 return rfMap.version
1529 def versionsHtml = ""
1530 def linkedVersions = []
1531 releaseFiles.reverse().each { rFile ->
1532 def (rMap, rContent) = mdFileComponents(rFile)
1534 def versionLink = ""
1535 def partialVersion = ""
1536 def firstPart = true
1537 rMap.version.split("\\.").each { part ->
1538 def displayPart = ( firstPart ? "" : "." ) + part
1539 partialVersion += displayPart
1541 linkedVersions.contains(partialVersion)
1542 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1544 versionLink += displayPart
1546 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1547 linkedVersions += partialVersion
1551 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1554 def rContentProcessed = ""
1555 rContent.eachLine { line ->
1556 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1557 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1558 } else if (lm = line =~ /^###([^#]+.*)$/) {
1559 line = "_${lm[0][1].trim()}_"
1561 rContentProcessed += line + "\n"
1564 def rContentSections = getMdSections(rContentProcessed)
1565 def rVersion = versionTemplate
1566 if (rVersion != "") {
1567 def rNewFeatures = rContentSections["new_features"]
1568 def rIssuesResolved = rContentSections["issues_resolved"]
1569 Node newFeaturesNode = parser.parse(rNewFeatures)
1570 String newFeaturesHtml = renderer.render(newFeaturesNode)
1571 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1572 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1573 rVersion = hugoTemplateSubstitutions(rVersion,
1575 VERSION: rMap.version,
1576 VERSION_LINK: versionLink,
1577 DISPLAY_DATE: displayDate,
1578 NEW_FEATURES: newFeaturesHtml,
1579 ISSUES_RESOLVED: issuesResolvedHtml
1582 versionsHtml += rVersion
1586 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1587 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1588 releasesHtmlFile.text = releasesTemplate
1590 if (whatsnewMdFile.exists()) {
1591 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1592 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1593 Node whatsnewNode = parser.parse(whatsnewMd)
1594 String whatsnewHtml = renderer.render(whatsnewNode)
1595 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1596 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1598 VERSION: JALVIEW_VERSION,
1599 DISPLAY_DATE: wnDisplayDate
1602 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1603 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1608 inputs.file(releasesTemplateFile)
1609 inputs.file(whatsnewTemplateFile)
1610 inputs.dir(releasesMdDir)
1611 inputs.dir(whatsnewMdDir)
1612 outputs.file(releasesHtmlFile)
1613 outputs.file(whatsnewHtmlFile)
1617 task copyResources(type: Copy) {
1619 description = "Copy (and make text substitutions in) the resources dir to the build area"
1621 def inputDir = resourceDir
1622 def outputDir = resourcesBuildDir
1626 include('**/*.html')
1628 filter(ReplaceTokens,
1632 'Version-Rel': JALVIEW_VERSION,
1633 'Year-Rel': getDate("yyyy")
1640 exclude('**/*.html')
1645 inputs.dir(inputDir)
1646 outputs.dir(outputDir)
1649 task copyChannelResources(type: Copy) {
1650 dependsOn copyResources
1652 description = "Copy the channel resources dir to the build resources area"
1654 def inputDir = "${channelDir}/${resource_dir}"
1655 def outputDir = resourcesBuildDir
1657 include(channel_props)
1658 filter(ReplaceTokens,
1662 'SUFFIX': channelSuffix
1667 exclude(channel_props)
1671 inputs.dir(inputDir)
1672 outputs.dir(outputDir)
1675 task createBuildProperties(type: WriteProperties) {
1676 dependsOn copyResources
1678 description = "Create the ${buildProperties} file"
1680 inputs.dir(sourceDir)
1681 inputs.dir(resourcesBuildDir)
1682 outputFile (buildProperties)
1683 // taking time specific comment out to allow better incremental builds
1684 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1685 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1686 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1687 property "VERSION", JALVIEW_VERSION
1688 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1689 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1690 if (getdownSetAppBaseProperty) {
1691 property "GETDOWNAPPBASE", getdownAppBase
1692 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1694 outputs.file(outputFile)
1698 task buildIndices(type: JavaExec) {
1700 classpath = sourceSets.main.compileClasspath
1701 main = "com.sun.java.help.search.Indexer"
1702 workingDir = "${helpBuildDir}/${help_dir}"
1705 inputs.dir("${workingDir}/${argDir}")
1707 outputs.dir("${classesDir}/doc")
1708 outputs.dir("${classesDir}/help")
1709 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1710 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1711 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1712 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1713 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1714 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1717 task buildResources {
1718 dependsOn copyResources
1719 dependsOn copyChannelResources
1720 dependsOn createBuildProperties
1724 dependsOn buildResources
1727 dependsOn releasesTemplates
1728 dependsOn convertMdFiles
1729 dependsOn buildIndices
1733 compileJava.dependsOn prepare
1734 run.dependsOn compileJava
1735 //run.dependsOn prepare
1738 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1743 dependsOn cloverClasses
1745 dependsOn compileJava //?
