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 $jalviewDir
1743 dependsOn cloverClasses
1745 dependsOn compileJava //?
1749 includeGroups testng_groups
1750 excludeGroups testng_excluded_groups
1752 useDefaultListeners=true
1755 maxHeapSize = "2048m"
1758 maxParallelForks = 1
1761 jvmArgs '-Xmx2048m', '-Xms2048m'
1764 workingDir = jalviewDir
1765 def testLaf = project.findProperty("test_laf")
1766 if (testLaf != null) {
1767 println("Setting Test LaF to '${testLaf}'")
1768 systemProperty "laf", testLaf
1770 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1771 if (testHiDPIScale != null) {
1772 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1773 systemProperty "sun.java2d.uiScale", testHiDPIScale
1775 sourceCompatibility = compile_source_compatibility
1776 targetCompatibility = compile_target_compatibility
1777 jvmArgs += additional_compiler_args
1781 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1787 task compileLinkCheck(type: JavaCompile) {
1789 classpath = files("${jalviewDir}/${utils_dir}")
1790 destinationDir = file("${jalviewDir}/${utils_dir}")
1791 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1793 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1794 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1795 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1796 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1800 task linkCheck(type: JavaExec) {
1802 dependsOn compileLinkCheck
1804 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1805 classpath = files("${jalviewDir}/${utils_dir}")
1806 main = "HelpLinksChecker"
1807 workingDir = "${helpBuildDir}"
1808 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1810 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1811 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1814 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1818 inputs.dir(helpBuildDir)
1819 outputs.file(helpLinksCheckerOutFile)
1823 // import the pubhtmlhelp target
1824 ant.properties.basedir = "${jalviewDir}"
1825 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1826 ant.importBuild "${utils_dir}/publishHelp.xml"
1829 task cleanPackageDir(type: Delete) {
1831 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1841 attributes "Main-Class": main_class,
1842 "Permissions": "all-permissions",
1843 "Application-Name": applicationName,
1844 "Codebase": application_codebase,
1845 "Implementation-Version": JALVIEW_VERSION
1848 def outputDir = "${jalviewDir}/${package_dir}"
1849 destinationDirectory = file(outputDir)
1850 archiveFileName = rootProject.name+".jar"
1851 duplicatesStrategy "EXCLUDE"
1858 exclude "**/*.jar.*"
1860 inputs.dir(sourceSets.main.java.outputDir)
1861 sourceSets.main.resources.srcDirs.each{ dir ->
1864 outputs.file("${outputDir}/${archiveFileName}")
1868 task copyJars(type: Copy) {
1869 from fileTree(dir: classesDir, include: "**/*.jar").files
1870 into "${jalviewDir}/${package_dir}"
1874 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1875 task syncJars(type: Sync) {
1877 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1878 into "${jalviewDir}/${package_dir}"
1880 include jar.archiveFileName.getOrNull()
1887 description = "Put all required libraries in dist"
1888 // order of "cleanPackageDir", "copyJars", "jar" important!
1889 jar.mustRunAfter cleanPackageDir
1890 syncJars.mustRunAfter cleanPackageDir
1891 dependsOn cleanPackageDir
1894 outputs.dir("${jalviewDir}/${package_dir}")
1899 dependsOn cleanPackageDir
1906 group = "distribution"
1907 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1911 from ("${jalviewDir}/${libDistDir}") {
1915 attributes "Implementation-Version": JALVIEW_VERSION,
1916 "Application-Name": applicationName
1919 duplicatesStrategy "INCLUDE"
1921 mainClassName = shadow_jar_main_class
1923 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1927 task getdownImagesCopy() {
1928 inputs.dir getdownImagesDir
1929 outputs.dir getdownImagesBuildDir
1933 from(getdownImagesDir) {
1934 include("*getdown*.png")
1936 into getdownImagesBuildDir
1941 task getdownImagesProcess() {
1942 dependsOn getdownImagesCopy
1945 if (backgroundImageText) {
1946 if (convertBinary == null) {
1947 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
1949 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
1950 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
1952 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
1954 executable convertBinary
1957 '-font', getdown_background_image_text_font,
1958 '-fill', getdown_background_image_text_colour,
1959 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
1960 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
1961 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
1970 task getdownImages() {
1971 dependsOn getdownImagesProcess
1974 task getdownWebsite() {
1975 group = "distribution"
1976 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1978 dependsOn getdownImages
1983 def getdownWebsiteResourceFilenames = []
1984 def getdownResourceDir = getdownResourceDir
1985 def getdownResourceFilenames = []
1988 // clean the getdown website and files dir before creating getdown folders
1989 delete getdownAppBaseDir
1990 delete getdownFilesDir
1993 from buildProperties
1994 rename(file(buildProperties).getName(), getdown_build_properties)
1997 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2000 from channelPropsFile
2001 filter(ReplaceTokens,
2005 'SUFFIX': channelSuffix
2008 into getdownAppBaseDir
2010 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2012 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2013 def props = project.properties.sort { it.key }
2014 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2015 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2017 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2018 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2020 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2021 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2023 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2024 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2025 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2026 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2027 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2028 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2029 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2032 props.put("getdown_txt_title", jalview_name)
2033 props.put("getdown_txt_ui.name", applicationName)
2035 // start with appbase
2036 getdownTextLines += "appbase = ${getdownAppBase}"
2037 props.each{ prop, val ->
2038 if (prop.startsWith("getdown_txt_") && val != null) {
2039 if (prop.startsWith("getdown_txt_multi_")) {
2040 def key = prop.substring(18)
2041 val.split(",").each{ v ->
2042 def line = "${key} = ${v}"
2043 getdownTextLines += line
2046 // file values rationalised
2047 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2049 if (val.indexOf('/') == 0) {
2052 } else if (val.indexOf('/') > 0) {
2053 // relative path (relative to jalviewDir)
2054 r = file( "${jalviewDir}/${val}" )
2057 val = "${getdown_resource_dir}/" + r.getName()
2058 getdownWebsiteResourceFilenames += val
2059 getdownResourceFilenames += r.getPath()
2062 if (! prop.startsWith("getdown_txt_resource")) {
2063 def line = prop.substring(12) + " = ${val}"
2064 getdownTextLines += line
2070 getdownWebsiteResourceFilenames.each{ filename ->
2071 getdownTextLines += "resource = ${filename}"
2073 getdownResourceFilenames.each{ filename ->
2076 into getdownResourceDir
2080 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2081 getdownWrapperScripts.each{ script ->
2082 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2086 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2088 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2093 fileTree(file(package_dir)).each{ f ->
2094 if (f.isDirectory()) {
2095 def files = fileTree(dir: f, include: ["*"]).getFiles()
2097 } else if (f.exists()) {
2101 def jalviewJar = jar.archiveFileName.getOrNull()
2102 // put jalview.jar first for CLASSPATH and .properties files reasons
2103 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2104 def name = f.getName()
2105 def line = "code = ${getdownAppDistDir}/${name}"
2106 getdownTextLines += line
2113 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2115 if (JAVA_VERSION.equals("11")) {
2116 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2117 j11libFiles.sort().each{f ->
2118 def name = f.getName()
2119 def line = "code = ${getdown_j11lib_dir}/${name}"
2120 getdownTextLines += line
2123 into getdownJ11libDir
2129 // 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.
