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 '2.1.1' // 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 compileTestJava.dependsOn compileJava
1738 ext.testsFailed = false
1739 /* testTask0 is the main test task */
1740 task testTask0(type: Test) {
1742 includeGroups testng_groups.split(",")
1743 excludeGroups testng_excluded_groups.split(",")
1744 tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
1746 useDefaultListeners=true
1750 /* separated tests */
1751 task testTask1(type: Test) {
1754 excludeGroups testng_excluded_groups.split(",")
1755 tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
1757 useDefaultListeners=true
1762 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1763 * to summarise test results from all Test tasks
1765 /* START of test tasks results summary */
1766 import groovy.time.TimeCategory
1767 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1768 import org.gradle.api.tasks.testing.logging.TestLogEvent
1770 rootProject.ext.testsResults = [] // Container for tests summaries
1772 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1774 // from original test task
1776 dependsOn cloverClasses
1778 dependsOn compileJava //?
1781 // run main tests first
1782 if (!testTask.name.equals("testTask0"))
1783 testTask.mustRunAfter "testTask0"
1785 testTask.testLogging { logging ->
1786 events TestLogEvent.FAILED,
1787 TestLogEvent.SKIPPED,
1788 TestLogEvent.STANDARD_OUT,
1789 TestLogEvent.STANDARD_ERROR
1791 exceptionFormat TestExceptionFormat.FULL
1794 showStackTraces true
1797 ignoreFailures = true // Always try to run all tests for all modules
1799 afterSuite { desc, result ->
1801 if (desc.parent) return // Only summarize results for whole modules
1803 String summary = "${testTask.project.name}:${testTask.name} results: ${result.resultType} " +
1805 "${result.testCount} tests, " +
1806 "${result.successfulTestCount} successes, " +
1807 "${result.failedTestCount} failures, " +
1808 "${result.skippedTestCount} skipped" +
1810 "in ${TimeCategory.minus(new Date(result.endTime), new Date(result.startTime))}" +
1812 "Report file: ${testTask.reports.html.entryPoint}"
1814 // Add reports in `testsResults`, keep failed suites at the end
1815 if (result.resultType == TestResult.ResultType.SUCCESS) {
1816 rootProject.ext.testsResults.add(0, summary)
1818 rootProject.ext.testsResults += summary
1821 if (result.resultType == TestResult.ResultType.FAILURE) {
1826 // from original test task
1827 maxHeapSize = "1024m"
1829 workingDir = jalviewDir
1830 def testLaf = project.findProperty("test_laf")
1831 if (testLaf != null) {
1832 println("Setting Test LaF to '${testLaf}'")
1833 systemProperty "laf", testLaf
1835 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1836 if (testHiDPIScale != null) {
1837 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1838 systemProperty "sun.java2d.uiScale", testHiDPIScale
1840 sourceCompatibility = compile_source_compatibility
1841 targetCompatibility = compile_target_compatibility
1842 jvmArgs += additional_compiler_args
1846 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1852 gradle.buildFinished {
1853 def allResults = rootProject.ext.testsResults
1855 if (!allResults.isEmpty()) {
1856 printResults allResults
1860 private static void printResults(allResults) {
1861 def maxLength = allResults*.readLines().flatten().collect { it.length() }.max()
1863 println "┌${"${"─" * maxLength}"}┐"
1865 println allResults.collect {
1866 it.readLines().collect {
1867 "│" + it + " " * (maxLength - it.length()) + "│"
1869 }.join("\n├${"${"─" * maxLength}"}┤\n")
1871 println "└${"${"─" * maxLength}"}┘"
1873 /* END of test tasks results summary */
1875 task verifyTestStatus {
1878 throw new GradleException("There were failing tests!")
1884 // from original test task
1887 dependsOn cloverClasses
1889 dependsOn compileJava //?
1891 dependsOn tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}
1892 finalizedBy verifyTestStatus
1895 // not running tests in this task
1900 task compileLinkCheck(type: JavaCompile) {
1902 classpath = files("${jalviewDir}/${utils_dir}")
1903 destinationDir = file("${jalviewDir}/${utils_dir}")
1904 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1906 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1907 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1908 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1909 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1913 task linkCheck(type: JavaExec) {
1915 dependsOn compileLinkCheck
1917 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1918 classpath = files("${jalviewDir}/${utils_dir}")
1919 main = "HelpLinksChecker"
1920 workingDir = "${helpBuildDir}"
1921 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1923 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1924 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1927 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1931 inputs.dir(helpBuildDir)
1932 outputs.file(helpLinksCheckerOutFile)
1936 // import the pubhtmlhelp target
1937 ant.properties.basedir = "${jalviewDir}"
1938 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1939 ant.importBuild "${utils_dir}/publishHelp.xml"
1942 task cleanPackageDir(type: Delete) {
1944 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1954 attributes "Main-Class": main_class,
1955 "Permissions": "all-permissions",
1956 "Application-Name": applicationName,
1957 "Codebase": application_codebase,
1958 "Implementation-Version": JALVIEW_VERSION
1961 def outputDir = "${jalviewDir}/${package_dir}"
1962 destinationDirectory = file(outputDir)
1963 archiveFileName = rootProject.name+".jar"
1964 duplicatesStrategy "EXCLUDE"
1971 exclude "**/*.jar.*"
1973 inputs.dir(sourceSets.main.java.outputDir)
1974 sourceSets.main.resources.srcDirs.each{ dir ->
1977 outputs.file("${outputDir}/${archiveFileName}")
1981 task copyJars(type: Copy) {
1982 from fileTree(dir: classesDir, include: "**/*.jar").files
1983 into "${jalviewDir}/${package_dir}"
1987 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1988 task syncJars(type: Sync) {
1990 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1991 into "${jalviewDir}/${package_dir}"
1993 include jar.archiveFileName.getOrNull()
2000 description = "Put all required libraries in dist"
2001 // order of "cleanPackageDir", "copyJars", "jar" important!
