1 /* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
2 * For properties set within build.gradle, use camelCaseNoSpace.
4 import org.apache.tools.ant.filters.ReplaceTokens
5 import org.gradle.internal.os.OperatingSystem
6 import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
7 import org.gradle.api.internal.PropertiesTransformer
8 import org.gradle.util.ConfigureUtil
9 import org.gradle.plugins.ide.eclipse.model.Output
10 import org.gradle.plugins.ide.eclipse.model.Library
11 import java.security.MessageDigest
12 import java.util.regex.Matcher
13 import groovy.transform.ExternalizeMethods
14 import groovy.util.XmlParser
15 import groovy.xml.XmlUtil
16 import groovy.json.JsonBuilder
17 import com.vladsch.flexmark.util.ast.Node
18 import com.vladsch.flexmark.html.HtmlRenderer
19 import com.vladsch.flexmark.parser.Parser
20 import com.vladsch.flexmark.util.data.MutableDataSet
21 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
22 import com.vladsch.flexmark.ext.tables.TablesExtension
23 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
24 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
25 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
26 import com.vladsch.flexmark.ext.toc.TocExtension
27 import com.google.common.hash.HashCode
28 import com.google.common.hash.Hashing
29 import com.google.common.io.Files
30 import org.jsoup.Jsoup
31 import org.jsoup.nodes.Element
39 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
40 classpath "org.jsoup:jsoup:1.14.3"
41 classpath "com.eowise:gradle-imagemagick:0.5.1"
50 id "com.diffplug.gradle.spotless" version "3.28.0"
51 id 'com.github.johnrengelman.shadow' version '4.0.3'
52 id 'com.install4j.gradle' version '10.0.3'
53 id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
54 id 'com.palantir.git-version' version '0.13.0' apply false
65 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
66 def string(Object o) {
67 return o == null ? "" : o.toString()
70 def overrideProperties(String propsFileName, boolean output = false) {
71 if (propsFileName == null) {
74 def propsFile = file(propsFileName)
75 if (propsFile != null && propsFile.exists()) {
76 println("Using properties from file '${propsFileName}'")
78 def p = new Properties()
79 def localPropsFIS = new FileInputStream(propsFile)
85 if (project.hasProperty(key)) {
86 oldval = project.findProperty(key)
87 project.setProperty(key, val)
89 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
92 ext.setProperty(key, val)
94 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
98 } catch (Exception e) {
99 println("Exception reading local.properties")
106 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
107 jalviewDirRelativePath = jalviewDir
110 getdownChannelName = CHANNEL.toLowerCase()
111 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
112 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
113 channelDirName = propertiesChannelName
114 // Import channel_properties
115 if (getdownChannelName.startsWith("develop-")) {
116 channelDirName = "develop-SUFFIX"
118 channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
119 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
120 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
121 overrideProperties(channelGradleProperties, false)
122 // local build environment properties
123 // can be "projectDir/local.properties"
124 overrideProperties("${projectDir}/local.properties", true)
125 // or "../projectDir_local.properties"
126 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
129 // Import releaseProps from the RELEASE file
130 // or a file specified via JALVIEW_RELEASE_FILE if defined
131 // Expect jalview.version and target release branch in jalview.release
132 releaseProps = new Properties();
133 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
134 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
136 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
137 releaseProps.load(it)
139 } catch (Exception fileLoadError) {
140 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
143 // Set JALVIEW_VERSION if it is not already set
144 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
145 JALVIEW_VERSION = releaseProps.get("jalview.version")
147 println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
149 // this property set when running Eclipse headlessly
150 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
151 // this property set by Eclipse
152 eclipseApplicationProperty = string("eclipse.application")
153 // CHECK IF RUNNING FROM WITHIN ECLIPSE
154 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
155 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
156 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
157 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
158 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
162 println("WITHIN ECLIPSE IDE")
164 println("HEADLESS BUILD")
167 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
169 println("J2S ENABLED")
172 System.properties.sort { it.key }.each {
173 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
176 if (false && IN_ECLIPSE) {
177 jalviewDir = jalviewDirAbsolutePath
182 buildDate = new Date().format("yyyyMMdd")
185 bareSourceDir = string(source_dir)
186 sourceDir = string("${jalviewDir}/${bareSourceDir}")
187 resourceDir = string("${jalviewDir}/${resource_dir}")
188 bareTestSourceDir = string(test_source_dir)
189 testDir = string("${jalviewDir}/${bareTestSourceDir}")
191 classesDir = string("${jalviewDir}/${classes_dir}")
194 useClover = clover.equals("true")
195 cloverBuildDir = "${buildDir}/clover"
196 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
197 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
198 cloverReportDir = file("${buildDir}/reports/clover")
199 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
200 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
201 //cloverTestClassesDir = cloverClassesDir
202 cloverDb = string("${cloverBuildDir}/clover.db")
204 testSourceDir = useClover ? cloverTestInstrDir : testDir
205 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
208 backgroundImageText = BACKGROUNDIMAGETEXT
209 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
210 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
211 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
212 getdownFullArchiveDir = null
