1 /* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
2 * For properties set within build.gradle, use camelCaseNoSpace.
4 import org.apache.tools.ant.filters.ReplaceTokens
5 import org.gradle.internal.os.OperatingSystem
6 import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
7 import org.gradle.api.internal.PropertiesTransformer
8 import org.gradle.util.ConfigureUtil
9 import org.gradle.plugins.ide.eclipse.model.Output
10 import org.gradle.plugins.ide.eclipse.model.Library
11 import java.security.MessageDigest
12 import java.util.regex.Matcher
13 import groovy.transform.ExternalizeMethods
14 import groovy.util.XmlParser
15 import groovy.xml.XmlUtil
16 import groovy.json.JsonBuilder
17 import com.vladsch.flexmark.util.ast.Node
18 import com.vladsch.flexmark.html.HtmlRenderer
19 import com.vladsch.flexmark.parser.Parser
20 import com.vladsch.flexmark.util.data.MutableDataSet
21 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
22 import com.vladsch.flexmark.ext.tables.TablesExtension
23 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
24 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
25 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
26 import com.vladsch.flexmark.ext.toc.TocExtension
27 import com.google.common.hash.HashCode
28 import com.google.common.hash.Hashing
29 import com.google.common.io.Files
30 import org.jsoup.Jsoup
31 import org.jsoup.nodes.Element
39 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
40 classpath "org.jsoup:jsoup:1.14.3"
41 classpath "com.eowise:gradle-imagemagick:0.5.1"
50 id "com.diffplug.gradle.spotless" version "3.28.0"
51 id 'com.github.johnrengelman.shadow' version '4.0.3'
52 id 'com.install4j.gradle' version '10.0.3'
53 id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
54 id 'com.palantir.git-version' version '0.13.0' apply false
65 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
66 def string(Object o) {
67 return o == null ? "" : o.toString()
70 def overrideProperties(String propsFileName, boolean output = false) {
71 if (propsFileName == null) {
74 def propsFile = file(propsFileName)
75 if (propsFile != null && propsFile.exists()) {
76 println("Using properties from file '${propsFileName}'")
78 def p = new Properties()
79 def localPropsFIS = new FileInputStream(propsFile)
85 if (project.hasProperty(key)) {
86 oldval = project.findProperty(key)
87 project.setProperty(key, val)
89 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
92 ext.setProperty(key, val)
94 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
98 } catch (Exception e) {
99 println("Exception reading local.properties")
106 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
107 jalviewDirRelativePath = jalviewDir
110 getdownChannelName = CHANNEL.toLowerCase()
111 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
112 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
113 channelDirName = propertiesChannelName
114 // Import channel_properties
115 if (getdownChannelName.startsWith("develop-")) {
116 channelDirName = "develop-SUFFIX"
118 channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
119 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
120 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
121 overrideProperties(channelGradleProperties, false)
122 // local build environment properties
123 // can be "projectDir/local.properties"
124 overrideProperties("${projectDir}/local.properties", true)
125 // or "../projectDir_local.properties"
126 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
129 // Import releaseProps from the RELEASE file
130 // or a file specified via JALVIEW_RELEASE_FILE if defined
131 // Expect jalview.version and target release branch in jalview.release
132 releaseProps = new Properties();
133 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
134 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
136 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
137 releaseProps.load(it)
139 } catch (Exception fileLoadError) {
140 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
143 // Set JALVIEW_VERSION if it is not already set
144 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
145 JALVIEW_VERSION = releaseProps.get("jalview.version")
147 println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
149 // this property set when running Eclipse headlessly
150 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
151 // this property set by Eclipse
152 eclipseApplicationProperty = string("eclipse.application")
153 // CHECK IF RUNNING FROM WITHIN ECLIPSE
154 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
155 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
156 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
157 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
158 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
162 println("WITHIN ECLIPSE IDE")
164 println("HEADLESS BUILD")
167 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
169 println("J2S ENABLED")
172 System.properties.sort { it.key }.each {
173 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
176 if (false && IN_ECLIPSE) {
177 jalviewDir = jalviewDirAbsolutePath
182 buildDate = new Date().format("yyyyMMdd")
185 bareSourceDir = string(source_dir)
186 sourceDir = string("${jalviewDir}/${bareSourceDir}")
187 resourceDir = string("${jalviewDir}/${resource_dir}")
188 bareTestSourceDir = string(test_source_dir)
189 testDir = string("${jalviewDir}/${bareTestSourceDir}")
191 classesDir = string("${jalviewDir}/${classes_dir}")
194 useClover = clover.equals("true")
195 cloverBuildDir = "${buildDir}/clover"
196 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
197 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
198 cloverReportDir = file("${buildDir}/reports/clover")
199 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
200 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
201 //cloverTestClassesDir = cloverClassesDir
202 cloverDb = string("${cloverBuildDir}/clover.db")
204 testSourceDir = useClover ? cloverTestInstrDir : testDir
205 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
208 backgroundImageText = BACKGROUNDIMAGETEXT
209 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
210 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
211 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
212 getdownFullArchiveDir = null
213 getdownTextLines = []
214 getdownLaunchJvl = null
215 getdownVersionLaunchJvl = null
217 buildProperties = null
219 // the following values might be overridden by the CHANNEL switch
220 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
221 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
222 getdownArchiveAppBase = getdown_archive_base
223 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
224 getdownAppDistDir = getdown_app_dir_alt
225 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
226 getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
227 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
228 reportRsyncCommand = false
229 jvlChannelName = CHANNEL.toLowerCase()
230 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
231 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
232 install4jDMGBackgroundImageDir = "${install4j_images_dir}"
233 install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
234 install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
235 install4jInstallerName = "${jalview_name} Non-Release Installer"
236 install4jExecutableName = install4j_executable_name
237 install4jExtraScheme = "jalviewx"
238 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
239 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
240 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
241 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
242 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
243 install4jCheckSums = true
245 applicationName = "${jalview_name}"
249 // TODO: get bamboo build artifact URL for getdown artifacts
250 getdown_channel_base = bamboo_channelbase
251 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
252 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
253 jvlChannelName += "_${getdownChannelName}"
254 // automatically add the test group Not-bamboo for exclusion
255 if ("".equals(testng_excluded_groups)) {
256 testng_excluded_groups = "Not-bamboo"
258 install4jExtraScheme = "jalviewb"
259 backgroundImageText = true
262 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
263 getdownAppDistDir = getdown_app_dir_release
264 getdownSetAppBaseProperty = true
265 reportRsyncCommand = true
267 install4jInstallerName = "${jalview_name} Installer"
271 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
272 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
273 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
274 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
275 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
277 package_dir = string("${ARCHIVEDIR}/${package_dir}")
278 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
281 reportRsyncCommand = true
282 install4jExtraScheme = "jalviewa"
286 getdownChannelName = string("archive/${JALVIEW_VERSION}")
287 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
288 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
289 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
290 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
292 package_dir = string("${ARCHIVEDIR}/${package_dir}")
293 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
296 reportRsyncCommand = true
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
298 install4jSuffix = "Archive"
299 install4jExtraScheme = "jalviewa"
302 case ~/^DEVELOP-([\.\-\w]*)$/:
303 def suffix = Matcher.lastMatcher[0][1]
304 reportRsyncCommand = true
305 getdownSetAppBaseProperty = true
306 JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
307 install4jSuffix = "Develop ${suffix}"
308 install4jExtraScheme = "jalviewd"
309 install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
310 getdownChannelName = string("develop-${suffix}")
311 getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
312 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
313 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
314 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
315 channelSuffix = string(suffix)
316 backgroundImageText = true
320 reportRsyncCommand = true
321 getdownSetAppBaseProperty = true
322 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
323 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
325 install4jSuffix = "Develop"
326 install4jExtraScheme = "jalviewd"
327 install4jInstallerName = "${jalview_name} Develop Installer"
328 backgroundImageText = true
332 reportRsyncCommand = true
333 getdownSetAppBaseProperty = true
334 // Don't ignore transpile errors for release build
335 if (jalviewjs_ignore_transpile_errors.equals("true")) {
336 jalviewjs_ignore_transpile_errors = "false"
337 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
339 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
340 install4jSuffix = "Test"
341 install4jExtraScheme = "jalviewt"
342 install4jInstallerName = "${jalview_name} Test Installer"
343 backgroundImageText = true
346 case ~/^SCRATCH(|-[-\w]*)$/:
347 getdownChannelName = CHANNEL
348 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
350 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
351 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
352 reportRsyncCommand = true
353 install4jSuffix = "Scratch"
357 if (!file("${LOCALDIR}").exists()) {
358 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
360 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
361 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
363 JALVIEW_VERSION = "TEST"
364 install4jSuffix = "Test-Local"
365 install4jExtraScheme = "jalviewt"
366 install4jInstallerName = "${jalview_name} Test Installer"
367 backgroundImageText = true
370 case [ "LOCAL", "JALVIEWJS" ]:
371 JALVIEW_VERSION = "TEST"
372 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
373 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
374 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
375 install4jExtraScheme = "jalviewl"
376 install4jCheckSums = false
379 default: // something wrong specified
380 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
384 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
385 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
386 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
387 // override getdownAppBase if requested
388 if (findProperty("getdown_appbase_override") != null) {
389 // revert to LOCAL if empty string
390 if (string(getdown_appbase_override) == "") {
391 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
392 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
393 } else if (string(getdown_appbase_override).startsWith("file://")) {
394 getdownAppBase = string(getdown_appbase_override)
395 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
397 getdownAppBase = string(getdown_appbase_override)
399 println("Overriding getdown appbase with '${getdownAppBase}'")
401 // sanitise file name for jalview launcher file for this channel
402 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
403 // install4j application and folder names
404 if (install4jSuffix == "") {
405 install4jBundleId = "${install4j_bundle_id}"
406 install4jWinApplicationId = install4j_release_win_application_id
408 applicationName = "${jalview_name} ${install4jSuffix}"
409 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
410 // add int hash of install4jSuffix to the last part of the application_id
411 def id = install4j_release_win_application_id
412 def idsplitreverse = id.split("-").reverse()
413 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
414 install4jWinApplicationId = idsplitreverse.reverse().join("-")
416 // sanitise folder and id names
417 // install4jApplicationFolder = e.g. "Jalview Build"
418 install4jApplicationFolder = applicationName
419 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
420 .replaceAll("_+", "_") // collapse __
421 install4jInternalId = applicationName
423 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
424 .replaceAll("_+", "") // collapse __
425 //.replaceAll("_*-_*", "-") // collapse _-_
426 install4jUnixApplicationFolder = applicationName
428 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
429 .replaceAll("_+", "_") // collapse __
430 .replaceAll("_*-_*", "-") // collapse _-_
433 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
434 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
435 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
436 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
437 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
438 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
439 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
440 /* compile without modules -- using classpath libraries
441 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
442 modules_runtimeClasspath = modules_compileClasspath
448 apply plugin: "com.palantir.git-version"
449 def details = versionDetails()
450 gitHash = details.gitHash
451 gitBranch = details.branchName
452 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
453 println("Not in a git repository. Using git values from RELEASE properties file.")