2130 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2131 getdownTextLines += "resource = ${getdown_launcher_new}"
2132 getdownTextLines += "class = ${main_class}"
2133 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2134 if (getdownSetAppBaseProperty) {
2135 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2136 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2139 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2140 getdownTxt.write(getdownTextLines.join("\n"))
2142 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2143 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2144 launchJvl.write("appbase=${getdownAppBase}")
2146 // files going into the getdown website dir: getdown-launcher.jar
2148 from getdownLauncher
2149 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2150 into getdownAppBaseDir
2153 // files going into the getdown website dir: getdown-launcher(-local).jar
2155 from getdownLauncher
2156 if (file(getdownLauncher).getName() != getdown_launcher) {
2157 rename(file(getdownLauncher).getName(), getdown_launcher)
2159 into getdownAppBaseDir
2162 // files going into the getdown website dir: ./install dir and files
2163 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2166 from getdownLauncher
2167 from "${getdownAppDir}/${getdown_build_properties}"
2168 if (file(getdownLauncher).getName() != getdown_launcher) {
2169 rename(file(getdownLauncher).getName(), getdown_launcher)
2171 into getdownInstallDir
2174 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2176 from getdownInstallDir
2177 into getdownFilesInstallDir
2181 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2185 from getdownLauncher
2186 from "${getdownAppBaseDir}/${getdown_build_properties}"
2187 from "${getdownAppBaseDir}/${channel_props}"
2188 if (file(getdownLauncher).getName() != getdown_launcher) {
2189 rename(file(getdownLauncher).getName(), getdown_launcher)
2191 into getdownFilesDir
2194 // and ./resource (not all downloaded by getdown)
2196 from getdownResourceDir
2197 into "${getdownFilesDir}/${getdown_resource_dir}"
2202 inputs.dir("${jalviewDir}/${package_dir}")
2204 outputs.dir(getdownAppBaseDir)
2205 outputs.dir(getdownFilesDir)
2209 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2210 task getdownDigestDir(type: JavaExec) {
2212 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2214 def digestDirPropertyName = "DIGESTDIR"
2216 classpath = files(getdownLauncher)
2217 def digestDir = findProperty(digestDirPropertyName)
2218 if (digestDir == null) {
2219 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2223 main = "com.threerings.getdown.tools.Digester"
2227 task getdownDigest(type: JavaExec) {
2228 group = "distribution"
2229 description = "Digest the getdown website folder"
2230 dependsOn getdownWebsite
2232 classpath = files(getdownLauncher)
2234 main = "com.threerings.getdown.tools.Digester"
2235 args getdownAppBaseDir
2236 inputs.dir(getdownAppBaseDir)
2237 outputs.file("${getdownAppBaseDir}/digest2.txt")
2242 group = "distribution"
2243 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2244 dependsOn getdownDigest
2246 if (reportRsyncCommand) {
2247 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2248 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2249 println "LIKELY RSYNC COMMAND:"
2250 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2251 if (RUNRSYNC == "true") {
2253 commandLine "mkdir", "-p", toDir
2256 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2264 task getdownArchiveBuild() {
2265 group = "distribution"
2266 description = "Put files in the archive dir to go on the website"
2268 dependsOn getdownWebsite
2270 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2271 def vDir = "${getdownArchiveDir}/${v}"
2272 getdownFullArchiveDir = "${vDir}/getdown"
2273 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2275 def vAltDir = "alt_${v}"
2276 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2279 // cleanup old "old" dir
2280 delete getdownArchiveDir
2282 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2283 getdownArchiveTxt.getParentFile().mkdirs()
2284 def getdownArchiveTextLines = []
2285 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2289 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2290 into "${getdownFullArchiveDir}/${vAltDir}"
2293 getdownTextLines.each { line ->
2294 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2295 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2296 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2297 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2298 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2299 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2300 // remove the existing resource = resource/ or bin/ lines
2301 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2302 getdownArchiveTextLines += line
2306 // the resource dir -- add these files as resource lines in getdown.txt
2308 from "${archiveImagesDir}"
2309 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2311 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2315 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2317 def vLaunchJvl = file(getdownVersionLaunchJvl)
2318 vLaunchJvl.getParentFile().mkdirs()
2319 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2320 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2321 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2322 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2323 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2324 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2326 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2328 from getdownLauncher
2329 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2330 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2331 from "${getdownAppBaseDir}/${channel_props}"
2332 if (file(getdownLauncher).getName() != getdown_launcher) {
2333 rename(file(getdownLauncher).getName(), getdown_launcher)
2335 into getdownFullArchiveDir
2341 task getdownArchiveDigest(type: JavaExec) {
2342 group = "distribution"
2343 description = "Digest the getdown archive folder"
2345 dependsOn getdownArchiveBuild
2348 classpath = files(getdownLauncher)
2349 args getdownFullArchiveDir
2351 main = "com.threerings.getdown.tools.Digester"
2352 inputs.dir(getdownFullArchiveDir)
2353 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2356 task getdownArchive() {