213 getdownTextLines = []
214 getdownLaunchJvl = null
215 getdownVersionLaunchJvl = null
217 buildProperties = null
219 // the following values might be overridden by the CHANNEL switch
220 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
221 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
222 getdownArchiveAppBase = getdown_archive_base
223 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
224 getdownAppDistDir = getdown_app_dir_alt
225 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
226 getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
227 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
228 reportRsyncCommand = false
229 jvlChannelName = CHANNEL.toLowerCase()
230 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
231 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
232 install4jDMGBackgroundImageDir = "${install4j_images_dir}"
233 install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
234 install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
235 install4jInstallerName = "${jalview_name} Non-Release Installer"
236 install4jExecutableName = install4j_executable_name
237 install4jExtraScheme = "jalviewx"
238 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
239 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
240 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
241 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
242 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
243 install4jCheckSums = true
245 applicationName = "${jalview_name}"
249 // TODO: get bamboo build artifact URL for getdown artifacts
250 getdown_channel_base = bamboo_channelbase
251 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
252 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
253 jvlChannelName += "_${getdownChannelName}"
254 // automatically add the test group Not-bamboo for exclusion
255 if ("".equals(testng_excluded_groups)) {
256 testng_excluded_groups = "Not-bamboo"
258 install4jExtraScheme = "jalviewb"
259 backgroundImageText = true
262 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
263 getdownAppDistDir = getdown_app_dir_release
264 getdownSetAppBaseProperty = true
265 reportRsyncCommand = true
267 install4jInstallerName = "${jalview_name} Installer"
271 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
272 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
273 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
274 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
275 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
277 package_dir = string("${ARCHIVEDIR}/${package_dir}")
278 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
281 reportRsyncCommand = true
282 install4jExtraScheme = "jalviewa"
286 getdownChannelName = string("archive/${JALVIEW_VERSION}")
287 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
288 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
289 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
290 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
292 package_dir = string("${ARCHIVEDIR}/${package_dir}")
293 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
296 reportRsyncCommand = true
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
298 install4jSuffix = "Archive"
299 install4jExtraScheme = "jalviewa"
302 case ~/^DEVELOP-([\.\-\w]*)$/:
303 def suffix = Matcher.lastMatcher[0][1]
304 reportRsyncCommand = true
305 getdownSetAppBaseProperty = true
306 JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
307 install4jSuffix = "Develop ${suffix}"
308 install4jExtraScheme = "jalviewd"
309 install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
310 getdownChannelName = string("develop-${suffix}")
311 getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
312 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
313 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
314 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
315 channelSuffix = string(suffix)
316 backgroundImageText = true
320 reportRsyncCommand = true
321 getdownSetAppBaseProperty = true
322 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
323 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
325 install4jSuffix = "Develop"
326 install4jExtraScheme = "jalviewd"
327 install4jInstallerName = "${jalview_name} Develop Installer"
328 backgroundImageText = true
332 reportRsyncCommand = true
333 getdownSetAppBaseProperty = true
334 // Don't ignore transpile errors for release build
335 if (jalviewjs_ignore_transpile_errors.equals("true")) {
336 jalviewjs_ignore_transpile_errors = "false"
337 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
339 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
340 install4jSuffix = "Test"
341 install4jExtraScheme = "jalviewt"
342 install4jInstallerName = "${jalview_name} Test Installer"
343 backgroundImageText = true
346 case ~/^SCRATCH(|-[-\w]*)$/:
347 getdownChannelName = CHANNEL
348 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
350 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
351 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
352 reportRsyncCommand = true
353 install4jSuffix = "Scratch"
357 if (!file("${LOCALDIR}").exists()) {
358 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
360 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
361 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
363 JALVIEW_VERSION = "TEST"
364 install4jSuffix = "Test-Local"
365 install4jExtraScheme = "jalviewt"
366 install4jInstallerName = "${jalview_name} Test Installer"
367 backgroundImageText = true
370 case [ "LOCAL", "JALVIEWJS" ]:
371 JALVIEW_VERSION = "TEST"
372 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
373 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
374 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
375 install4jExtraScheme = "jalviewl"
376 install4jCheckSums = false
379 default: // something wrong specified
380 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
384 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
385 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
386 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
387 // override getdownAppBase if requested
388 if (findProperty("getdown_appbase_override") != null) {
389 // revert to LOCAL if empty string
390 if (string(getdown_appbase_override) == "") {
391 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