2002 jar.mustRunAfter cleanPackageDir
2003 syncJars.mustRunAfter cleanPackageDir
2004 dependsOn cleanPackageDir
2007 outputs.dir("${jalviewDir}/${package_dir}")
2012 dependsOn cleanPackageDir
2019 group = "distribution"
2020 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2024 from ("${jalviewDir}/${libDistDir}") {
2028 attributes "Implementation-Version": JALVIEW_VERSION,
2029 "Application-Name": applicationName
2032 duplicatesStrategy "INCLUDE"
2034 mainClassName = shadow_jar_main_class
2036 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2040 task getdownImagesCopy() {
2041 inputs.dir getdownImagesDir
2042 outputs.dir getdownImagesBuildDir
2046 from(getdownImagesDir) {
2047 include("*getdown*.png")
2049 into getdownImagesBuildDir
2054 task getdownImagesProcess() {
2055 dependsOn getdownImagesCopy
2058 if (backgroundImageText) {
2059 if (convertBinary == null) {
2060 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2062 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2063 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2065 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2067 executable convertBinary
2070 '-font', getdown_background_image_text_font,
2071 '-fill', getdown_background_image_text_colour,
2072 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2073 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2074 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2083 task getdownImages() {
2084 dependsOn getdownImagesProcess
2087 task getdownWebsite() {
2088 group = "distribution"
2089 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2091 dependsOn getdownImages
2096 def getdownWebsiteResourceFilenames = []
2097 def getdownResourceDir = getdownResourceDir
2098 def getdownResourceFilenames = []
2101 // clean the getdown website and files dir before creating getdown folders
2102 delete getdownAppBaseDir
2103 delete getdownFilesDir
2106 from buildProperties
2107 rename(file(buildProperties).getName(), getdown_build_properties)
2110 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2113 from channelPropsFile
2114 filter(ReplaceTokens,
2118 'SUFFIX': channelSuffix
2121 into getdownAppBaseDir
2123 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2125 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2126 def props = project.properties.sort { it.key }
2127 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2128 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2130 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2131 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2133 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2134 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2136 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2137 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2138 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2139 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2140 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2141 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2142 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2145 props.put("getdown_txt_title", jalview_name)
2146 props.put("getdown_txt_ui.name", applicationName)
2148 // start with appbase
2149 getdownTextLines += "appbase = ${getdownAppBase}"
2150 props.each{ prop, val ->
2151 if (prop.startsWith("getdown_txt_") && val != null) {
2152 if (prop.startsWith("getdown_txt_multi_")) {
2153 def key = prop.substring(18)
2154 val.split(",").each{ v ->
2155 def line = "${key} = ${v}"
2156 getdownTextLines += line
2159 // file values rationalised
2160 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2162 if (val.indexOf('/') == 0) {
2165 } else if (val.indexOf('/') > 0) {
2166 // relative path (relative to jalviewDir)
2167 r = file( "${jalviewDir}/${val}" )
2170 val = "${getdown_resource_dir}/" + r.getName()
2171 getdownWebsiteResourceFilenames += val
2172 getdownResourceFilenames += r.getPath()
2175 if (! prop.startsWith("getdown_txt_resource")) {
2176 def line = prop.substring(12) + " = ${val}"
2177 getdownTextLines += line
2183 getdownWebsiteResourceFilenames.each{ filename ->
2184 getdownTextLines += "resource = ${filename}"
2186 getdownResourceFilenames.each{ filename ->
2189 into getdownResourceDir
2193 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2194 getdownWrapperScripts.each{ script ->
2195 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2199 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2201 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2206 fileTree(file(package_dir)).each{ f ->
2207 if (f.isDirectory()) {
2208 def files = fileTree(dir: f, include: ["*"]).getFiles()
2210 } else if (f.exists()) {
2214 def jalviewJar = jar.archiveFileName.getOrNull()
2215 // put jalview.jar first for CLASSPATH and .properties files reasons
2216 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2217 def name = f.getName()
2218 def line = "code = ${getdownAppDistDir}/${name}"
2219 getdownTextLines += line
2226 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2228 if (JAVA_VERSION.equals("11")) {
2229 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2230 j11libFiles.sort().each{f ->
2231 def name = f.getName()
2232 def line = "code = ${getdown_j11lib_dir}/${name}"
2233 getdownTextLines += line
2236 into getdownJ11libDir
2242 // 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.