2357 group = "distribution"
2358 description = "Build the website archive dir with getdown digest"
2360 dependsOn getdownArchiveBuild
2361 dependsOn getdownArchiveDigest
2364 tasks.withType(JavaCompile) {
2365 options.encoding = 'UTF-8'
2371 delete getdownAppBaseDir
2372 delete getdownFilesDir
2373 delete getdownArchiveDir
2379 if (file(install4jHomeDir).exists()) {
2381 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2382 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2383 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2384 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2386 installDir(file(install4jHomeDir))
2388 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2392 task copyInstall4jTemplate {
2393 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2394 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2395 inputs.file(install4jTemplateFile)
2396 inputs.file(install4jFileAssociationsFile)
2397 inputs.property("CHANNEL", { CHANNEL })
2398 outputs.file(install4jConfFile)
2401 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2403 // turn off code signing if no OSX_KEYPASS
2404 if (OSX_KEYPASS == "") {
2405 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2406 codeSigning.'@macEnabled' = "false"
2408 install4jConfigXml.'**'.windows.each { windows ->
2409 windows.'@runPostProcessor' = "false"
2413 // disable install screen for OSX dmg (for 2.11.2.0)
2414 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2415 macosArchive.attributes().remove('executeSetupApp')
2416 macosArchive.attributes().remove('setupAppId')
2419 // turn off checksum creation for LOCAL channel
2420 def e = install4jConfigXml.application[0]
2421 e.'@createChecksums' = string(install4jCheckSums)
2423 // put file association actions where placeholder action is
2424 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2425 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2426 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2427 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2428 def parent = a.parent()
2430 fileAssociationActions.each { faa ->
2433 // don't need to continue in .any loop once replacements have been made
2438 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2439 // NB we're deleting the /other/ one!
2440 // Also remove the examples subdir from non-release versions
2441 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2442 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2443 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2444 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2446 // remove the examples subdir from Full File Set
2447 def files = install4jConfigXml.files[0]
2448 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2449 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2450 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2451 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2452 dirEntry.parent().remove(dirEntry)
2454 install4jConfigXml.'**'.action.any { a ->
2455 if (a.'@customizedId' == customizedIdToDelete) {
2456 def parent = a.parent()
2462 // write install4j file
2463 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2470 delete install4jConfFile
2474 task cleanInstallersDataFiles {
2475 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2476 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2477 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2479 delete installersOutputTxt
2480 delete installersSha256
2481 delete hugoDataJsonFile
2485 task install4jDMGBackgroundImageCopy {
2486 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2487 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2490 from(install4jDMGBackgroundImageDir) {
2491 include(install4jDMGBackgroundImageFile)
2493 into install4jDMGBackgroundImageBuildDir
2498 task install4jDMGBackgroundImageProcess {
2499 dependsOn install4jDMGBackgroundImageCopy
2502 if (backgroundImageText) {
2503 if (convertBinary == null) {
2504 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2506 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2507 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2509 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2511 executable convertBinary
2514 '-font', install4j_background_image_text_font,
2515 '-fill', install4j_background_image_text_colour,
2516 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2517 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2518 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2527 task install4jDMGBackgroundImage {
2528 dependsOn install4jDMGBackgroundImageProcess
2531 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2532 group = "distribution"
2533 description = "Create the install4j installers"
2535 dependsOn copyInstall4jTemplate
2536 dependsOn cleanInstallersDataFiles
2537 dependsOn install4jDMGBackgroundImage
2539 projectFile = install4jConfFile
2541 // create an md5 for the input files to use as version for install4j conf file
2542 def digest = MessageDigest.getInstance("MD5")
2544 (file("${install4jDir}/${install4j_template}").text +
2545 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2546 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2547 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2548 if (filesMd5.length() >= 8) {
2549 filesMd5 = filesMd5.substring(0,8)
2551 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2554 'JALVIEW_NAME': jalview_name,
2555 'JALVIEW_APPLICATION_NAME': applicationName,
2556 'JALVIEW_DIR': "../..",
2557 'OSX_KEYSTORE': OSX_KEYSTORE,
2558 'OSX_APPLEID': OSX_APPLEID,
2559 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2560 'JSIGN_SH': JSIGN_SH,
2561 'JRE_DIR': getdown_app_dir_java,
2562 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2563 'JALVIEW_VERSION': JALVIEW_VERSION,
2564 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2565 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2566 'JAVA_VERSION': JAVA_VERSION,
2567 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2568 'VERSION': JALVIEW_VERSION,
2569 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2570 'BUNDLE_ID': install4jBundleId,
2571 'INTERNAL_ID': install4jInternalId,
2572 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2573 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2574 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2575 'WRAPPER_LINK': getdownWrapperLink,