392 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
393 } else if (string(getdown_appbase_override).startsWith("file://")) {
394 getdownAppBase = string(getdown_appbase_override)
395 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
397 getdownAppBase = string(getdown_appbase_override)
399 println("Overriding getdown appbase with '${getdownAppBase}'")
401 // sanitise file name for jalview launcher file for this channel
402 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
403 // install4j application and folder names
404 if (install4jSuffix == "") {
405 install4jBundleId = "${install4j_bundle_id}"
406 install4jWinApplicationId = install4j_release_win_application_id
408 applicationName = "${jalview_name} ${install4jSuffix}"
409 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
410 // add int hash of install4jSuffix to the last part of the application_id
411 def id = install4j_release_win_application_id
412 def idsplitreverse = id.split("-").reverse()
413 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
414 install4jWinApplicationId = idsplitreverse.reverse().join("-")
416 // sanitise folder and id names
417 // install4jApplicationFolder = e.g. "Jalview Build"
418 install4jApplicationFolder = applicationName
419 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
420 .replaceAll("_+", "_") // collapse __
421 install4jInternalId = applicationName
423 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
424 .replaceAll("_+", "") // collapse __
425 //.replaceAll("_*-_*", "-") // collapse _-_
426 install4jUnixApplicationFolder = applicationName
428 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
429 .replaceAll("_+", "_") // collapse __
430 .replaceAll("_*-_*", "-") // collapse _-_
433 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
434 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
435 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
436 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
437 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
438 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
439 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
440 /* compile without modules -- using classpath libraries
441 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
442 modules_runtimeClasspath = modules_compileClasspath
448 apply plugin: "com.palantir.git-version"
449 def details = versionDetails()
450 gitHash = details.gitHash
451 gitBranch = details.branchName
452 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
453 println("Not in a git repository. Using git values from RELEASE properties file.")
454 gitHash = releaseProps.getProperty("git.hash")
455 gitBranch = releaseProps.getProperty("git.branch")
456 } catch(java.lang.RuntimeException e1) {
457 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
460 println("Using a ${CHANNEL} profile.")
462 additional_compiler_args = []
463 // configure classpath/args for j8/j11 compilation
464 if (JAVA_VERSION.equals("1.8")) {
465 JAVA_INTEGER_VERSION = string("8")
468 libDistDir = j8libDir
469 compile_source_compatibility = 1.8
470 compile_target_compatibility = 1.8
471 // these are getdown.txt properties defined dependent on the JAVA_VERSION
472 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
473 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
474 // this property is assigned below and expanded to multiple lines in the getdown task
475 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
476 // this property is for the Java library used in eclipse
477 eclipseJavaRuntimeName = string("JavaSE-1.8")
478 } else if (JAVA_VERSION.equals("11")) {
479 JAVA_INTEGER_VERSION = string("11")
481 libDistDir = j11libDir
482 compile_source_compatibility = 11
483 compile_target_compatibility = 11
484 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
485 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
486 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
487 eclipseJavaRuntimeName = string("JavaSE-11")
488 /* compile without modules -- using classpath libraries
489 additional_compiler_args += [
490 '--module-path', modules_compileClasspath.asPath,
491 '--add-modules', j11modules
494 } else if (JAVA_VERSION.equals("17")) {
495 JAVA_INTEGER_VERSION = string("17")
497 libDistDir = j17libDir
498 compile_source_compatibility = 17
499 compile_target_compatibility = 17
500 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
501 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
502 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
503 eclipseJavaRuntimeName = string("JavaSE-17")
504 /* compile without modules -- using classpath libraries
505 additional_compiler_args += [
506 '--module-path', modules_compileClasspath.asPath,
507 '--add-modules', j11modules
511 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
516 JAVA_MIN_VERSION = JAVA_VERSION
517 JAVA_MAX_VERSION = JAVA_VERSION
518 jreInstallsDir = string(jre_installs_dir)
519 if (jreInstallsDir.startsWith("~/")) {
520 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
522 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
523 install4jConfFileName = string("jalview-install4j-conf.install4j")
524 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
525 install4jHomeDir = install4j_home_dir
526 if (install4jHomeDir.startsWith("~/")) {
527 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
530 resourceBuildDir = string("${buildDir}/resources")
531 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
532 helpBuildDir = string("${resourceBuildDir}/help_build")
533 docBuildDir = string("${resourceBuildDir}/doc_build")
535 if (buildProperties == null) {
536 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
538 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
539 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
540 helpSourceDir = string("${helpParentDir}/${help_dir}")
541 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
544 convertBinaryExpectedLocation = imagemagick_convert
545 if (convertBinaryExpectedLocation.startsWith("~/")) {
546 convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
548 if (file(convertBinaryExpectedLocation).exists()) {
549 convertBinary = convertBinaryExpectedLocation
552 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
553 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