1749 includeGroups testng_groups
1750 excludeGroups testng_excluded_groups
1752 useDefaultListeners=true
1755 maxHeapSize = "1024m"
1758 maxParallelForks = 1
1762 workingDir = jalviewDir
1763 def testLaf = project.findProperty("test_laf")
1764 if (testLaf != null) {
1765 println("Setting Test LaF to '${testLaf}'")
1766 systemProperty "laf", testLaf
1768 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1769 if (testHiDPIScale != null) {
1770 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1771 systemProperty "sun.java2d.uiScale", testHiDPIScale
1773 sourceCompatibility = compile_source_compatibility
1774 targetCompatibility = compile_target_compatibility
1775 jvmArgs += additional_compiler_args
1779 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1785 task compileLinkCheck(type: JavaCompile) {
1787 classpath = files("${jalviewDir}/${utils_dir}")
1788 destinationDir = file("${jalviewDir}/${utils_dir}")
1789 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1791 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1792 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1793 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1794 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1798 task linkCheck(type: JavaExec) {
1800 dependsOn compileLinkCheck
1802 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1803 classpath = files("${jalviewDir}/${utils_dir}")
1804 main = "HelpLinksChecker"
1805 workingDir = "${helpBuildDir}"
1806 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1808 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1809 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1812 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1816 inputs.dir(helpBuildDir)
1817 outputs.file(helpLinksCheckerOutFile)
1821 // import the pubhtmlhelp target
1822 ant.properties.basedir = "${jalviewDir}"
1823 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1824 ant.importBuild "${utils_dir}/publishHelp.xml"
1827 task cleanPackageDir(type: Delete) {
1829 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1839 attributes "Main-Class": main_class,
1840 "Permissions": "all-permissions",
1841 "Application-Name": applicationName,
1842 "Codebase": application_codebase,
1843 "Implementation-Version": JALVIEW_VERSION
1846 def outputDir = "${jalviewDir}/${package_dir}"
1847 destinationDirectory = file(outputDir)
1848 archiveFileName = rootProject.name+".jar"
1849 duplicatesStrategy "EXCLUDE"
1856 exclude "**/*.jar.*"
1858 inputs.dir(sourceSets.main.java.outputDir)
1859 sourceSets.main.resources.srcDirs.each{ dir ->
1862 outputs.file("${outputDir}/${archiveFileName}")
1866 task copyJars(type: Copy) {
1867 from fileTree(dir: classesDir, include: "**/*.jar").files
1868 into "${jalviewDir}/${package_dir}"
1872 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1873 task syncJars(type: Sync) {
1875 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1876 into "${jalviewDir}/${package_dir}"
1878 include jar.archiveFileName.getOrNull()
1885 description = "Put all required libraries in dist"
1886 // order of "cleanPackageDir", "copyJars", "jar" important!
1887 jar.mustRunAfter cleanPackageDir
1888 syncJars.mustRunAfter cleanPackageDir
1889 dependsOn cleanPackageDir
1892 outputs.dir("${jalviewDir}/${package_dir}")
1897 dependsOn cleanPackageDir
1904 group = "distribution"
1905 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1909 from ("${jalviewDir}/${libDistDir}") {
1913 attributes "Implementation-Version": JALVIEW_VERSION,
1914 "Application-Name": applicationName
1917 duplicatesStrategy "INCLUDE"
1919 mainClassName = shadow_jar_main_class
1921 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1925 task getdownImagesCopy() {
1926 inputs.dir getdownImagesDir
1927 outputs.dir getdownImagesBuildDir
1931 from(getdownImagesDir) {
1932 include("*getdown*.png")
1934 into getdownImagesBuildDir
1939 task getdownImagesProcess() {
1940 dependsOn getdownImagesCopy
1943 if (backgroundImageText) {
1944 if (convertBinary == null) {
1945 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
1947 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
1948 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
1950 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
1952 executable convertBinary
1955 '-font', getdown_background_image_text_font,
1956 '-fill', getdown_background_image_text_colour,
1957 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
1958 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
1959 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
1968 task getdownImages() {
1969 dependsOn getdownImagesProcess
1972 task getdownWebsite() {
1973 group = "distribution"
1974 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1976 dependsOn getdownImages
1981 def getdownWebsiteResourceFilenames = []
1982 def getdownResourceDir = getdownResourceDir
1983 def getdownResourceFilenames = []
1986 // clean the getdown website and files dir before creating getdown folders
1987 delete getdownAppBaseDir
1988 delete getdownFilesDir
1991 from buildProperties
1992 rename(file(buildProperties).getName(), getdown_build_properties)
1995 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1998 from channelPropsFile
1999 filter(ReplaceTokens,
2003 'SUFFIX': channelSuffix
2006 into getdownAppBaseDir
2008 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2010 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2011 def props = project.properties.sort { it.key }
2012 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2013 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2015 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2016 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2018 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2019 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2021 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2022 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2023 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2024 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2025 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2026 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2027 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2030 props.put("getdown_txt_title", jalview_name)
2031 props.put("getdown_txt_ui.name", applicationName)
2033 // start with appbase
2034 getdownTextLines += "appbase = ${getdownAppBase}"
2035 props.each{ prop, val ->
2036 if (prop.startsWith("getdown_txt_") && val != null) {
2037 if (prop.startsWith("getdown_txt_multi_")) {
2038 def key = prop.substring(18)
2039 val.split(",").each{ v ->
2040 def line = "${key} = ${v}"
2041 getdownTextLines += line
2044 // file values rationalised
2045 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2047 if (val.indexOf('/') == 0) {
2050 } else if (val.indexOf('/') > 0) {
2051 // relative path (relative to jalviewDir)
2052 r = file( "${jalviewDir}/${val}" )
2055 val = "${getdown_resource_dir}/" + r.getName()
2056 getdownWebsiteResourceFilenames += val
2057 getdownResourceFilenames += r.getPath()
2060 if (! prop.startsWith("getdown_txt_resource")) {
2061 def line = prop.substring(12) + " = ${val}"
2062 getdownTextLines += line
2068 getdownWebsiteResourceFilenames.each{ filename ->
2069 getdownTextLines += "resource = ${filename}"
2071 getdownResourceFilenames.each{ filename ->
2074 into getdownResourceDir
2078 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2079 getdownWrapperScripts.each{ script ->
2080 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2084 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2086 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2091 fileTree(file(package_dir)).each{ f ->
2092 if (f.isDirectory()) {
2093 def files = fileTree(dir: f, include: ["*"]).getFiles()
2095 } else if (f.exists()) {
2099 def jalviewJar = jar.archiveFileName.getOrNull()
2100 // put jalview.jar first for CLASSPATH and .properties files reasons
2101 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2102 def name = f.getName()
2103 def line = "code = ${getdownAppDistDir}/${name}"
2104 getdownTextLines += line
2111 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2113 if (JAVA_VERSION.equals("11")) {
2114 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2115 j11libFiles.sort().each{f ->
2116 def name = f.getName()
2117 def line = "code = ${getdown_j11lib_dir}/${name}"
2118 getdownTextLines += line
2121 into getdownJ11libDir
2127 // 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.