454 gitHash = releaseProps.getProperty("git.hash")
455 gitBranch = releaseProps.getProperty("git.branch")
456 } catch(java.lang.RuntimeException e1) {
457 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
460 println("Using a ${CHANNEL} profile.")
462 additional_compiler_args = []
463 // configure classpath/args for j8/j11 compilation
464 if (JAVA_VERSION.equals("1.8")) {
465 JAVA_INTEGER_VERSION = string("8")
468 libDistDir = j8libDir
469 compile_source_compatibility = 1.8
470 compile_target_compatibility = 1.8
471 // these are getdown.txt properties defined dependent on the JAVA_VERSION
472 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
473 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
474 // this property is assigned below and expanded to multiple lines in the getdown task
475 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
476 // this property is for the Java library used in eclipse
477 eclipseJavaRuntimeName = string("JavaSE-1.8")
478 } else if (JAVA_VERSION.equals("11")) {
479 JAVA_INTEGER_VERSION = string("11")
481 libDistDir = j11libDir
482 compile_source_compatibility = 11
483 compile_target_compatibility = 11
484 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
485 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
486 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
487 eclipseJavaRuntimeName = string("JavaSE-11")
488 /* compile without modules -- using classpath libraries
489 additional_compiler_args += [
490 '--module-path', modules_compileClasspath.asPath,
491 '--add-modules', j11modules
494 } else if (JAVA_VERSION.equals("17")) {
495 JAVA_INTEGER_VERSION = string("17")
497 libDistDir = j17libDir
498 compile_source_compatibility = 17
499 compile_target_compatibility = 17
500 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
501 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
502 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
503 eclipseJavaRuntimeName = string("JavaSE-17")
504 /* compile without modules -- using classpath libraries
505 additional_compiler_args += [
506 '--module-path', modules_compileClasspath.asPath,
507 '--add-modules', j11modules
511 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
516 JAVA_MIN_VERSION = JAVA_VERSION
517 JAVA_MAX_VERSION = JAVA_VERSION
518 jreInstallsDir = string(jre_installs_dir)
519 if (jreInstallsDir.startsWith("~/")) {
520 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
522 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
523 install4jConfFileName = string("jalview-install4j-conf.install4j")
524 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
525 install4jHomeDir = install4j_home_dir
526 if (install4jHomeDir.startsWith("~/")) {
527 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
530 resourceBuildDir = string("${buildDir}/resources")
531 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
532 helpBuildDir = string("${resourceBuildDir}/help_build")
533 docBuildDir = string("${resourceBuildDir}/doc_build")
535 if (buildProperties == null) {
536 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
538 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
539 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
540 helpSourceDir = string("${helpParentDir}/${help_dir}")
541 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
544 convertBinaryExpectedLocation = imagemagick_convert
545 if (convertBinaryExpectedLocation.startsWith("~/")) {
546 convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
548 if (file(convertBinaryExpectedLocation).exists()) {
549 convertBinary = convertBinaryExpectedLocation
552 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
553 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
554 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
556 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
558 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
560 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
561 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
562 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
563 jalviewjsJalviewCoreHtmlFile = string("")
564 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
565 jalviewjsCoreClasslists = []
566 jalviewjsJalviewTemplateName = string(jalviewjs_name)
567 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
568 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
569 jalviewjsJ2sProps = null
570 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
572 eclipseWorkspace = null
573 eclipseBinary = string("")
574 eclipseVersion = string("")
584 outputDir = file(classesDir)
588 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
591 compileClasspath = files(sourceSets.main.java.outputDir)
592 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
594 runtimeClasspath = compileClasspath
595 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
600 srcDirs cloverInstrDir
601 outputDir = cloverClassesDir
605 srcDirs = sourceSets.main.resources.srcDirs
608 compileClasspath = files( sourceSets.clover.java.outputDir )
609 //compileClasspath += files( testClassesDir )
610 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
611 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
612 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
614 runtimeClasspath = compileClasspath
619 srcDirs testSourceDir
620 outputDir = file(testClassesDir)
624 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
627 compileClasspath = files( sourceSets.test.java.outputDir )
628 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
629 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
631 runtimeClasspath = compileClasspath
632 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
638 // eclipse project and settings files creation, also used by buildship
641 name = eclipse_project_name
643 natures 'org.eclipse.jdt.core.javanature',
644 'org.eclipse.jdt.groovy.core.groovyNature',
645 'org.eclipse.buildship.core.gradleprojectnature'
647 buildCommand 'org.eclipse.jdt.core.javabuilder'
648 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
652 //defaultOutputDir = sourceSets.main.java.outputDir
653 configurations.each{ c->
654 if (c.isCanBeResolved()) {
655 minusConfigurations += [c]
659 plusConfigurations = [ ]
663 def removeTheseToo = []
664 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
665 cp.entries.each { entry ->
666 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
667 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
668 // we add the resources and help/help dirs in as libs afterwards (see below)
669 if (entry.kind == 'src') {
670 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
671 removeTheseToo += entry
673 alreadyAddedSrcPath.putAt(entry.path, true)
678 cp.entries.removeAll(removeTheseToo)
680 //cp.entries += new Output("${eclipse_bin_dir}/main")
681 if (file(helpParentDir).isDirectory()) {
682 cp.entries += new Library(fileReference(helpParentDir))
684 if (file(resourceDir).isDirectory()) {
685 cp.entries += new Library(fileReference(resourceDir))
688 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
690 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
691 //don't want to add outputDir as eclipse is using its own output dir in bin/main
692 if (it.isDirectory() || ! it.exists()) {
693 // don't add dirs to classpath, especially if they don't exist
694 return false // groovy "continue" in .any closure
696 def itPath = it.toString()
697 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
698 // make relative path
699 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
701 if (alreadyAddedLibPath.get(itPath)) {
702 //println("Not adding duplicate entry "+itPath)
704 //println("Adding entry "+itPath)
705 cp.entries += new Library(fileReference(itPath))
706 alreadyAddedLibPath.put(itPath, true)
710 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
711 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
712 if (it.isDirectory() || ! it.exists()) {
713 // don't add dirs to classpath
714 return false // groovy "continue" in .any closure
717 def itPath = it.toString()
718 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
719 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
721 if (alreadyAddedLibPath.get(itPath)) {
724 def lib = new Library(fileReference(itPath))
725 lib.entryAttributes["test"] = "true"
727 alreadyAddedLibPath.put(itPath, true)
735 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
740 // for the IDE, use java 11 compatibility
741 sourceCompatibility = compile_source_compatibility
742 targetCompatibility = compile_target_compatibility
743 javaRuntimeName = eclipseJavaRuntimeName
745 // add in jalview project specific properties/preferences into eclipse core preferences
747 withProperties { props ->
748 def jalview_prefs = new Properties()
749 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
750 jalview_prefs.load(ins)
752 jalview_prefs.forEach { t, v ->
753 if (props.getAt(t) == null) {
757 // codestyle file -- overrides previous formatter prefs
758 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
759 if (csFile.exists()) {
760 XmlParser parser = new XmlParser()
761 def profiles = parser.parse(csFile)
762 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
763 if (profile != null) {
764 profile.'setting'.each { s ->
766 def value = s.'@value'
767 if (id != null && value != null) {
768 props.putAt(id, value)
779 // Don't want these to be activated if in headless build
780 synchronizationTasks "eclipseSynchronizationTask"
781 //autoBuildTasks "eclipseAutoBuildTask"
787 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
788 // Class to allow updating arbitrary properties files
789 class PropertiesFile extends PropertiesPersistableConfigurationObject {
790 public PropertiesFile(PropertiesTransformer t) { super(t); }
791 @Override protected void load(Properties properties) { }
792 @Override protected void store(Properties properties) { }
793 @Override protected String getDefaultResourceName() { return ""; }
794 // This is necessary, because PropertiesPersistableConfigurationObject fails
795 // if no default properties file exists.