2576 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2577 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2578 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2579 'INSTALLER_NAME': install4jInstallerName,
2580 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2581 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2582 'GETDOWN_FILES_DIR': getdown_files_dir,
2583 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2584 'GETDOWN_DIST_DIR': getdownAppDistDir,
2585 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2586 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2587 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2588 'BUILD_DIR': install4jBuildDir,
2589 'APPLICATION_CATEGORIES': install4j_application_categories,
2590 'APPLICATION_FOLDER': install4jApplicationFolder,
2591 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2592 'EXECUTABLE_NAME': install4jExecutableName,
2593 'EXTRA_SCHEME': install4jExtraScheme,
2594 'MAC_ICONS_FILE': install4jMacIconsFile,
2595 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2596 'PNG_ICON_FILE': install4jPngIconFile,
2597 'BACKGROUND': install4jBackground,
2602 'windows': 'WINDOWS',
2606 // these are the bundled OS/architecture VMs needed by install4j
2609 [ "mac", "aarch64" ],
2610 [ "windows", "x64" ],
2612 [ "linux", "aarch64" ]
2614 osArch.forEach { os, arch ->
2615 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)
2616 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2617 // otherwise running `gradle installers` generates a non-useful error:
2618 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2619 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)
2622 //println("INSTALL4J VARIABLES:")
2623 //variables.each{k,v->println("${k}=${v}")}
2625 destination = "${jalviewDir}/${install4jBuildDir}"
2626 buildSelected = true
2628 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2630 disableSigning = true
2631 disableNotarization = true
2635 macKeystorePassword = OSX_KEYPASS
2638 if (OSX_ALTOOLPASS) {
2639 appleIdPassword = OSX_ALTOOLPASS
2640 disableNotarization = false
2642 disableNotarization = true
2646 println("Using projectFile "+projectFile)
2647 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2651 inputs.dir(getdownAppBaseDir)
2652 inputs.file(install4jConfFile)
2653 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2654 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2657 def getDataHash(File myFile) {
2658 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2659 return myFile.exists()
2661 "file" : myFile.getName(),
2662 "filesize" : myFile.length(),
2663 "sha256" : hash.toString()
2668 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2670 "channel" : getdownChannelName,
2671 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2672 "git-commit" : "${gitHash} [${gitBranch}]",
2673 "version" : JALVIEW_VERSION
2675 // install4j installer files
2676 if (installersOutputTxt.exists()) {
2678 installersOutputTxt.readLines().each { def line ->
2679 if (line.startsWith("#")) {
2682 line.replaceAll("\n","")
2683 def vals = line.split("\t")
2684 def filename = vals[3]
2685 def filesize = file(filename).length()
2686 filename = filename.replaceAll(/^.*\//, "")
2687 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2688 idHash."${filename}" = vals[0]
2690 if (install4jCheckSums && installersSha256.exists()) {
2691 installersSha256.readLines().each { def line ->
2692 if (line.startsWith("#")) {
2695 line.replaceAll("\n","")
2696 def vals = line.split(/\s+\*?/)
2697 def filename = vals[1]
2698 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2704 "JAR": shadowJar.archiveFile, // executable JAR
2705 "JVL": getdownVersionLaunchJvl, // version JVL
2706 "SOURCE": sourceDist.archiveFile // source TGZ
2707 ].each { key, value ->
2708 def file = file(value)
2709 if (file.exists()) {
2710 def fileHash = getDataHash(file)
2711 if (fileHash != null) {
2712 hash."${key}" = fileHash;
2716 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2719 task staticMakeInstallersJsonFile {
2721 def output = findProperty("i4j_output")
2722 def sha256 = findProperty("i4j_sha256")
2723 def json = findProperty("i4j_json")
2724 if (output == null || sha256 == null || json == null) {
2725 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2727 writeDataJsonFile(file(output), file(sha256), file(json))
2732 dependsOn installerFiles
2738 eclipse().configFile(eclipse_codestyle_file)
2742 task createSourceReleaseProperties(type: WriteProperties) {
2743 group = "distribution"
2744 description = "Create the source RELEASE properties file"
2746 def sourceTarBuildDir = "${buildDir}/sourceTar"
2747 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2748 outputFile (sourceReleasePropertiesFile)
2751 releaseProps.each{ key, val -> property key, val }
2752 property "git.branch", gitBranch
2753 property "git.hash", gitHash
2756 outputs.file(outputFile)
2759 task sourceDist(type: Tar) {
2760 group "distribution"
2761 description "Create a source .tar.gz file for distribution"
2763 dependsOn createBuildProperties
2764 dependsOn convertMdFiles
2765 dependsOn eclipseAllPreferences
2766 dependsOn createSourceReleaseProperties
2769 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2770 archiveFileName = outputFileName
2772 compression Compression.GZIP
2787 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2789 "utils/InstallAnywhere",
2804 "gradle.properties",
2816 ".settings/org.eclipse.buildship.core.prefs",
2817 ".settings/org.eclipse.jdt.core.prefs"
2821 exclude (EXCLUDE_FILES)
2822 include (PROCESS_FILES)
2823 filter(ReplaceTokens,
2827 'Version-Rel': JALVIEW_VERSION,
2828 'Year-Rel': getDate("yyyy")
2833 exclude (EXCLUDE_FILES)
2834 exclude (PROCESS_FILES)
2835 exclude ("appletlib")
2836 exclude ("**/*locales")
2837 exclude ("*locales/**")
2838 exclude ("utils/InstallAnywhere")
2840 exclude (getdown_files_dir)
2841 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2842 //exclude (getdown_website_dir)
2843 //exclude (getdown_archive_dir)
2845 // exluding these as not using jars as modules yet
2846 exclude ("${j11modDir}/**/*.jar")
2849 include(INCLUDE_FILES)
2851 // from (jalviewDir) {
2852 // // explicit includes for stuff that seemed to not get included
2853 // include(fileTree("test/**/*."))