2243 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2244 getdownTextLines += "resource = ${getdown_launcher_new}"
2245 getdownTextLines += "class = ${main_class}"
2246 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2247 if (getdownSetAppBaseProperty) {
2248 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2249 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2252 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2253 getdownTxt.write(getdownTextLines.join("\n"))
2255 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2256 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2257 launchJvl.write("appbase=${getdownAppBase}")
2259 // files going into the getdown website dir: getdown-launcher.jar
2261 from getdownLauncher
2262 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2263 into getdownAppBaseDir
2266 // files going into the getdown website dir: getdown-launcher(-local).jar
2268 from getdownLauncher
2269 if (file(getdownLauncher).getName() != getdown_launcher) {
2270 rename(file(getdownLauncher).getName(), getdown_launcher)
2272 into getdownAppBaseDir
2275 // files going into the getdown website dir: ./install dir and files
2276 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2279 from getdownLauncher
2280 from "${getdownAppDir}/${getdown_build_properties}"
2281 if (file(getdownLauncher).getName() != getdown_launcher) {
2282 rename(file(getdownLauncher).getName(), getdown_launcher)
2284 into getdownInstallDir
2287 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2289 from getdownInstallDir
2290 into getdownFilesInstallDir
2294 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2298 from getdownLauncher
2299 from "${getdownAppBaseDir}/${getdown_build_properties}"
2300 from "${getdownAppBaseDir}/${channel_props}"
2301 if (file(getdownLauncher).getName() != getdown_launcher) {
2302 rename(file(getdownLauncher).getName(), getdown_launcher)
2304 into getdownFilesDir
2307 // and ./resource (not all downloaded by getdown)
2309 from getdownResourceDir
2310 into "${getdownFilesDir}/${getdown_resource_dir}"
2315 inputs.dir("${jalviewDir}/${package_dir}")
2317 outputs.dir(getdownAppBaseDir)
2318 outputs.dir(getdownFilesDir)
2322 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2323 task getdownDigestDir(type: JavaExec) {
2325 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2327 def digestDirPropertyName = "DIGESTDIR"
2329 classpath = files(getdownLauncher)
2330 def digestDir = findProperty(digestDirPropertyName)
2331 if (digestDir == null) {
2332 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2336 main = "com.threerings.getdown.tools.Digester"
2340 task getdownDigest(type: JavaExec) {
2341 group = "distribution"
2342 description = "Digest the getdown website folder"
2343 dependsOn getdownWebsite
2345 classpath = files(getdownLauncher)
2347 main = "com.threerings.getdown.tools.Digester"
2348 args getdownAppBaseDir
2349 inputs.dir(getdownAppBaseDir)
2350 outputs.file("${getdownAppBaseDir}/digest2.txt")
2355 group = "distribution"
2356 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2357 dependsOn getdownDigest
2359 if (reportRsyncCommand) {
2360 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2361 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2362 println "LIKELY RSYNC COMMAND:"
2363 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2364 if (RUNRSYNC == "true") {
2366 commandLine "mkdir", "-p", toDir
2369 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2377 task getdownArchiveBuild() {
2378 group = "distribution"
2379 description = "Put files in the archive dir to go on the website"
2381 dependsOn getdownWebsite
2383 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2384 def vDir = "${getdownArchiveDir}/${v}"
2385 getdownFullArchiveDir = "${vDir}/getdown"
2386 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2388 def vAltDir = "alt_${v}"
2389 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2392 // cleanup old "old" dir
2393 delete getdownArchiveDir
2395 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2396 getdownArchiveTxt.getParentFile().mkdirs()
2397 def getdownArchiveTextLines = []
2398 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2402 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2403 into "${getdownFullArchiveDir}/${vAltDir}"
2406 getdownTextLines.each { line ->
2407 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2408 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2409 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2410 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2411 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2412 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2413 // remove the existing resource = resource/ or bin/ lines
2414 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2415 getdownArchiveTextLines += line
2419 // the resource dir -- add these files as resource lines in getdown.txt
2421 from "${archiveImagesDir}"
2422 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2424 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2428 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2430 def vLaunchJvl = file(getdownVersionLaunchJvl)
2431 vLaunchJvl.getParentFile().mkdirs()
2432 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2433 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2434 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2435 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2436 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2437 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2439 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2441 from getdownLauncher
2442 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2443 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2444 from "${getdownAppBaseDir}/${channel_props}"
2445 if (file(getdownLauncher).getName() != getdown_launcher) {
2446 rename(file(getdownLauncher).getName(), getdown_launcher)
2448 into getdownFullArchiveDir
2454 task getdownArchiveDigest(type: JavaExec) {
2455 group = "distribution"
2456 description = "Digest the getdown archive folder"
2458 dependsOn getdownArchiveBuild
2461 classpath = files(getdownLauncher)
2462 args getdownFullArchiveDir
2464 main = "com.threerings.getdown.tools.Digester"
2465 inputs.dir(getdownFullArchiveDir)
2466 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2469 task getdownArchive() {
2470 group = "distribution"
2471 description = "Build the website archive dir with getdown digest"
2473 dependsOn getdownArchiveBuild
2474 dependsOn getdownArchiveDigest
2477 tasks.withType(JavaCompile) {
2478 options.encoding = 'UTF-8'
2484 delete getdownAppBaseDir
2485 delete getdownFilesDir
2486 delete getdownArchiveDir
2492 if (file(install4jHomeDir).exists()) {
2494 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2495 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2496 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2497 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2499 installDir(file(install4jHomeDir))
2501 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2505 task copyInstall4jTemplate {
2506 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2507 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2508 inputs.file(install4jTemplateFile)
2509 inputs.file(install4jFileAssociationsFile)
2510 inputs.property("CHANNEL", { CHANNEL })
2511 outputs.file(install4jConfFile)
2514 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2516 // turn off code signing if no OSX_KEYPASS
2517 if (OSX_KEYPASS == "") {
2518 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2519 codeSigning.'@macEnabled' = "false"
2521 install4jConfigXml.'**'.windows.each { windows ->
2522 windows.'@runPostProcessor' = "false"
2526 // disable install screen for OSX dmg (for 2.11.2.0)
2527 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2528 macosArchive.attributes().remove('executeSetupApp')
2529 macosArchive.attributes().remove('setupAppId')
2532 // turn off checksum creation for LOCAL channel
2533 def e = install4jConfigXml.application[0]
2534 e.'@createChecksums' = string(install4jCheckSums)
2536 // put file association actions where placeholder action is
2537 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2538 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2539 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2540 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2541 def parent = a.parent()
2543 fileAssociationActions.each { faa ->
2546 // don't need to continue in .any loop once replacements have been made
2551 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2552 // NB we're deleting the /other/ one!