554 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
556 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
558 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
560 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
561 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
562 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
563 jalviewjsJalviewCoreHtmlFile = string("")
564 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
565 jalviewjsCoreClasslists = []
566 jalviewjsJalviewTemplateName = string(jalviewjs_name)
567 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
568 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
569 jalviewjsJ2sProps = null
570 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
572 eclipseWorkspace = null
573 eclipseBinary = string("")
574 eclipseVersion = string("")
584 outputDir = file(classesDir)
588 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
591 compileClasspath = files(sourceSets.main.java.outputDir)
592 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
594 runtimeClasspath = compileClasspath
595 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
600 srcDirs cloverInstrDir
601 outputDir = cloverClassesDir
605 srcDirs = sourceSets.main.resources.srcDirs
608 compileClasspath = files( sourceSets.clover.java.outputDir )
609 //compileClasspath += files( testClassesDir )
610 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
611 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
612 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
614 runtimeClasspath = compileClasspath
619 srcDirs testSourceDir
620 outputDir = file(testClassesDir)
624 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
627 compileClasspath = files( sourceSets.test.java.outputDir )
628 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
629 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
631 runtimeClasspath = compileClasspath
632 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
638 // eclipse project and settings files creation, also used by buildship
641 name = eclipse_project_name
643 natures 'org.eclipse.jdt.core.javanature',
644 'org.eclipse.jdt.groovy.core.groovyNature',
645 'org.eclipse.buildship.core.gradleprojectnature'
647 buildCommand 'org.eclipse.jdt.core.javabuilder'
648 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
652 //defaultOutputDir = sourceSets.main.java.outputDir
653 configurations.each{ c->
654 if (c.isCanBeResolved()) {
655 minusConfigurations += [c]
659 plusConfigurations = [ ]
663 def removeTheseToo = []
664 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
665 cp.entries.each { entry ->
666 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
667 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
668 // we add the resources and help/help dirs in as libs afterwards (see below)
669 if (entry.kind == 'src') {
670 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
671 removeTheseToo += entry
673 alreadyAddedSrcPath.putAt(entry.path, true)
678 cp.entries.removeAll(removeTheseToo)
680 //cp.entries += new Output("${eclipse_bin_dir}/main")
681 if (file(helpParentDir).isDirectory()) {
682 cp.entries += new Library(fileReference(helpParentDir))
684 if (file(resourceDir).isDirectory()) {
685 cp.entries += new Library(fileReference(resourceDir))
688 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
690 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
691 //don't want to add outputDir as eclipse is using its own output dir in bin/main
692 if (it.isDirectory() || ! it.exists()) {
693 // don't add dirs to classpath, especially if they don't exist
694 return false // groovy "continue" in .any closure
696 def itPath = it.toString()
697 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
698 // make relative path
699 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
701 if (alreadyAddedLibPath.get(itPath)) {
702 //println("Not adding duplicate entry "+itPath)
704 //println("Adding entry "+itPath)
705 cp.entries += new Library(fileReference(itPath))
706 alreadyAddedLibPath.put(itPath, true)
710 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
711 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
712 if (it.isDirectory() || ! it.exists()) {
713 // don't add dirs to classpath
714 return false // groovy "continue" in .any closure
717 def itPath = it.toString()
718 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
719 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
721 if (alreadyAddedLibPath.get(itPath)) {
724 def lib = new Library(fileReference(itPath))
725 lib.entryAttributes["test"] = "true"
727 alreadyAddedLibPath.put(itPath, true)
735 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
740 // for the IDE, use java 11 compatibility
741 sourceCompatibility = compile_source_compatibility
742 targetCompatibility = compile_target_compatibility
743 javaRuntimeName = eclipseJavaRuntimeName
745 // add in jalview project specific properties/preferences into eclipse core preferences
747 withProperties { props ->
748 def jalview_prefs = new Properties()
749 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
750 jalview_prefs.load(ins)
752 jalview_prefs.forEach { t, v ->
753 if (props.getAt(t) == null) {
757 // codestyle file -- overrides previous formatter prefs
758 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
759 if (csFile.exists()) {
760 XmlParser parser = new XmlParser()
761 def profiles = parser.parse(csFile)
762 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
763 if (profile != null) {
764 profile.'setting'.each { s ->
766 def value = s.'@value'
767 if (id != null && value != null) {
768 props.putAt(id, value)
779 // Don't want these to be activated if in headless build
780 synchronizationTasks "eclipseSynchronizationTask"
781 //autoBuildTasks "eclipseAutoBuildTask"
787 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
788 // Class to allow updating arbitrary properties files
789 class PropertiesFile extends PropertiesPersistableConfigurationObject {
790 public PropertiesFile(PropertiesTransformer t) { super(t); }
791 @Override protected void load(Properties properties) { }
792 @Override protected void store(Properties properties) { }
793 @Override protected String getDefaultResourceName() { return ""; }
794 // This is necessary, because PropertiesPersistableConfigurationObject fails
795 // if no default properties file exists.
