1 /* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
2 * For properties set within build.gradle, use camelCaseNoSpace.
4 import org.apache.tools.ant.filters.ReplaceTokens
5 import org.gradle.internal.os.OperatingSystem
6 import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
7 import org.gradle.api.internal.PropertiesTransformer
8 import org.gradle.util.ConfigureUtil
9 import org.gradle.plugins.ide.eclipse.model.Output
10 import org.gradle.plugins.ide.eclipse.model.Library
11 import java.security.MessageDigest
12 import java.util.regex.Matcher
13 import groovy.transform.ExternalizeMethods
14 import groovy.util.XmlParser
15 import groovy.xml.XmlUtil
16 import groovy.json.JsonBuilder
17 import com.vladsch.flexmark.util.ast.Node
18 import com.vladsch.flexmark.html.HtmlRenderer
19 import com.vladsch.flexmark.parser.Parser
20 import com.vladsch.flexmark.util.data.MutableDataSet
21 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
22 import com.vladsch.flexmark.ext.tables.TablesExtension
23 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
24 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
25 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
26 import com.vladsch.flexmark.ext.toc.TocExtension
27 import com.google.common.hash.HashCode
28 import com.google.common.hash.Hashing
29 import com.google.common.io.Files
30 import org.jsoup.Jsoup
31 import org.jsoup.nodes.Element
39 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
40 classpath "org.jsoup:jsoup:1.14.3"
41 classpath "com.eowise:gradle-imagemagick:0.5.1"
50 id "com.diffplug.gradle.spotless" version "3.28.0"
51 id 'com.github.johnrengelman.shadow' version '4.0.3'
52 id 'com.install4j.gradle' version '10.0.3'
53 id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
54 id 'com.palantir.git-version' version '0.13.0' apply false
65 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
66 def string(Object o) {
67 return o == null ? "" : o.toString()
70 def overrideProperties(String propsFileName, boolean output = false) {
71 if (propsFileName == null) {
74 def propsFile = file(propsFileName)
75 if (propsFile != null && propsFile.exists()) {
76 println("Using properties from file '${propsFileName}'")
78 def p = new Properties()
79 def localPropsFIS = new FileInputStream(propsFile)
85 if (project.hasProperty(key)) {
86 oldval = project.findProperty(key)
87 project.setProperty(key, val)
89 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
92 ext.setProperty(key, val)
94 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
98 } catch (Exception e) {
99 println("Exception reading local.properties")
106 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
107 jalviewDirRelativePath = jalviewDir
110 getdownChannelName = CHANNEL.toLowerCase()
111 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
112 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
113 channelDirName = propertiesChannelName
114 // Import channel_properties
115 if (getdownChannelName.startsWith("develop-")) {
116 channelDirName = "develop-SUFFIX"
118 channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
119 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
120 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
121 overrideProperties(channelGradleProperties, false)
122 // local build environment properties
123 // can be "projectDir/local.properties"
124 overrideProperties("${projectDir}/local.properties", true)
125 // or "../projectDir_local.properties"
126 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
129 // Import releaseProps from the RELEASE file
130 // or a file specified via JALVIEW_RELEASE_FILE if defined
131 // Expect jalview.version and target release branch in jalview.release
132 releaseProps = new Properties();
133 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
134 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
136 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
137 releaseProps.load(it)
139 } catch (Exception fileLoadError) {
140 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
143 // Set JALVIEW_VERSION if it is not already set
144 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
145 JALVIEW_VERSION = releaseProps.get("jalview.version")
147 println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
149 // this property set when running Eclipse headlessly
150 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
151 // this property set by Eclipse
152 eclipseApplicationProperty = string("eclipse.application")
153 // CHECK IF RUNNING FROM WITHIN ECLIPSE
154 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
155 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
156 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
157 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
158 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
162 println("WITHIN ECLIPSE IDE")
164 println("HEADLESS BUILD")
167 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
169 println("J2S ENABLED")
172 System.properties.sort { it.key }.each {
173 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
176 if (false && IN_ECLIPSE) {
177 jalviewDir = jalviewDirAbsolutePath
182 buildDate = new Date().format("yyyyMMdd")
185 bareSourceDir = string(source_dir)
186 sourceDir = string("${jalviewDir}/${bareSourceDir}")
187 resourceDir = string("${jalviewDir}/${resource_dir}")
188 bareTestSourceDir = string(test_source_dir)
189 testDir = string("${jalviewDir}/${bareTestSourceDir}")
191 classesDir = string("${jalviewDir}/${classes_dir}")
194 useClover = clover.equals("true")
195 cloverBuildDir = "${buildDir}/clover"
196 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
197 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
198 cloverReportDir = file("${buildDir}/reports/clover")
199 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
200 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
201 //cloverTestClassesDir = cloverClassesDir
202 cloverDb = string("${cloverBuildDir}/clover.db")
204 testSourceDir = useClover ? cloverTestInstrDir : testDir
205 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
208 backgroundImageText = BACKGROUNDIMAGETEXT
209 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
210 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
211 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
212 getdownFullArchiveDir = null
213 getdownTextLines = []
214 getdownLaunchJvl = null
215 getdownVersionLaunchJvl = null
217 buildProperties = null
219 // the following values might be overridden by the CHANNEL switch
220 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
221 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
222 getdownArchiveAppBase = getdown_archive_base
223 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
224 getdownAppDistDir = getdown_app_dir_alt
225 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
226 getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
227 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
228 reportRsyncCommand = false
229 jvlChannelName = CHANNEL.toLowerCase()
230 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
231 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
232 install4jDMGBackgroundImageDir = "${install4j_images_dir}"
233 install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
234 install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
235 install4jInstallerName = "${jalview_name} Non-Release Installer"
236 install4jExecutableName = install4j_executable_name
237 install4jExtraScheme = "jalviewx"
238 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
239 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
240 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
241 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
242 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
243 install4jCheckSums = true
245 applicationName = "${jalview_name}"
249 // TODO: get bamboo build artifact URL for getdown artifacts
250 getdown_channel_base = bamboo_channelbase
251 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
252 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
253 jvlChannelName += "_${getdownChannelName}"
254 // automatically add the test group Not-bamboo for exclusion
255 if ("".equals(testng_excluded_groups)) {
256 testng_excluded_groups = "Not-bamboo"
258 install4jExtraScheme = "jalviewb"
259 backgroundImageText = true
262 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
263 getdownAppDistDir = getdown_app_dir_release
264 getdownSetAppBaseProperty = true
265 reportRsyncCommand = true
267 install4jInstallerName = "${jalview_name} Installer"
271 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
272 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
273 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
274 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
275 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
277 package_dir = string("${ARCHIVEDIR}/${package_dir}")
278 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
281 reportRsyncCommand = true
282 install4jExtraScheme = "jalviewa"
286 getdownChannelName = string("archive/${JALVIEW_VERSION}")
287 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
288 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
289 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
290 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
292 package_dir = string("${ARCHIVEDIR}/${package_dir}")
293 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
296 reportRsyncCommand = true
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
298 install4jSuffix = "Archive"
299 install4jExtraScheme = "jalviewa"
302 case ~/^DEVELOP-([\.\-\w]*)$/:
303 def suffix = Matcher.lastMatcher[0][1]
304 reportRsyncCommand = true
305 getdownSetAppBaseProperty = true
306 JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
307 install4jSuffix = "Develop ${suffix}"
308 install4jExtraScheme = "jalviewd"
309 install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
310 getdownChannelName = string("develop-${suffix}")
311 getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
312 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
313 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
314 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
315 channelSuffix = string(suffix)
316 backgroundImageText = true
320 reportRsyncCommand = true
321 getdownSetAppBaseProperty = true
322 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
323 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
325 install4jSuffix = "Develop"
326 install4jExtraScheme = "jalviewd"
327 install4jInstallerName = "${jalview_name} Develop Installer"
328 backgroundImageText = true
332 reportRsyncCommand = true
333 getdownSetAppBaseProperty = true
334 // Don't ignore transpile errors for release build
335 if (jalviewjs_ignore_transpile_errors.equals("true")) {
336 jalviewjs_ignore_transpile_errors = "false"
337 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
339 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
340 install4jSuffix = "Test"
341 install4jExtraScheme = "jalviewt"
342 install4jInstallerName = "${jalview_name} Test Installer"
343 backgroundImageText = true
346 case ~/^SCRATCH(|-[-\w]*)$/:
347 getdownChannelName = CHANNEL
348 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
350 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
351 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
352 reportRsyncCommand = true
353 install4jSuffix = "Scratch"
357 if (!file("${LOCALDIR}").exists()) {
358 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
360 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
361 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
363 JALVIEW_VERSION = "TEST"
364 install4jSuffix = "Test-Local"
365 install4jExtraScheme = "jalviewt"
366 install4jInstallerName = "${jalview_name} Test Installer"
367 backgroundImageText = true
370 case [ "LOCAL", "JALVIEWJS" ]:
371 JALVIEW_VERSION = "TEST"
372 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
373 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
374 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
375 install4jExtraScheme = "jalviewl"
376 install4jCheckSums = false
379 default: // something wrong specified
380 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
384 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
385 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
386 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
387 // override getdownAppBase if requested
388 if (findProperty("getdown_appbase_override") != null) {
389 // revert to LOCAL if empty string
390 if (string(getdown_appbase_override) == "") {
391 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
392 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
393 } else if (string(getdown_appbase_override).startsWith("file://")) {
394 getdownAppBase = string(getdown_appbase_override)
395 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
397 getdownAppBase = string(getdown_appbase_override)
399 println("Overriding getdown appbase with '${getdownAppBase}'")
401 // sanitise file name for jalview launcher file for this channel
402 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
403 // install4j application and folder names
404 if (install4jSuffix == "") {
405 install4jBundleId = "${install4j_bundle_id}"
406 install4jWinApplicationId = install4j_release_win_application_id
408 applicationName = "${jalview_name} ${install4jSuffix}"
409 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
410 // add int hash of install4jSuffix to the last part of the application_id
411 def id = install4j_release_win_application_id
412 def idsplitreverse = id.split("-").reverse()
413 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
414 install4jWinApplicationId = idsplitreverse.reverse().join("-")
416 // sanitise folder and id names
417 // install4jApplicationFolder = e.g. "Jalview Build"
418 install4jApplicationFolder = applicationName
419 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
420 .replaceAll("_+", "_") // collapse __
421 install4jInternalId = applicationName
423 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
424 .replaceAll("_+", "") // collapse __
425 //.replaceAll("_*-_*", "-") // collapse _-_
426 install4jUnixApplicationFolder = applicationName
428 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
429 .replaceAll("_+", "_") // collapse __
430 .replaceAll("_*-_*", "-") // collapse _-_
433 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
434 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
435 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
436 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
437 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
438 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
439 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
440 /* compile without modules -- using classpath libraries
441 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
442 modules_runtimeClasspath = modules_compileClasspath
448 apply plugin: "com.palantir.git-version"
449 def details = versionDetails()
450 gitHash = details.gitHash
451 gitBranch = details.branchName
452 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
453 println("Not in a git repository. Using git values from RELEASE properties file.")