2553 // Also remove the examples subdir from non-release versions
2554 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2555 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2556 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2557 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2559 // remove the examples subdir from Full File Set
2560 def files = install4jConfigXml.files[0]
2561 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2562 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2563 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2564 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2565 dirEntry.parent().remove(dirEntry)
2567 install4jConfigXml.'**'.action.any { a ->
2568 if (a.'@customizedId' == customizedIdToDelete) {
2569 def parent = a.parent()
2575 // write install4j file
2576 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2583 delete install4jConfFile
2587 task cleanInstallersDataFiles {
2588 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2589 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2590 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2592 delete installersOutputTxt
2593 delete installersSha256
2594 delete hugoDataJsonFile
2598 task install4jDMGBackgroundImageCopy {
2599 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2600 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2603 from(install4jDMGBackgroundImageDir) {
2604 include(install4jDMGBackgroundImageFile)
2606 into install4jDMGBackgroundImageBuildDir
2611 task install4jDMGBackgroundImageProcess {
2612 dependsOn install4jDMGBackgroundImageCopy
2615 if (backgroundImageText) {
2616 if (convertBinary == null) {
2617 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2619 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2620 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2622 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2624 executable convertBinary
2627 '-font', install4j_background_image_text_font,
2628 '-fill', install4j_background_image_text_colour,
2629 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2630 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2631 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2640 task install4jDMGBackgroundImage {
2641 dependsOn install4jDMGBackgroundImageProcess
2644 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2645 group = "distribution"
2646 description = "Create the install4j installers"
2648 dependsOn copyInstall4jTemplate
2649 dependsOn cleanInstallersDataFiles
2650 dependsOn install4jDMGBackgroundImage
2652 projectFile = install4jConfFile
2654 // create an md5 for the input files to use as version for install4j conf file
2655 def digest = MessageDigest.getInstance("MD5")
2657 (file("${install4jDir}/${install4j_template}").text +
2658 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2659 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2660 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2661 if (filesMd5.length() >= 8) {
2662 filesMd5 = filesMd5.substring(0,8)
2664 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2667 'JALVIEW_NAME': jalview_name,
2668 'JALVIEW_APPLICATION_NAME': applicationName,
2669 'JALVIEW_DIR': "../..",
2670 'OSX_KEYSTORE': OSX_KEYSTORE,
2671 'OSX_APPLEID': OSX_APPLEID,
2672 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2673 'JSIGN_SH': JSIGN_SH,
2674 'JRE_DIR': getdown_app_dir_java,
2675 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2676 'JALVIEW_VERSION': JALVIEW_VERSION,
2677 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2678 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2679 'JAVA_VERSION': JAVA_VERSION,
2680 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2681 'VERSION': JALVIEW_VERSION,
2682 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2683 'BUNDLE_ID': install4jBundleId,
2684 'INTERNAL_ID': install4jInternalId,
2685 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2686 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2687 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2688 'WRAPPER_LINK': getdownWrapperLink,
2689 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2690 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2691 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2692 'INSTALLER_NAME': install4jInstallerName,
2693 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2694 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2695 'GETDOWN_FILES_DIR': getdown_files_dir,
2696 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2697 'GETDOWN_DIST_DIR': getdownAppDistDir,
2698 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2699 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2700 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2701 'BUILD_DIR': install4jBuildDir,
2702 'APPLICATION_CATEGORIES': install4j_application_categories,
2703 'APPLICATION_FOLDER': install4jApplicationFolder,
2704 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2705 'EXECUTABLE_NAME': install4jExecutableName,
2706 'EXTRA_SCHEME': install4jExtraScheme,
2707 'MAC_ICONS_FILE': install4jMacIconsFile,
2708 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2709 'PNG_ICON_FILE': install4jPngIconFile,
2710 'BACKGROUND': install4jBackground,
2715 'windows': 'WINDOWS',
2719 // these are the bundled OS/architecture VMs needed by install4j
2722 [ "mac", "aarch64" ],
2723 [ "windows", "x64" ],
2725 [ "linux", "aarch64" ]
2727 osArch.forEach { os, arch ->
2728 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)
2729 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2730 // otherwise running `gradle installers` generates a non-useful error:
2731 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2732 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)
2735 //println("INSTALL4J VARIABLES:")
2736 //variables.each{k,v->println("${k}=${v}")}
2738 destination = "${jalviewDir}/${install4jBuildDir}"
2739 buildSelected = true
2741 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2743 disableSigning = true
2744 disableNotarization = true
2748 macKeystorePassword = OSX_KEYPASS
2751 if (OSX_ALTOOLPASS) {
2752 appleIdPassword = OSX_ALTOOLPASS
2753 disableNotarization = false
2755 disableNotarization = true
2759 println("Using projectFile "+projectFile)
2760 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2764 inputs.dir(getdownAppBaseDir)
2765 inputs.file(install4jConfFile)
2766 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2767 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2770 def getDataHash(File myFile) {
2771 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2772 return myFile.exists()
2774 "file" : myFile.getName(),
2775 "filesize" : myFile.length(),
2776 "sha256" : hash.toString()
2781 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2783 "channel" : getdownChannelName,
2784 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2785 "git-commit" : "${gitHash} [${gitBranch}]",
2786 "version" : JALVIEW_VERSION
2788 // install4j installer files
2789 if (installersOutputTxt.exists()) {
2791 installersOutputTxt.readLines().each { def line ->
2792 if (line.startsWith("#")) {
2795 line.replaceAll("\n","")
2796 def vals = line.split("\t")
2797 def filename = vals[3]
2798 def filesize = file(filename).length()
2799 filename = filename.replaceAll(/^.*\//, "")
2800 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2801 idHash."${filename}" = vals[0]
2803 if (install4jCheckSums && installersSha256.exists()) {
2804 installersSha256.readLines().each { def line ->
2805 if (line.startsWith("#")) {
2808 line.replaceAll("\n","")
2809 def vals = line.split(/\s+\*?/)
2810 def filename = vals[1]
2811 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2817 "JAR": shadowJar.archiveFile, // executable JAR
2818 "JVL": getdownVersionLaunchJvl, // version JVL
2819 "SOURCE": sourceDist.archiveFile // source TGZ
2820 ].each { key, value ->
2821 def file = file(value)
2822 if (file.exists()) {
2823 def fileHash = getDataHash(file)
2824 if (fileHash != null) {
2825 hash."${key}" = fileHash;
2829 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2832 task staticMakeInstallersJsonFile {
2834 def output = findProperty("i4j_output")
2835 def sha256 = findProperty("i4j_sha256")
2836 def json = findProperty("i4j_json")
2837 if (output == null || sha256 == null || json == null) {
2838 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2840 writeDataJsonFile(file(output), file(sha256), file(json))
2845 dependsOn installerFiles
2851 eclipse().configFile(eclipse_codestyle_file)
2855 task createSourceReleaseProperties(type: WriteProperties) {
2856 group = "distribution"
2857 description = "Create the source RELEASE properties file"
2859 def sourceTarBuildDir = "${buildDir}/sourceTar"
2860 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2861 outputFile (sourceReleasePropertiesFile)
2864 releaseProps.each{ key, val -> property key, val }
2865 property "git.branch", gitBranch
2866 property "git.hash", gitHash
2869 outputs.file(outputFile)
2872 task sourceDist(type: Tar) {
2873 group "distribution"
2874 description "Create a source .tar.gz file for distribution"
2876 dependsOn createBuildProperties
2877 dependsOn convertMdFiles
2878 dependsOn eclipseAllPreferences
2879 dependsOn createSourceReleaseProperties
2882 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2883 archiveFileName = outputFileName
2885 compression Compression.GZIP
2900 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2902 "utils/InstallAnywhere",
2917 "gradle.properties",
2929 ".settings/org.eclipse.buildship.core.prefs",
2930 ".settings/org.eclipse.jdt.core.prefs"
2934 exclude (EXCLUDE_FILES)
2935 include (PROCESS_FILES)
2936 filter(ReplaceTokens,
2940 'Version-Rel': JALVIEW_VERSION,
2941 'Year-Rel': getDate("yyyy")
2946 exclude (EXCLUDE_FILES)
2947 exclude (PROCESS_FILES)
2948 exclude ("appletlib")
2949 exclude ("**/*locales")
2950 exclude ("*locales/**")
2951 exclude ("utils/InstallAnywhere")
2953 exclude (getdown_files_dir)
2954 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2955 //exclude (getdown_website_dir)
2956 //exclude (getdown_archive_dir)
2958 // exluding these as not using jars as modules yet
2959 exclude ("${j11modDir}/**/*.jar")
2962 include(INCLUDE_FILES)
2964 // from (jalviewDir) {
2965 // // explicit includes for stuff that seemed to not get included
2966 // include(fileTree("test/**/*."))