2128 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2129 getdownTextLines += "resource = ${getdown_launcher_new}"
2130 getdownTextLines += "class = ${main_class}"
2131 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2132 if (getdownSetAppBaseProperty) {
2133 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2134 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2137 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2138 getdownTxt.write(getdownTextLines.join("\n"))
2140 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2141 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2142 launchJvl.write("appbase=${getdownAppBase}")
2144 // files going into the getdown website dir: getdown-launcher.jar
2146 from getdownLauncher
2147 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2148 into getdownAppBaseDir
2151 // files going into the getdown website dir: getdown-launcher(-local).jar
2153 from getdownLauncher
2154 if (file(getdownLauncher).getName() != getdown_launcher) {
2155 rename(file(getdownLauncher).getName(), getdown_launcher)
2157 into getdownAppBaseDir
2160 // files going into the getdown website dir: ./install dir and files
2161 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2164 from getdownLauncher
2165 from "${getdownAppDir}/${getdown_build_properties}"
2166 if (file(getdownLauncher).getName() != getdown_launcher) {
2167 rename(file(getdownLauncher).getName(), getdown_launcher)
2169 into getdownInstallDir
2172 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2174 from getdownInstallDir
2175 into getdownFilesInstallDir
2179 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2183 from getdownLauncher
2184 from "${getdownAppBaseDir}/${getdown_build_properties}"
2185 from "${getdownAppBaseDir}/${channel_props}"
2186 if (file(getdownLauncher).getName() != getdown_launcher) {
2187 rename(file(getdownLauncher).getName(), getdown_launcher)
2189 into getdownFilesDir
2192 // and ./resource (not all downloaded by getdown)
2194 from getdownResourceDir
2195 into "${getdownFilesDir}/${getdown_resource_dir}"
2200 inputs.dir("${jalviewDir}/${package_dir}")
2202 outputs.dir(getdownAppBaseDir)
2203 outputs.dir(getdownFilesDir)
2207 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2208 task getdownDigestDir(type: JavaExec) {
2210 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2212 def digestDirPropertyName = "DIGESTDIR"
2214 classpath = files(getdownLauncher)
2215 def digestDir = findProperty(digestDirPropertyName)
2216 if (digestDir == null) {
2217 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2221 main = "com.threerings.getdown.tools.Digester"
2225 task getdownDigest(type: JavaExec) {
2226 group = "distribution"
2227 description = "Digest the getdown website folder"
2228 dependsOn getdownWebsite
2230 classpath = files(getdownLauncher)
2232 main = "com.threerings.getdown.tools.Digester"
2233 args getdownAppBaseDir
2234 inputs.dir(getdownAppBaseDir)
2235 outputs.file("${getdownAppBaseDir}/digest2.txt")
2240 group = "distribution"
2241 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2242 dependsOn getdownDigest
2244 if (reportRsyncCommand) {
2245 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2246 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2247 println "LIKELY RSYNC COMMAND:"
2248 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2249 if (RUNRSYNC == "true") {
2251 commandLine "mkdir", "-p", toDir
2254 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2262 task getdownArchiveBuild() {
2263 group = "distribution"
2264 description = "Put files in the archive dir to go on the website"
2266 dependsOn getdownWebsite
2268 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2269 def vDir = "${getdownArchiveDir}/${v}"
2270 getdownFullArchiveDir = "${vDir}/getdown"
2271 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2273 def vAltDir = "alt_${v}"
2274 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2277 // cleanup old "old" dir
2278 delete getdownArchiveDir
2280 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2281 getdownArchiveTxt.getParentFile().mkdirs()
2282 def getdownArchiveTextLines = []
2283 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2287 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2288 into "${getdownFullArchiveDir}/${vAltDir}"
2291 getdownTextLines.each { line ->
2292 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2293 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2294 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2295 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2296 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2297 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2298 // remove the existing resource = resource/ or bin/ lines
2299 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2300 getdownArchiveTextLines += line
2304 // the resource dir -- add these files as resource lines in getdown.txt
2306 from "${archiveImagesDir}"
2307 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2309 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2313 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2315 def vLaunchJvl = file(getdownVersionLaunchJvl)
2316 vLaunchJvl.getParentFile().mkdirs()
2317 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2318 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2319 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2320 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2321 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2322 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2324 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2326 from getdownLauncher
2327 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2328 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2329 from "${getdownAppBaseDir}/${channel_props}"
2330 if (file(getdownLauncher).getName() != getdown_launcher) {
2331 rename(file(getdownLauncher).getName(), getdown_launcher)
2333 into getdownFullArchiveDir
2339 task getdownArchiveDigest(type: JavaExec) {
2340 group = "distribution"
2341 description = "Digest the getdown archive folder"
2343 dependsOn getdownArchiveBuild
2346 classpath = files(getdownLauncher)
2347 args getdownFullArchiveDir
2349 main = "com.threerings.getdown.tools.Digester"
2350 inputs.dir(getdownFullArchiveDir)
2351 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2354 task getdownArchive() {
2355 group = "distribution"
2356 description = "Build the website archive dir with getdown digest"
2358 dependsOn getdownArchiveBuild
2359 dependsOn getdownArchiveDigest
2362 tasks.withType(JavaCompile) {
2363 options.encoding = 'UTF-8'
2369 delete getdownAppBaseDir
2370 delete getdownFilesDir
2371 delete getdownArchiveDir
2377 if (file(install4jHomeDir).exists()) {
2379 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2380 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2381 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2382 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2384 installDir(file(install4jHomeDir))
2386 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2390 task copyInstall4jTemplate {
2391 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2392 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2393 inputs.file(install4jTemplateFile)
2394 inputs.file(install4jFileAssociationsFile)
2395 inputs.property("CHANNEL", { CHANNEL })
2396 outputs.file(install4jConfFile)
2399 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2401 // turn off code signing if no OSX_KEYPASS
2402 if (OSX_KEYPASS == "") {
2403 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2404 codeSigning.'@macEnabled' = "false"
2406 install4jConfigXml.'**'.windows.each { windows ->
2407 windows.'@runPostProcessor' = "false"
2411 // disable install screen for OSX dmg (for 2.11.2.0)
2412 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2413 macosArchive.attributes().remove('executeSetupApp')
2414 macosArchive.attributes().remove('setupAppId')
2417 // turn off checksum creation for LOCAL channel
2418 def e = install4jConfigXml.application[0]
2419 e.'@createChecksums' = string(install4jCheckSums)
2421 // put file association actions where placeholder action is
2422 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2423 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2424 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2425 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2426 def parent = a.parent()
2428 fileAssociationActions.each { faa ->
2431 // don't need to continue in .any loop once replacements have been made
2436 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2437 // NB we're deleting the /other/ one!