454 gitHash = releaseProps.getProperty("git.hash")
455 gitBranch = releaseProps.getProperty("git.branch")
456 } catch(java.lang.RuntimeException e1) {
457 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
460 println("Using a ${CHANNEL} profile.")
462 additional_compiler_args = []
463 // configure classpath/args for j8/j11 compilation
464 if (JAVA_VERSION.equals("1.8")) {
465 JAVA_INTEGER_VERSION = string("8")
468 libDistDir = j8libDir
469 compile_source_compatibility = 1.8
470 compile_target_compatibility = 1.8
471 // these are getdown.txt properties defined dependent on the JAVA_VERSION
472 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
473 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
474 // this property is assigned below and expanded to multiple lines in the getdown task
475 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
476 // this property is for the Java library used in eclipse
477 eclipseJavaRuntimeName = string("JavaSE-1.8")
478 } else if (JAVA_VERSION.equals("11")) {
479 JAVA_INTEGER_VERSION = string("11")
481 libDistDir = j11libDir
482 compile_source_compatibility = 11
483 compile_target_compatibility = 11
484 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
485 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
486 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
487 eclipseJavaRuntimeName = string("JavaSE-11")
488 /* compile without modules -- using classpath libraries
489 additional_compiler_args += [
490 '--module-path', modules_compileClasspath.asPath,
491 '--add-modules', j11modules
494 } else if (JAVA_VERSION.equals("17")) {
495 JAVA_INTEGER_VERSION = string("17")
497 libDistDir = j17libDir
498 compile_source_compatibility = 17
499 compile_target_compatibility = 17
500 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
501 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
502 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
503 eclipseJavaRuntimeName = string("JavaSE-17")
504 /* compile without modules -- using classpath libraries
505 additional_compiler_args += [
506 '--module-path', modules_compileClasspath.asPath,
507 '--add-modules', j11modules
511 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
516 JAVA_MIN_VERSION = JAVA_VERSION
517 JAVA_MAX_VERSION = JAVA_VERSION
518 jreInstallsDir = string(jre_installs_dir)
519 if (jreInstallsDir.startsWith("~/")) {
520 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
522 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
523 install4jConfFileName = string("jalview-install4j-conf.install4j")
524 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
525 install4jHomeDir = install4j_home_dir
526 if (install4jHomeDir.startsWith("~/")) {
527 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
530 resourceBuildDir = string("${buildDir}/resources")
531 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
532 helpBuildDir = string("${resourceBuildDir}/help_build")
533 docBuildDir = string("${resourceBuildDir}/doc_build")
535 if (buildProperties == null) {
536 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
538 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
539 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
540 helpSourceDir = string("${helpParentDir}/${help_dir}")
541 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
544 convertBinaryExpectedLocation = imagemagick_convert
545 if (convertBinaryExpectedLocation.startsWith("~/")) {
546 convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
548 if (file(convertBinaryExpectedLocation).exists()) {
549 convertBinary = convertBinaryExpectedLocation
552 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
553 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
554 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
556 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
558 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
560 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
561 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
562 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
563 jalviewjsJalviewCoreHtmlFile = string("")
564 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
565 jalviewjsCoreClasslists = []
566 jalviewjsJalviewTemplateName = string(jalviewjs_name)
567 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
568 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
569 jalviewjsJ2sProps = null
570 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
572 eclipseWorkspace = null
573 eclipseBinary = string("")
574 eclipseVersion = string("")
584 outputDir = file(classesDir)
588 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
591 compileClasspath = files(sourceSets.main.java.outputDir)
592 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
594 runtimeClasspath = compileClasspath
595 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
600 srcDirs cloverInstrDir
601 outputDir = cloverClassesDir
605 srcDirs = sourceSets.main.resources.srcDirs
608 compileClasspath = files( sourceSets.clover.java.outputDir )
609 //compileClasspath += files( testClassesDir )
610 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
611 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
612 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
614 runtimeClasspath = compileClasspath
619 srcDirs testSourceDir
620 outputDir = file(testClassesDir)
624 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
627 compileClasspath = files( sourceSets.test.java.outputDir )
628 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
629 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
631 runtimeClasspath = compileClasspath
632 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
638 // eclipse project and settings files creation, also used by buildship
641 name = eclipse_project_name
643 natures 'org.eclipse.jdt.core.javanature',
644 'org.eclipse.jdt.groovy.core.groovyNature',
645 'org.eclipse.buildship.core.gradleprojectnature'
647 buildCommand 'org.eclipse.jdt.core.javabuilder'
648 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
652 //defaultOutputDir = sourceSets.main.java.outputDir
653 configurations.each{ c->
654 if (c.isCanBeResolved()) {
655 minusConfigurations += [c]
659 plusConfigurations = [ ]
663 def removeTheseToo = []
664 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
665 cp.entries.each { entry ->
666 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
667 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
668 // we add the resources and help/help dirs in as libs afterwards (see below)
669 if (entry.kind == 'src') {
670 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
671 removeTheseToo += entry
673 alreadyAddedSrcPath.putAt(entry.path, true)
678 cp.entries.removeAll(removeTheseToo)
680 //cp.entries += new Output("${eclipse_bin_dir}/main")
681 if (file(helpParentDir).isDirectory()) {
682 cp.entries += new Library(fileReference(helpParentDir))
684 if (file(resourceDir).isDirectory()) {
685 cp.entries += new Library(fileReference(resourceDir))
688 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
690 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
691 //don't want to add outputDir as eclipse is using its own output dir in bin/main
692 if (it.isDirectory() || ! it.exists()) {
693 // don't add dirs to classpath, especially if they don't exist
694 return false // groovy "continue" in .any closure
696 def itPath = it.toString()
697 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
698 // make relative path
699 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
701 if (alreadyAddedLibPath.get(itPath)) {
702 //println("Not adding duplicate entry "+itPath)
704 //println("Adding entry "+itPath)
705 cp.entries += new Library(fileReference(itPath))
706 alreadyAddedLibPath.put(itPath, true)
710 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
711 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
712 if (it.isDirectory() || ! it.exists()) {
713 // don't add dirs to classpath
714 return false // groovy "continue" in .any closure
717 def itPath = it.toString()
718 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
719 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
721 if (alreadyAddedLibPath.get(itPath)) {
724 def lib = new Library(fileReference(itPath))
725 lib.entryAttributes["test"] = "true"
727 alreadyAddedLibPath.put(itPath, true)
735 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
740 // for the IDE, use java 11 compatibility
741 sourceCompatibility = compile_source_compatibility
742 targetCompatibility = compile_target_compatibility
743 javaRuntimeName = eclipseJavaRuntimeName
745 // add in jalview project specific properties/preferences into eclipse core preferences
747 withProperties { props ->
748 def jalview_prefs = new Properties()
749 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
750 jalview_prefs.load(ins)
752 jalview_prefs.forEach { t, v ->
753 if (props.getAt(t) == null) {
757 // codestyle file -- overrides previous formatter prefs
758 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
759 if (csFile.exists()) {
760 XmlParser parser = new XmlParser()
761 def profiles = parser.parse(csFile)
762 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
763 if (profile != null) {
764 profile.'setting'.each { s ->
766 def value = s.'@value'
767 if (id != null && value != null) {
768 props.putAt(id, value)
779 // Don't want these to be activated if in headless build
780 synchronizationTasks "eclipseSynchronizationTask"
781 //autoBuildTasks "eclipseAutoBuildTask"
787 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
788 // Class to allow updating arbitrary properties files
789 class PropertiesFile extends PropertiesPersistableConfigurationObject {
790 public PropertiesFile(PropertiesTransformer t) { super(t); }
791 @Override protected void load(Properties properties) { }
792 @Override protected void store(Properties properties) { }
793 @Override protected String getDefaultResourceName() { return ""; }
794 // This is necessary, because PropertiesPersistableConfigurationObject fails
795 // if no default properties file exists.