2967 // exclude(EXCLUDE_FILES)
2968 // exclude(PROCESS_FILES)
2971 from(file(buildProperties).getParent()) {
2972 include(file(buildProperties).getName())
2973 rename(file(buildProperties).getName(), "build_properties")
2975 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2979 def sourceTarBuildDir = "${buildDir}/sourceTar"
2980 from(sourceTarBuildDir) {
2981 // this includes the appended RELEASE properties file
2985 task dataInstallersJson {
2987 description "Create the installers-VERSION.json data file for installer files created"
2989 mustRunAfter installers
2990 mustRunAfter shadowJar
2991 mustRunAfter sourceDist
2992 mustRunAfter getdownArchive
2994 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2995 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2997 if (installersOutputTxt.exists()) {
2998 inputs.file(installersOutputTxt)
3000 if (install4jCheckSums && installersSha256.exists()) {
3001 inputs.file(installersSha256)
3004 shadowJar.archiveFile, // executable JAR
3005 getdownVersionLaunchJvl, // version JVL
3006 sourceDist.archiveFile // source TGZ
3007 ].each { fileName ->
3008 if (file(fileName).exists()) {
3009 inputs.file(fileName)
3013 outputs.file(hugoDataJsonFile)
3016 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3022 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3025 dependsOn pubhtmlhelp
3027 inputs.dir("${helpBuildDir}/${help_dir}")
3028 outputs.dir("${buildDir}/distributions/${help_dir}")
3032 task j2sSetHeadlessBuild {
3039 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3041 description "Enable the alternative J2S Config file for headless build"
3043 outputFile = jalviewjsJ2sSettingsFileName
3044 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3045 def j2sProps = new Properties()
3046 if (j2sPropsFile.exists()) {
3048 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3049 j2sProps.load(j2sPropsFileFIS)
3050 j2sPropsFileFIS.close()
3052 j2sProps.each { prop, val ->
3055 } catch (Exception e) {
3056 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3060 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3061 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3066 task jalviewjsSetEclipseWorkspace {
3067 def propKey = "jalviewjs_eclipse_workspace"
3069 if (project.hasProperty(propKey)) {
3070 propVal = project.getProperty(propKey)
3071 if (propVal.startsWith("~/")) {
3072 propVal = System.getProperty("user.home") + propVal.substring(1)
3075 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3076 def propsFile = file(propsFileName)
3077 def eclipseWsDir = propVal
3078 def props = new Properties()
3080 def writeProps = true
3081 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3082 def ins = new FileInputStream(propsFileName)
3085 if (props.getProperty(propKey, null) != null) {
3086 eclipseWsDir = props.getProperty(propKey)
3091 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3092 def tempDir = File.createTempDir()
3093 eclipseWsDir = tempDir.getAbsolutePath()
3096 eclipseWorkspace = file(eclipseWsDir)
3099 // do not run a headless transpile when we claim to be in Eclipse
3101 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3102 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3104 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3108 props.setProperty(propKey, eclipseWsDir)
3109 propsFile.parentFile.mkdirs()
3110 def bytes = new ByteArrayOutputStream()
3111 props.store(bytes, null)
3112 def propertiesString = bytes.toString()
3113 propsFile.text = propertiesString
3119 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3122 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3123 outputs.file(propsFileName)
3124 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3128 task jalviewjsEclipsePaths {
3131 def eclipseRoot = jalviewjs_eclipse_root
3132 if (eclipseRoot.startsWith("~/")) {
3133 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3135 if (OperatingSystem.current().isMacOsX()) {
3136 eclipseRoot += "/Eclipse.app"
3137 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3138 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3139 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3140 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3141 eclipseRoot += "/eclipse"
3143 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3144 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3145 } else { // linux or unix
3146 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3147 eclipseRoot += "/eclipse"
3148 println("eclipseDir exists")
3150 eclipseBinary = "${eclipseRoot}/eclipse"
3151 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3154 eclipseVersion = "4.13" // default
3155 def assumedVersion = true
3156 if (file(eclipseProduct).exists()) {
3157 def fis = new FileInputStream(eclipseProduct)
3158 def props = new Properties()
3160 eclipseVersion = props.getProperty("version")
3162 assumedVersion = false
3165 def propKey = "eclipse_debug"
3166 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3169 // do not run a headless transpile when we claim to be in Eclipse
3171 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3172 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3174 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3177 if (!assumedVersion) {
3178 println("ECLIPSE VERSION=${eclipseVersion}")
3184 task printProperties {
3186 description "Output to console all System.properties"
3188 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3194 dependsOn eclipseProject
3195 dependsOn eclipseClasspath
3196 dependsOn eclipseJdt
3200 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3201 task jalviewjsEclipseCopyDropins(type: Copy) {
3202 dependsOn jalviewjsEclipsePaths
3204 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3205 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3206 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3213 // this eclipse -clean doesn't actually work
3214 task jalviewjsCleanEclipse(type: Exec) {
3215 dependsOn eclipseSetup
3216 dependsOn jalviewjsEclipsePaths
3217 dependsOn jalviewjsEclipseCopyDropins
3219 executable(eclipseBinary)
3220 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3226 def inputString = """exit
3229 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3230 standardInput = inputByteStream
3233 /* not really working yet
3234 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3238 task jalviewjsTransferUnzipSwingJs {
3239 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3243 from zipTree(file_zip)
3244 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3248 inputs.file file_zip
3249 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3253 task jalviewjsTransferUnzipLib {
3254 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3257 zipFiles.each { file_zip ->
3259 from zipTree(file_zip)
3260 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3265 inputs.files zipFiles
3266 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3270 task jalviewjsTransferUnzipAllLibs {
3271 dependsOn jalviewjsTransferUnzipSwingJs
3272 dependsOn jalviewjsTransferUnzipLib
3276 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3278 description "Create the alternative j2s file from the j2s.* properties"
3280 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3281 def siteDirProperty = "j2s.site.directory"