2438 // Also remove the examples subdir from non-release versions
2439 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2440 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2441 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2442 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2444 // remove the examples subdir from Full File Set
2445 def files = install4jConfigXml.files[0]
2446 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2447 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2448 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2449 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2450 dirEntry.parent().remove(dirEntry)
2452 install4jConfigXml.'**'.action.any { a ->
2453 if (a.'@customizedId' == customizedIdToDelete) {
2454 def parent = a.parent()
2460 // write install4j file
2461 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2468 delete install4jConfFile
2472 task cleanInstallersDataFiles {
2473 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2474 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2475 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2477 delete installersOutputTxt
2478 delete installersSha256
2479 delete hugoDataJsonFile
2483 task install4jDMGBackgroundImageCopy {
2484 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2485 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2488 from(install4jDMGBackgroundImageDir) {
2489 include(install4jDMGBackgroundImageFile)
2491 into install4jDMGBackgroundImageBuildDir
2496 task install4jDMGBackgroundImageProcess {
2497 dependsOn install4jDMGBackgroundImageCopy
2500 if (backgroundImageText) {
2501 if (convertBinary == null) {
2502 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2504 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2505 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2507 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2509 executable convertBinary
2512 '-font', install4j_background_image_text_font,
2513 '-fill', install4j_background_image_text_colour,
2514 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2515 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2516 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2525 task install4jDMGBackgroundImage {
2526 dependsOn install4jDMGBackgroundImageProcess
2529 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2530 group = "distribution"
2531 description = "Create the install4j installers"
2533 dependsOn copyInstall4jTemplate
2534 dependsOn cleanInstallersDataFiles
2535 dependsOn install4jDMGBackgroundImage
2537 projectFile = install4jConfFile
2539 // create an md5 for the input files to use as version for install4j conf file
2540 def digest = MessageDigest.getInstance("MD5")
2542 (file("${install4jDir}/${install4j_template}").text +
2543 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2544 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2545 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2546 if (filesMd5.length() >= 8) {
2547 filesMd5 = filesMd5.substring(0,8)
2549 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2552 'JALVIEW_NAME': jalview_name,
2553 'JALVIEW_APPLICATION_NAME': applicationName,
2554 'JALVIEW_DIR': "../..",
2555 'OSX_KEYSTORE': OSX_KEYSTORE,
2556 'OSX_APPLEID': OSX_APPLEID,
2557 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2558 'JSIGN_SH': JSIGN_SH,
2559 'JRE_DIR': getdown_app_dir_java,
2560 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2561 'JALVIEW_VERSION': JALVIEW_VERSION,
2562 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2563 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2564 'JAVA_VERSION': JAVA_VERSION,
2565 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2566 'VERSION': JALVIEW_VERSION,
2567 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2568 'BUNDLE_ID': install4jBundleId,
2569 'INTERNAL_ID': install4jInternalId,
2570 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2571 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2572 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2573 'WRAPPER_LINK': getdownWrapperLink,
2574 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2575 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2576 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2577 'INSTALLER_NAME': install4jInstallerName,
2578 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2579 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2580 'GETDOWN_FILES_DIR': getdown_files_dir,
2581 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2582 'GETDOWN_DIST_DIR': getdownAppDistDir,
2583 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2584 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2585 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2586 'BUILD_DIR': install4jBuildDir,
2587 'APPLICATION_CATEGORIES': install4j_application_categories,
2588 'APPLICATION_FOLDER': install4jApplicationFolder,
2589 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2590 'EXECUTABLE_NAME': install4jExecutableName,
2591 'EXTRA_SCHEME': install4jExtraScheme,
2592 'MAC_ICONS_FILE': install4jMacIconsFile,
2593 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2594 'PNG_ICON_FILE': install4jPngIconFile,
2595 'BACKGROUND': install4jBackground,
2600 'windows': 'WINDOWS',
2604 // these are the bundled OS/architecture VMs needed by install4j
2607 [ "mac", "aarch64" ],
2608 [ "windows", "x64" ],
2610 [ "linux", "aarch64" ]
2612 osArch.forEach { os, arch ->
2613 variables[ sprintf("%s_%s_JAVA_VM_DIR", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/jre-%s-%s-%s/jre", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
2614 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2615 // otherwise running `gradle installers` generates a non-useful error:
2616 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2617 variables[ sprintf("%s_%s_JAVA_VM_TGZ", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/tgz/jre_%s_%s_%s.tar.gz", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
2620 //println("INSTALL4J VARIABLES:")
2621 //variables.each{k,v->println("${k}=${v}")}
2623 destination = "${jalviewDir}/${install4jBuildDir}"
2624 buildSelected = true
2626 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2628 disableSigning = true
2629 disableNotarization = true
2633 macKeystorePassword = OSX_KEYPASS
2636 if (OSX_ALTOOLPASS) {
2637 appleIdPassword = OSX_ALTOOLPASS
2638 disableNotarization = false
2640 disableNotarization = true
2644 println("Using projectFile "+projectFile)
2645 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2649 inputs.dir(getdownAppBaseDir)
2650 inputs.file(install4jConfFile)
2651 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2652 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2655 def getDataHash(File myFile) {
2656 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2657 return myFile.exists()
2659 "file" : myFile.getName(),
2660 "filesize" : myFile.length(),
2661 "sha256" : hash.toString()
2666 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2668 "channel" : getdownChannelName,
2669 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2670 "git-commit" : "${gitHash} [${gitBranch}]",
2671 "version" : JALVIEW_VERSION
2673 // install4j installer files
2674 if (installersOutputTxt.exists()) {
2676 installersOutputTxt.readLines().each { def line ->
2677 if (line.startsWith("#")) {
2680 line.replaceAll("\n","")
2681 def vals = line.split("\t")
2682 def filename = vals[3]
2683 def filesize = file(filename).length()
2684 filename = filename.replaceAll(/^.*\//, "")
2685 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2686 idHash."${filename}" = vals[0]
2688 if (install4jCheckSums && installersSha256.exists()) {
2689 installersSha256.readLines().each { def line ->
2690 if (line.startsWith("#")) {
2693 line.replaceAll("\n","")
2694 def vals = line.split(/\s+\*?/)
2695 def filename = vals[1]
2696 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2702 "JAR": shadowJar.archiveFile, // executable JAR
2703 "JVL": getdownVersionLaunchJvl, // version JVL
2704 "SOURCE": sourceDist.archiveFile // source TGZ
2705 ].each { key, value ->