796 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
799 // Task to update arbitrary properties files (set outputFile)
800 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
801 private final PropertiesFileContentMerger file;
802 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
803 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
804 protected void configure(PropertiesFile props) {
805 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
807 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
810 task eclipseUIPreferences(type: PropertiesFileTask) {
811 description = "Generate Eclipse additional settings"
812 def filename = "org.eclipse.jdt.ui.prefs"
813 outputFile = "$projectDir/.settings/${filename}" as File
816 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
821 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
822 description = "Generate Eclipse additional settings"
823 def filename = "org.eclipse.jdt.groovy.core.prefs"
824 outputFile = "$projectDir/.settings/${filename}" as File
827 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
832 task eclipseAllPreferences {
834 dependsOn eclipseUIPreferences
835 dependsOn eclipseGroovyCorePreferences
838 eclipseUIPreferences.mustRunAfter eclipseJdt
839 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
841 /* end of eclipse preferences hack */
849 delete cloverBuildDir
850 delete cloverReportDir
855 task cloverInstrJava(type: JavaExec) {
856 group = "Verification"
857 description = "Create clover instrumented source java files"
859 dependsOn cleanClover
861 inputs.files(sourceSets.main.allJava)
862 outputs.dir(cloverInstrDir)
864 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
865 classpath = sourceSets.clover.compileClasspath
866 main = "com.atlassian.clover.CloverInstr"
874 cloverInstrDir.getPath(),
876 def srcFiles = sourceSets.main.allJava.files
879 { file -> file.absolutePath }
882 args argsList.toArray()
885 delete cloverInstrDir
886 println("Clover: About to instrument "+srcFiles.size() +" files")
891 task cloverInstrTests(type: JavaExec) {
892 group = "Verification"
893 description = "Create clover instrumented source test files"
895 dependsOn cleanClover
897 inputs.files(testDir)
898 outputs.dir(cloverTestInstrDir)
900 classpath = sourceSets.clover.compileClasspath
901 main = "com.atlassian.clover.CloverInstr"
911 cloverTestInstrDir.getPath(),
913 args argsList.toArray()
916 delete cloverTestInstrDir
917 println("Clover: About to instrument test files")
923 group = "Verification"
924 description = "Create clover instrumented all source files"
926 dependsOn cloverInstrJava
927 dependsOn cloverInstrTests
931 cloverClasses.dependsOn cloverInstr
934 task cloverConsoleReport(type: JavaExec) {
935 group = "Verification"
936 description = "Creates clover console report"
939 file(cloverDb).exists()
942 inputs.dir cloverClassesDir
944 classpath = sourceSets.clover.runtimeClasspath
945 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
947 if (cloverreport_mem.length() > 0) {
948 maxHeapSize = cloverreport_mem
950 if (cloverreport_jvmargs.length() > 0) {
951 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
961 args argsList.toArray()
965 task cloverHtmlReport(type: JavaExec) {
966 group = "Verification"
967 description = "Creates clover HTML report"
970 file(cloverDb).exists()
973 def cloverHtmlDir = cloverReportDir
974 inputs.dir cloverClassesDir
975 outputs.dir cloverHtmlDir
977 classpath = sourceSets.clover.runtimeClasspath
978 main = "com.atlassian.clover.reporters.html.HtmlReporter"
980 if (cloverreport_mem.length() > 0) {
981 maxHeapSize = cloverreport_mem
983 if (cloverreport_jvmargs.length() > 0) {
984 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
995 if (cloverreport_html_options.length() > 0) {
996 argsList += cloverreport_html_options.split(" ")
999 args argsList.toArray()
1003 task cloverXmlReport(type: JavaExec) {
1004 group = "Verification"
1005 description = "Creates clover XML report"
1008 file(cloverDb).exists()
1011 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1012 inputs.dir cloverClassesDir
1013 outputs.file cloverXmlFile
1015 classpath = sourceSets.clover.runtimeClasspath
1016 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1018 if (cloverreport_mem.length() > 0) {
1019 maxHeapSize = cloverreport_mem
1021 if (cloverreport_jvmargs.length() > 0) {
1022 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1033 if (cloverreport_xml_options.length() > 0) {
1034 argsList += cloverreport_xml_options.split(" ")
1037 args argsList.toArray()
1042 group = "Verification"
1043 description = "Creates clover reports"
1045 dependsOn cloverXmlReport
1046 dependsOn cloverHtmlReport
1053 sourceCompatibility = compile_source_compatibility
1054 targetCompatibility = compile_target_compatibility
1055 options.compilerArgs += additional_compiler_args
1056 print ("Setting target compatibility to "+targetCompatibility+"\n")
1058 //classpath += configurations.cloverRuntime
1064 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1065 sourceCompatibility = compile_source_compatibility
1066 targetCompatibility = compile_target_compatibility
1067 options.compilerArgs = additional_compiler_args
1068 options.encoding = "UTF-8"
1070 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1077 sourceCompatibility = compile_source_compatibility
1078 targetCompatibility = compile_target_compatibility
1079 options.compilerArgs = additional_compiler_args
1081 print ("Setting target compatibility to "+targetCompatibility+"\n")
1088 delete sourceSets.main.java.outputDir
1094 dependsOn cleanClover
1096 delete sourceSets.test.java.outputDir
1101 // format is a string like date.format("dd MMMM yyyy")
1102 def getDate(format) {
1103 return date.format(format)
1107 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1108 MutableDataSet options = new MutableDataSet()
1110 def extensions = new ArrayList<>()
1111 extensions.add(AnchorLinkExtension.create())
1112 extensions.add(AutolinkExtension.create())
1113 extensions.add(StrikethroughExtension.create())
1114 extensions.add(TaskListExtension.create())
1115 extensions.add(TablesExtension.create())
1116 extensions.add(TocExtension.create())
1118 options.set(Parser.EXTENSIONS, extensions)
1120 // set GFM table parsing options
1121 options.set(TablesExtension.WITH_CAPTION, false)
1122 options.set(TablesExtension.COLUMN_SPANS, false)
1123 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1124 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1125 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1126 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1127 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1129 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1130 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1131 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1132 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1134 Parser parser = Parser.builder(options).build()
1135 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1137 mdFiles.each { mdFile ->
1138 // add table of contents
1139 def mdText = "[TOC]\n"+mdFile.text
1141 // grab the first top-level title
1143 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1144 def matcher = mdText =~ titleRegex
1145 if (matcher.size() > 0) {
1146 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1147 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1149 // or use the filename if none found
1150 if (title == null) {
1151 title = mdFile.getName()
1154 Node document = parser.parse(mdText)
1155 String htmlBody = renderer.render(document)
1156 def htmlText = '''<html>
1157 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1158 <html xmlns="http://www.w3.org/1999/xhtml">
1160 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1161 <meta http-equiv="Content-Style-Type" content="text/css" />
1162 <meta name="generator" content="flexmark" />
1164 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1166 <style type="text/css">code{white-space: pre;}</style>
1168 htmlText += ((cssFile != null) ? cssFile.text : '')
1169 htmlText += '''</head>
1172 htmlText += htmlBody
1178 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1179 def htmlFile = file(htmlFilePath)
1180 println("Creating ${htmlFilePath}")
1181 htmlFile.text = htmlText
1186 task copyDocs(type: Copy) {
1187 def inputDir = "${jalviewDir}/${doc_dir}"
1188 def outputDir = "${docBuildDir}/${doc_dir}"
1192 include('**/*.html')
1194 filter(ReplaceTokens,
1198 'Version-Rel': JALVIEW_VERSION,
1199 'Year-Rel': getDate("yyyy")
1206 exclude('**/*.html')
1211 inputs.dir(inputDir)
1212 outputs.dir(outputDir)
1216 task convertMdFiles {
1218 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1219 def cssFile = file("${jalviewDir}/${flexmark_css}")
1222 convertMdToHtml(mdFiles, cssFile)
1225 inputs.files(mdFiles)
1226 inputs.file(cssFile)
1229 mdFiles.each { mdFile ->
1230 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1231 htmlFiles.add(file(htmlFilePath))
1233 outputs.files(htmlFiles)
1237 def hugoTemplateSubstitutions(String input, Map extras=null) {
1238 def replacements = [
1239 DATE: getDate("yyyy-MM-dd"),
1240 CHANNEL: propertiesChannelName,
1241 APPLICATION_NAME: applicationName,
1243 GIT_BRANCH: gitBranch,
1244 VERSION: JALVIEW_VERSION,
1245 JAVA_VERSION: JAVA_VERSION,
1246 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1251 if (extras != null) {
1252 extras.each{ k, v ->
1253 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1256 replacements.each{ k, v ->
1257 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1262 def mdFileComponents(File mdFile, def dateOnly=false) {
1265 if (mdFile.exists()) {
1266 def inFrontMatter = false
1267 def firstLine = true
1268 mdFile.eachLine { line ->
1269 if (line.matches("---")) {
1270 def prev = inFrontMatter
1271 inFrontMatter = firstLine
1272 if (inFrontMatter != prev)
1275 if (inFrontMatter) {
1277 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1278 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1279 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1280 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1281 } else if (m = line =~ /^channel:\s*(\S+)/) {
1282 map["channel"] = m[0][1]
1283 } else if (m = line =~ /^version:\s*(\S+)/) {
1284 map["version"] = m[0][1]
1285 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1286 map[ m[0][1] ] = m[0][2]
1288 if (dateOnly && map["date"] != null) {
1294 content += line+"\n"
1299 return dateOnly ? map["date"] : [map, content]
1302 task hugoTemplates {
1304 description "Create partially populated md pages for hugo website build"
1306 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1307 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1308 def templateFiles = fileTree(dir: hugoTemplatesDir)
1309 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1310 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1311 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1312 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1315 // specific release template for version archive
1318 def givenDate = null
1319 def givenChannel = null
1320 def givenVersion = null
1321 if (CHANNEL == "RELEASE") {
1322 def (map, content) = mdFileComponents(releaseMdFile)
1323 givenDate = map.date
1324 givenChannel = map.channel
1325 givenVersion = map.version
1327 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1328 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1331 if (whatsnewMdFile.exists())
1332 whatsnew = whatsnewMdFile.text
1335 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1336 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1338 def changesHugo = null
1339 if (changes != null) {
1340 changesHugo = '<div class="release_notes">\n\n'
1341 def inSection = false
1342 changes.eachLine { line ->
1344 if (m = line =~ /^##([^#].*)$/) {
1346 changesHugo += "</div>\n\n"
1348 def section = m[0][1].trim()
1349 section = section.toLowerCase()
1350 section = section.replaceAll(/ +/, "_")
1351 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1352 changesHugo += "<div class=\"${section}\">\n\n"
1354 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1355 def comment = m[0][2].trim()
1356 if (comment != "") {
1357 comment = comment.replaceAll('"', """)