796 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
799 // Task to update arbitrary properties files (set outputFile)
800 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
801 private final PropertiesFileContentMerger file;
802 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
803 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
804 protected void configure(PropertiesFile props) {
805 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
807 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
810 task eclipseUIPreferences(type: PropertiesFileTask) {
811 description = "Generate Eclipse additional settings"
812 def filename = "org.eclipse.jdt.ui.prefs"
813 outputFile = "$projectDir/.settings/${filename}" as File
816 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
821 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
822 description = "Generate Eclipse additional settings"
823 def filename = "org.eclipse.jdt.groovy.core.prefs"
824 outputFile = "$projectDir/.settings/${filename}" as File
827 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
832 task eclipseAllPreferences {
834 dependsOn eclipseUIPreferences
835 dependsOn eclipseGroovyCorePreferences
838 eclipseUIPreferences.mustRunAfter eclipseJdt
839 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
841 /* end of eclipse preferences hack */
849 delete cloverBuildDir
850 delete cloverReportDir
855 task cloverInstrJava(type: JavaExec) {
856 group = "Verification"
857 description = "Create clover instrumented source java files"
859 dependsOn cleanClover
861 inputs.files(sourceSets.main.allJava)
862 outputs.dir(cloverInstrDir)
864 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
865 classpath = sourceSets.clover.compileClasspath
866 main = "com.atlassian.clover.CloverInstr"
874 cloverInstrDir.getPath(),
876 def srcFiles = sourceSets.main.allJava.files
879 { file -> file.absolutePath }
882 args argsList.toArray()
885 delete cloverInstrDir
886 println("Clover: About to instrument "+srcFiles.size() +" files")
891 task cloverInstrTests(type: JavaExec) {
892 group = "Verification"
893 description = "Create clover instrumented source test files"
895 dependsOn cleanClover
897 inputs.files(testDir)
898 outputs.dir(cloverTestInstrDir)
900 classpath = sourceSets.clover.compileClasspath
901 main = "com.atlassian.clover.CloverInstr"
911 cloverTestInstrDir.getPath(),
913 args argsList.toArray()
916 delete cloverTestInstrDir
917 println("Clover: About to instrument test files")
923 group = "Verification"
924 description = "Create clover instrumented all source files"
926 dependsOn cloverInstrJava
927 dependsOn cloverInstrTests
931 cloverClasses.dependsOn cloverInstr
934 task cloverConsoleReport(type: JavaExec) {
935 group = "Verification"
936 description = "Creates clover console report"
939 file(cloverDb).exists()
942 inputs.dir cloverClassesDir
944 classpath = sourceSets.clover.runtimeClasspath
945 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
947 if (cloverreport_mem.length() > 0) {
948 maxHeapSize = cloverreport_mem
950 if (cloverreport_jvmargs.length() > 0) {
951 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
961 args argsList.toArray()
965 task cloverHtmlReport(type: JavaExec) {
966 group = "Verification"
967 description = "Creates clover HTML report"
970 file(cloverDb).exists()
973 def cloverHtmlDir = cloverReportDir
974 inputs.dir cloverClassesDir
975 outputs.dir cloverHtmlDir
977 classpath = sourceSets.clover.runtimeClasspath
978 main = "com.atlassian.clover.reporters.html.HtmlReporter"
980 if (cloverreport_mem.length() > 0) {
981 maxHeapSize = cloverreport_mem
983 if (cloverreport_jvmargs.length() > 0) {
984 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
995 if (cloverreport_html_options.length() > 0) {
996 argsList += cloverreport_html_options.split(" ")
999 args argsList.toArray()
1003 task cloverXmlReport(type: JavaExec) {
1004 group = "Verification"
1005 description = "Creates clover XML report"
1008 file(cloverDb).exists()
1011 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1012 inputs.dir cloverClassesDir
1013 outputs.file cloverXmlFile
1015 classpath = sourceSets.clover.runtimeClasspath
1016 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1018 if (cloverreport_mem.length() > 0) {
1019 maxHeapSize = cloverreport_mem
1021 if (cloverreport_jvmargs.length() > 0) {
1022 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1033 if (cloverreport_xml_options.length() > 0) {
1034 argsList += cloverreport_xml_options.split(" ")
1037 args argsList.toArray()
1042 group = "Verification"
1043 description = "Creates clover reports"
1045 dependsOn cloverXmlReport
1046 dependsOn cloverHtmlReport
1053 sourceCompatibility = compile_source_compatibility
1054 targetCompatibility = compile_target_compatibility
1055 options.compilerArgs += additional_compiler_args
1056 print ("Setting target compatibility to "+targetCompatibility+"\n")
1058 //classpath += configurations.cloverRuntime
1064 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1065 sourceCompatibility = compile_source_compatibility
1066 targetCompatibility = compile_target_compatibility
1067 options.compilerArgs = additional_compiler_args
1068 options.encoding = "UTF-8"
1070 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1077 sourceCompatibility = compile_source_compatibility
1078 targetCompatibility = compile_target_compatibility
1079 options.compilerArgs = additional_compiler_args
1081 print ("Setting target compatibility to "+targetCompatibility+"\n")
1088 delete sourceSets.main.java.outputDir
1094 dependsOn cleanClover
1096 delete sourceSets.test.java.outputDir
1101 // format is a string like date.format("dd MMMM yyyy")
1102 def getDate(format) {
1103 return date.format(format)
1107 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1108 MutableDataSet options = new MutableDataSet()
1110 def extensions = new ArrayList<>()
1111 extensions.add(AnchorLinkExtension.create())
1112 extensions.add(AutolinkExtension.create())
1113 extensions.add(StrikethroughExtension.create())
1114 extensions.add(TaskListExtension.create())
1115 extensions.add(TablesExtension.create())
1116 extensions.add(TocExtension.create())
1118 options.set(Parser.EXTENSIONS, extensions)
1120 // set GFM table parsing options
1121 options.set(TablesExtension.WITH_CAPTION, false)
1122 options.set(TablesExtension.COLUMN_SPANS, false)
1123 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1124 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1125 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1126 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1127 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1129 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1130 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1131 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1132 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1134 Parser parser = Parser.builder(options).build()
1135 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1137 mdFiles.each { mdFile ->
1138 // add table of contents
1139 def mdText = "[TOC]\n"+mdFile.text
1141 // grab the first top-level title
1143 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1144 def matcher = mdText =~ titleRegex
1145 if (matcher.size() > 0) {
1146 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1147 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1149 // or use the filename if none found
1150 if (title == null) {
1151 title = mdFile.getName()
1154 Node document = parser.parse(mdText)
1155 String htmlBody = renderer.render(document)
1156 def htmlText = '''<html>
1157 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1158 <html xmlns="http://www.w3.org/1999/xhtml">
1160 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1161 <meta http-equiv="Content-Style-Type" content="text/css" />
1162 <meta name="generator" content="flexmark" />
1164 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1166 <style type="text/css">code{white-space: pre;}</style>
1168 htmlText += ((cssFile != null) ? cssFile.text : '')
1169 htmlText += '''</head>
1172 htmlText += htmlBody
1178 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1179 def htmlFile = file(htmlFilePath)
1180 println("Creating ${htmlFilePath}")
1181 htmlFile.text = htmlText
1186 task copyDocs(type: Copy) {
1187 def inputDir = "${jalviewDir}/${doc_dir}"
1188 def outputDir = "${docBuildDir}/${doc_dir}"
1192 include('**/*.html')
1194 filter(ReplaceTokens,
1198 'Version-Rel': JALVIEW_VERSION,
1199 'Year-Rel': getDate("yyyy")
1206 exclude('**/*.html')
1211 inputs.dir(inputDir)
1212 outputs.dir(outputDir)
1216 task convertMdFiles {
1218 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1219 def cssFile = file("${jalviewDir}/${flexmark_css}")
1222 convertMdToHtml(mdFiles, cssFile)
1225 inputs.files(mdFiles)
1226 inputs.file(cssFile)
1229 mdFiles.each { mdFile ->
1230 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1231 htmlFiles.add(file(htmlFilePath))
1233 outputs.files(htmlFiles)
1237 def hugoTemplateSubstitutions(String input, Map extras=null) {
1238 def replacements = [
1239 DATE: getDate("yyyy-MM-dd"),
1240 CHANNEL: propertiesChannelName,
1241 APPLICATION_NAME: applicationName,
1243 GIT_BRANCH: gitBranch,
1244 VERSION: JALVIEW_VERSION,
1245 JAVA_VERSION: JAVA_VERSION,
1246 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1251 if (extras != null) {
1252 extras.each{ k, v ->
1253 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1256 replacements.each{ k, v ->
1257 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1262 def mdFileComponents(File mdFile, def dateOnly=false) {
1265 if (mdFile.exists()) {
1266 def inFrontMatter = false
1267 def firstLine = true
1268 mdFile.eachLine { line ->
1269 if (line.matches("---")) {
1270 def prev = inFrontMatter
1271 inFrontMatter = firstLine
1272 if (inFrontMatter != prev)
1275 if (inFrontMatter) {
1277 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1278 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1279 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1280 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1281 } else if (m = line =~ /^channel:\s*(\S+)/) {
1282 map["channel"] = m[0][1]
1283 } else if (m = line =~ /^version:\s*(\S+)/) {
1284 map["version"] = m[0][1]
1285 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1286 map[ m[0][1] ] = m[0][2]
1288 if (dateOnly && map["date"] != null) {
1294 content += line+"\n"
1299 return dateOnly ? map["date"] : [map, content]
1302 task hugoTemplates {
1304 description "Create partially populated md pages for hugo website build"
1306 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1307 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1308 def templateFiles = fileTree(dir: hugoTemplatesDir)
1309 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1310 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1311 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1312 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1315 // specific release template for version archive
1318 def givenDate = null
1319 def givenChannel = null
1320 def givenVersion = null
1321 if (CHANNEL == "RELEASE") {
1322 def (map, content) = mdFileComponents(releaseMdFile)
1323 givenDate = map.date
1324 givenChannel = map.channel
1325 givenVersion = map.version
1327 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1328 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1331 if (whatsnewMdFile.exists())
1332 whatsnew = whatsnewMdFile.text
1335 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1336 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1338 def changesHugo = null
1339 if (changes != null) {
1340 changesHugo = '<div class="release_notes">\n\n'
1341 def inSection = false
1342 changes.eachLine { line ->
1344 if (m = line =~ /^##([^#].*)$/) {
1346 changesHugo += "</div>\n\n"
1348 def section = m[0][1].trim()
1349 section = section.toLowerCase()
1350 section = section.replaceAll(/ +/, "_")
1351 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1352 changesHugo += "<div class=\"${section}\">\n\n"
1354 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1355 def comment = m[0][2].trim()
1356 if (comment != "") {
1357 comment = comment.replaceAll('"', """)
1359 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1360 def newline = m[0][1]
1361 if (comment.trim() != "")
1362 newline += "{{<comment>}}${comment}{{</comment>}} "
1363 newline += m[0][3].trim()
1364 if (issuekeys.size() > 0)
1365 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1366 if (m[0][4] != null)
1371 changesHugo += line+"\n"
1374 changesHugo += "\n</div>\n\n"
1376 changesHugo += '</div>'
1379 templateFiles.each{ templateFile ->
1380 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1381 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1382 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1384 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1388 rename(templateFile.getName(), newFileName)
1392 def newFile = file("${outPathName}/${newFileName}".toString())
1393 def content = newFile.text
1394 newFile.text = hugoTemplateSubstitutions(content,
1397 CHANGES: changesHugo,
1398 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1399 DRAFT: givenDate == null ? "true" : "false",