2854 // exclude(EXCLUDE_FILES)
2855 // exclude(PROCESS_FILES)
2858 from(file(buildProperties).getParent()) {
2859 include(file(buildProperties).getName())
2860 rename(file(buildProperties).getName(), "build_properties")
2862 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2866 def sourceTarBuildDir = "${buildDir}/sourceTar"
2867 from(sourceTarBuildDir) {
2868 // this includes the appended RELEASE properties file
2872 task dataInstallersJson {
2874 description "Create the installers-VERSION.json data file for installer files created"
2876 mustRunAfter installers
2877 mustRunAfter shadowJar
2878 mustRunAfter sourceDist
2879 mustRunAfter getdownArchive
2881 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2882 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2884 if (installersOutputTxt.exists()) {
2885 inputs.file(installersOutputTxt)
2887 if (install4jCheckSums && installersSha256.exists()) {
2888 inputs.file(installersSha256)
2891 shadowJar.archiveFile, // executable JAR
2892 getdownVersionLaunchJvl, // version JVL
2893 sourceDist.archiveFile // source TGZ
2894 ].each { fileName ->
2895 if (file(fileName).exists()) {
2896 inputs.file(fileName)
2900 outputs.file(hugoDataJsonFile)
2903 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
2909 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
2912 dependsOn pubhtmlhelp
2914 inputs.dir("${helpBuildDir}/${help_dir}")
2915 outputs.dir("${buildDir}/distributions/${help_dir}")
2919 task j2sSetHeadlessBuild {
2926 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2928 description "Enable the alternative J2S Config file for headless build"
2930 outputFile = jalviewjsJ2sSettingsFileName
2931 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2932 def j2sProps = new Properties()
2933 if (j2sPropsFile.exists()) {
2935 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2936 j2sProps.load(j2sPropsFileFIS)
2937 j2sPropsFileFIS.close()
2939 j2sProps.each { prop, val ->
2942 } catch (Exception e) {
2943 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2947 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2948 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2953 task jalviewjsSetEclipseWorkspace {
2954 def propKey = "jalviewjs_eclipse_workspace"
2956 if (project.hasProperty(propKey)) {
2957 propVal = project.getProperty(propKey)
2958 if (propVal.startsWith("~/")) {
2959 propVal = System.getProperty("user.home") + propVal.substring(1)
2962 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2963 def propsFile = file(propsFileName)
2964 def eclipseWsDir = propVal
2965 def props = new Properties()
2967 def writeProps = true
2968 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2969 def ins = new FileInputStream(propsFileName)
2972 if (props.getProperty(propKey, null) != null) {
2973 eclipseWsDir = props.getProperty(propKey)
2978 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2979 def tempDir = File.createTempDir()
2980 eclipseWsDir = tempDir.getAbsolutePath()
2983 eclipseWorkspace = file(eclipseWsDir)
2986 // do not run a headless transpile when we claim to be in Eclipse
2988 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2989 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2991 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2995 props.setProperty(propKey, eclipseWsDir)
2996 propsFile.parentFile.mkdirs()
2997 def bytes = new ByteArrayOutputStream()
2998 props.store(bytes, null)
2999 def propertiesString = bytes.toString()
3000 propsFile.text = propertiesString
3006 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3009 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3010 outputs.file(propsFileName)
3011 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3015 task jalviewjsEclipsePaths {
3018 def eclipseRoot = jalviewjs_eclipse_root
3019 if (eclipseRoot.startsWith("~/")) {
3020 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3022 if (OperatingSystem.current().isMacOsX()) {
3023 eclipseRoot += "/Eclipse.app"
3024 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3025 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3026 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3027 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3028 eclipseRoot += "/eclipse"
3030 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3031 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3032 } else { // linux or unix
3033 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3034 eclipseRoot += "/eclipse"
3035 println("eclipseDir exists")
3037 eclipseBinary = "${eclipseRoot}/eclipse"
3038 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3041 eclipseVersion = "4.13" // default
3042 def assumedVersion = true
3043 if (file(eclipseProduct).exists()) {
3044 def fis = new FileInputStream(eclipseProduct)
3045 def props = new Properties()
3047 eclipseVersion = props.getProperty("version")
3049 assumedVersion = false
3052 def propKey = "eclipse_debug"
3053 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3056 // do not run a headless transpile when we claim to be in Eclipse
3058 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3059 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3061 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3064 if (!assumedVersion) {
3065 println("ECLIPSE VERSION=${eclipseVersion}")
3071 task printProperties {
3073 description "Output to console all System.properties"
3075 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3081 dependsOn eclipseProject
3082 dependsOn eclipseClasspath
3083 dependsOn eclipseJdt
3087 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3088 task jalviewjsEclipseCopyDropins(type: Copy) {
3089 dependsOn jalviewjsEclipsePaths
3091 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3092 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3093 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3100 // this eclipse -clean doesn't actually work
3101 task jalviewjsCleanEclipse(type: Exec) {
3102 dependsOn eclipseSetup
3103 dependsOn jalviewjsEclipsePaths
3104 dependsOn jalviewjsEclipseCopyDropins
3106 executable(eclipseBinary)
3107 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3113 def inputString = """exit
3116 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3117 standardInput = inputByteStream
3120 /* not really working yet
3121 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3125 task jalviewjsTransferUnzipSwingJs {
3126 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3130 from zipTree(file_zip)
3131 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3135 inputs.file file_zip
3136 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3140 task jalviewjsTransferUnzipLib {
3141 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3144 zipFiles.each { file_zip ->
3146 from zipTree(file_zip)
3147 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3152 inputs.files zipFiles
3153 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3157 task jalviewjsTransferUnzipAllLibs {
3158 dependsOn jalviewjsTransferUnzipSwingJs
3159 dependsOn jalviewjsTransferUnzipLib
3163 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3165 description "Create the alternative j2s file from the j2s.* properties"
3167 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3168 def siteDirProperty = "j2s.site.directory"
3169 def setSiteDir = false
3170 jalviewjsJ2sProps.each { prop, val ->
3172 if (prop == siteDirProperty) {
3173 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3174 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3180 if (!setSiteDir) { // default site location, don't override specifically set property
3181 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3184 outputFile = jalviewjsJ2sAltSettingsFileName
3187 inputs.properties(jalviewjsJ2sProps)
3188 outputs.file(jalviewjsJ2sAltSettingsFileName)
3193 task jalviewjsEclipseSetup {
3194 dependsOn jalviewjsEclipseCopyDropins
3195 dependsOn jalviewjsSetEclipseWorkspace
3196 dependsOn jalviewjsCreateJ2sSettings
3200 task jalviewjsSyncAllLibs (type: Sync) {
3201 dependsOn jalviewjsTransferUnzipAllLibs
3202 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3203 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3204 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3208 def outputFiles = []
3209 rename { filename ->
3210 outputFiles += "${outputDir}/${filename}"
3217 // should this be exclude really ?