796 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
799 // Task to update arbitrary properties files (set outputFile)
800 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
801 private final PropertiesFileContentMerger file;
802 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
803 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
804 protected void configure(PropertiesFile props) {
805 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
807 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
810 task eclipseUIPreferences(type: PropertiesFileTask) {
811 description = "Generate Eclipse additional settings"
812 def filename = "org.eclipse.jdt.ui.prefs"
813 outputFile = "$projectDir/.settings/${filename}" as File
816 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
821 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
822 description = "Generate Eclipse additional settings"
823 def filename = "org.eclipse.jdt.groovy.core.prefs"
824 outputFile = "$projectDir/.settings/${filename}" as File
827 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
832 task eclipseAllPreferences {
834 dependsOn eclipseUIPreferences
835 dependsOn eclipseGroovyCorePreferences
838 eclipseUIPreferences.mustRunAfter eclipseJdt
839 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
841 /* end of eclipse preferences hack */
849 delete cloverBuildDir
850 delete cloverReportDir
855 task cloverInstrJava(type: JavaExec) {
856 group = "Verification"
857 description = "Create clover instrumented source java files"
859 dependsOn cleanClover
861 inputs.files(sourceSets.main.allJava)
862 outputs.dir(cloverInstrDir)
864 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
865 classpath = sourceSets.clover.compileClasspath
866 main = "com.atlassian.clover.CloverInstr"
874 cloverInstrDir.getPath(),
876 def srcFiles = sourceSets.main.allJava.files
879 { file -> file.absolutePath }
882 args argsList.toArray()
885 delete cloverInstrDir
886 println("Clover: About to instrument "+srcFiles.size() +" files")
891 task cloverInstrTests(type: JavaExec) {
892 group = "Verification"
893 description = "Create clover instrumented source test files"
895 dependsOn cleanClover
897 inputs.files(testDir)
898 outputs.dir(cloverTestInstrDir)
900 classpath = sourceSets.clover.compileClasspath
901 main = "com.atlassian.clover.CloverInstr"
911 cloverTestInstrDir.getPath(),
913 args argsList.toArray()
916 delete cloverTestInstrDir
917 println("Clover: About to instrument test files")
923 group = "Verification"
924 description = "Create clover instrumented all source files"
926 dependsOn cloverInstrJava
927 dependsOn cloverInstrTests
931 cloverClasses.dependsOn cloverInstr
934 task cloverConsoleReport(type: JavaExec) {
935 group = "Verification"
936 description = "Creates clover console report"
939 file(cloverDb).exists()
942 inputs.dir cloverClassesDir
944 classpath = sourceSets.clover.runtimeClasspath
945 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
947 if (cloverreport_mem.length() > 0) {
948 maxHeapSize = cloverreport_mem
950 if (cloverreport_jvmargs.length() > 0) {
951 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
961 args argsList.toArray()
965 task cloverHtmlReport(type: JavaExec) {
966 group = "Verification"
967 description = "Creates clover HTML report"
970 file(cloverDb).exists()
973 def cloverHtmlDir = cloverReportDir
974 inputs.dir cloverClassesDir
975 outputs.dir cloverHtmlDir
977 classpath = sourceSets.clover.runtimeClasspath
978 main = "com.atlassian.clover.reporters.html.HtmlReporter"
980 if (cloverreport_mem.length() > 0) {
981 maxHeapSize = cloverreport_mem
983 if (cloverreport_jvmargs.length() > 0) {
984 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
995 if (cloverreport_html_options.length() > 0) {
996 argsList += cloverreport_html_options.split(" ")
999 args argsList.toArray()
1003 task cloverXmlReport(type: JavaExec) {
1004 group = "Verification"
1005 description = "Creates clover XML report"
1008 file(cloverDb).exists()
1011 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1012 inputs.dir cloverClassesDir
1013 outputs.file cloverXmlFile
1015 classpath = sourceSets.clover.runtimeClasspath
1016 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1018 if (cloverreport_mem.length() > 0) {
1019 maxHeapSize = cloverreport_mem
1021 if (cloverreport_jvmargs.length() > 0) {
1022 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1033 if (cloverreport_xml_options.length() > 0) {
1034 argsList += cloverreport_xml_options.split(" ")
1037 args argsList.toArray()
1042 group = "Verification"
1043 description = "Creates clover reports"
1045 dependsOn cloverXmlReport
1046 dependsOn cloverHtmlReport
1053 sourceCompatibility = compile_source_compatibility