1400 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1401 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1408 inputs.file(oldJvlFile)
1409 inputs.dir(hugoTemplatesDir)
1410 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1411 inputs.property("CHANNEL", { CHANNEL })
1414 def getMdDate(File mdFile) {
1415 return mdFileComponents(mdFile, true)
1418 def getMdSections(String content) {
1420 def sectionContent = ""
1421 def sectionName = null
1422 content.eachLine { line ->
1424 if (m = line =~ /^##([^#].*)$/) {
1425 if (sectionName != null) {
1426 sections[sectionName] = sectionContent
1430 sectionName = m[0][1].trim()
1431 sectionName = sectionName.toLowerCase()
1432 sectionName = sectionName.replaceAll(/ +/, "_")
1433 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1434 } else if (sectionName != null) {
1435 sectionContent += line+"\n"
1438 if (sectionContent != null) {
1439 sections[sectionName] = sectionContent
1445 task copyHelp(type: Copy) {
1446 def inputDir = helpSourceDir
1447 def outputDir = "${helpBuildDir}/${help_dir}"
1451 include('**/*.html')
1455 filter(ReplaceTokens,
1459 'Version-Rel': JALVIEW_VERSION,
1460 'Year-Rel': getDate("yyyy")
1467 exclude('**/*.html')
1474 inputs.dir(inputDir)
1475 outputs.files(helpFile)
1476 outputs.dir(outputDir)
1480 task releasesTemplates {
1482 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1486 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1487 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1488 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1489 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1490 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1491 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1494 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1495 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1497 if (CHANNEL == "RELEASE") {
1498 if (!releaseMdFile.exists()) {
1499 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1501 if (!whatsnewMdFile.exists()) {
1502 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1506 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1507 def releaseFilesDates = releaseFiles.collectEntries {
1508 [(it): getMdDate(it)]
1510 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1512 def releasesTemplate = releasesTemplateFile.text
1513 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1514 def versionTemplate = m[0][1]
1516 MutableDataSet options = new MutableDataSet()
1518 def extensions = new ArrayList<>()
1519 options.set(Parser.EXTENSIONS, extensions)
1520 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1522 Parser parser = Parser.builder(options).build()
1523 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1525 def actualVersions = releaseFiles.collect { rf ->
1526 def (rfMap, rfContent) = mdFileComponents(rf)
1527 return rfMap.version
1529 def versionsHtml = ""
1530 def linkedVersions = []
1531 releaseFiles.reverse().each { rFile ->
1532 def (rMap, rContent) = mdFileComponents(rFile)
1534 def versionLink = ""
1535 def partialVersion = ""
1536 def firstPart = true
1537 rMap.version.split("\\.").each { part ->
1538 def displayPart = ( firstPart ? "" : "." ) + part
1539 partialVersion += displayPart
1541 linkedVersions.contains(partialVersion)
1542 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1544 versionLink += displayPart
1546 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1547 linkedVersions += partialVersion
1551 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1554 def rContentProcessed = ""
1555 rContent.eachLine { line ->
1556 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1557 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1558 } else if (lm = line =~ /^###([^#]+.*)$/) {
1559 line = "_${lm[0][1].trim()}_"
1561 rContentProcessed += line + "\n"
1564 def rContentSections = getMdSections(rContentProcessed)
1565 def rVersion = versionTemplate
1566 if (rVersion != "") {
1567 def rNewFeatures = rContentSections["new_features"]
1568 def rIssuesResolved = rContentSections["issues_resolved"]
1569 Node newFeaturesNode = parser.parse(rNewFeatures)
1570 String newFeaturesHtml = renderer.render(newFeaturesNode)
1571 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1572 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1573 rVersion = hugoTemplateSubstitutions(rVersion,
1575 VERSION: rMap.version,
1576 VERSION_LINK: versionLink,
1577 DISPLAY_DATE: displayDate,
1578 NEW_FEATURES: newFeaturesHtml,
1579 ISSUES_RESOLVED: issuesResolvedHtml
1582 versionsHtml += rVersion
1586 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1587 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1588 releasesHtmlFile.text = releasesTemplate
1590 if (whatsnewMdFile.exists()) {
1591 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1592 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1593 Node whatsnewNode = parser.parse(whatsnewMd)
1594 String whatsnewHtml = renderer.render(whatsnewNode)
1595 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1596 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1598 VERSION: JALVIEW_VERSION,
1599 DISPLAY_DATE: wnDisplayDate
1602 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1603 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1608 inputs.file(releasesTemplateFile)
1609 inputs.file(whatsnewTemplateFile)
1610 inputs.dir(releasesMdDir)
1611 inputs.dir(whatsnewMdDir)
1612 outputs.file(releasesHtmlFile)
1613 outputs.file(whatsnewHtmlFile)
1617 task copyResources(type: Copy) {
1619 description = "Copy (and make text substitutions in) the resources dir to the build area"
1621 def inputDir = resourceDir
1622 def outputDir = resourcesBuildDir
1626 include('**/*.html')
1628 filter(ReplaceTokens,
1632 'Version-Rel': JALVIEW_VERSION,
1633 'Year-Rel': getDate("yyyy")
1640 exclude('**/*.html')
1645 inputs.dir(inputDir)
1646 outputs.dir(outputDir)
1649 task copyChannelResources(type: Copy) {
1650 dependsOn copyResources
1652 description = "Copy the channel resources dir to the build resources area"
1654 def inputDir = "${channelDir}/${resource_dir}"
1655 def outputDir = resourcesBuildDir
1657 include(channel_props)
1658 filter(ReplaceTokens,
1662 'SUFFIX': channelSuffix
1667 exclude(channel_props)
1671 inputs.dir(inputDir)
1672 outputs.dir(outputDir)
1675 task createBuildProperties(type: WriteProperties) {
1676 dependsOn copyResources
1678 description = "Create the ${buildProperties} file"
1680 inputs.dir(sourceDir)
1681 inputs.dir(resourcesBuildDir)
1682 outputFile (buildProperties)
1683 // taking time specific comment out to allow better incremental builds
1684 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1685 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1686 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1687 property "VERSION", JALVIEW_VERSION
1688 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1689 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1690 if (getdownSetAppBaseProperty) {
1691 property "GETDOWNAPPBASE", getdownAppBase
1692 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1694 outputs.file(outputFile)
1698 task buildIndices(type: JavaExec) {
1700 classpath = sourceSets.main.compileClasspath
1701 main = "com.sun.java.help.search.Indexer"
1702 workingDir = "${helpBuildDir}/${help_dir}"
1705 inputs.dir("${workingDir}/${argDir}")
1707 outputs.dir("${classesDir}/doc")
1708 outputs.dir("${classesDir}/help")
1709 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1710 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1711 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1712 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1713 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1714 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1717 task buildResources {
1718 dependsOn copyResources
1719 dependsOn copyChannelResources
1720 dependsOn createBuildProperties
1724 dependsOn buildResources
1727 dependsOn releasesTemplates
1728 dependsOn convertMdFiles
1729 dependsOn buildIndices
1733 compileJava.dependsOn prepare
1734 run.dependsOn compileJava
1735 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 allprojects { project ->
1773 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1775 // run main tests first
1776 // if (!testTask.name.equals("testTask0"))
1777 // testTask.mustRunAfter testTask0
1779 testTask.testLogging { logging ->
1780 events TestLogEvent.FAILED,
1781 TestLogEvent.SKIPPED,
1782 TestLogEvent.STANDARD_OUT,
1783 TestLogEvent.STANDARD_ERROR
1785 exceptionFormat TestExceptionFormat.FULL
1788 showStackTraces true
1791 ignoreFailures = true // Always try to run all tests for all modules
1793 afterSuite { desc, result ->
1795 if (desc.parent) return // Only summarize results for whole modules
1797 String summary = "${testTask.project.name}:${testTask.name} results: ${result.resultType} " +
1799 "${result.testCount} tests, " +
1800 "${result.successfulTestCount} successes, " +
1801 "${result.failedTestCount} failures, " +
1802 "${result.skippedTestCount} skipped" +
1804 "in ${TimeCategory.minus(new Date(result.endTime), new Date(result.startTime))}" +
1806 "Report file: ${testTask.reports.html.entryPoint}"
1808 // Add reports in `testsResults`, keep failed suites at the end
1809 if (result.resultType == TestResult.ResultType.SUCCESS) {
1810 rootProject.ext.testsResults.add(0, summary)
1812 rootProject.ext.testsResults += summary
1814 if (result.resultType == TestResult.ResultType.FAILURE) {
1819 // from original test task
1821 dependsOn cloverClasses
1823 dependsOn compileJava //?
1825 maxHeapSize = "1024m"
1827 workingDir = jalviewDir
1828 def testLaf = project.findProperty("test_laf")
1829 if (testLaf != null) {
1830 println("Setting Test LaF to '${testLaf}'")
1831 systemProperty "laf", testLaf
1833 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1834 if (testHiDPIScale != null) {
1835 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1836 systemProperty "sun.java2d.uiScale", testHiDPIScale
1838 sourceCompatibility = compile_source_compatibility
1839 targetCompatibility = compile_target_compatibility
1840 jvmArgs += additional_compiler_args
1844 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1851 gradle.buildFinished {
1852 def allResults = rootProject.ext.testsResults
1854 if (!allResults.isEmpty()) {
1855 printResults allResults
1859 private static void printResults(allResults) {
1860 def maxLength = allResults*.readLines().flatten().collect { it.length() }.max()
1862 println "┌${"${"─" * maxLength}"}┐"
1864 println allResults.collect {
1865 it.readLines().collect {
1866 "│" + it + " " * (maxLength - it.length()) + "│"
1868 }.join("\n├${"${"─" * maxLength}"}┤\n")
1870 println "└${"${"─" * maxLength}"}┘"
1872 /* END of test tasks results summary */
1874 task verifyTestStatus {
1877 throw new GradleException("There were failing tests!")
1883 dependsOn tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}
1884 finalizedBy verifyTestStatus
1886 // not running tests in this task
1891 task compileLinkCheck(type: JavaCompile) {
1893 classpath = files("${jalviewDir}/${utils_dir}")
1894 destinationDir = file("${jalviewDir}/${utils_dir}")
1895 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1897 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1898 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1899 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1900 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1904 task linkCheck(type: JavaExec) {
1906 dependsOn compileLinkCheck
1908 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1909 classpath = files("${jalviewDir}/${utils_dir}")
1910 main = "HelpLinksChecker"
1911 workingDir = "${helpBuildDir}"
1912 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1914 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1915 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1918 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1922 inputs.dir(helpBuildDir)
1923 outputs.file(helpLinksCheckerOutFile)
1927 // import the pubhtmlhelp target
1928 ant.properties.basedir = "${jalviewDir}"
1929 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1930 ant.importBuild "${utils_dir}/publishHelp.xml"
1933 task cleanPackageDir(type: Delete) {
1935 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1945 attributes "Main-Class": main_class,
1946 "Permissions": "all-permissions",
1947 "Application-Name": applicationName,
1948 "Codebase": application_codebase,
1949 "Implementation-Version": JALVIEW_VERSION
1952 def outputDir = "${jalviewDir}/${package_dir}"
1953 destinationDirectory = file(outputDir)
1954 archiveFileName = rootProject.name+".jar"
1955 duplicatesStrategy "EXCLUDE"
1962 exclude "**/*.jar.*"
1964 inputs.dir(sourceSets.main.java.outputDir)
1965 sourceSets.main.resources.srcDirs.each{ dir ->
1968 outputs.file("${outputDir}/${archiveFileName}")
1972 task copyJars(type: Copy) {
1973 from fileTree(dir: classesDir, include: "**/*.jar").files
1974 into "${jalviewDir}/${package_dir}"
1978 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1979 task syncJars(type: Sync) {
1981 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1982 into "${jalviewDir}/${package_dir}"
1984 include jar.archiveFileName.getOrNull()
1991 description = "Put all required libraries in dist"
1992 // order of "cleanPackageDir", "copyJars", "jar" important!