3282 def setSiteDir = false
3283 jalviewjsJ2sProps.each { prop, val ->
3285 if (prop == siteDirProperty) {
3286 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3287 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3293 if (!setSiteDir) { // default site location, don't override specifically set property
3294 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3297 outputFile = jalviewjsJ2sAltSettingsFileName
3300 inputs.properties(jalviewjsJ2sProps)
3301 outputs.file(jalviewjsJ2sAltSettingsFileName)
3306 task jalviewjsEclipseSetup {
3307 dependsOn jalviewjsEclipseCopyDropins
3308 dependsOn jalviewjsSetEclipseWorkspace
3309 dependsOn jalviewjsCreateJ2sSettings
3313 task jalviewjsSyncAllLibs (type: Sync) {
3314 dependsOn jalviewjsTransferUnzipAllLibs
3315 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3316 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3317 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3321 def outputFiles = []
3322 rename { filename ->
3323 outputFiles += "${outputDir}/${filename}"
3330 // should this be exclude really ?
3331 duplicatesStrategy "INCLUDE"
3333 outputs.files outputFiles
3334 inputs.files inputFiles
3338 task jalviewjsSyncResources (type: Sync) {
3339 dependsOn buildResources
3341 def inputFiles = fileTree(dir: resourcesBuildDir)
3342 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3346 def outputFiles = []
3347 rename { filename ->
3348 outputFiles += "${outputDir}/${filename}"
3354 outputs.files outputFiles
3355 inputs.files inputFiles
3359 task jalviewjsSyncSiteResources (type: Sync) {
3360 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3361 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3365 def outputFiles = []
3366 rename { filename ->
3367 outputFiles += "${outputDir}/${filename}"
3373 outputs.files outputFiles
3374 inputs.files inputFiles
3378 task jalviewjsSyncBuildProperties (type: Sync) {
3379 dependsOn createBuildProperties
3380 def inputFiles = [file(buildProperties)]
3381 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3385 def outputFiles = []
3386 rename { filename ->
3387 outputFiles += "${outputDir}/${filename}"
3393 outputs.files outputFiles
3394 inputs.files inputFiles
3398 task jalviewjsProjectImport(type: Exec) {
3399 dependsOn eclipseSetup
3400 dependsOn jalviewjsEclipsePaths
3401 dependsOn jalviewjsEclipseSetup
3404 // do not run a headless import when we claim to be in Eclipse
3406 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3407 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3409 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3413 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3414 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3415 executable(eclipseBinary)
3416 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3420 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3422 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3423 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3426 inputs.file("${jalviewDir}/.project")
3427 outputs.upToDateWhen {
3428 file(projdir).exists()
3433 task jalviewjsTranspile(type: Exec) {
3434 dependsOn jalviewjsEclipseSetup
3435 dependsOn jalviewjsProjectImport
3436 dependsOn jalviewjsEclipsePaths
3438 dependsOn jalviewjsEnableAltFileProperty
3442 // do not run a headless transpile when we claim to be in Eclipse
3444 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3445 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3447 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3451 executable(eclipseBinary)
3452 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3456 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3458 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3459 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3465 stdout = new ByteArrayOutputStream()
3466 stderr = new ByteArrayOutputStream()
3468 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3469 def logOutFile = file(logOutFileName)
3470 logOutFile.createNewFile()
3471 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3472 BINARY: ${eclipseBinary}
3473 VERSION: ${eclipseVersion}
3474 WORKSPACE: ${eclipseWorkspace}
3475 DEBUG: ${eclipseDebug}
3478 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3479 // combine stdout and stderr
3480 def logErrFOS = logOutFOS
3482 if (jalviewjs_j2s_to_console.equals("true")) {
3483 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3484 new org.apache.tools.ant.util.TeeOutputStream(
3488 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3489 new org.apache.tools.ant.util.TeeOutputStream(
3494 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3497 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3504 if (stdout.toString().contains("Error processing ")) {
3505 // j2s did not complete transpile
3506 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3507 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3508 println("IGNORING TRANSPILE ERRORS")
3509 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3511 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3516 inputs.dir("${jalviewDir}/${sourceDir}")
3517 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3518 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3522 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3524 def stdout = new ByteArrayOutputStream()
3525 def stderr = new ByteArrayOutputStream()
3527 def coreFile = file(jsfile)
3529 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3531 logOutFile.createNewFile()
3532 logOutFile.append(msg+"\n")
3534 def coreTop = file(prefixFile)
3535 def coreBottom = file(suffixFile)
3536 coreFile.getParentFile().mkdirs()
3537 coreFile.createNewFile()
3538 coreFile.write( coreTop.getText("UTF-8") )
3542 def t = f.getText("UTF-8")
3543 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3544 coreFile.append( t )
3546 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3548 logOutFile.append(msg+"\n")
3551 coreFile.append( coreBottom.getText("UTF-8") )
3553 msg = "Generating ${zjsfile}"
3555 logOutFile.append(msg+"\n")
3556 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3557 def logErrFOS = logOutFOS
3560 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3561 main = "com.google.javascript.jscomp.CommandLineRunner"
3562 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3563 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3566 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3568 logOutFile.append(msg+"\n")
3570 if (logOutConsole) {
3571 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3572 new org.apache.tools.ant.util.TeeOutputStream(
3576 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3577 new org.apache.tools.ant.util.TeeOutputStream(
3582 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3585 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3592 logOutFile.append(msg+"\n")
3596 task jalviewjsBuildAllCores {
3598 description "Build the core js lib closures listed in the classlists dir"
3599 dependsOn jalviewjsTranspile
3600 dependsOn jalviewjsTransferUnzipSwingJs
3602 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3603 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3604 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3605 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3606 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3607 def prefixFile = "${jsDir}/core/coretop2.js"