1054 targetCompatibility = compile_target_compatibility
1055 options.compilerArgs += additional_compiler_args
1056 print ("Setting target compatibility to "+targetCompatibility+"\n")
1058 //classpath += configurations.cloverRuntime
1064 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1065 sourceCompatibility = compile_source_compatibility
1066 targetCompatibility = compile_target_compatibility
1067 options.compilerArgs += additional_compiler_args
1068 options.encoding = "UTF-8"
1070 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1077 sourceCompatibility = compile_source_compatibility
1078 targetCompatibility = compile_target_compatibility
1079 options.compilerArgs += additional_compiler_args
1081 print ("Setting target compatibility to "+targetCompatibility+"\n")
1088 delete sourceSets.main.java.outputDir
1094 dependsOn cleanClover
1096 delete sourceSets.test.java.outputDir
1101 // format is a string like date.format("dd MMMM yyyy")
1102 def getDate(format) {
1103 return date.format(format)
1107 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1108 MutableDataSet options = new MutableDataSet()
1110 def extensions = new ArrayList<>()
1111 extensions.add(AnchorLinkExtension.create())
1112 extensions.add(AutolinkExtension.create())
1113 extensions.add(StrikethroughExtension.create())
1114 extensions.add(TaskListExtension.create())
1115 extensions.add(TablesExtension.create())
1116 extensions.add(TocExtension.create())
1118 options.set(Parser.EXTENSIONS, extensions)
1120 // set GFM table parsing options
1121 options.set(TablesExtension.WITH_CAPTION, false)
1122 options.set(TablesExtension.COLUMN_SPANS, false)
1123 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1124 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1125 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1126 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1127 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1129 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1130 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1131 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1132 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1134 Parser parser = Parser.builder(options).build()
1135 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1137 mdFiles.each { mdFile ->
1138 // add table of contents
1139 def mdText = "[TOC]\n"+mdFile.text
1141 // grab the first top-level title
1143 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1144 def matcher = mdText =~ titleRegex
1145 if (matcher.size() > 0) {
1146 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1147 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1149 // or use the filename if none found
1150 if (title == null) {
1151 title = mdFile.getName()
1154 Node document = parser.parse(mdText)
1155 String htmlBody = renderer.render(document)
1156 def htmlText = '''<html>
1157 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1158 <html xmlns="http://www.w3.org/1999/xhtml">
1160 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1161 <meta http-equiv="Content-Style-Type" content="text/css" />
1162 <meta name="generator" content="flexmark" />
1164 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1166 <style type="text/css">code{white-space: pre;}</style>
1168 htmlText += ((cssFile != null) ? cssFile.text : '')
1169 htmlText += '''</head>
1172 htmlText += htmlBody
1178 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1179 def htmlFile = file(htmlFilePath)
1180 println("Creating ${htmlFilePath}")
1181 htmlFile.text = htmlText
1186 task copyDocs(type: Copy) {
1187 def inputDir = "${jalviewDir}/${doc_dir}"
1188 def outputDir = "${docBuildDir}/${doc_dir}"
1192 include('**/*.html')
1194 filter(ReplaceTokens,
1198 'Version-Rel': JALVIEW_VERSION,
1199 'Year-Rel': getDate("yyyy")
1206 exclude('**/*.html')
1211 inputs.dir(inputDir)
1212 outputs.dir(outputDir)
1216 task convertMdFiles {
1218 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1219 def cssFile = file("${jalviewDir}/${flexmark_css}")
1222 convertMdToHtml(mdFiles, cssFile)
1225 inputs.files(mdFiles)
1226 inputs.file(cssFile)
1229 mdFiles.each { mdFile ->
1230 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1231 htmlFiles.add(file(htmlFilePath))
1233 outputs.files(htmlFiles)
1237 def hugoTemplateSubstitutions(String input, Map extras=null) {
1238 def replacements = [
1239 DATE: getDate("yyyy-MM-dd"),
1240 CHANNEL: propertiesChannelName,
1241 APPLICATION_NAME: applicationName,
1243 GIT_BRANCH: gitBranch,
1244 VERSION: JALVIEW_VERSION,
1245 JAVA_VERSION: JAVA_VERSION,
1246 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1251 if (extras != null) {
1252 extras.each{ k, v ->
1253 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1256 replacements.each{ k, v ->