1993 jar.mustRunAfter cleanPackageDir
1994 syncJars.mustRunAfter cleanPackageDir
1995 dependsOn cleanPackageDir
1998 outputs.dir("${jalviewDir}/${package_dir}")
2003 dependsOn cleanPackageDir
2010 group = "distribution"
2011 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2015 from ("${jalviewDir}/${libDistDir}") {
2019 attributes "Implementation-Version": JALVIEW_VERSION,
2020 "Application-Name": applicationName
2023 duplicatesStrategy "INCLUDE"
2025 mainClassName = shadow_jar_main_class
2027 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2031 task getdownImagesCopy() {
2032 inputs.dir getdownImagesDir
2033 outputs.dir getdownImagesBuildDir
2037 from(getdownImagesDir) {
2038 include("*getdown*.png")
2040 into getdownImagesBuildDir
2045 task getdownImagesProcess() {
2046 dependsOn getdownImagesCopy
2049 if (backgroundImageText) {
2050 if (convertBinary == null) {
2051 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2053 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2054 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2056 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2058 executable convertBinary
2061 '-font', getdown_background_image_text_font,
2062 '-fill', getdown_background_image_text_colour,
2063 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2064 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2065 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2074 task getdownImages() {
2075 dependsOn getdownImagesProcess
2078 task getdownWebsite() {
2079 group = "distribution"
2080 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2082 dependsOn getdownImages
2087 def getdownWebsiteResourceFilenames = []
2088 def getdownResourceDir = getdownResourceDir
2089 def getdownResourceFilenames = []
2092 // clean the getdown website and files dir before creating getdown folders
2093 delete getdownAppBaseDir
2094 delete getdownFilesDir
2097 from buildProperties
2098 rename(file(buildProperties).getName(), getdown_build_properties)
2101 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2104 from channelPropsFile
2105 filter(ReplaceTokens,
2109 'SUFFIX': channelSuffix
2112 into getdownAppBaseDir
2114 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2116 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2117 def props = project.properties.sort { it.key }
2118 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2119 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2121 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2122 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2124 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2125 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2127 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2128 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2129 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2130 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2131 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2132 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2133 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2136 props.put("getdown_txt_title", jalview_name)
2137 props.put("getdown_txt_ui.name", applicationName)
2139 // start with appbase
2140 getdownTextLines += "appbase = ${getdownAppBase}"
2141 props.each{ prop, val ->
2142 if (prop.startsWith("getdown_txt_") && val != null) {
2143 if (prop.startsWith("getdown_txt_multi_")) {
2144 def key = prop.substring(18)
2145 val.split(",").each{ v ->
2146 def line = "${key} = ${v}"
2147 getdownTextLines += line
2150 // file values rationalised
2151 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2153 if (val.indexOf('/') == 0) {
2156 } else if (val.indexOf('/') > 0) {
2157 // relative path (relative to jalviewDir)
2158 r = file( "${jalviewDir}/${val}" )
2161 val = "${getdown_resource_dir}/" + r.getName()
2162 getdownWebsiteResourceFilenames += val
2163 getdownResourceFilenames += r.getPath()
2166 if (! prop.startsWith("getdown_txt_resource")) {
2167 def line = prop.substring(12) + " = ${val}"
2168 getdownTextLines += line
2174 getdownWebsiteResourceFilenames.each{ filename ->
2175 getdownTextLines += "resource = ${filename}"
2177 getdownResourceFilenames.each{ filename ->
2180 into getdownResourceDir
2184 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2185 getdownWrapperScripts.each{ script ->
2186 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2190 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2192 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2197 fileTree(file(package_dir)).each{ f ->
2198 if (f.isDirectory()) {
2199 def files = fileTree(dir: f, include: ["*"]).getFiles()
2201 } else if (f.exists()) {
2205 def jalviewJar = jar.archiveFileName.getOrNull()
2206 // put jalview.jar first for CLASSPATH and .properties files reasons
2207 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2208 def name = f.getName()
2209 def line = "code = ${getdownAppDistDir}/${name}"
2210 getdownTextLines += line
2217 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2219 if (JAVA_VERSION.equals("11")) {
2220 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2221 j11libFiles.sort().each{f ->
2222 def name = f.getName()
2223 def line = "code = ${getdown_j11lib_dir}/${name}"
2224 getdownTextLines += line
2227 into getdownJ11libDir
2233 // 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.
2234 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2235 getdownTextLines += "resource = ${getdown_launcher_new}"
2236 getdownTextLines += "class = ${main_class}"
2237 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2238 if (getdownSetAppBaseProperty) {
2239 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2240 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2243 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2244 getdownTxt.write(getdownTextLines.join("\n"))
2246 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2247 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2248 launchJvl.write("appbase=${getdownAppBase}")
2250 // files going into the getdown website dir: getdown-launcher.jar
2252 from getdownLauncher
2253 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2254 into getdownAppBaseDir
2257 // files going into the getdown website dir: getdown-launcher(-local).jar
2259 from getdownLauncher
2260 if (file(getdownLauncher).getName() != getdown_launcher) {
2261 rename(file(getdownLauncher).getName(), getdown_launcher)
2263 into getdownAppBaseDir
2266 // files going into the getdown website dir: ./install dir and files
2267 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2270 from getdownLauncher
2271 from "${getdownAppDir}/${getdown_build_properties}"
2272 if (file(getdownLauncher).getName() != getdown_launcher) {
2273 rename(file(getdownLauncher).getName(), getdown_launcher)
2275 into getdownInstallDir
2278 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2280 from getdownInstallDir
2281 into getdownFilesInstallDir
2285 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2289 from getdownLauncher
2290 from "${getdownAppBaseDir}/${getdown_build_properties}"
2291 from "${getdownAppBaseDir}/${channel_props}"
2292 if (file(getdownLauncher).getName() != getdown_launcher) {
2293 rename(file(getdownLauncher).getName(), getdown_launcher)
2295 into getdownFilesDir
2298 // and ./resource (not all downloaded by getdown)
2300 from getdownResourceDir
2301 into "${getdownFilesDir}/${getdown_resource_dir}"
2306 inputs.dir("${jalviewDir}/${package_dir}")
2308 outputs.dir(getdownAppBaseDir)
2309 outputs.dir(getdownFilesDir)
2313 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2314 task getdownDigestDir(type: JavaExec) {
2316 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2318 def digestDirPropertyName = "DIGESTDIR"
2320 classpath = files(getdownLauncher)
2321 def digestDir = findProperty(digestDirPropertyName)
2322 if (digestDir == null) {
2323 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2327 main = "com.threerings.getdown.tools.Digester"
2331 task getdownDigest(type: JavaExec) {
2332 group = "distribution"
2333 description = "Digest the getdown website folder"
2334 dependsOn getdownWebsite
2336 classpath = files(getdownLauncher)
2338 main = "com.threerings.getdown.tools.Digester"
2339 args getdownAppBaseDir
2340 inputs.dir(getdownAppBaseDir)
2341 outputs.file("${getdownAppBaseDir}/digest2.txt")
2346 group = "distribution"
2347 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2348 dependsOn getdownDigest
2350 if (reportRsyncCommand) {
2351 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2352 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2353 println "LIKELY RSYNC COMMAND:"
2354 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2355 if (RUNRSYNC == "true") {
2357 commandLine "mkdir", "-p", toDir
2360 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2368 task getdownArchiveBuild() {
2369 group = "distribution"
2370 description = "Put files in the archive dir to go on the website"
2372 dependsOn getdownWebsite
2374 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2375 def vDir = "${getdownArchiveDir}/${v}"
2376 getdownFullArchiveDir = "${vDir}/getdown"
2377 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2379 def vAltDir = "alt_${v}"
2380 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2383 // cleanup old "old" dir
2384 delete getdownArchiveDir
2386 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2387 getdownArchiveTxt.getParentFile().mkdirs()
2388 def getdownArchiveTextLines = []
2389 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2393 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2394 into "${getdownFullArchiveDir}/${vAltDir}"
2397 getdownTextLines.each { line ->
2398 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2399 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2400 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2401 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2402 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2403 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2404 // remove the existing resource = resource/ or bin/ lines
2405 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2406 getdownArchiveTextLines += line
2410 // the resource dir -- add these files as resource lines in getdown.txt
2412 from "${archiveImagesDir}"
2413 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2415 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2419 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2421 def vLaunchJvl = file(getdownVersionLaunchJvl)
2422 vLaunchJvl.getParentFile().mkdirs()
2423 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2424 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2425 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2426 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2427 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2428 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2430 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2432 from getdownLauncher
2433 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2434 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2435 from "${getdownAppBaseDir}/${channel_props}"
2436 if (file(getdownLauncher).getName() != getdown_launcher) {
2437 rename(file(getdownLauncher).getName(), getdown_launcher)
2439 into getdownFullArchiveDir
2445 task getdownArchiveDigest(type: JavaExec) {
2446 group = "distribution"
2447 description = "Digest the getdown archive folder"
2449 dependsOn getdownArchiveBuild
2452 classpath = files(getdownLauncher)
2453 args getdownFullArchiveDir
2455 main = "com.threerings.getdown.tools.Digester"
2456 inputs.dir(getdownFullArchiveDir)
2457 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2460 task getdownArchive() {
2461 group = "distribution"
2462 description = "Build the website archive dir with getdown digest"
2464 dependsOn getdownArchiveBuild
2465 dependsOn getdownArchiveDigest
2468 tasks.withType(JavaCompile) {
2469 options.encoding = 'UTF-8'
2475 delete getdownAppBaseDir
2476 delete getdownFilesDir
2477 delete getdownArchiveDir
2483 if (file(install4jHomeDir).exists()) {
2485 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2486 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2487 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2488 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2490 installDir(file(install4jHomeDir))
2492 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2496 task copyInstall4jTemplate {
2497 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2498 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2499 inputs.file(install4jTemplateFile)
2500 inputs.file(install4jFileAssociationsFile)
2501 inputs.property("CHANNEL", { CHANNEL })
2502 outputs.file(install4jConfFile)
2505 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2507 // turn off code signing if no OSX_KEYPASS
2508 if (OSX_KEYPASS == "") {
2509 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2510 codeSigning.'@macEnabled' = "false"
2512 install4jConfigXml.'**'.windows.each { windows ->
2513 windows.'@runPostProcessor' = "false"
2517 // disable install screen for OSX dmg (for 2.11.2.0)
2518 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2519 macosArchive.attributes().remove('executeSetupApp')
2520 macosArchive.attributes().remove('setupAppId')
2523 // turn off checksum creation for LOCAL channel
2524 def e = install4jConfigXml.application[0]
2525 e.'@createChecksums' = string(install4jCheckSums)
2527 // put file association actions where placeholder action is
2528 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2529 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2530 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2531 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2532 def parent = a.parent()
2534 fileAssociationActions.each { faa ->
2537 // don't need to continue in .any loop once replacements have been made
2542 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2543 // NB we're deleting the /other/ one!