3218 duplicatesStrategy "INCLUDE"
3220 outputs.files outputFiles
3221 inputs.files inputFiles
3225 task jalviewjsSyncResources (type: Sync) {
3226 dependsOn buildResources
3228 def inputFiles = fileTree(dir: resourcesBuildDir)
3229 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3233 def outputFiles = []
3234 rename { filename ->
3235 outputFiles += "${outputDir}/${filename}"
3241 outputs.files outputFiles
3242 inputs.files inputFiles
3246 task jalviewjsSyncSiteResources (type: Sync) {
3247 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3248 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3252 def outputFiles = []
3253 rename { filename ->
3254 outputFiles += "${outputDir}/${filename}"
3260 outputs.files outputFiles
3261 inputs.files inputFiles
3265 task jalviewjsSyncBuildProperties (type: Sync) {
3266 dependsOn createBuildProperties
3267 def inputFiles = [file(buildProperties)]
3268 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3272 def outputFiles = []
3273 rename { filename ->
3274 outputFiles += "${outputDir}/${filename}"
3280 outputs.files outputFiles
3281 inputs.files inputFiles
3285 task jalviewjsProjectImport(type: Exec) {
3286 dependsOn eclipseSetup
3287 dependsOn jalviewjsEclipsePaths
3288 dependsOn jalviewjsEclipseSetup
3291 // do not run a headless import when we claim to be in Eclipse
3293 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3294 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3296 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3300 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3301 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3302 executable(eclipseBinary)
3303 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3307 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3309 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3310 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3313 inputs.file("${jalviewDir}/.project")
3314 outputs.upToDateWhen {
3315 file(projdir).exists()
3320 task jalviewjsTranspile(type: Exec) {
3321 dependsOn jalviewjsEclipseSetup
3322 dependsOn jalviewjsProjectImport
3323 dependsOn jalviewjsEclipsePaths
3325 dependsOn jalviewjsEnableAltFileProperty
3329 // do not run a headless transpile when we claim to be in Eclipse
3331 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3332 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3334 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3338 executable(eclipseBinary)
3339 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3343 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3345 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3346 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3352 stdout = new ByteArrayOutputStream()
3353 stderr = new ByteArrayOutputStream()
3355 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3356 def logOutFile = file(logOutFileName)
3357 logOutFile.createNewFile()
3358 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3359 BINARY: ${eclipseBinary}
3360 VERSION: ${eclipseVersion}
3361 WORKSPACE: ${eclipseWorkspace}
3362 DEBUG: ${eclipseDebug}
3365 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3366 // combine stdout and stderr
3367 def logErrFOS = logOutFOS
3369 if (jalviewjs_j2s_to_console.equals("true")) {
3370 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3371 new org.apache.tools.ant.util.TeeOutputStream(
3375 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3376 new org.apache.tools.ant.util.TeeOutputStream(
3381 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3384 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3391 if (stdout.toString().contains("Error processing ")) {
3392 // j2s did not complete transpile
3393 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3394 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3395 println("IGNORING TRANSPILE ERRORS")
3396 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3398 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3403 inputs.dir("${jalviewDir}/${sourceDir}")
3404 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3405 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3409 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3411 def stdout = new ByteArrayOutputStream()
3412 def stderr = new ByteArrayOutputStream()
3414 def coreFile = file(jsfile)
3416 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3418 logOutFile.createNewFile()
3419 logOutFile.append(msg+"\n")
3421 def coreTop = file(prefixFile)
3422 def coreBottom = file(suffixFile)
3423 coreFile.getParentFile().mkdirs()
3424 coreFile.createNewFile()
3425 coreFile.write( coreTop.getText("UTF-8") )
3429 def t = f.getText("UTF-8")
3430 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3431 coreFile.append( t )
3433 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3435 logOutFile.append(msg+"\n")
3438 coreFile.append( coreBottom.getText("UTF-8") )
3440 msg = "Generating ${zjsfile}"
3442 logOutFile.append(msg+"\n")
3443 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3444 def logErrFOS = logOutFOS
3447 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3448 main = "com.google.javascript.jscomp.CommandLineRunner"
3449 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3450 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3453 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3455 logOutFile.append(msg+"\n")
3457 if (logOutConsole) {
3458 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3459 new org.apache.tools.ant.util.TeeOutputStream(
3463 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3464 new org.apache.tools.ant.util.TeeOutputStream(
3469 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3472 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3479 logOutFile.append(msg+"\n")
3483 task jalviewjsBuildAllCores {
3485 description "Build the core js lib closures listed in the classlists dir"
3486 dependsOn jalviewjsTranspile
3487 dependsOn jalviewjsTransferUnzipSwingJs
3489 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3490 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3491 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3492 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3493 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3494 def prefixFile = "${jsDir}/core/coretop2.js"
3495 def suffixFile = "${jsDir}/core/corebottom2.js"
3497 inputs.file prefixFile
3498 inputs.file suffixFile
3500 def classlistFiles = []
3501 // add the classlists found int the jalviewjs_classlists_dir
3502 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3504 def name = file.getName() - ".txt"
3511 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3512 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3513 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3515 jalviewjsCoreClasslists = []