1359 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1360 def newline = m[0][1]
1361 if (comment.trim() != "")
1362 newline += "{{<comment>}}${comment}{{</comment>}} "
1363 newline += m[0][3].trim()
1364 if (issuekeys.size() > 0)
1365 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1366 if (m[0][4] != null)
1371 changesHugo += line+"\n"
1374 changesHugo += "\n</div>\n\n"
1376 changesHugo += '</div>'
1379 templateFiles.each{ templateFile ->
1380 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1381 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1382 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1384 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1388 rename(templateFile.getName(), newFileName)
1392 def newFile = file("${outPathName}/${newFileName}".toString())
1393 def content = newFile.text
1394 newFile.text = hugoTemplateSubstitutions(content,
1397 CHANGES: changesHugo,
1398 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1399 DRAFT: givenDate == null ? "true" : "false",
1400 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1401 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1408 inputs.file(oldJvlFile)
1409 inputs.dir(hugoTemplatesDir)
1410 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1411 inputs.property("CHANNEL", { CHANNEL })
1414 def getMdDate(File mdFile) {
1415 return mdFileComponents(mdFile, true)
1418 def getMdSections(String content) {
1420 def sectionContent = ""
1421 def sectionName = null
1422 content.eachLine { line ->
1424 if (m = line =~ /^##([^#].*)$/) {
1425 if (sectionName != null) {
1426 sections[sectionName] = sectionContent
1430 sectionName = m[0][1].trim()
1431 sectionName = sectionName.toLowerCase()
1432 sectionName = sectionName.replaceAll(/ +/, "_")
1433 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1434 } else if (sectionName != null) {
1435 sectionContent += line+"\n"
1438 if (sectionContent != null) {
1439 sections[sectionName] = sectionContent
1445 task copyHelp(type: Copy) {
1446 def inputDir = helpSourceDir
1447 def outputDir = "${helpBuildDir}/${help_dir}"
1451 include('**/*.html')
1455 filter(ReplaceTokens,
1459 'Version-Rel': JALVIEW_VERSION,
1460 'Year-Rel': getDate("yyyy")
1467 exclude('**/*.html')
1474 inputs.dir(inputDir)
1475 outputs.files(helpFile)
1476 outputs.dir(outputDir)
1480 task releasesTemplates {
1482 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1486 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1487 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1488 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1489 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1490 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1491 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1494 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1495 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1497 if (CHANNEL == "RELEASE") {
1498 if (!releaseMdFile.exists()) {
1499 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1501 if (!whatsnewMdFile.exists()) {
1502 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1506 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1507 def releaseFilesDates = releaseFiles.collectEntries {
1508 [(it): getMdDate(it)]
1510 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1512 def releasesTemplate = releasesTemplateFile.text
1513 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1514 def versionTemplate = m[0][1]
1516 MutableDataSet options = new MutableDataSet()
1518 def extensions = new ArrayList<>()
1519 options.set(Parser.EXTENSIONS, extensions)
1520 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1522 Parser parser = Parser.builder(options).build()
1523 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1525 def actualVersions = releaseFiles.collect { rf ->
1526 def (rfMap, rfContent) = mdFileComponents(rf)
1527 return rfMap.version
1529 def versionsHtml = ""
1530 def linkedVersions = []
1531 releaseFiles.reverse().each { rFile ->
1532 def (rMap, rContent) = mdFileComponents(rFile)
1534 def versionLink = ""
1535 def partialVersion = ""
1536 def firstPart = true
1537 rMap.version.split("\\.").each { part ->
1538 def displayPart = ( firstPart ? "" : "." ) + part
1539 partialVersion += displayPart
1541 linkedVersions.contains(partialVersion)
1542 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1544 versionLink += displayPart
1546 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1547 linkedVersions += partialVersion
1551 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1554 def rContentProcessed = ""
1555 rContent.eachLine { line ->
1556 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1557 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1558 } else if (lm = line =~ /^###([^#]+.*)$/) {
1559 line = "_${lm[0][1].trim()}_"
1561 rContentProcessed += line + "\n"
1564 def rContentSections = getMdSections(rContentProcessed)
1565 def rVersion = versionTemplate
1566 if (rVersion != "") {
1567 def rNewFeatures = rContentSections["new_features"]
1568 def rIssuesResolved = rContentSections["issues_resolved"]
1569 Node newFeaturesNode = parser.parse(rNewFeatures)
1570 String newFeaturesHtml = renderer.render(newFeaturesNode)
1571 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1572 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1573 rVersion = hugoTemplateSubstitutions(rVersion,
1575 VERSION: rMap.version,
1576 VERSION_LINK: versionLink,
1577 DISPLAY_DATE: displayDate,
1578 NEW_FEATURES: newFeaturesHtml,
1579 ISSUES_RESOLVED: issuesResolvedHtml
1582 versionsHtml += rVersion
1586 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1587 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1588 releasesHtmlFile.text = releasesTemplate
1590 if (whatsnewMdFile.exists()) {
1591 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1592 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1593 Node whatsnewNode = parser.parse(whatsnewMd)
1594 String whatsnewHtml = renderer.render(whatsnewNode)
1595 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1596 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1598 VERSION: JALVIEW_VERSION,
1599 DISPLAY_DATE: wnDisplayDate
1602 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1603 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1608 inputs.file(releasesTemplateFile)
1609 inputs.file(whatsnewTemplateFile)
1610 inputs.dir(releasesMdDir)
1611 inputs.dir(whatsnewMdDir)
1612 outputs.file(releasesHtmlFile)
1613 outputs.file(whatsnewHtmlFile)
1617 task copyResources(type: Copy) {
1619 description = "Copy (and make text substitutions in) the resources dir to the build area"
1621 def inputDir = resourceDir
1622 def outputDir = resourcesBuildDir
1626 include('**/*.html')
1628 filter(ReplaceTokens,
1632 'Version-Rel': JALVIEW_VERSION,
1633 'Year-Rel': getDate("yyyy")
1640 exclude('**/*.html')
1645 inputs.dir(inputDir)
1646 outputs.dir(outputDir)
1649 task copyChannelResources(type: Copy) {
1650 dependsOn copyResources
1652 description = "Copy the channel resources dir to the build resources area"
1654 def inputDir = "${channelDir}/${resource_dir}"
1655 def outputDir = resourcesBuildDir
1657 include(channel_props)
1658 filter(ReplaceTokens,
1662 'SUFFIX': channelSuffix
1667 exclude(channel_props)
1671 inputs.dir(inputDir)
1672 outputs.dir(outputDir)
1675 task createBuildProperties(type: WriteProperties) {
1676 dependsOn copyResources
1678 description = "Create the ${buildProperties} file"
1680 inputs.dir(sourceDir)
1681 inputs.dir(resourcesBuildDir)
1682 outputFile (buildProperties)
1683 // taking time specific comment out to allow better incremental builds
1684 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1685 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1686 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1687 property "VERSION", JALVIEW_VERSION
1688 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1689 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1690 if (getdownSetAppBaseProperty) {
1691 property "GETDOWNAPPBASE", getdownAppBase
1692 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1694 outputs.file(outputFile)
1698 task buildIndices(type: JavaExec) {
1700 classpath = sourceSets.main.compileClasspath
1701 main = "com.sun.java.help.search.Indexer"
1702 workingDir = "${helpBuildDir}/${help_dir}"
1705 inputs.dir("${workingDir}/${argDir}")
1707 outputs.dir("${classesDir}/doc")
1708 outputs.dir("${classesDir}/help")
1709 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1710 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1711 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1712 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1713 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1714 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1717 task buildResources {
1718 dependsOn copyResources
1719 dependsOn copyChannelResources
1720 dependsOn createBuildProperties
1724 dependsOn buildResources
1727 dependsOn releasesTemplates
1728 dependsOn convertMdFiles
1729 dependsOn buildIndices
1733 compileJava.dependsOn prepare
1734 run.dependsOn compileJava
1735 //run.dependsOn prepare
1738 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1743 dependsOn cloverClasses
1745 dependsOn compileJava //?
1749 includeGroups testng_groups
1750 excludeGroups testng_excluded_groups
1752 useDefaultListeners=true
1755 maxHeapSize = "1024m"
1757 workingDir = jalviewDir
1758 def testLaf = project.findProperty("test_laf")
1759 if (testLaf != null) {
1760 println("Setting Test LaF to '${testLaf}'")
1761 systemProperty "laf", testLaf
1763 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1764 if (testHiDPIScale != null) {
1765 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1766 systemProperty "sun.java2d.uiScale", testHiDPIScale
1768 sourceCompatibility = compile_source_compatibility
1769 targetCompatibility = compile_target_compatibility
1770 jvmArgs += additional_compiler_args
1774 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1780 task compileLinkCheck(type: JavaCompile) {
1782 classpath = files("${jalviewDir}/${utils_dir}")
1783 destinationDir = file("${jalviewDir}/${utils_dir}")
1784 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1786 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1787 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1788 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1789 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1793 task linkCheck(type: JavaExec) {
1795 dependsOn compileLinkCheck
1797 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1798 classpath = files("${jalviewDir}/${utils_dir}")
1799 main = "HelpLinksChecker"
1800 workingDir = "${helpBuildDir}"
1801 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1803 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1804 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1807 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1811 inputs.dir(helpBuildDir)
1812 outputs.file(helpLinksCheckerOutFile)
1816 // import the pubhtmlhelp target
1817 ant.properties.basedir = "${jalviewDir}"
1818 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1819 ant.importBuild "${utils_dir}/publishHelp.xml"
1822 task cleanPackageDir(type: Delete) {
1824 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1834 attributes "Main-Class": main_class,
1835 "Permissions": "all-permissions",
1836 "Application-Name": applicationName,
1837 "Codebase": application_codebase,
1838 "Implementation-Version": JALVIEW_VERSION
1841 def outputDir = "${jalviewDir}/${package_dir}"
1842 destinationDirectory = file(outputDir)
1843 archiveFileName = rootProject.name+".jar"
1844 duplicatesStrategy "EXCLUDE"
1851 exclude "**/*.jar.*"
1853 inputs.dir(sourceSets.main.java.outputDir)
1854 sourceSets.main.resources.srcDirs.each{ dir ->
1857 outputs.file("${outputDir}/${archiveFileName}")
1861 task copyJars(type: Copy) {
1862 from fileTree(dir: classesDir, include: "**/*.jar").files
1863 into "${jalviewDir}/${package_dir}"
1867 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1868 task syncJars(type: Sync) {
1870 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1871 into "${jalviewDir}/${package_dir}"
1873 include jar.archiveFileName.getOrNull()
1880 description = "Put all required libraries in dist"
1881 // order of "cleanPackageDir", "copyJars", "jar" important!