2544 // Also remove the examples subdir from non-release versions
2545 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2546 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2547 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2548 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2550 // remove the examples subdir from Full File Set
2551 def files = install4jConfigXml.files[0]
2552 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2553 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2554 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2555 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2556 dirEntry.parent().remove(dirEntry)
2558 install4jConfigXml.'**'.action.any { a ->
2559 if (a.'@customizedId' == customizedIdToDelete) {
2560 def parent = a.parent()
2566 // write install4j file
2567 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2574 delete install4jConfFile
2578 task cleanInstallersDataFiles {
2579 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2580 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2581 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2583 delete installersOutputTxt
2584 delete installersSha256
2585 delete hugoDataJsonFile
2589 task install4jDMGBackgroundImageCopy {
2590 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2591 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2594 from(install4jDMGBackgroundImageDir) {
2595 include(install4jDMGBackgroundImageFile)
2597 into install4jDMGBackgroundImageBuildDir
2602 task install4jDMGBackgroundImageProcess {
2603 dependsOn install4jDMGBackgroundImageCopy
2606 if (backgroundImageText) {
2607 if (convertBinary == null) {
2608 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2610 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2611 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2613 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2615 executable convertBinary
2618 '-font', install4j_background_image_text_font,
2619 '-fill', install4j_background_image_text_colour,
2620 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2621 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2622 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2631 task install4jDMGBackgroundImage {
2632 dependsOn install4jDMGBackgroundImageProcess
2635 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2636 group = "distribution"
2637 description = "Create the install4j installers"
2639 dependsOn copyInstall4jTemplate
2640 dependsOn cleanInstallersDataFiles
2641 dependsOn install4jDMGBackgroundImage
2643 projectFile = install4jConfFile
2645 // create an md5 for the input files to use as version for install4j conf file
2646 def digest = MessageDigest.getInstance("MD5")
2648 (file("${install4jDir}/${install4j_template}").text +
2649 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2650 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2651 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2652 if (filesMd5.length() >= 8) {
2653 filesMd5 = filesMd5.substring(0,8)
2655 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2658 'JALVIEW_NAME': jalview_name,
2659 'JALVIEW_APPLICATION_NAME': applicationName,
2660 'JALVIEW_DIR': "../..",
2661 'OSX_KEYSTORE': OSX_KEYSTORE,
2662 'OSX_APPLEID': OSX_APPLEID,
2663 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2664 'JSIGN_SH': JSIGN_SH,
2665 'JRE_DIR': getdown_app_dir_java,
2666 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2667 'JALVIEW_VERSION': JALVIEW_VERSION,
2668 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2669 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2670 'JAVA_VERSION': JAVA_VERSION,
2671 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2672 'VERSION': JALVIEW_VERSION,
2673 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2674 'BUNDLE_ID': install4jBundleId,
2675 'INTERNAL_ID': install4jInternalId,
2676 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2677 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2678 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2679 'WRAPPER_LINK': getdownWrapperLink,
2680 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2681 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2682 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2683 'INSTALLER_NAME': install4jInstallerName,
2684 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2685 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2686 'GETDOWN_FILES_DIR': getdown_files_dir,
2687 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2688 'GETDOWN_DIST_DIR': getdownAppDistDir,
2689 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2690 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2691 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2692 'BUILD_DIR': install4jBuildDir,
2693 'APPLICATION_CATEGORIES': install4j_application_categories,
2694 'APPLICATION_FOLDER': install4jApplicationFolder,
2695 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2696 'EXECUTABLE_NAME': install4jExecutableName,
2697 'EXTRA_SCHEME': install4jExtraScheme,
2698 'MAC_ICONS_FILE': install4jMacIconsFile,
2699 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2700 'PNG_ICON_FILE': install4jPngIconFile,
2701 'BACKGROUND': install4jBackground,
2706 'windows': 'WINDOWS',
2710 // these are the bundled OS/architecture VMs needed by install4j
2713 [ "mac", "aarch64" ],
2714 [ "windows", "x64" ],
2716 [ "linux", "aarch64" ]
2718 osArch.forEach { os, arch ->
2719 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)
2720 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2721 // otherwise running `gradle installers` generates a non-useful error:
2722 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2723 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)
2726 //println("INSTALL4J VARIABLES:")
2727 //variables.each{k,v->println("${k}=${v}")}
2729 destination = "${jalviewDir}/${install4jBuildDir}"
2730 buildSelected = true
2732 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2734 disableSigning = true
2735 disableNotarization = true
2739 macKeystorePassword = OSX_KEYPASS
2742 if (OSX_ALTOOLPASS) {
2743 appleIdPassword = OSX_ALTOOLPASS
2744 disableNotarization = false
2746 disableNotarization = true
2750 println("Using projectFile "+projectFile)
2751 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2755 inputs.dir(getdownAppBaseDir)
2756 inputs.file(install4jConfFile)
2757 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2758 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2761 def getDataHash(File myFile) {
2762 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2763 return myFile.exists()
2765 "file" : myFile.getName(),
2766 "filesize" : myFile.length(),
2767 "sha256" : hash.toString()
2772 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2774 "channel" : getdownChannelName,
2775 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2776 "git-commit" : "${gitHash} [${gitBranch}]",
2777 "version" : JALVIEW_VERSION
2779 // install4j installer files
2780 if (installersOutputTxt.exists()) {
2782 installersOutputTxt.readLines().each { def line ->
2783 if (line.startsWith("#")) {
2786 line.replaceAll("\n","")
2787 def vals = line.split("\t")
2788 def filename = vals[3]
2789 def filesize = file(filename).length()
2790 filename = filename.replaceAll(/^.*\//, "")
2791 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2792 idHash."${filename}" = vals[0]
2794 if (install4jCheckSums && installersSha256.exists()) {
2795 installersSha256.readLines().each { def line ->
2796 if (line.startsWith("#")) {
2799 line.replaceAll("\n","")
2800 def vals = line.split(/\s+\*?/)
2801 def filename = vals[1]
2802 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2808 "JAR": shadowJar.archiveFile, // executable JAR
2809 "JVL": getdownVersionLaunchJvl, // version JVL
2810 "SOURCE": sourceDist.archiveFile // source TGZ
2811 ].each { key, value ->
2812 def file = file(value)
2813 if (file.exists()) {
2814 def fileHash = getDataHash(file)
2815 if (fileHash != null) {
2816 hash."${key}" = fileHash;
2820 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2823 task staticMakeInstallersJsonFile {
2825 def output = findProperty("i4j_output")
2826 def sha256 = findProperty("i4j_sha256")
2827 def json = findProperty("i4j_json")
2828 if (output == null || sha256 == null || json == null) {
2829 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2831 writeDataJsonFile(file(output), file(sha256), file(json))
2836 dependsOn installerFiles
2842 eclipse().configFile(eclipse_codestyle_file)
2846 task createSourceReleaseProperties(type: WriteProperties) {
2847 group = "distribution"
2848 description = "Create the source RELEASE properties file"
2850 def sourceTarBuildDir = "${buildDir}/sourceTar"
2851 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2852 outputFile (sourceReleasePropertiesFile)
2855 releaseProps.each{ key, val -> property key, val }
2856 property "git.branch", gitBranch
2857 property "git.hash", gitHash
2860 outputs.file(outputFile)
2863 task sourceDist(type: Tar) {
2864 group "distribution"
2865 description "Create a source .tar.gz file for distribution"
2867 dependsOn createBuildProperties
2868 dependsOn convertMdFiles
2869 dependsOn eclipseAllPreferences
2870 dependsOn createSourceReleaseProperties
2873 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2874 archiveFileName = outputFileName
2876 compression Compression.GZIP
2891 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2893 "utils/InstallAnywhere",
2908 "gradle.properties",
2920 ".settings/org.eclipse.buildship.core.prefs",
2921 ".settings/org.eclipse.jdt.core.prefs"
2925 exclude (EXCLUDE_FILES)
2926 include (PROCESS_FILES)
2927 filter(ReplaceTokens,
2931 'Version-Rel': JALVIEW_VERSION,
2932 'Year-Rel': getDate("yyyy")
2937 exclude (EXCLUDE_FILES)
2938 exclude (PROCESS_FILES)
2939 exclude ("appletlib")
2940 exclude ("**/*locales")
2941 exclude ("*locales/**")
2942 exclude ("utils/InstallAnywhere")
2944 exclude (getdown_files_dir)
2945 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2946 //exclude (getdown_website_dir)
2947 //exclude (getdown_archive_dir)
2949 // exluding these as not using jars as modules yet
2950 exclude ("${j11modDir}/**/*.jar")
2953 include(INCLUDE_FILES)
2955 // from (jalviewDir) {
2956 // // explicit includes for stuff that seemed to not get included
2957 // include(fileTree("test/**/*."))