2706 def file = file(value)
2707 if (file.exists()) {
2708 def fileHash = getDataHash(file)
2709 if (fileHash != null) {
2710 hash."${key}" = fileHash;
2714 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2717 task staticMakeInstallersJsonFile {
2719 def output = findProperty("i4j_output")
2720 def sha256 = findProperty("i4j_sha256")
2721 def json = findProperty("i4j_json")
2722 if (output == null || sha256 == null || json == null) {
2723 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2725 writeDataJsonFile(file(output), file(sha256), file(json))
2730 dependsOn installerFiles
2736 eclipse().configFile(eclipse_codestyle_file)
2740 task createSourceReleaseProperties(type: WriteProperties) {
2741 group = "distribution"
2742 description = "Create the source RELEASE properties file"
2744 def sourceTarBuildDir = "${buildDir}/sourceTar"
2745 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2746 outputFile (sourceReleasePropertiesFile)
2749 releaseProps.each{ key, val -> property key, val }
2750 property "git.branch", gitBranch
2751 property "git.hash", gitHash
2754 outputs.file(outputFile)
2757 task sourceDist(type: Tar) {
2758 group "distribution"
2759 description "Create a source .tar.gz file for distribution"
2761 dependsOn createBuildProperties
2762 dependsOn convertMdFiles
2763 dependsOn eclipseAllPreferences
2764 dependsOn createSourceReleaseProperties
2767 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2768 archiveFileName = outputFileName
2770 compression Compression.GZIP
2785 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2787 "utils/InstallAnywhere",
2802 "gradle.properties",
2814 ".settings/org.eclipse.buildship.core.prefs",
2815 ".settings/org.eclipse.jdt.core.prefs"
2819 exclude (EXCLUDE_FILES)
2820 include (PROCESS_FILES)
2821 filter(ReplaceTokens,
2825 'Version-Rel': JALVIEW_VERSION,
2826 'Year-Rel': getDate("yyyy")
2831 exclude (EXCLUDE_FILES)
2832 exclude (PROCESS_FILES)
2833 exclude ("appletlib")
2834 exclude ("**/*locales")
2835 exclude ("*locales/**")
2836 exclude ("utils/InstallAnywhere")
2838 exclude (getdown_files_dir)
2839 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2840 //exclude (getdown_website_dir)
2841 //exclude (getdown_archive_dir)
2843 // exluding these as not using jars as modules yet
2844 exclude ("${j11modDir}/**/*.jar")
2847 include(INCLUDE_FILES)
2849 // from (jalviewDir) {
2850 // // explicit includes for stuff that seemed to not get included
2851 // include(fileTree("test/**/*."))
2852 // exclude(EXCLUDE_FILES)
2853 // exclude(PROCESS_FILES)
2856 from(file(buildProperties).getParent()) {
2857 include(file(buildProperties).getName())
2858 rename(file(buildProperties).getName(), "build_properties")
2860 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2864 def sourceTarBuildDir = "${buildDir}/sourceTar"
2865 from(sourceTarBuildDir) {
2866 // this includes the appended RELEASE properties file
2870 task dataInstallersJson {
2872 description "Create the installers-VERSION.json data file for installer files created"
2874 mustRunAfter installers
2875 mustRunAfter shadowJar
2876 mustRunAfter sourceDist
2877 mustRunAfter getdownArchive
2879 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2880 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2882 if (installersOutputTxt.exists()) {
2883 inputs.file(installersOutputTxt)
2885 if (install4jCheckSums && installersSha256.exists()) {
2886 inputs.file(installersSha256)
2889 shadowJar.archiveFile, // executable JAR
2890 getdownVersionLaunchJvl, // version JVL
2891 sourceDist.archiveFile // source TGZ
2892 ].each { fileName ->
2893 if (file(fileName).exists()) {
2894 inputs.file(fileName)
2898 outputs.file(hugoDataJsonFile)
2901 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
2907 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
2910 dependsOn pubhtmlhelp
2912 inputs.dir("${helpBuildDir}/${help_dir}")
2913 outputs.dir("${buildDir}/distributions/${help_dir}")
2917 task j2sSetHeadlessBuild {
2924 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2926 description "Enable the alternative J2S Config file for headless build"
2928 outputFile = jalviewjsJ2sSettingsFileName
2929 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2930 def j2sProps = new Properties()
2931 if (j2sPropsFile.exists()) {
2933 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2934 j2sProps.load(j2sPropsFileFIS)
2935 j2sPropsFileFIS.close()
2937 j2sProps.each { prop, val ->
2940 } catch (Exception e) {
2941 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2945 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2946 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2951 task jalviewjsSetEclipseWorkspace {
2952 def propKey = "jalviewjs_eclipse_workspace"
2954 if (project.hasProperty(propKey)) {
2955 propVal = project.getProperty(propKey)
2956 if (propVal.startsWith("~/")) {
2957 propVal = System.getProperty("user.home") + propVal.substring(1)
2960 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2961 def propsFile = file(propsFileName)
2962 def eclipseWsDir = propVal
2963 def props = new Properties()
2965 def writeProps = true
2966 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2967 def ins = new FileInputStream(propsFileName)
2970 if (props.getProperty(propKey, null) != null) {
2971 eclipseWsDir = props.getProperty(propKey)
2976 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2977 def tempDir = File.createTempDir()
2978 eclipseWsDir = tempDir.getAbsolutePath()
2981 eclipseWorkspace = file(eclipseWsDir)
2984 // do not run a headless transpile when we claim to be in Eclipse
2986 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2987 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2989 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2993 props.setProperty(propKey, eclipseWsDir)
2994 propsFile.parentFile.mkdirs()
2995 def bytes = new ByteArrayOutputStream()
2996 props.store(bytes, null)
2997 def propertiesString = bytes.toString()
2998 propsFile.text = propertiesString
3004 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3007 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3008 outputs.file(propsFileName)
3009 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3013 task jalviewjsEclipsePaths {
3016 def eclipseRoot = jalviewjs_eclipse_root
3017 if (eclipseRoot.startsWith("~/")) {
3018 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3020 if (OperatingSystem.current().isMacOsX()) {
3021 eclipseRoot += "/Eclipse.app"
3022 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3023 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3024 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3025 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3026 eclipseRoot += "/eclipse"
3028 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3029 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3030 } else { // linux or unix
3031 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3032 eclipseRoot += "/eclipse"
3033 println("eclipseDir exists")
3035 eclipseBinary = "${eclipseRoot}/eclipse"
3036 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3039 eclipseVersion = "4.13" // default
3040 def assumedVersion = true
3041 if (file(eclipseProduct).exists()) {
3042 def fis = new FileInputStream(eclipseProduct)
3043 def props = new Properties()
3045 eclipseVersion = props.getProperty("version")
3047 assumedVersion = false
3050 def propKey = "eclipse_debug"
3051 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3054 // do not run a headless transpile when we claim to be in Eclipse
3056 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3057 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3059 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3062 if (!assumedVersion) {
3063 println("ECLIPSE VERSION=${eclipseVersion}")
3069 task printProperties {
3071 description "Output to console all System.properties"
3073 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3079 dependsOn eclipseProject
3080 dependsOn eclipseClasspath
3081 dependsOn eclipseJdt
3085 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3086 task jalviewjsEclipseCopyDropins(type: Copy) {