1882 jar.mustRunAfter cleanPackageDir
1883 syncJars.mustRunAfter cleanPackageDir
1884 dependsOn cleanPackageDir
1887 outputs.dir("${jalviewDir}/${package_dir}")
1892 dependsOn cleanPackageDir
1899 group = "distribution"
1900 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1904 from ("${jalviewDir}/${libDistDir}") {
1908 attributes "Implementation-Version": JALVIEW_VERSION,
1909 "Application-Name": applicationName
1912 duplicatesStrategy "INCLUDE"
1914 mainClassName = shadow_jar_main_class
1916 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1920 task getdownImagesCopy() {
1921 inputs.dir getdownImagesDir
1922 outputs.dir getdownImagesBuildDir
1926 from(getdownImagesDir) {
1927 include("*getdown*.png")
1929 into getdownImagesBuildDir
1934 task getdownImagesProcess() {
1935 dependsOn getdownImagesCopy
1938 if (backgroundImageText) {
1939 if (convertBinary == null) {
1940 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
1942 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
1943 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
1945 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
1947 executable convertBinary
1950 '-font', getdown_background_image_text_font,
1951 '-fill', getdown_background_image_text_colour,
1952 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
1953 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
1954 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
1963 task getdownImages() {
1964 dependsOn getdownImagesProcess
1967 task getdownWebsite() {
1968 group = "distribution"
1969 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1971 dependsOn getdownImages
1976 def getdownWebsiteResourceFilenames = []
1977 def getdownResourceDir = getdownResourceDir
1978 def getdownResourceFilenames = []
1981 // clean the getdown website and files dir before creating getdown folders
1982 delete getdownAppBaseDir
1983 delete getdownFilesDir
1986 from buildProperties
1987 rename(file(buildProperties).getName(), getdown_build_properties)
1990 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
1993 from channelPropsFile
1994 filter(ReplaceTokens,
1998 'SUFFIX': channelSuffix
2001 into getdownAppBaseDir
2003 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2005 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2006 def props = project.properties.sort { it.key }
2007 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2008 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2010 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2011 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2013 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2014 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2016 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2017 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2018 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2019 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2020 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2021 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2022 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2025 props.put("getdown_txt_title", jalview_name)
2026 props.put("getdown_txt_ui.name", applicationName)
2028 // start with appbase
2029 getdownTextLines += "appbase = ${getdownAppBase}"
2030 props.each{ prop, val ->
2031 if (prop.startsWith("getdown_txt_") && val != null) {
2032 if (prop.startsWith("getdown_txt_multi_")) {
2033 def key = prop.substring(18)
2034 val.split(",").each{ v ->
2035 def line = "${key} = ${v}"
2036 getdownTextLines += line
2039 // file values rationalised
2040 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2042 if (val.indexOf('/') == 0) {
2045 } else if (val.indexOf('/') > 0) {
2046 // relative path (relative to jalviewDir)
2047 r = file( "${jalviewDir}/${val}" )
2050 val = "${getdown_resource_dir}/" + r.getName()
2051 getdownWebsiteResourceFilenames += val
2052 getdownResourceFilenames += r.getPath()
2055 if (! prop.startsWith("getdown_txt_resource")) {
2056 def line = prop.substring(12) + " = ${val}"
2057 getdownTextLines += line
2063 getdownWebsiteResourceFilenames.each{ filename ->
2064 getdownTextLines += "resource = ${filename}"
2066 getdownResourceFilenames.each{ filename ->
2069 into getdownResourceDir
2073 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2074 getdownWrapperScripts.each{ script ->
2075 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2079 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2081 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2086 fileTree(file(package_dir)).each{ f ->
2087 if (f.isDirectory()) {
2088 def files = fileTree(dir: f, include: ["*"]).getFiles()
2090 } else if (f.exists()) {
2094 def jalviewJar = jar.archiveFileName.getOrNull()
2095 // put jalview.jar first for CLASSPATH and .properties files reasons
2096 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2097 def name = f.getName()
2098 def line = "code = ${getdownAppDistDir}/${name}"
2099 getdownTextLines += line
2106 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2108 if (JAVA_VERSION.equals("11")) {
2109 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2110 j11libFiles.sort().each{f ->
2111 def name = f.getName()
2112 def line = "code = ${getdown_j11lib_dir}/${name}"
2113 getdownTextLines += line
2116 into getdownJ11libDir
2122 // 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.
2123 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2124 getdownTextLines += "resource = ${getdown_launcher_new}"
2125 getdownTextLines += "class = ${main_class}"
2126 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2127 if (getdownSetAppBaseProperty) {
2128 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2129 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2132 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2133 getdownTxt.write(getdownTextLines.join("\n"))
2135 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2136 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2137 launchJvl.write("appbase=${getdownAppBase}")
2139 // files going into the getdown website dir: getdown-launcher.jar
2141 from getdownLauncher
2142 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2143 into getdownAppBaseDir
2146 // files going into the getdown website dir: getdown-launcher(-local).jar
2148 from getdownLauncher
2149 if (file(getdownLauncher).getName() != getdown_launcher) {
2150 rename(file(getdownLauncher).getName(), getdown_launcher)
2152 into getdownAppBaseDir
2155 // files going into the getdown website dir: ./install dir and files
2156 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2159 from getdownLauncher
2160 from "${getdownAppDir}/${getdown_build_properties}"
2161 if (file(getdownLauncher).getName() != getdown_launcher) {
2162 rename(file(getdownLauncher).getName(), getdown_launcher)
2164 into getdownInstallDir
2167 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2169 from getdownInstallDir
2170 into getdownFilesInstallDir
2174 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2178 from getdownLauncher
2179 from "${getdownAppBaseDir}/${getdown_build_properties}"
2180 from "${getdownAppBaseDir}/${channel_props}"
2181 if (file(getdownLauncher).getName() != getdown_launcher) {
2182 rename(file(getdownLauncher).getName(), getdown_launcher)
2184 into getdownFilesDir
2187 // and ./resource (not all downloaded by getdown)
2189 from getdownResourceDir
2190 into "${getdownFilesDir}/${getdown_resource_dir}"
2195 inputs.dir("${jalviewDir}/${package_dir}")
2197 outputs.dir(getdownAppBaseDir)
2198 outputs.dir(getdownFilesDir)
2202 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2203 task getdownDigestDir(type: JavaExec) {
2205 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2207 def digestDirPropertyName = "DIGESTDIR"
2209 classpath = files(getdownLauncher)
2210 def digestDir = findProperty(digestDirPropertyName)
2211 if (digestDir == null) {
2212 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2216 main = "com.threerings.getdown.tools.Digester"
2220 task getdownDigest(type: JavaExec) {
2221 group = "distribution"
2222 description = "Digest the getdown website folder"
2223 dependsOn getdownWebsite
2225 classpath = files(getdownLauncher)
2227 main = "com.threerings.getdown.tools.Digester"
2228 args getdownAppBaseDir
2229 inputs.dir(getdownAppBaseDir)
2230 outputs.file("${getdownAppBaseDir}/digest2.txt")
2235 group = "distribution"
2236 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2237 dependsOn getdownDigest
2239 if (reportRsyncCommand) {
2240 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2241 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2242 println "LIKELY RSYNC COMMAND:"
2243 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2244 if (RUNRSYNC == "true") {
2246 commandLine "mkdir", "-p", toDir
2249 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2257 task getdownArchiveBuild() {
2258 group = "distribution"
2259 description = "Put files in the archive dir to go on the website"
2261 dependsOn getdownWebsite
2263 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2264 def vDir = "${getdownArchiveDir}/${v}"
2265 getdownFullArchiveDir = "${vDir}/getdown"
2266 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2268 def vAltDir = "alt_${v}"
2269 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2272 // cleanup old "old" dir
2273 delete getdownArchiveDir
2275 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2276 getdownArchiveTxt.getParentFile().mkdirs()
2277 def getdownArchiveTextLines = []
2278 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2282 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2283 into "${getdownFullArchiveDir}/${vAltDir}"
2286 getdownTextLines.each { line ->
2287 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2288 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2289 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2290 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2291 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2292 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2293 // remove the existing resource = resource/ or bin/ lines
2294 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2295 getdownArchiveTextLines += line
2299 // the resource dir -- add these files as resource lines in getdown.txt
2301 from "${archiveImagesDir}"
2302 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2304 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2308 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2310 def vLaunchJvl = file(getdownVersionLaunchJvl)
2311 vLaunchJvl.getParentFile().mkdirs()
2312 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2313 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2314 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2315 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2316 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2317 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2319 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2321 from getdownLauncher
2322 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2323 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2324 from "${getdownAppBaseDir}/${channel_props}"
2325 if (file(getdownLauncher).getName() != getdown_launcher) {
2326 rename(file(getdownLauncher).getName(), getdown_launcher)
2328 into getdownFullArchiveDir
2334 task getdownArchiveDigest(type: JavaExec) {
2335 group = "distribution"
2336 description = "Digest the getdown archive folder"
2338 dependsOn getdownArchiveBuild
2341 classpath = files(getdownLauncher)
2342 args getdownFullArchiveDir
2344 main = "com.threerings.getdown.tools.Digester"
2345 inputs.dir(getdownFullArchiveDir)
2346 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2349 task getdownArchive() {
2350 group = "distribution"
2351 description = "Build the website archive dir with getdown digest"
2353 dependsOn getdownArchiveBuild
2354 dependsOn getdownArchiveDigest
2357 tasks.withType(JavaCompile) {
2358 options.encoding = 'UTF-8'
2364 delete getdownAppBaseDir
2365 delete getdownFilesDir
2366 delete getdownArchiveDir
2372 if (file(install4jHomeDir).exists()) {
2374 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2375 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2376 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2377 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2379 installDir(file(install4jHomeDir))
2381 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2385 task copyInstall4jTemplate {
2386 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2387 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2388 inputs.file(install4jTemplateFile)
2389 inputs.file(install4jFileAssociationsFile)
2390 inputs.property("CHANNEL", { CHANNEL })
2391 outputs.file(install4jConfFile)
2394 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2396 // turn off code signing if no OSX_KEYPASS
2397 if (OSX_KEYPASS == "") {
2398 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2399 codeSigning.'@macEnabled' = "false"
2401 install4jConfigXml.'**'.windows.each { windows ->
2402 windows.'@runPostProcessor' = "false"
2406 // disable install screen for OSX dmg (for 2.11.2.0)
2407 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2408 macosArchive.attributes().remove('executeSetupApp')
2409 macosArchive.attributes().remove('setupAppId')
2412 // turn off checksum creation for LOCAL channel
2413 def e = install4jConfigXml.application[0]
2414 e.'@createChecksums' = string(install4jCheckSums)
2416 // put file association actions where placeholder action is
2417 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2418 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2419 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2420 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2421 def parent = a.parent()
2423 fileAssociationActions.each { faa ->
2426 // don't need to continue in .any loop once replacements have been made
2431 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2432 // NB we're deleting the /other/ one!