1257 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1262 def mdFileComponents(File mdFile, def dateOnly=false) {
1265 if (mdFile.exists()) {
1266 def inFrontMatter = false
1267 def firstLine = true
1268 mdFile.eachLine { line ->
1269 if (line.matches("---")) {
1270 def prev = inFrontMatter
1271 inFrontMatter = firstLine
1272 if (inFrontMatter != prev)
1275 if (inFrontMatter) {
1277 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1278 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1279 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1280 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1281 } else if (m = line =~ /^channel:\s*(\S+)/) {
1282 map["channel"] = m[0][1]
1283 } else if (m = line =~ /^version:\s*(\S+)/) {
1284 map["version"] = m[0][1]
1285 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1286 map[ m[0][1] ] = m[0][2]
1288 if (dateOnly && map["date"] != null) {
1294 content += line+"\n"
1299 return dateOnly ? map["date"] : [map, content]
1302 task hugoTemplates {
1304 description "Create partially populated md pages for hugo website build"
1306 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1307 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1308 def templateFiles = fileTree(dir: hugoTemplatesDir)
1309 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1310 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1311 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1312 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1315 // specific release template for version archive
1318 def givenDate = null
1319 def givenChannel = null
1320 def givenVersion = null
1321 if (CHANNEL == "RELEASE") {
1322 def (map, content) = mdFileComponents(releaseMdFile)
1323 givenDate = map.date
1324 givenChannel = map.channel
1325 givenVersion = map.version
1327 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1328 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1331 if (whatsnewMdFile.exists())
1332 whatsnew = whatsnewMdFile.text
1335 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1336 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1338 def changesHugo = null
1339 if (changes != null) {
1340 changesHugo = '<div class="release_notes">\n\n'
1341 def inSection = false
1342 changes.eachLine { line ->
1344 if (m = line =~ /^##([^#].*)$/) {
1346 changesHugo += "</div>\n\n"
1348 def section = m[0][1].trim()
1349 section = section.toLowerCase()
1350 section = section.replaceAll(/ +/, "_")
1351 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1352 changesHugo += "<div class=\"${section}\">\n\n"
1354 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1355 def comment = m[0][2].trim()
1356 if (comment != "") {
1357 comment = comment.replaceAll('"', """)
1359 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1360 def newline = m[0][1]
1361 if (comment.trim() != "")
1362 newline += "{{<comment>}}${comment}{{</comment>}} "
1363 newline += m[0][3].trim()
1364 if (issuekeys.size() > 0)
1365 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1366 if (m[0][4] != null)
1371 changesHugo += line+"\n"
1374 changesHugo += "\n</div>\n\n"
1376 changesHugo += '</div>'
1379 templateFiles.each{ templateFile ->
1380 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1381 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1382 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1384 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1388 rename(templateFile.getName(), newFileName)
1392 def newFile = file("${outPathName}/${newFileName}".toString())
1393 def content = newFile.text
1394 newFile.text = hugoTemplateSubstitutions(content,
1397 CHANGES: changesHugo,
1398 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1399 DRAFT: givenDate == null ? "true" : "false",
1400 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1401 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1408 inputs.file(oldJvlFile)
1409 inputs.dir(hugoTemplatesDir)
1410 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1411 inputs.property("CHANNEL", { CHANNEL })
1414 def getMdDate(File mdFile) {
1415 return mdFileComponents(mdFile, true)
1418 def getMdSections(String content) {
1420 def sectionContent = ""
1421 def sectionName = null
1422 content.eachLine { line ->
1424 if (m = line =~ /^##([^#].*)$/) {
1425 if (sectionName != null) {
1426 sections[sectionName] = sectionContent
1430 sectionName = m[0][1].trim()
1431 sectionName = sectionName.toLowerCase()
1432 sectionName = sectionName.replaceAll(/ +/, "_")
1433 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1434 } else if (sectionName != null) {
1435 sectionContent += line+"\n"
1438 if (sectionContent != null) {
1439 sections[sectionName] = sectionContent
1445 task copyHelp(type: Copy) {
1446 def inputDir = helpSourceDir