3087 dependsOn jalviewjsEclipsePaths
3089 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3090 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3091 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3098 // this eclipse -clean doesn't actually work
3099 task jalviewjsCleanEclipse(type: Exec) {
3100 dependsOn eclipseSetup
3101 dependsOn jalviewjsEclipsePaths
3102 dependsOn jalviewjsEclipseCopyDropins
3104 executable(eclipseBinary)
3105 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3111 def inputString = """exit
3114 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3115 standardInput = inputByteStream
3118 /* not really working yet
3119 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3123 task jalviewjsTransferUnzipSwingJs {
3124 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3128 from zipTree(file_zip)
3129 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3133 inputs.file file_zip
3134 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3138 task jalviewjsTransferUnzipLib {
3139 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3142 zipFiles.each { file_zip ->
3144 from zipTree(file_zip)
3145 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3150 inputs.files zipFiles
3151 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3155 task jalviewjsTransferUnzipAllLibs {
3156 dependsOn jalviewjsTransferUnzipSwingJs
3157 dependsOn jalviewjsTransferUnzipLib
3161 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3163 description "Create the alternative j2s file from the j2s.* properties"
3165 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3166 def siteDirProperty = "j2s.site.directory"
3167 def setSiteDir = false
3168 jalviewjsJ2sProps.each { prop, val ->
3170 if (prop == siteDirProperty) {
3171 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3172 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3178 if (!setSiteDir) { // default site location, don't override specifically set property
3179 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3182 outputFile = jalviewjsJ2sAltSettingsFileName
3185 inputs.properties(jalviewjsJ2sProps)
3186 outputs.file(jalviewjsJ2sAltSettingsFileName)
3191 task jalviewjsEclipseSetup {
3192 dependsOn jalviewjsEclipseCopyDropins
3193 dependsOn jalviewjsSetEclipseWorkspace
3194 dependsOn jalviewjsCreateJ2sSettings
3198 task jalviewjsSyncAllLibs (type: Sync) {
3199 dependsOn jalviewjsTransferUnzipAllLibs
3200 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3201 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3202 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3206 def outputFiles = []
3207 rename { filename ->
3208 outputFiles += "${outputDir}/${filename}"
3215 // should this be exclude really ?
3216 duplicatesStrategy "INCLUDE"
3218 outputs.files outputFiles
3219 inputs.files inputFiles
3223 task jalviewjsSyncResources (type: Sync) {
3224 dependsOn buildResources
3226 def inputFiles = fileTree(dir: resourcesBuildDir)
3227 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3231 def outputFiles = []
3232 rename { filename ->
3233 outputFiles += "${outputDir}/${filename}"
3239 outputs.files outputFiles
3240 inputs.files inputFiles
3244 task jalviewjsSyncSiteResources (type: Sync) {
3245 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3246 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3250 def outputFiles = []
3251 rename { filename ->
3252 outputFiles += "${outputDir}/${filename}"
3258 outputs.files outputFiles
3259 inputs.files inputFiles
3263 task jalviewjsSyncBuildProperties (type: Sync) {
3264 dependsOn createBuildProperties
3265 def inputFiles = [file(buildProperties)]
3266 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3270 def outputFiles = []
3271 rename { filename ->
3272 outputFiles += "${outputDir}/${filename}"
3278 outputs.files outputFiles
3279 inputs.files inputFiles
3283 task jalviewjsProjectImport(type: Exec) {
3284 dependsOn eclipseSetup
3285 dependsOn jalviewjsEclipsePaths
3286 dependsOn jalviewjsEclipseSetup
3289 // do not run a headless import when we claim to be in Eclipse
3291 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3292 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3294 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3298 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3299 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3300 executable(eclipseBinary)
3301 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3305 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3307 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3308 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3311 inputs.file("${jalviewDir}/.project")
3312 outputs.upToDateWhen {
3313 file(projdir).exists()
3318 task jalviewjsTranspile(type: Exec) {
3319 dependsOn jalviewjsEclipseSetup
3320 dependsOn jalviewjsProjectImport
3321 dependsOn jalviewjsEclipsePaths
3323 dependsOn jalviewjsEnableAltFileProperty
3327 // do not run a headless transpile when we claim to be in Eclipse
3329 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3330 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3332 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3336 executable(eclipseBinary)
3337 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3341 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3343 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3344 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3350 stdout = new ByteArrayOutputStream()
3351 stderr = new ByteArrayOutputStream()
3353 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3354 def logOutFile = file(logOutFileName)
3355 logOutFile.createNewFile()
3356 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3357 BINARY: ${eclipseBinary}
3358 VERSION: ${eclipseVersion}
3359 WORKSPACE: ${eclipseWorkspace}
3360 DEBUG: ${eclipseDebug}
3363 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3364 // combine stdout and stderr
3365 def logErrFOS = logOutFOS
3367 if (jalviewjs_j2s_to_console.equals("true")) {
3368 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3369 new org.apache.tools.ant.util.TeeOutputStream(
3373 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3374 new org.apache.tools.ant.util.TeeOutputStream(
3379 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3382 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3389 if (stdout.toString().contains("Error processing ")) {
3390 // j2s did not complete transpile
3391 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3392 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3393 println("IGNORING TRANSPILE ERRORS")
3394 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3396 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3401 inputs.dir("${jalviewDir}/${sourceDir}")
3402 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3403 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3407 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3409 def stdout = new ByteArrayOutputStream()
3410 def stderr = new ByteArrayOutputStream()
3412 def coreFile = file(jsfile)
3414 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3416 logOutFile.createNewFile()
3417 logOutFile.append(msg+"\n")
3419 def coreTop = file(prefixFile)
3420 def coreBottom = file(suffixFile)
3421 coreFile.getParentFile().mkdirs()
3422 coreFile.createNewFile()
3423 coreFile.write( coreTop.getText("UTF-8") )
3427 def t = f.getText("UTF-8")
3428 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3429 coreFile.append( t )
3431 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3433 logOutFile.append(msg+"\n")
3436 coreFile.append( coreBottom.getText("UTF-8") )
3438 msg = "Generating ${zjsfile}"
3440 logOutFile.append(msg+"\n")
3441 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3442 def logErrFOS = logOutFOS
3445 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3446 main = "com.google.javascript.jscomp.CommandLineRunner"
3447 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3448 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3451 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3453 logOutFile.append(msg+"\n")