2433 // Also remove the examples subdir from non-release versions
2434 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2435 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2436 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2437 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2439 // remove the examples subdir from Full File Set
2440 def files = install4jConfigXml.files[0]
2441 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2442 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2443 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2444 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2445 dirEntry.parent().remove(dirEntry)
2447 install4jConfigXml.'**'.action.any { a ->
2448 if (a.'@customizedId' == customizedIdToDelete) {
2449 def parent = a.parent()
2455 // write install4j file
2456 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2463 delete install4jConfFile
2467 task cleanInstallersDataFiles {
2468 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2469 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2470 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2472 delete installersOutputTxt
2473 delete installersSha256
2474 delete hugoDataJsonFile
2478 task install4jDMGBackgroundImageCopy {
2479 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2480 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2483 from(install4jDMGBackgroundImageDir) {
2484 include(install4jDMGBackgroundImageFile)
2486 into install4jDMGBackgroundImageBuildDir
2491 task install4jDMGBackgroundImageProcess {
2492 dependsOn install4jDMGBackgroundImageCopy
2495 if (backgroundImageText) {
2496 if (convertBinary == null) {
2497 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2499 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2500 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2502 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2504 executable convertBinary
2507 '-font', install4j_background_image_text_font,
2508 '-fill', install4j_background_image_text_colour,
2509 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2510 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2511 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2520 task install4jDMGBackgroundImage {
2521 dependsOn install4jDMGBackgroundImageProcess
2524 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2525 group = "distribution"
2526 description = "Create the install4j installers"
2528 dependsOn copyInstall4jTemplate
2529 dependsOn cleanInstallersDataFiles
2530 dependsOn install4jDMGBackgroundImage
2532 projectFile = install4jConfFile
2534 // create an md5 for the input files to use as version for install4j conf file
2535 def digest = MessageDigest.getInstance("MD5")
2537 (file("${install4jDir}/${install4j_template}").text +
2538 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2539 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2540 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2541 if (filesMd5.length() >= 8) {
2542 filesMd5 = filesMd5.substring(0,8)
2544 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2547 'JALVIEW_NAME': jalview_name,
2548 'JALVIEW_APPLICATION_NAME': applicationName,
2549 'JALVIEW_DIR': "../..",
2550 'OSX_KEYSTORE': OSX_KEYSTORE,
2551 'OSX_APPLEID': OSX_APPLEID,
2552 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2553 'JSIGN_SH': JSIGN_SH,
2554 'JRE_DIR': getdown_app_dir_java,
2555 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2556 'JALVIEW_VERSION': JALVIEW_VERSION,
2557 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2558 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2559 'JAVA_VERSION': JAVA_VERSION,
2560 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2561 'VERSION': JALVIEW_VERSION,
2562 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2563 'BUNDLE_ID': install4jBundleId,
2564 'INTERNAL_ID': install4jInternalId,
2565 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2566 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2567 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2568 'WRAPPER_LINK': getdownWrapperLink,
2569 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2570 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2571 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2572 'INSTALLER_NAME': install4jInstallerName,
2573 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2574 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2575 'GETDOWN_FILES_DIR': getdown_files_dir,
2576 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2577 'GETDOWN_DIST_DIR': getdownAppDistDir,
2578 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2579 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2580 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2581 'BUILD_DIR': install4jBuildDir,
2582 'APPLICATION_CATEGORIES': install4j_application_categories,
2583 'APPLICATION_FOLDER': install4jApplicationFolder,
2584 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2585 'EXECUTABLE_NAME': install4jExecutableName,
2586 'EXTRA_SCHEME': install4jExtraScheme,
2587 'MAC_ICONS_FILE': install4jMacIconsFile,
2588 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2589 'PNG_ICON_FILE': install4jPngIconFile,
2590 'BACKGROUND': install4jBackground,
2595 'windows': 'WINDOWS',
2599 // these are the bundled OS/architecture VMs needed by install4j
2602 [ "mac", "aarch64" ],
2603 [ "windows", "x64" ],
2605 [ "linux", "aarch64" ]
2607 osArch.forEach { os, arch ->
2608 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)
2609 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2610 // otherwise running `gradle installers` generates a non-useful error:
2611 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2612 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)
2615 //println("INSTALL4J VARIABLES:")
2616 //variables.each{k,v->println("${k}=${v}")}
2618 destination = "${jalviewDir}/${install4jBuildDir}"
2619 buildSelected = true
2621 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2623 disableSigning = true
2624 disableNotarization = true
2628 macKeystorePassword = OSX_KEYPASS
2631 if (OSX_ALTOOLPASS) {
2632 appleIdPassword = OSX_ALTOOLPASS
2633 disableNotarization = false
2635 disableNotarization = true
2639 println("Using projectFile "+projectFile)
2640 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2644 inputs.dir(getdownAppBaseDir)
2645 inputs.file(install4jConfFile)
2646 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2647 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2650 def getDataHash(File myFile) {
2651 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2652 return myFile.exists()
2654 "file" : myFile.getName(),
2655 "filesize" : myFile.length(),
2656 "sha256" : hash.toString()
2661 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2663 "channel" : getdownChannelName,
2664 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2665 "git-commit" : "${gitHash} [${gitBranch}]",
2666 "version" : JALVIEW_VERSION
2668 // install4j installer files
2669 if (installersOutputTxt.exists()) {
2671 installersOutputTxt.readLines().each { def line ->
2672 if (line.startsWith("#")) {
2675 line.replaceAll("\n","")
2676 def vals = line.split("\t")
2677 def filename = vals[3]
2678 def filesize = file(filename).length()
2679 filename = filename.replaceAll(/^.*\//, "")
2680 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2681 idHash."${filename}" = vals[0]
2683 if (install4jCheckSums && installersSha256.exists()) {
2684 installersSha256.readLines().each { def line ->
2685 if (line.startsWith("#")) {
2688 line.replaceAll("\n","")
2689 def vals = line.split(/\s+\*?/)
2690 def filename = vals[1]
2691 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2697 "JAR": shadowJar.archiveFile, // executable JAR
2698 "JVL": getdownVersionLaunchJvl, // version JVL
2699 "SOURCE": sourceDist.archiveFile // source TGZ
2700 ].each { key, value ->
2701 def file = file(value)
2702 if (file.exists()) {
2703 def fileHash = getDataHash(file)
2704 if (fileHash != null) {
2705 hash."${key}" = fileHash;
2709 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2712 task staticMakeInstallersJsonFile {
2714 def output = findProperty("i4j_output")
2715 def sha256 = findProperty("i4j_sha256")
2716 def json = findProperty("i4j_json")
2717 if (output == null || sha256 == null || json == null) {
2718 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2720 writeDataJsonFile(file(output), file(sha256), file(json))
2725 dependsOn installerFiles
2731 eclipse().configFile(eclipse_codestyle_file)
2735 task createSourceReleaseProperties(type: WriteProperties) {
2736 group = "distribution"
2737 description = "Create the source RELEASE properties file"
2739 def sourceTarBuildDir = "${buildDir}/sourceTar"
2740 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2741 outputFile (sourceReleasePropertiesFile)
2744 releaseProps.each{ key, val -> property key, val }
2745 property "git.branch", gitBranch
2746 property "git.hash", gitHash
2749 outputs.file(outputFile)
2752 task sourceDist(type: Tar) {
2753 group "distribution"
2754 description "Create a source .tar.gz file for distribution"
2756 dependsOn createBuildProperties
2757 dependsOn convertMdFiles
2758 dependsOn eclipseAllPreferences
2759 dependsOn createSourceReleaseProperties
2762 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2763 archiveFileName = outputFileName
2765 compression Compression.GZIP
2780 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2782 "utils/InstallAnywhere",
2797 "gradle.properties",
2809 ".settings/org.eclipse.buildship.core.prefs",
2810 ".settings/org.eclipse.jdt.core.prefs"
2814 exclude (EXCLUDE_FILES)
2815 include (PROCESS_FILES)
2816 filter(ReplaceTokens,
2820 'Version-Rel': JALVIEW_VERSION,
2821 'Year-Rel': getDate("yyyy")
2826 exclude (EXCLUDE_FILES)
2827 exclude (PROCESS_FILES)
2828 exclude ("appletlib")
2829 exclude ("**/*locales")
2830 exclude ("*locales/**")
2831 exclude ("utils/InstallAnywhere")
2833 exclude (getdown_files_dir)
2834 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2835 //exclude (getdown_website_dir)
2836 //exclude (getdown_archive_dir)
2838 // exluding these as not using jars as modules yet
2839 exclude ("${j11modDir}/**/*.jar")
2842 include(INCLUDE_FILES)
2844 // from (jalviewDir) {
2845 // // explicit includes for stuff that seemed to not get included
2846 // include(fileTree("test/**/*."))