2958 // exclude(EXCLUDE_FILES)
2959 // exclude(PROCESS_FILES)
2962 from(file(buildProperties).getParent()) {
2963 include(file(buildProperties).getName())
2964 rename(file(buildProperties).getName(), "build_properties")
2966 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2970 def sourceTarBuildDir = "${buildDir}/sourceTar"
2971 from(sourceTarBuildDir) {
2972 // this includes the appended RELEASE properties file
2976 task dataInstallersJson {
2978 description "Create the installers-VERSION.json data file for installer files created"
2980 mustRunAfter installers
2981 mustRunAfter shadowJar
2982 mustRunAfter sourceDist
2983 mustRunAfter getdownArchive
2985 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2986 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2988 if (installersOutputTxt.exists()) {
2989 inputs.file(installersOutputTxt)
2991 if (install4jCheckSums && installersSha256.exists()) {
2992 inputs.file(installersSha256)
2995 shadowJar.archiveFile, // executable JAR
2996 getdownVersionLaunchJvl, // version JVL
2997 sourceDist.archiveFile // source TGZ
2998 ].each { fileName ->
2999 if (file(fileName).exists()) {
3000 inputs.file(fileName)
3004 outputs.file(hugoDataJsonFile)
3007 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3013 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3016 dependsOn pubhtmlhelp
3018 inputs.dir("${helpBuildDir}/${help_dir}")
3019 outputs.dir("${buildDir}/distributions/${help_dir}")
3023 task j2sSetHeadlessBuild {
3030 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3032 description "Enable the alternative J2S Config file for headless build"
3034 outputFile = jalviewjsJ2sSettingsFileName
3035 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3036 def j2sProps = new Properties()
3037 if (j2sPropsFile.exists()) {
3039 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3040 j2sProps.load(j2sPropsFileFIS)
3041 j2sPropsFileFIS.close()
3043 j2sProps.each { prop, val ->
3046 } catch (Exception e) {
3047 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3051 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3052 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3057 task jalviewjsSetEclipseWorkspace {
3058 def propKey = "jalviewjs_eclipse_workspace"
3060 if (project.hasProperty(propKey)) {
3061 propVal = project.getProperty(propKey)
3062 if (propVal.startsWith("~/")) {
3063 propVal = System.getProperty("user.home") + propVal.substring(1)
3066 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3067 def propsFile = file(propsFileName)
3068 def eclipseWsDir = propVal
3069 def props = new Properties()
3071 def writeProps = true
3072 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3073 def ins = new FileInputStream(propsFileName)
3076 if (props.getProperty(propKey, null) != null) {
3077 eclipseWsDir = props.getProperty(propKey)
3082 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3083 def tempDir = File.createTempDir()
3084 eclipseWsDir = tempDir.getAbsolutePath()
3087 eclipseWorkspace = file(eclipseWsDir)
3090 // do not run a headless transpile when we claim to be in Eclipse
3092 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3093 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3095 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3099 props.setProperty(propKey, eclipseWsDir)
3100 propsFile.parentFile.mkdirs()
3101 def bytes = new ByteArrayOutputStream()
3102 props.store(bytes, null)
3103 def propertiesString = bytes.toString()
3104 propsFile.text = propertiesString
3110 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3113 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3114 outputs.file(propsFileName)
3115 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3119 task jalviewjsEclipsePaths {
3122 def eclipseRoot = jalviewjs_eclipse_root
3123 if (eclipseRoot.startsWith("~/")) {
3124 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3126 if (OperatingSystem.current().isMacOsX()) {
3127 eclipseRoot += "/Eclipse.app"
3128 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3129 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3130 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3131 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3132 eclipseRoot += "/eclipse"
3134 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3135 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3136 } else { // linux or unix
3137 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3138 eclipseRoot += "/eclipse"
3139 println("eclipseDir exists")
3141 eclipseBinary = "${eclipseRoot}/eclipse"
3142 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3145 eclipseVersion = "4.13" // default
3146 def assumedVersion = true
3147 if (file(eclipseProduct).exists()) {
3148 def fis = new FileInputStream(eclipseProduct)
3149 def props = new Properties()
3151 eclipseVersion = props.getProperty("version")
3153 assumedVersion = false
3156 def propKey = "eclipse_debug"
3157 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3160 // do not run a headless transpile when we claim to be in Eclipse
3162 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3163 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3165 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3168 if (!assumedVersion) {
3169 println("ECLIPSE VERSION=${eclipseVersion}")
3175 task printProperties {
3177 description "Output to console all System.properties"
3179 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3185 dependsOn eclipseProject
3186 dependsOn eclipseClasspath
3187 dependsOn eclipseJdt
3191 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3192 task jalviewjsEclipseCopyDropins(type: Copy) {
3193 dependsOn jalviewjsEclipsePaths
3195 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3196 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3197 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3204 // this eclipse -clean doesn't actually work
3205 task jalviewjsCleanEclipse(type: Exec) {
3206 dependsOn eclipseSetup
3207 dependsOn jalviewjsEclipsePaths
3208 dependsOn jalviewjsEclipseCopyDropins
3210 executable(eclipseBinary)
3211 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3217 def inputString = """exit
3220 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3221 standardInput = inputByteStream
3224 /* not really working yet
3225 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3229 task jalviewjsTransferUnzipSwingJs {
3230 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3234 from zipTree(file_zip)
3235 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3239 inputs.file file_zip
3240 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3244 task jalviewjsTransferUnzipLib {
3245 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3248 zipFiles.each { file_zip ->
3250 from zipTree(file_zip)
3251 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3256 inputs.files zipFiles
3257 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3261 task jalviewjsTransferUnzipAllLibs {
3262 dependsOn jalviewjsTransferUnzipSwingJs
3263 dependsOn jalviewjsTransferUnzipLib
3267 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3269 description "Create the alternative j2s file from the j2s.* properties"
3271 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3272 def siteDirProperty = "j2s.site.directory"
3273 def setSiteDir = false
3274 jalviewjsJ2sProps.each { prop, val ->
3276 if (prop == siteDirProperty) {
3277 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3278 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3284 if (!setSiteDir) { // default site location, don't override specifically set property
3285 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3288 outputFile = jalviewjsJ2sAltSettingsFileName
3291 inputs.properties(jalviewjsJ2sProps)
3292 outputs.file(jalviewjsJ2sAltSettingsFileName)
3297 task jalviewjsEclipseSetup {
3298 dependsOn jalviewjsEclipseCopyDropins
3299 dependsOn jalviewjsSetEclipseWorkspace
3300 dependsOn jalviewjsCreateJ2sSettings
3304 task jalviewjsSyncAllLibs (type: Sync) {
3305 dependsOn jalviewjsTransferUnzipAllLibs
3306 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3307 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3308 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3312 def outputFiles = []
3313 rename { filename ->
3314 outputFiles += "${outputDir}/${filename}"
3321 // should this be exclude really ?
3322 duplicatesStrategy "INCLUDE"
3324 outputs.files outputFiles
3325 inputs.files inputFiles
3329 task jalviewjsSyncResources (type: Sync) {
3330 dependsOn buildResources
3332 def inputFiles = fileTree(dir: resourcesBuildDir)
3333 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3337 def outputFiles = []
3338 rename { filename ->
3339 outputFiles += "${outputDir}/${filename}"
3345 outputs.files outputFiles
3346 inputs.files inputFiles
3350 task jalviewjsSyncSiteResources (type: Sync) {
3351 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3352 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3356 def outputFiles = []
3357 rename { filename ->
3358 outputFiles += "${outputDir}/${filename}"
3364 outputs.files outputFiles
3365 inputs.files inputFiles
3369 task jalviewjsSyncBuildProperties (type: Sync) {
3370 dependsOn createBuildProperties
3371 def inputFiles = [file(buildProperties)]
3372 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3376 def outputFiles = []
3377 rename { filename ->
3378 outputFiles += "${outputDir}/${filename}"
3384 outputs.files outputFiles
3385 inputs.files inputFiles
3389 task jalviewjsProjectImport(type: Exec) {
3390 dependsOn eclipseSetup
3391 dependsOn jalviewjsEclipsePaths
3392 dependsOn jalviewjsEclipseSetup
3395 // do not run a headless import when we claim to be in Eclipse
3397 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3398 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3400 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3404 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3405 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3406 executable(eclipseBinary)
3407 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3411 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3413 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3414 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3417 inputs.file("${jalviewDir}/.project")
3418 outputs.upToDateWhen {
3419 file(projdir).exists()
3424 task jalviewjsTranspile(type: Exec) {
3425 dependsOn jalviewjsEclipseSetup
3426 dependsOn jalviewjsProjectImport
3427 dependsOn jalviewjsEclipsePaths
3429 dependsOn jalviewjsEnableAltFileProperty
3433 // do not run a headless transpile when we claim to be in Eclipse
3435 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3436 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3438 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3442 executable(eclipseBinary)
3443 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3447 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3449 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3450 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3456 stdout = new ByteArrayOutputStream()
3457 stderr = new ByteArrayOutputStream()
3459 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3460 def logOutFile = file(logOutFileName)
3461 logOutFile.createNewFile()
3462 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3463 BINARY: ${eclipseBinary}
3464 VERSION: ${eclipseVersion}
3465 WORKSPACE: ${eclipseWorkspace}
3466 DEBUG: ${eclipseDebug}
3469 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3470 // combine stdout and stderr
3471 def logErrFOS = logOutFOS
3473 if (jalviewjs_j2s_to_console.equals("true")) {
3474 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3475 new org.apache.tools.ant.util.TeeOutputStream(
3479 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3480 new org.apache.tools.ant.util.TeeOutputStream(
3485 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3488 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3495 if (stdout.toString().contains("Error processing ")) {
3496 // j2s did not complete transpile
3497 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3498 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3499 println("IGNORING TRANSPILE ERRORS")
3500 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3502 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3507 inputs.dir("${jalviewDir}/${sourceDir}")
3508 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3509 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3513 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3515 def stdout = new ByteArrayOutputStream()
3516 def stderr = new ByteArrayOutputStream()
3518 def coreFile = file(jsfile)
3520 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3522 logOutFile.createNewFile()
3523 logOutFile.append(msg+"\n")
3525 def coreTop = file(prefixFile)
3526 def coreBottom = file(suffixFile)
3527 coreFile.getParentFile().mkdirs()
3528 coreFile.createNewFile()
3529 coreFile.write( coreTop.getText("UTF-8") )
3533 def t = f.getText("UTF-8")
3534 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3535 coreFile.append( t )
3537 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3539 logOutFile.append(msg+"\n")
3542 coreFile.append( coreBottom.getText("UTF-8") )
3544 msg = "Generating ${zjsfile}"
3546 logOutFile.append(msg+"\n")
3547 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3548 def logErrFOS = logOutFOS
3551 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3552 main = "com.google.javascript.jscomp.CommandLineRunner"