3608 def suffixFile = "${jsDir}/core/corebottom2.js"
3610 inputs.file prefixFile
3611 inputs.file suffixFile
3613 def classlistFiles = []
3614 // add the classlists found int the jalviewjs_classlists_dir
3615 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3617 def name = file.getName() - ".txt"
3624 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3625 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3626 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3628 jalviewjsCoreClasslists = []
3630 classlistFiles.each {
3633 def file = hash['file']
3634 if (! file.exists()) {
3635 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3636 return false // this is a "continue" in groovy .each closure
3638 def name = hash['name']
3640 name = file.getName() - ".txt"
3648 def list = fileTree(dir: j2sDir, includes: filelist)
3650 def jsfile = "${outputDir}/core${name}.js"
3651 def zjsfile = "${outputDir}/core${name}.z.js"
3653 jalviewjsCoreClasslists += [
3662 outputs.file(jsfile)
3663 outputs.file(zjsfile)
3666 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3667 def stevesoftClasslistName = "_stevesoft"
3668 def stevesoftClasslist = [
3669 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3670 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3671 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3672 'name': stevesoftClasslistName
3674 jalviewjsCoreClasslists += stevesoftClasslist
3675 inputs.files(stevesoftClasslist['list'])
3676 outputs.file(stevesoftClasslist['jsfile'])
3677 outputs.file(stevesoftClasslist['zjsfile'])
3680 def allClasslistName = "_all"
3681 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3682 allJsFiles += fileTree(
3686 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3687 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3688 "**/org/jmol/export/JSExporter.js"
3691 allJsFiles += fileTree(
3695 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3696 "**/sun/misc/Unsafe.js",
3697 "**/swingjs/jquery/jquery-editable-select.js",
3698 "**/swingjs/jquery/j2sComboBox.js",
3699 "**/sun/misc/FloatingDecimal.js"
3702 def allClasslist = [
3703 'jsfile': "${outputDir}/core${allClasslistName}.js",
3704 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3706 'name': allClasslistName
3708 // not including this version of "all" core at the moment
3709 //jalviewjsCoreClasslists += allClasslist
3710 inputs.files(allClasslist['list'])
3711 outputs.file(allClasslist['jsfile'])
3712 outputs.file(allClasslist['zjsfile'])
3715 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3716 logOutFile.getParentFile().mkdirs()
3717 logOutFile.createNewFile()
3718 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3720 jalviewjsCoreClasslists.each {
3721 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3728 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3731 into file(outputFile).getParentFile()
3732 rename { filename ->
3733 if (filename.equals(inputFile.getName())) {
3734 return file(outputFile).getName()
3738 filter(ReplaceTokens,
3742 'MAIN': '"'+main_class+'"',
3744 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3745 'COREKEY': jalviewjs_core_key,
3746 'CORENAME': coreName
3753 task jalviewjsPublishCoreTemplates {
3754 dependsOn jalviewjsBuildAllCores
3755 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3756 def inputFile = file(inputFileName)
3757 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3759 def outputFiles = []
3760 jalviewjsCoreClasslists.each { cl ->
3761 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3762 cl['outputfile'] = outputFile
3763 outputFiles += outputFile
3767 jalviewjsCoreClasslists.each { cl ->
3768 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3771 inputs.file(inputFile)
3772 outputs.files(outputFiles)
3776 task jalviewjsSyncCore (type: Sync) {
3777 dependsOn jalviewjsBuildAllCores
3778 dependsOn jalviewjsPublishCoreTemplates
3779 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3780 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3784 def outputFiles = []
3785 rename { filename ->
3786 outputFiles += "${outputDir}/${filename}"
3792 outputs.files outputFiles
3793 inputs.files inputFiles
3797 // this Copy version of TransferSiteJs will delete anything else in the target dir
3798 task jalviewjsCopyTransferSiteJs(type: Copy) {
3799 dependsOn jalviewjsTranspile
3800 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3801 into "${jalviewDir}/${jalviewjsSiteDir}"
3805 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3806 task jalviewjsSyncTransferSiteJs(type: Sync) {
3807 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3809 into "${jalviewDir}/${jalviewjsSiteDir}"
3816 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3817 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3818 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3819 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3821 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3822 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3823 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3824 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3827 task jalviewjsPrepareSite {
3829 description "Prepares the website folder including unzipping files and copying resources"
3830 dependsOn jalviewjsSyncAllLibs
3831 dependsOn jalviewjsSyncResources
3832 dependsOn jalviewjsSyncSiteResources
3833 dependsOn jalviewjsSyncBuildProperties
3834 dependsOn jalviewjsSyncCore
3838 task jalviewjsBuildSite {
3840 description "Builds the whole website including transpiled code"
3841 dependsOn jalviewjsCopyTransferSiteJs
3842 dependsOn jalviewjsPrepareSite
3846 task cleanJalviewjsTransferSite {
3848 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3849 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3850 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3851 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3856 task cleanJalviewjsSite {
3857 dependsOn cleanJalviewjsTransferSite
3859 delete "${jalviewDir}/${jalviewjsSiteDir}"
3864 task jalviewjsSiteTar(type: Tar) {
3866 description "Creates a tar.gz file for the website"
3867 dependsOn jalviewjsBuildSite
3868 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3869 archiveFileName = outputFilename
3871 compression Compression.GZIP
3873 from "${jalviewDir}/${jalviewjsSiteDir}"
3874 into jalviewjs_site_dir // this is inside the tar file
3876 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3880 task jalviewjsServer {
3882 def filename = "jalviewjsTest.html"
3883 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3884 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3889 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3890 factory = f.newInstance()
3891 } catch (ClassNotFoundException e) {
3892 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3894 def port = Integer.valueOf(jalviewjs_server_port)
3899 while(port < start+1000 && !running) {
3901 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3902 jalviewjsServer = factory.start(doc_root, port)
3904 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3905 println("SERVER STARTED with document root ${doc_root}.")