2847 // exclude(EXCLUDE_FILES)
2848 // exclude(PROCESS_FILES)
2851 from(file(buildProperties).getParent()) {
2852 include(file(buildProperties).getName())
2853 rename(file(buildProperties).getName(), "build_properties")
2855 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2859 def sourceTarBuildDir = "${buildDir}/sourceTar"
2860 from(sourceTarBuildDir) {
2861 // this includes the appended RELEASE properties file
2865 task dataInstallersJson {
2867 description "Create the installers-VERSION.json data file for installer files created"
2869 mustRunAfter installers
2870 mustRunAfter shadowJar
2871 mustRunAfter sourceDist
2872 mustRunAfter getdownArchive
2874 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2875 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2877 if (installersOutputTxt.exists()) {
2878 inputs.file(installersOutputTxt)
2880 if (install4jCheckSums && installersSha256.exists()) {
2881 inputs.file(installersSha256)
2884 shadowJar.archiveFile, // executable JAR
2885 getdownVersionLaunchJvl, // version JVL
2886 sourceDist.archiveFile // source TGZ
2887 ].each { fileName ->
2888 if (file(fileName).exists()) {
2889 inputs.file(fileName)
2893 outputs.file(hugoDataJsonFile)
2896 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
2902 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
2905 dependsOn pubhtmlhelp
2907 inputs.dir("${helpBuildDir}/${help_dir}")
2908 outputs.dir("${buildDir}/distributions/${help_dir}")
2912 task j2sSetHeadlessBuild {
2919 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2921 description "Enable the alternative J2S Config file for headless build"
2923 outputFile = jalviewjsJ2sSettingsFileName
2924 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2925 def j2sProps = new Properties()
2926 if (j2sPropsFile.exists()) {
2928 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2929 j2sProps.load(j2sPropsFileFIS)
2930 j2sPropsFileFIS.close()
2932 j2sProps.each { prop, val ->
2935 } catch (Exception e) {
2936 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2940 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2941 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2946 task jalviewjsSetEclipseWorkspace {
2947 def propKey = "jalviewjs_eclipse_workspace"
2949 if (project.hasProperty(propKey)) {
2950 propVal = project.getProperty(propKey)
2951 if (propVal.startsWith("~/")) {
2952 propVal = System.getProperty("user.home") + propVal.substring(1)
2955 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2956 def propsFile = file(propsFileName)
2957 def eclipseWsDir = propVal
2958 def props = new Properties()
2960 def writeProps = true
2961 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2962 def ins = new FileInputStream(propsFileName)
2965 if (props.getProperty(propKey, null) != null) {
2966 eclipseWsDir = props.getProperty(propKey)
2971 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2972 def tempDir = File.createTempDir()
2973 eclipseWsDir = tempDir.getAbsolutePath()
2976 eclipseWorkspace = file(eclipseWsDir)
2979 // do not run a headless transpile when we claim to be in Eclipse
2981 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2982 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2984 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2988 props.setProperty(propKey, eclipseWsDir)
2989 propsFile.parentFile.mkdirs()
2990 def bytes = new ByteArrayOutputStream()
2991 props.store(bytes, null)
2992 def propertiesString = bytes.toString()
2993 propsFile.text = propertiesString
2999 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3002 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3003 outputs.file(propsFileName)
3004 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3008 task jalviewjsEclipsePaths {
3011 def eclipseRoot = jalviewjs_eclipse_root
3012 if (eclipseRoot.startsWith("~/")) {
3013 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3015 if (OperatingSystem.current().isMacOsX()) {
3016 eclipseRoot += "/Eclipse.app"
3017 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3018 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3019 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3020 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3021 eclipseRoot += "/eclipse"
3023 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3024 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3025 } else { // linux or unix
3026 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3027 eclipseRoot += "/eclipse"
3028 println("eclipseDir exists")
3030 eclipseBinary = "${eclipseRoot}/eclipse"
3031 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3034 eclipseVersion = "4.13" // default
3035 def assumedVersion = true
3036 if (file(eclipseProduct).exists()) {
3037 def fis = new FileInputStream(eclipseProduct)
3038 def props = new Properties()
3040 eclipseVersion = props.getProperty("version")
3042 assumedVersion = false
3045 def propKey = "eclipse_debug"
3046 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3049 // do not run a headless transpile when we claim to be in Eclipse
3051 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3052 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3054 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3057 if (!assumedVersion) {
3058 println("ECLIPSE VERSION=${eclipseVersion}")
3064 task printProperties {
3066 description "Output to console all System.properties"
3068 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3074 dependsOn eclipseProject
3075 dependsOn eclipseClasspath
3076 dependsOn eclipseJdt
3080 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3081 task jalviewjsEclipseCopyDropins(type: Copy) {
3082 dependsOn jalviewjsEclipsePaths
3084 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3085 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3086 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3093 // this eclipse -clean doesn't actually work
3094 task jalviewjsCleanEclipse(type: Exec) {
3095 dependsOn eclipseSetup
3096 dependsOn jalviewjsEclipsePaths
3097 dependsOn jalviewjsEclipseCopyDropins
3099 executable(eclipseBinary)
3100 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3106 def inputString = """exit
3109 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3110 standardInput = inputByteStream
3113 /* not really working yet
3114 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3118 task jalviewjsTransferUnzipSwingJs {
3119 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3123 from zipTree(file_zip)
3124 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3128 inputs.file file_zip
3129 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3133 task jalviewjsTransferUnzipLib {
3134 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3137 zipFiles.each { file_zip ->
3139 from zipTree(file_zip)
3140 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3145 inputs.files zipFiles
3146 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3150 task jalviewjsTransferUnzipAllLibs {
3151 dependsOn jalviewjsTransferUnzipSwingJs
3152 dependsOn jalviewjsTransferUnzipLib
3156 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3158 description "Create the alternative j2s file from the j2s.* properties"
3160 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3161 def siteDirProperty = "j2s.site.directory"
3162 def setSiteDir = false
3163 jalviewjsJ2sProps.each { prop, val ->
3165 if (prop == siteDirProperty) {
3166 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3167 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3173 if (!setSiteDir) { // default site location, don't override specifically set property
3174 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3177 outputFile = jalviewjsJ2sAltSettingsFileName
3180 inputs.properties(jalviewjsJ2sProps)
3181 outputs.file(jalviewjsJ2sAltSettingsFileName)
3186 task jalviewjsEclipseSetup {
3187 dependsOn jalviewjsEclipseCopyDropins
3188 dependsOn jalviewjsSetEclipseWorkspace
3189 dependsOn jalviewjsCreateJ2sSettings
3193 task jalviewjsSyncAllLibs (type: Sync) {
3194 dependsOn jalviewjsTransferUnzipAllLibs
3195 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3196 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3197 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3201 def outputFiles = []
3202 rename { filename ->
3203 outputFiles += "${outputDir}/${filename}"
3210 // should this be exclude really ?
3211 duplicatesStrategy "INCLUDE"
3213 outputs.files outputFiles
3214 inputs.files inputFiles
3218 task jalviewjsSyncResources (type: Sync) {
3219 dependsOn buildResources
3221 def inputFiles = fileTree(dir: resourcesBuildDir)
3222 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3226 def outputFiles = []
3227 rename { filename ->
3228 outputFiles += "${outputDir}/${filename}"
3234 outputs.files outputFiles
3235 inputs.files inputFiles
3239 task jalviewjsSyncSiteResources (type: Sync) {
3240 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3241 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3245 def outputFiles = []
3246 rename { filename ->
3247 outputFiles += "${outputDir}/${filename}"
3253 outputs.files outputFiles
3254 inputs.files inputFiles
3258 task jalviewjsSyncBuildProperties (type: Sync) {
3259 dependsOn createBuildProperties
3260 def inputFiles = [file(buildProperties)]
3261 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3265 def outputFiles = []
3266 rename { filename ->
3267 outputFiles += "${outputDir}/${filename}"
3273 outputs.files outputFiles
3274 inputs.files inputFiles
3278 task jalviewjsProjectImport(type: Exec) {
3279 dependsOn eclipseSetup
3280 dependsOn jalviewjsEclipsePaths
3281 dependsOn jalviewjsEclipseSetup
3284 // do not run a headless import when we claim to be in Eclipse
3286 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3287 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3289 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3293 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3294 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3295 executable(eclipseBinary)
3296 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3300 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3302 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3303 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3306 inputs.file("${jalviewDir}/.project")
3307 outputs.upToDateWhen {
3308 file(projdir).exists()
3313 task jalviewjsTranspile(type: Exec) {
3314 dependsOn jalviewjsEclipseSetup
3315 dependsOn jalviewjsProjectImport
3316 dependsOn jalviewjsEclipsePaths
3318 dependsOn jalviewjsEnableAltFileProperty
3322 // do not run a headless transpile when we claim to be in Eclipse
3324 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3325 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3327 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3331 executable(eclipseBinary)
3332 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3336 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3338 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3339 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3345 stdout = new ByteArrayOutputStream()
3346 stderr = new ByteArrayOutputStream()
3348 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3349 def logOutFile = file(logOutFileName)
3350 logOutFile.createNewFile()
3351 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3352 BINARY: ${eclipseBinary}
3353 VERSION: ${eclipseVersion}
3354 WORKSPACE: ${eclipseWorkspace}
3355 DEBUG: ${eclipseDebug}
3358 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3359 // combine stdout and stderr
3360 def logErrFOS = logOutFOS
3362 if (jalviewjs_j2s_to_console.equals("true")) {
3363 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3364 new org.apache.tools.ant.util.TeeOutputStream(
3368 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3369 new org.apache.tools.ant.util.TeeOutputStream(
3374 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3377 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3384 if (stdout.toString().contains("Error processing ")) {
3385 // j2s did not complete transpile
3386 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3387 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3388 println("IGNORING TRANSPILE ERRORS")
3389 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3391 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3396 inputs.dir("${jalviewDir}/${sourceDir}")
3397 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3398 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3402 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3404 def stdout = new ByteArrayOutputStream()
3405 def stderr = new ByteArrayOutputStream()
3407 def coreFile = file(jsfile)
3409 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3411 logOutFile.createNewFile()
3412 logOutFile.append(msg+"\n")
3414 def coreTop = file(prefixFile)
3415 def coreBottom = file(suffixFile)
3416 coreFile.getParentFile().mkdirs()
3417 coreFile.createNewFile()
3418 coreFile.write( coreTop.getText("UTF-8") )
3422 def t = f.getText("UTF-8")
3423 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3424 coreFile.append( t )
3426 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3428 logOutFile.append(msg+"\n")
3431 coreFile.append( coreBottom.getText("UTF-8") )
3433 msg = "Generating ${zjsfile}"
3435 logOutFile.append(msg+"\n")
3436 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3437 def logErrFOS = logOutFOS
3440 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3441 main = "com.google.javascript.jscomp.CommandLineRunner"