3517 classlistFiles.each {
3520 def file = hash['file']
3521 if (! file.exists()) {
3522 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3523 return false // this is a "continue" in groovy .each closure
3525 def name = hash['name']
3527 name = file.getName() - ".txt"
3535 def list = fileTree(dir: j2sDir, includes: filelist)
3537 def jsfile = "${outputDir}/core${name}.js"
3538 def zjsfile = "${outputDir}/core${name}.z.js"
3540 jalviewjsCoreClasslists += [
3549 outputs.file(jsfile)
3550 outputs.file(zjsfile)
3553 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3554 def stevesoftClasslistName = "_stevesoft"
3555 def stevesoftClasslist = [
3556 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3557 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3558 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3559 'name': stevesoftClasslistName
3561 jalviewjsCoreClasslists += stevesoftClasslist
3562 inputs.files(stevesoftClasslist['list'])
3563 outputs.file(stevesoftClasslist['jsfile'])
3564 outputs.file(stevesoftClasslist['zjsfile'])
3567 def allClasslistName = "_all"
3568 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3569 allJsFiles += fileTree(
3573 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3574 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3575 "**/org/jmol/export/JSExporter.js"
3578 allJsFiles += fileTree(
3582 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3583 "**/sun/misc/Unsafe.js",
3584 "**/swingjs/jquery/jquery-editable-select.js",
3585 "**/swingjs/jquery/j2sComboBox.js",
3586 "**/sun/misc/FloatingDecimal.js"
3589 def allClasslist = [
3590 'jsfile': "${outputDir}/core${allClasslistName}.js",
3591 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3593 'name': allClasslistName
3595 // not including this version of "all" core at the moment
3596 //jalviewjsCoreClasslists += allClasslist
3597 inputs.files(allClasslist['list'])
3598 outputs.file(allClasslist['jsfile'])
3599 outputs.file(allClasslist['zjsfile'])
3602 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3603 logOutFile.getParentFile().mkdirs()
3604 logOutFile.createNewFile()
3605 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3607 jalviewjsCoreClasslists.each {
3608 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3615 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3618 into file(outputFile).getParentFile()
3619 rename { filename ->
3620 if (filename.equals(inputFile.getName())) {
3621 return file(outputFile).getName()
3625 filter(ReplaceTokens,
3629 'MAIN': '"'+main_class+'"',
3631 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3632 'COREKEY': jalviewjs_core_key,
3633 'CORENAME': coreName
3640 task jalviewjsPublishCoreTemplates {
3641 dependsOn jalviewjsBuildAllCores
3642 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3643 def inputFile = file(inputFileName)
3644 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3646 def outputFiles = []
3647 jalviewjsCoreClasslists.each { cl ->
3648 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3649 cl['outputfile'] = outputFile
3650 outputFiles += outputFile
3654 jalviewjsCoreClasslists.each { cl ->
3655 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3658 inputs.file(inputFile)
3659 outputs.files(outputFiles)
3663 task jalviewjsSyncCore (type: Sync) {
3664 dependsOn jalviewjsBuildAllCores
3665 dependsOn jalviewjsPublishCoreTemplates
3666 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3667 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3671 def outputFiles = []
3672 rename { filename ->
3673 outputFiles += "${outputDir}/${filename}"
3679 outputs.files outputFiles
3680 inputs.files inputFiles
3684 // this Copy version of TransferSiteJs will delete anything else in the target dir
3685 task jalviewjsCopyTransferSiteJs(type: Copy) {
3686 dependsOn jalviewjsTranspile
3687 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3688 into "${jalviewDir}/${jalviewjsSiteDir}"
3692 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3693 task jalviewjsSyncTransferSiteJs(type: Sync) {
3694 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3696 into "${jalviewDir}/${jalviewjsSiteDir}"
3703 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3704 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3705 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3706 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3708 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3709 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3710 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3711 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3714 task jalviewjsPrepareSite {
3716 description "Prepares the website folder including unzipping files and copying resources"
3717 dependsOn jalviewjsSyncAllLibs
3718 dependsOn jalviewjsSyncResources
3719 dependsOn jalviewjsSyncSiteResources
3720 dependsOn jalviewjsSyncBuildProperties
3721 dependsOn jalviewjsSyncCore
3725 task jalviewjsBuildSite {
3727 description "Builds the whole website including transpiled code"
3728 dependsOn jalviewjsCopyTransferSiteJs
3729 dependsOn jalviewjsPrepareSite
3733 task cleanJalviewjsTransferSite {
3735 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3736 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3737 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3738 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3743 task cleanJalviewjsSite {
3744 dependsOn cleanJalviewjsTransferSite
3746 delete "${jalviewDir}/${jalviewjsSiteDir}"
3751 task jalviewjsSiteTar(type: Tar) {
3753 description "Creates a tar.gz file for the website"
3754 dependsOn jalviewjsBuildSite
3755 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3756 archiveFileName = outputFilename
3758 compression Compression.GZIP
3760 from "${jalviewDir}/${jalviewjsSiteDir}"
3761 into jalviewjs_site_dir // this is inside the tar file
3763 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3767 task jalviewjsServer {
3769 def filename = "jalviewjsTest.html"
3770 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3771 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3776 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3777 factory = f.newInstance()
3778 } catch (ClassNotFoundException e) {
3779 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3781 def port = Integer.valueOf(jalviewjs_server_port)
3786 while(port < start+1000 && !running) {
3788 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3789 jalviewjsServer = factory.start(doc_root, port)
3791 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3792 println("SERVER STARTED with document root ${doc_root}.")