3553 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3554 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3557 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3559 logOutFile.append(msg+"\n")
3561 if (logOutConsole) {
3562 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3563 new org.apache.tools.ant.util.TeeOutputStream(
3567 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3568 new org.apache.tools.ant.util.TeeOutputStream(
3573 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3576 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3583 logOutFile.append(msg+"\n")
3587 task jalviewjsBuildAllCores {
3589 description "Build the core js lib closures listed in the classlists dir"
3590 dependsOn jalviewjsTranspile
3591 dependsOn jalviewjsTransferUnzipSwingJs
3593 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3594 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3595 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3596 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3597 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3598 def prefixFile = "${jsDir}/core/coretop2.js"
3599 def suffixFile = "${jsDir}/core/corebottom2.js"
3601 inputs.file prefixFile
3602 inputs.file suffixFile
3604 def classlistFiles = []
3605 // add the classlists found int the jalviewjs_classlists_dir
3606 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3608 def name = file.getName() - ".txt"
3615 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3616 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3617 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3619 jalviewjsCoreClasslists = []
3621 classlistFiles.each {
3624 def file = hash['file']
3625 if (! file.exists()) {
3626 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3627 return false // this is a "continue" in groovy .each closure
3629 def name = hash['name']
3631 name = file.getName() - ".txt"
3639 def list = fileTree(dir: j2sDir, includes: filelist)
3641 def jsfile = "${outputDir}/core${name}.js"
3642 def zjsfile = "${outputDir}/core${name}.z.js"
3644 jalviewjsCoreClasslists += [
3653 outputs.file(jsfile)
3654 outputs.file(zjsfile)
3657 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3658 def stevesoftClasslistName = "_stevesoft"
3659 def stevesoftClasslist = [
3660 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3661 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3662 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3663 'name': stevesoftClasslistName
3665 jalviewjsCoreClasslists += stevesoftClasslist
3666 inputs.files(stevesoftClasslist['list'])
3667 outputs.file(stevesoftClasslist['jsfile'])
3668 outputs.file(stevesoftClasslist['zjsfile'])
3671 def allClasslistName = "_all"
3672 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3673 allJsFiles += fileTree(
3677 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3678 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3679 "**/org/jmol/export/JSExporter.js"
3682 allJsFiles += fileTree(
3686 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3687 "**/sun/misc/Unsafe.js",
3688 "**/swingjs/jquery/jquery-editable-select.js",
3689 "**/swingjs/jquery/j2sComboBox.js",
3690 "**/sun/misc/FloatingDecimal.js"
3693 def allClasslist = [
3694 'jsfile': "${outputDir}/core${allClasslistName}.js",
3695 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3697 'name': allClasslistName
3699 // not including this version of "all" core at the moment
3700 //jalviewjsCoreClasslists += allClasslist
3701 inputs.files(allClasslist['list'])
3702 outputs.file(allClasslist['jsfile'])
3703 outputs.file(allClasslist['zjsfile'])
3706 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3707 logOutFile.getParentFile().mkdirs()
3708 logOutFile.createNewFile()
3709 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3711 jalviewjsCoreClasslists.each {
3712 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3719 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3722 into file(outputFile).getParentFile()
3723 rename { filename ->
3724 if (filename.equals(inputFile.getName())) {
3725 return file(outputFile).getName()
3729 filter(ReplaceTokens,
3733 'MAIN': '"'+main_class+'"',
3735 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3736 'COREKEY': jalviewjs_core_key,
3737 'CORENAME': coreName
3744 task jalviewjsPublishCoreTemplates {
3745 dependsOn jalviewjsBuildAllCores
3746 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3747 def inputFile = file(inputFileName)
3748 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3750 def outputFiles = []
3751 jalviewjsCoreClasslists.each { cl ->
3752 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3753 cl['outputfile'] = outputFile
3754 outputFiles += outputFile
3758 jalviewjsCoreClasslists.each { cl ->
3759 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3762 inputs.file(inputFile)
3763 outputs.files(outputFiles)
3767 task jalviewjsSyncCore (type: Sync) {
3768 dependsOn jalviewjsBuildAllCores
3769 dependsOn jalviewjsPublishCoreTemplates
3770 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3771 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3775 def outputFiles = []
3776 rename { filename ->
3777 outputFiles += "${outputDir}/${filename}"
3783 outputs.files outputFiles
3784 inputs.files inputFiles
3788 // this Copy version of TransferSiteJs will delete anything else in the target dir
3789 task jalviewjsCopyTransferSiteJs(type: Copy) {
3790 dependsOn jalviewjsTranspile
3791 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3792 into "${jalviewDir}/${jalviewjsSiteDir}"
3796 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3797 task jalviewjsSyncTransferSiteJs(type: Sync) {
3798 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3800 into "${jalviewDir}/${jalviewjsSiteDir}"
3807 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3808 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3809 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3810 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3812 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3813 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3814 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3815 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3818 task jalviewjsPrepareSite {
3820 description "Prepares the website folder including unzipping files and copying resources"
3821 dependsOn jalviewjsSyncAllLibs
3822 dependsOn jalviewjsSyncResources
3823 dependsOn jalviewjsSyncSiteResources
3824 dependsOn jalviewjsSyncBuildProperties
3825 dependsOn jalviewjsSyncCore
3829 task jalviewjsBuildSite {
3831 description "Builds the whole website including transpiled code"
3832 dependsOn jalviewjsCopyTransferSiteJs
3833 dependsOn jalviewjsPrepareSite
3837 task cleanJalviewjsTransferSite {
3839 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3840 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3841 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3842 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3847 task cleanJalviewjsSite {
3848 dependsOn cleanJalviewjsTransferSite
3850 delete "${jalviewDir}/${jalviewjsSiteDir}"
3855 task jalviewjsSiteTar(type: Tar) {
3857 description "Creates a tar.gz file for the website"
3858 dependsOn jalviewjsBuildSite
3859 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3860 archiveFileName = outputFilename
3862 compression Compression.GZIP
3864 from "${jalviewDir}/${jalviewjsSiteDir}"
3865 into jalviewjs_site_dir // this is inside the tar file
3867 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3871 task jalviewjsServer {
3873 def filename = "jalviewjsTest.html"
3874 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3875 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3880 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3881 factory = f.newInstance()
3882 } catch (ClassNotFoundException e) {
3883 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3885 def port = Integer.valueOf(jalviewjs_server_port)
3890 while(port < start+1000 && !running) {
3892 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3893 jalviewjsServer = factory.start(doc_root, port)
3895 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3896 println("SERVER STARTED with document root ${doc_root}.")
3897 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3898 println("For debug: "+url+"?j2sdebug")
3899 println("For verbose: "+url+"?j2sverbose")
3900 } catch (Exception e) {
3905 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3906 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3907 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3909 jalviewjsCoreClasslists.each { cl ->
3910 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3912 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3914 println("For core ${cl.name}: "+urlcore)
3917 file(htmlFile).text = htmlText
3920 outputs.file(htmlFile)
3921 outputs.upToDateWhen({false})
3925 task cleanJalviewjsAll {
3927 description "Delete all configuration and build artifacts to do with JalviewJS build"
3928 dependsOn cleanJalviewjsSite
3929 dependsOn jalviewjsEclipsePaths
3932 delete "${jalviewDir}/${jalviewjsBuildDir}"
3933 delete "${jalviewDir}/${eclipse_bin_dir}"
3934 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3935 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3937 delete jalviewjsJ2sAltSettingsFileName
3940 outputs.upToDateWhen( { false } )
3944 task jalviewjsIDE_checkJ2sPlugin {
3945 group "00 JalviewJS in Eclipse"
3946 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3949 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3950 def j2sPluginFile = file(j2sPlugin)
3951 def eclipseHome = System.properties["eclipse.home.location"]
3952 if (eclipseHome == null || ! IN_ECLIPSE) {
3953 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3955 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3956 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3957 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3958 eclipseJ2sPluginDirs += altPluginsDir
3960 def foundPlugin = false
3961 def j2sPluginFileName = j2sPluginFile.getName()
3962 def eclipseJ2sPlugin
3963 def eclipseJ2sPluginFile
3964 eclipseJ2sPluginDirs.any { dir ->
3965 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3966 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3967 if (eclipseJ2sPluginFile.exists()) {
3973 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3974 System.err.println(msg)
3975 throw new StopExecutionException(msg)
3978 def digest = MessageDigest.getInstance("MD5")
3980 digest.update(j2sPluginFile.text.bytes)
3981 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3983 digest.update(eclipseJ2sPluginFile.text.bytes)
3984 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3986 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3987 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3988 System.err.println(msg)
3989 throw new StopExecutionException(msg)
3991 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3997 task jalviewjsIDE_copyJ2sPlugin {
3998 group "00 JalviewJS in Eclipse"
3999 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4002 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4003 def j2sPluginFile = file(j2sPlugin)
4004 def eclipseHome = System.properties["eclipse.home.location"]
4005 if (eclipseHome == null || ! IN_ECLIPSE) {
4006 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4008 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4009 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4010 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4011 System.err.println(msg)
4014 eclipseJ2sPluginFile.getParentFile().mkdirs()
4015 into eclipseJ2sPluginFile.getParent()
4021 task jalviewjsIDE_j2sFile {
4022 group "00 JalviewJS in Eclipse"
4023 description "Creates the .j2s file"
4024 dependsOn jalviewjsCreateJ2sSettings
4028 task jalviewjsIDE_SyncCore {
4029 group "00 JalviewJS in Eclipse"
4030 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4031 dependsOn jalviewjsSyncCore
4035 task jalviewjsIDE_SyncSiteAll {
4036 dependsOn jalviewjsSyncAllLibs
4037 dependsOn jalviewjsSyncResources
4038 dependsOn jalviewjsSyncSiteResources
4039 dependsOn jalviewjsSyncBuildProperties
4043 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4046 task jalviewjsIDE_PrepareSite {
4047 group "00 JalviewJS in Eclipse"
4048 description "Sync libs and resources to site dir, but not closure cores"
4050 dependsOn jalviewjsIDE_SyncSiteAll
4051 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4055 task jalviewjsIDE_AssembleSite {
4056 group "00 JalviewJS in Eclipse"
4057 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4058 dependsOn jalviewjsPrepareSite
4062 task jalviewjsIDE_SiteClean {
4063 group "00 JalviewJS in Eclipse"
4064 description "Deletes the Eclipse transpiled site"
4065 dependsOn cleanJalviewjsSite
4069 task jalviewjsIDE_Server {
4070 group "00 JalviewJS in Eclipse"
4071 description "Starts a webserver on localhost to test the website"
4072 dependsOn jalviewjsServer
4076 // buildship runs this at import or gradle refresh
4077 task eclipseSynchronizationTask {
4078 //dependsOn eclipseSetup
4079 dependsOn createBuildProperties
4081 dependsOn jalviewjsIDE_j2sFile
4082 dependsOn jalviewjsIDE_checkJ2sPlugin
4083 dependsOn jalviewjsIDE_PrepareSite
4088 // buildship runs this at build time or project refresh
4089 task eclipseAutoBuildTask {
4090 //dependsOn jalviewjsIDE_checkJ2sPlugin
4091 //dependsOn jalviewjsIDE_PrepareSite
4097 description "Build the site"
4098 dependsOn jalviewjsBuildSite