3455 if (logOutConsole) {
3456 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3457 new org.apache.tools.ant.util.TeeOutputStream(
3461 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3462 new org.apache.tools.ant.util.TeeOutputStream(
3467 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3470 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3477 logOutFile.append(msg+"\n")
3481 task jalviewjsBuildAllCores {
3483 description "Build the core js lib closures listed in the classlists dir"
3484 dependsOn jalviewjsTranspile
3485 dependsOn jalviewjsTransferUnzipSwingJs
3487 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3488 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3489 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3490 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3491 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3492 def prefixFile = "${jsDir}/core/coretop2.js"
3493 def suffixFile = "${jsDir}/core/corebottom2.js"
3495 inputs.file prefixFile
3496 inputs.file suffixFile
3498 def classlistFiles = []
3499 // add the classlists found int the jalviewjs_classlists_dir
3500 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3502 def name = file.getName() - ".txt"
3509 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3510 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3511 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3513 jalviewjsCoreClasslists = []
3515 classlistFiles.each {
3518 def file = hash['file']
3519 if (! file.exists()) {
3520 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3521 return false // this is a "continue" in groovy .each closure
3523 def name = hash['name']
3525 name = file.getName() - ".txt"
3533 def list = fileTree(dir: j2sDir, includes: filelist)
3535 def jsfile = "${outputDir}/core${name}.js"
3536 def zjsfile = "${outputDir}/core${name}.z.js"
3538 jalviewjsCoreClasslists += [
3547 outputs.file(jsfile)
3548 outputs.file(zjsfile)
3551 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3552 def stevesoftClasslistName = "_stevesoft"
3553 def stevesoftClasslist = [
3554 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3555 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3556 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3557 'name': stevesoftClasslistName
3559 jalviewjsCoreClasslists += stevesoftClasslist
3560 inputs.files(stevesoftClasslist['list'])
3561 outputs.file(stevesoftClasslist['jsfile'])
3562 outputs.file(stevesoftClasslist['zjsfile'])
3565 def allClasslistName = "_all"
3566 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3567 allJsFiles += fileTree(
3571 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3572 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3573 "**/org/jmol/export/JSExporter.js"
3576 allJsFiles += fileTree(
3580 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3581 "**/sun/misc/Unsafe.js",
3582 "**/swingjs/jquery/jquery-editable-select.js",
3583 "**/swingjs/jquery/j2sComboBox.js",
3584 "**/sun/misc/FloatingDecimal.js"
3587 def allClasslist = [
3588 'jsfile': "${outputDir}/core${allClasslistName}.js",
3589 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3591 'name': allClasslistName
3593 // not including this version of "all" core at the moment
3594 //jalviewjsCoreClasslists += allClasslist
3595 inputs.files(allClasslist['list'])
3596 outputs.file(allClasslist['jsfile'])
3597 outputs.file(allClasslist['zjsfile'])
3600 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3601 logOutFile.getParentFile().mkdirs()
3602 logOutFile.createNewFile()
3603 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3605 jalviewjsCoreClasslists.each {
3606 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3613 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3616 into file(outputFile).getParentFile()
3617 rename { filename ->
3618 if (filename.equals(inputFile.getName())) {
3619 return file(outputFile).getName()
3623 filter(ReplaceTokens,
3627 'MAIN': '"'+main_class+'"',
3629 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3630 'COREKEY': jalviewjs_core_key,
3631 'CORENAME': coreName
3638 task jalviewjsPublishCoreTemplates {
3639 dependsOn jalviewjsBuildAllCores
3640 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3641 def inputFile = file(inputFileName)
3642 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3644 def outputFiles = []
3645 jalviewjsCoreClasslists.each { cl ->
3646 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3647 cl['outputfile'] = outputFile
3648 outputFiles += outputFile
3652 jalviewjsCoreClasslists.each { cl ->
3653 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3656 inputs.file(inputFile)
3657 outputs.files(outputFiles)
3661 task jalviewjsSyncCore (type: Sync) {
3662 dependsOn jalviewjsBuildAllCores
3663 dependsOn jalviewjsPublishCoreTemplates
3664 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3665 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3669 def outputFiles = []
3670 rename { filename ->
3671 outputFiles += "${outputDir}/${filename}"
3677 outputs.files outputFiles
3678 inputs.files inputFiles
3682 // this Copy version of TransferSiteJs will delete anything else in the target dir
3683 task jalviewjsCopyTransferSiteJs(type: Copy) {
3684 dependsOn jalviewjsTranspile
3685 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3686 into "${jalviewDir}/${jalviewjsSiteDir}"
3690 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3691 task jalviewjsSyncTransferSiteJs(type: Sync) {
3692 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3694 into "${jalviewDir}/${jalviewjsSiteDir}"
3701 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3702 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3703 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3704 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3706 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3707 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3708 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3709 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3712 task jalviewjsPrepareSite {
3714 description "Prepares the website folder including unzipping files and copying resources"
3715 dependsOn jalviewjsSyncAllLibs
3716 dependsOn jalviewjsSyncResources
3717 dependsOn jalviewjsSyncSiteResources
3718 dependsOn jalviewjsSyncBuildProperties
3719 dependsOn jalviewjsSyncCore
3723 task jalviewjsBuildSite {
3725 description "Builds the whole website including transpiled code"
3726 dependsOn jalviewjsCopyTransferSiteJs
3727 dependsOn jalviewjsPrepareSite
3731 task cleanJalviewjsTransferSite {
3733 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3734 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3735 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3736 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3741 task cleanJalviewjsSite {
3742 dependsOn cleanJalviewjsTransferSite
3744 delete "${jalviewDir}/${jalviewjsSiteDir}"
3749 task jalviewjsSiteTar(type: Tar) {
3751 description "Creates a tar.gz file for the website"
3752 dependsOn jalviewjsBuildSite
3753 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3754 archiveFileName = outputFilename
3756 compression Compression.GZIP
3758 from "${jalviewDir}/${jalviewjsSiteDir}"
3759 into jalviewjs_site_dir // this is inside the tar file
3761 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3765 task jalviewjsServer {
3767 def filename = "jalviewjsTest.html"
3768 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3769 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3774 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3775 factory = f.newInstance()
3776 } catch (ClassNotFoundException e) {
3777 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3779 def port = Integer.valueOf(jalviewjs_server_port)
3784 while(port < start+1000 && !running) {
3786 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3787 jalviewjsServer = factory.start(doc_root, port)
3789 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3790 println("SERVER STARTED with document root ${doc_root}.")