3793 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3794 println("For debug: "+url+"?j2sdebug")
3795 println("For verbose: "+url+"?j2sverbose")
3796 } catch (Exception e) {
3801 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3802 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3803 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3805 jalviewjsCoreClasslists.each { cl ->
3806 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3808 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3810 println("For core ${cl.name}: "+urlcore)
3813 file(htmlFile).text = htmlText
3816 outputs.file(htmlFile)
3817 outputs.upToDateWhen({false})
3821 task cleanJalviewjsAll {
3823 description "Delete all configuration and build artifacts to do with JalviewJS build"
3824 dependsOn cleanJalviewjsSite
3825 dependsOn jalviewjsEclipsePaths
3828 delete "${jalviewDir}/${jalviewjsBuildDir}"
3829 delete "${jalviewDir}/${eclipse_bin_dir}"
3830 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3831 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3833 delete jalviewjsJ2sAltSettingsFileName
3836 outputs.upToDateWhen( { false } )
3840 task jalviewjsIDE_checkJ2sPlugin {
3841 group "00 JalviewJS in Eclipse"
3842 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3845 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3846 def j2sPluginFile = file(j2sPlugin)
3847 def eclipseHome = System.properties["eclipse.home.location"]
3848 if (eclipseHome == null || ! IN_ECLIPSE) {
3849 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3851 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3852 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3853 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3854 eclipseJ2sPluginDirs += altPluginsDir
3856 def foundPlugin = false
3857 def j2sPluginFileName = j2sPluginFile.getName()
3858 def eclipseJ2sPlugin
3859 def eclipseJ2sPluginFile
3860 eclipseJ2sPluginDirs.any { dir ->
3861 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3862 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3863 if (eclipseJ2sPluginFile.exists()) {
3869 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3870 System.err.println(msg)
3871 throw new StopExecutionException(msg)
3874 def digest = MessageDigest.getInstance("MD5")
3876 digest.update(j2sPluginFile.text.bytes)
3877 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3879 digest.update(eclipseJ2sPluginFile.text.bytes)
3880 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3882 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3883 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3884 System.err.println(msg)
3885 throw new StopExecutionException(msg)
3887 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3893 task jalviewjsIDE_copyJ2sPlugin {
3894 group "00 JalviewJS in Eclipse"
3895 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3898 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3899 def j2sPluginFile = file(j2sPlugin)
3900 def eclipseHome = System.properties["eclipse.home.location"]
3901 if (eclipseHome == null || ! IN_ECLIPSE) {
3902 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3904 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3905 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3906 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3907 System.err.println(msg)
3910 eclipseJ2sPluginFile.getParentFile().mkdirs()
3911 into eclipseJ2sPluginFile.getParent()
3917 task jalviewjsIDE_j2sFile {
3918 group "00 JalviewJS in Eclipse"
3919 description "Creates the .j2s file"
3920 dependsOn jalviewjsCreateJ2sSettings
3924 task jalviewjsIDE_SyncCore {
3925 group "00 JalviewJS in Eclipse"
3926 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3927 dependsOn jalviewjsSyncCore
3931 task jalviewjsIDE_SyncSiteAll {
3932 dependsOn jalviewjsSyncAllLibs
3933 dependsOn jalviewjsSyncResources
3934 dependsOn jalviewjsSyncSiteResources
3935 dependsOn jalviewjsSyncBuildProperties
3939 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3942 task jalviewjsIDE_PrepareSite {
3943 group "00 JalviewJS in Eclipse"
3944 description "Sync libs and resources to site dir, but not closure cores"
3946 dependsOn jalviewjsIDE_SyncSiteAll
3947 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3951 task jalviewjsIDE_AssembleSite {
3952 group "00 JalviewJS in Eclipse"
3953 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3954 dependsOn jalviewjsPrepareSite
3958 task jalviewjsIDE_SiteClean {
3959 group "00 JalviewJS in Eclipse"
3960 description "Deletes the Eclipse transpiled site"
3961 dependsOn cleanJalviewjsSite
3965 task jalviewjsIDE_Server {
3966 group "00 JalviewJS in Eclipse"
3967 description "Starts a webserver on localhost to test the website"
3968 dependsOn jalviewjsServer
3972 // buildship runs this at import or gradle refresh
3973 task eclipseSynchronizationTask {
3974 //dependsOn eclipseSetup
3975 dependsOn createBuildProperties
3977 dependsOn jalviewjsIDE_j2sFile
3978 dependsOn jalviewjsIDE_checkJ2sPlugin
3979 dependsOn jalviewjsIDE_PrepareSite
3984 // buildship runs this at build time or project refresh
3985 task eclipseAutoBuildTask {
3986 //dependsOn jalviewjsIDE_checkJ2sPlugin
3987 //dependsOn jalviewjsIDE_PrepareSite
3993 description "Build the site"
3994 dependsOn jalviewjsBuildSite