3442 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3443 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3446 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3448 logOutFile.append(msg+"\n")
3450 if (logOutConsole) {
3451 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3452 new org.apache.tools.ant.util.TeeOutputStream(
3456 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3457 new org.apache.tools.ant.util.TeeOutputStream(
3462 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3465 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3472 logOutFile.append(msg+"\n")
3476 task jalviewjsBuildAllCores {
3478 description "Build the core js lib closures listed in the classlists dir"
3479 dependsOn jalviewjsTranspile
3480 dependsOn jalviewjsTransferUnzipSwingJs
3482 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3483 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3484 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3485 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3486 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3487 def prefixFile = "${jsDir}/core/coretop2.js"
3488 def suffixFile = "${jsDir}/core/corebottom2.js"
3490 inputs.file prefixFile
3491 inputs.file suffixFile
3493 def classlistFiles = []
3494 // add the classlists found int the jalviewjs_classlists_dir
3495 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3497 def name = file.getName() - ".txt"
3504 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3505 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3506 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3508 jalviewjsCoreClasslists = []
3510 classlistFiles.each {
3513 def file = hash['file']
3514 if (! file.exists()) {
3515 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3516 return false // this is a "continue" in groovy .each closure
3518 def name = hash['name']
3520 name = file.getName() - ".txt"
3528 def list = fileTree(dir: j2sDir, includes: filelist)
3530 def jsfile = "${outputDir}/core${name}.js"
3531 def zjsfile = "${outputDir}/core${name}.z.js"
3533 jalviewjsCoreClasslists += [
3542 outputs.file(jsfile)
3543 outputs.file(zjsfile)
3546 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3547 def stevesoftClasslistName = "_stevesoft"
3548 def stevesoftClasslist = [
3549 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3550 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3551 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3552 'name': stevesoftClasslistName
3554 jalviewjsCoreClasslists += stevesoftClasslist
3555 inputs.files(stevesoftClasslist['list'])
3556 outputs.file(stevesoftClasslist['jsfile'])
3557 outputs.file(stevesoftClasslist['zjsfile'])
3560 def allClasslistName = "_all"
3561 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3562 allJsFiles += fileTree(
3566 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3567 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3568 "**/org/jmol/export/JSExporter.js"
3571 allJsFiles += fileTree(
3575 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3576 "**/sun/misc/Unsafe.js",
3577 "**/swingjs/jquery/jquery-editable-select.js",
3578 "**/swingjs/jquery/j2sComboBox.js",
3579 "**/sun/misc/FloatingDecimal.js"
3582 def allClasslist = [
3583 'jsfile': "${outputDir}/core${allClasslistName}.js",
3584 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3586 'name': allClasslistName
3588 // not including this version of "all" core at the moment
3589 //jalviewjsCoreClasslists += allClasslist
3590 inputs.files(allClasslist['list'])
3591 outputs.file(allClasslist['jsfile'])
3592 outputs.file(allClasslist['zjsfile'])
3595 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3596 logOutFile.getParentFile().mkdirs()
3597 logOutFile.createNewFile()
3598 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3600 jalviewjsCoreClasslists.each {
3601 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3608 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3611 into file(outputFile).getParentFile()
3612 rename { filename ->
3613 if (filename.equals(inputFile.getName())) {
3614 return file(outputFile).getName()
3618 filter(ReplaceTokens,
3622 'MAIN': '"'+main_class+'"',
3624 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3625 'COREKEY': jalviewjs_core_key,
3626 'CORENAME': coreName
3633 task jalviewjsPublishCoreTemplates {
3634 dependsOn jalviewjsBuildAllCores
3635 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3636 def inputFile = file(inputFileName)
3637 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3639 def outputFiles = []
3640 jalviewjsCoreClasslists.each { cl ->
3641 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3642 cl['outputfile'] = outputFile
3643 outputFiles += outputFile
3647 jalviewjsCoreClasslists.each { cl ->
3648 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3651 inputs.file(inputFile)
3652 outputs.files(outputFiles)
3656 task jalviewjsSyncCore (type: Sync) {
3657 dependsOn jalviewjsBuildAllCores
3658 dependsOn jalviewjsPublishCoreTemplates
3659 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3660 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3664 def outputFiles = []
3665 rename { filename ->
3666 outputFiles += "${outputDir}/${filename}"
3672 outputs.files outputFiles
3673 inputs.files inputFiles
3677 // this Copy version of TransferSiteJs will delete anything else in the target dir
3678 task jalviewjsCopyTransferSiteJs(type: Copy) {
3679 dependsOn jalviewjsTranspile
3680 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3681 into "${jalviewDir}/${jalviewjsSiteDir}"
3685 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3686 task jalviewjsSyncTransferSiteJs(type: Sync) {
3687 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3689 into "${jalviewDir}/${jalviewjsSiteDir}"
3696 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3697 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3698 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3699 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3701 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3702 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3703 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3704 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3707 task jalviewjsPrepareSite {
3709 description "Prepares the website folder including unzipping files and copying resources"
3710 dependsOn jalviewjsSyncAllLibs
3711 dependsOn jalviewjsSyncResources
3712 dependsOn jalviewjsSyncSiteResources
3713 dependsOn jalviewjsSyncBuildProperties
3714 dependsOn jalviewjsSyncCore
3718 task jalviewjsBuildSite {
3720 description "Builds the whole website including transpiled code"
3721 dependsOn jalviewjsCopyTransferSiteJs
3722 dependsOn jalviewjsPrepareSite
3726 task cleanJalviewjsTransferSite {
3728 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3729 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3730 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3731 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3736 task cleanJalviewjsSite {
3737 dependsOn cleanJalviewjsTransferSite
3739 delete "${jalviewDir}/${jalviewjsSiteDir}"
3744 task jalviewjsSiteTar(type: Tar) {
3746 description "Creates a tar.gz file for the website"
3747 dependsOn jalviewjsBuildSite
3748 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3749 archiveFileName = outputFilename
3751 compression Compression.GZIP
3753 from "${jalviewDir}/${jalviewjsSiteDir}"
3754 into jalviewjs_site_dir // this is inside the tar file
3756 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3760 task jalviewjsServer {
3762 def filename = "jalviewjsTest.html"
3763 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3764 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3769 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3770 factory = f.newInstance()
3771 } catch (ClassNotFoundException e) {
3772 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3774 def port = Integer.valueOf(jalviewjs_server_port)
3779 while(port < start+1000 && !running) {
3781 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3782 jalviewjsServer = factory.start(doc_root, port)
3784 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3785 println("SERVER STARTED with document root ${doc_root}.")
3786 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3787 println("For debug: "+url+"?j2sdebug")
3788 println("For verbose: "+url+"?j2sverbose")
3789 } catch (Exception e) {
3794 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3795 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3796 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3798 jalviewjsCoreClasslists.each { cl ->
3799 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3801 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3803 println("For core ${cl.name}: "+urlcore)
3806 file(htmlFile).text = htmlText
3809 outputs.file(htmlFile)
3810 outputs.upToDateWhen({false})
3814 task cleanJalviewjsAll {
3816 description "Delete all configuration and build artifacts to do with JalviewJS build"
3817 dependsOn cleanJalviewjsSite
3818 dependsOn jalviewjsEclipsePaths
3821 delete "${jalviewDir}/${jalviewjsBuildDir}"
3822 delete "${jalviewDir}/${eclipse_bin_dir}"
3823 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3824 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3826 delete jalviewjsJ2sAltSettingsFileName
3829 outputs.upToDateWhen( { false } )
3833 task jalviewjsIDE_checkJ2sPlugin {
3834 group "00 JalviewJS in Eclipse"
3835 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3838 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3839 def j2sPluginFile = file(j2sPlugin)
3840 def eclipseHome = System.properties["eclipse.home.location"]
3841 if (eclipseHome == null || ! IN_ECLIPSE) {
3842 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3844 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3845 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3846 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3847 eclipseJ2sPluginDirs += altPluginsDir
3849 def foundPlugin = false
3850 def j2sPluginFileName = j2sPluginFile.getName()
3851 def eclipseJ2sPlugin
3852 def eclipseJ2sPluginFile
3853 eclipseJ2sPluginDirs.any { dir ->
3854 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3855 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3856 if (eclipseJ2sPluginFile.exists()) {
3862 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3863 System.err.println(msg)
3864 throw new StopExecutionException(msg)
3867 def digest = MessageDigest.getInstance("MD5")
3869 digest.update(j2sPluginFile.text.bytes)
3870 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3872 digest.update(eclipseJ2sPluginFile.text.bytes)
3873 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3875 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3876 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3877 System.err.println(msg)
3878 throw new StopExecutionException(msg)
3880 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3886 task jalviewjsIDE_copyJ2sPlugin {
3887 group "00 JalviewJS in Eclipse"
3888 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3891 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3892 def j2sPluginFile = file(j2sPlugin)
3893 def eclipseHome = System.properties["eclipse.home.location"]
3894 if (eclipseHome == null || ! IN_ECLIPSE) {
3895 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3897 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3898 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3899 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3900 System.err.println(msg)
3903 eclipseJ2sPluginFile.getParentFile().mkdirs()
3904 into eclipseJ2sPluginFile.getParent()
3910 task jalviewjsIDE_j2sFile {
3911 group "00 JalviewJS in Eclipse"
3912 description "Creates the .j2s file"
3913 dependsOn jalviewjsCreateJ2sSettings
3917 task jalviewjsIDE_SyncCore {
3918 group "00 JalviewJS in Eclipse"
3919 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3920 dependsOn jalviewjsSyncCore
3924 task jalviewjsIDE_SyncSiteAll {
3925 dependsOn jalviewjsSyncAllLibs
3926 dependsOn jalviewjsSyncResources
3927 dependsOn jalviewjsSyncSiteResources
3928 dependsOn jalviewjsSyncBuildProperties
3932 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3935 task jalviewjsIDE_PrepareSite {
3936 group "00 JalviewJS in Eclipse"
3937 description "Sync libs and resources to site dir, but not closure cores"
3939 dependsOn jalviewjsIDE_SyncSiteAll
3940 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3944 task jalviewjsIDE_AssembleSite {
3945 group "00 JalviewJS in Eclipse"
3946 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3947 dependsOn jalviewjsPrepareSite
3951 task jalviewjsIDE_SiteClean {
3952 group "00 JalviewJS in Eclipse"
3953 description "Deletes the Eclipse transpiled site"
3954 dependsOn cleanJalviewjsSite
3958 task jalviewjsIDE_Server {
3959 group "00 JalviewJS in Eclipse"
3960 description "Starts a webserver on localhost to test the website"
3961 dependsOn jalviewjsServer
3965 // buildship runs this at import or gradle refresh
3966 task eclipseSynchronizationTask {
3967 //dependsOn eclipseSetup
3968 dependsOn createBuildProperties
3970 dependsOn jalviewjsIDE_j2sFile
3971 dependsOn jalviewjsIDE_checkJ2sPlugin
3972 dependsOn jalviewjsIDE_PrepareSite
3977 // buildship runs this at build time or project refresh
3978 task eclipseAutoBuildTask {
3979 //dependsOn jalviewjsIDE_checkJ2sPlugin
3980 //dependsOn jalviewjsIDE_PrepareSite
3986 description "Build the site"
3987 dependsOn jalviewjsBuildSite