3906 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3907 println("For debug: "+url+"?j2sdebug")
3908 println("For verbose: "+url+"?j2sverbose")
3909 } catch (Exception e) {
3914 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3915 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3916 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3918 jalviewjsCoreClasslists.each { cl ->
3919 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3921 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3923 println("For core ${cl.name}: "+urlcore)
3926 file(htmlFile).text = htmlText
3929 outputs.file(htmlFile)
3930 outputs.upToDateWhen({false})
3934 task cleanJalviewjsAll {
3936 description "Delete all configuration and build artifacts to do with JalviewJS build"
3937 dependsOn cleanJalviewjsSite
3938 dependsOn jalviewjsEclipsePaths
3941 delete "${jalviewDir}/${jalviewjsBuildDir}"
3942 delete "${jalviewDir}/${eclipse_bin_dir}"
3943 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3944 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3946 delete jalviewjsJ2sAltSettingsFileName
3949 outputs.upToDateWhen( { false } )
3953 task jalviewjsIDE_checkJ2sPlugin {
3954 group "00 JalviewJS in Eclipse"
3955 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3958 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3959 def j2sPluginFile = file(j2sPlugin)
3960 def eclipseHome = System.properties["eclipse.home.location"]
3961 if (eclipseHome == null || ! IN_ECLIPSE) {
3962 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3964 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3965 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3966 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3967 eclipseJ2sPluginDirs += altPluginsDir
3969 def foundPlugin = false
3970 def j2sPluginFileName = j2sPluginFile.getName()
3971 def eclipseJ2sPlugin
3972 def eclipseJ2sPluginFile
3973 eclipseJ2sPluginDirs.any { dir ->
3974 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3975 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3976 if (eclipseJ2sPluginFile.exists()) {
3982 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3983 System.err.println(msg)
3984 throw new StopExecutionException(msg)
3987 def digest = MessageDigest.getInstance("MD5")
3989 digest.update(j2sPluginFile.text.bytes)
3990 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3992 digest.update(eclipseJ2sPluginFile.text.bytes)
3993 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3995 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3996 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3997 System.err.println(msg)
3998 throw new StopExecutionException(msg)
4000 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4006 task jalviewjsIDE_copyJ2sPlugin {
4007 group "00 JalviewJS in Eclipse"
4008 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4011 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4012 def j2sPluginFile = file(j2sPlugin)
4013 def eclipseHome = System.properties["eclipse.home.location"]
4014 if (eclipseHome == null || ! IN_ECLIPSE) {
4015 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4017 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4018 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4019 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4020 System.err.println(msg)
4023 eclipseJ2sPluginFile.getParentFile().mkdirs()
4024 into eclipseJ2sPluginFile.getParent()
4030 task jalviewjsIDE_j2sFile {
4031 group "00 JalviewJS in Eclipse"
4032 description "Creates the .j2s file"
4033 dependsOn jalviewjsCreateJ2sSettings
4037 task jalviewjsIDE_SyncCore {
4038 group "00 JalviewJS in Eclipse"
4039 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4040 dependsOn jalviewjsSyncCore
4044 task jalviewjsIDE_SyncSiteAll {
4045 dependsOn jalviewjsSyncAllLibs
4046 dependsOn jalviewjsSyncResources
4047 dependsOn jalviewjsSyncSiteResources
4048 dependsOn jalviewjsSyncBuildProperties
4052 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4055 task jalviewjsIDE_PrepareSite {
4056 group "00 JalviewJS in Eclipse"
4057 description "Sync libs and resources to site dir, but not closure cores"
4059 dependsOn jalviewjsIDE_SyncSiteAll
4060 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4064 task jalviewjsIDE_AssembleSite {
4065 group "00 JalviewJS in Eclipse"
4066 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4067 dependsOn jalviewjsPrepareSite
4071 task jalviewjsIDE_SiteClean {
4072 group "00 JalviewJS in Eclipse"
4073 description "Deletes the Eclipse transpiled site"
4074 dependsOn cleanJalviewjsSite
4078 task jalviewjsIDE_Server {
4079 group "00 JalviewJS in Eclipse"
4080 description "Starts a webserver on localhost to test the website"
4081 dependsOn jalviewjsServer
4085 // buildship runs this at import or gradle refresh
4086 task eclipseSynchronizationTask {
4087 //dependsOn eclipseSetup
4088 dependsOn createBuildProperties
4090 dependsOn jalviewjsIDE_j2sFile
4091 dependsOn jalviewjsIDE_checkJ2sPlugin
4092 dependsOn jalviewjsIDE_PrepareSite
4097 // buildship runs this at build time or project refresh
4098 task eclipseAutoBuildTask {
4099 //dependsOn jalviewjsIDE_checkJ2sPlugin
4100 //dependsOn jalviewjsIDE_PrepareSite
4106 description "Build the site"
4107 dependsOn jalviewjsBuildSite