3791 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3792 println("For debug: "+url+"?j2sdebug")
3793 println("For verbose: "+url+"?j2sverbose")
3794 } catch (Exception e) {
3799 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3800 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3801 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3803 jalviewjsCoreClasslists.each { cl ->
3804 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3806 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3808 println("For core ${cl.name}: "+urlcore)
3811 file(htmlFile).text = htmlText
3814 outputs.file(htmlFile)
3815 outputs.upToDateWhen({false})
3819 task cleanJalviewjsAll {
3821 description "Delete all configuration and build artifacts to do with JalviewJS build"
3822 dependsOn cleanJalviewjsSite
3823 dependsOn jalviewjsEclipsePaths
3826 delete "${jalviewDir}/${jalviewjsBuildDir}"
3827 delete "${jalviewDir}/${eclipse_bin_dir}"
3828 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3829 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3831 delete jalviewjsJ2sAltSettingsFileName
3834 outputs.upToDateWhen( { false } )
3838 task jalviewjsIDE_checkJ2sPlugin {
3839 group "00 JalviewJS in Eclipse"
3840 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3843 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3844 def j2sPluginFile = file(j2sPlugin)
3845 def eclipseHome = System.properties["eclipse.home.location"]
3846 if (eclipseHome == null || ! IN_ECLIPSE) {
3847 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3849 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3850 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3851 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3852 eclipseJ2sPluginDirs += altPluginsDir
3854 def foundPlugin = false
3855 def j2sPluginFileName = j2sPluginFile.getName()
3856 def eclipseJ2sPlugin
3857 def eclipseJ2sPluginFile
3858 eclipseJ2sPluginDirs.any { dir ->
3859 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3860 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3861 if (eclipseJ2sPluginFile.exists()) {
3867 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3868 System.err.println(msg)
3869 throw new StopExecutionException(msg)
3872 def digest = MessageDigest.getInstance("MD5")
3874 digest.update(j2sPluginFile.text.bytes)
3875 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3877 digest.update(eclipseJ2sPluginFile.text.bytes)
3878 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3880 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3881 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3882 System.err.println(msg)
3883 throw new StopExecutionException(msg)
3885 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3891 task jalviewjsIDE_copyJ2sPlugin {
3892 group "00 JalviewJS in Eclipse"
3893 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3896 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3897 def j2sPluginFile = file(j2sPlugin)
3898 def eclipseHome = System.properties["eclipse.home.location"]
3899 if (eclipseHome == null || ! IN_ECLIPSE) {
3900 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3902 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3903 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3904 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3905 System.err.println(msg)
3908 eclipseJ2sPluginFile.getParentFile().mkdirs()
3909 into eclipseJ2sPluginFile.getParent()
3915 task jalviewjsIDE_j2sFile {
3916 group "00 JalviewJS in Eclipse"
3917 description "Creates the .j2s file"
3918 dependsOn jalviewjsCreateJ2sSettings
3922 task jalviewjsIDE_SyncCore {
3923 group "00 JalviewJS in Eclipse"
3924 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3925 dependsOn jalviewjsSyncCore
3929 task jalviewjsIDE_SyncSiteAll {
3930 dependsOn jalviewjsSyncAllLibs
3931 dependsOn jalviewjsSyncResources
3932 dependsOn jalviewjsSyncSiteResources
3933 dependsOn jalviewjsSyncBuildProperties
3937 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3940 task jalviewjsIDE_PrepareSite {
3941 group "00 JalviewJS in Eclipse"
3942 description "Sync libs and resources to site dir, but not closure cores"
3944 dependsOn jalviewjsIDE_SyncSiteAll
3945 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3949 task jalviewjsIDE_AssembleSite {
3950 group "00 JalviewJS in Eclipse"
3951 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3952 dependsOn jalviewjsPrepareSite
3956 task jalviewjsIDE_SiteClean {
3957 group "00 JalviewJS in Eclipse"
3958 description "Deletes the Eclipse transpiled site"
3959 dependsOn cleanJalviewjsSite
3963 task jalviewjsIDE_Server {
3964 group "00 JalviewJS in Eclipse"
3965 description "Starts a webserver on localhost to test the website"
3966 dependsOn jalviewjsServer
3970 // buildship runs this at import or gradle refresh
3971 task eclipseSynchronizationTask {
3972 //dependsOn eclipseSetup
3973 dependsOn createBuildProperties
3975 dependsOn jalviewjsIDE_j2sFile
3976 dependsOn jalviewjsIDE_checkJ2sPlugin
3977 dependsOn jalviewjsIDE_PrepareSite
3982 // buildship runs this at build time or project refresh
3983 task eclipseAutoBuildTask {
3984 //dependsOn jalviewjsIDE_checkJ2sPlugin
3985 //dependsOn jalviewjsIDE_PrepareSite
3991 description "Build the site"
3992 dependsOn jalviewjsBuildSite