1447 def outputDir = "${helpBuildDir}/${help_dir}"
1451 include('**/*.html')
1455 filter(ReplaceTokens,
1459 'Version-Rel': JALVIEW_VERSION,
1460 'Year-Rel': getDate("yyyy")
1467 exclude('**/*.html')
1474 inputs.dir(inputDir)
1475 outputs.files(helpFile)
1476 outputs.dir(outputDir)
1480 task releasesTemplates {
1482 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1486 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1487 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1488 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1489 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1490 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1491 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1494 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1495 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1497 if (CHANNEL == "RELEASE") {
1498 if (!releaseMdFile.exists()) {
1499 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1501 if (!whatsnewMdFile.exists()) {
1502 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1506 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1507 def releaseFilesDates = releaseFiles.collectEntries {
1508 [(it): getMdDate(it)]
1510 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1512 def releasesTemplate = releasesTemplateFile.text
1513 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1514 def versionTemplate = m[0][1]
1516 MutableDataSet options = new MutableDataSet()
1518 def extensions = new ArrayList<>()
1519 options.set(Parser.EXTENSIONS, extensions)
1520 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1522 Parser parser = Parser.builder(options).build()
1523 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1525 def actualVersions = releaseFiles.collect { rf ->
1526 def (rfMap, rfContent) = mdFileComponents(rf)
1527 return rfMap.version
1529 def versionsHtml = ""
1530 def linkedVersions = []
1531 releaseFiles.reverse().each { rFile ->
1532 def (rMap, rContent) = mdFileComponents(rFile)
1534 def versionLink = ""
1535 def partialVersion = ""
1536 def firstPart = true
1537 rMap.version.split("\\.").each { part ->
1538 def displayPart = ( firstPart ? "" : "." ) + part
1539 partialVersion += displayPart
1541 linkedVersions.contains(partialVersion)
1542 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1544 versionLink += displayPart
1546 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1547 linkedVersions += partialVersion
1551 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1554 def rContentProcessed = ""
1555 rContent.eachLine { line ->
1556 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1557 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1558 } else if (lm = line =~ /^###([^#]+.*)$/) {
1559 line = "_${lm[0][1].trim()}_"
1561 rContentProcessed += line + "\n"
1564 def rContentSections = getMdSections(rContentProcessed)
1565 def rVersion = versionTemplate
1566 if (rVersion != "") {
1567 def rNewFeatures = rContentSections["new_features"]
1568 def rIssuesResolved = rContentSections["issues_resolved"]
1569 Node newFeaturesNode = parser.parse(rNewFeatures)
1570 String newFeaturesHtml = renderer.render(newFeaturesNode)
1571 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1572 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1573 rVersion = hugoTemplateSubstitutions(rVersion,
1575 VERSION: rMap.version,
1576 VERSION_LINK: versionLink,
1577 DISPLAY_DATE: displayDate,
1578 NEW_FEATURES: newFeaturesHtml,
1579 ISSUES_RESOLVED: issuesResolvedHtml
1582 versionsHtml += rVersion
1586 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1587 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1588 releasesHtmlFile.text = releasesTemplate
1590 if (whatsnewMdFile.exists()) {
1591 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1592 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1593 Node whatsnewNode = parser.parse(whatsnewMd)
1594 String whatsnewHtml = renderer.render(whatsnewNode)
1595 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1596 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1598 VERSION: JALVIEW_VERSION,
1599 DISPLAY_DATE: wnDisplayDate
1602 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1603 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1608 inputs.file(releasesTemplateFile)
1609 inputs.file(whatsnewTemplateFile)
1610 inputs.dir(releasesMdDir)
1611 inputs.dir(whatsnewMdDir)
1612 outputs.file(releasesHtmlFile)
1613 outputs.file(whatsnewHtmlFile)
1617 task copyResources(type: Copy) {
1619 description = "Copy (and make text substitutions in) the resources dir to the build area"
1621 def inputDir = resourceDir
1622 def outputDir = resourcesBuildDir
1626 include('**/*.html')
1628 filter(ReplaceTokens,
1632 'Version-Rel': JALVIEW_VERSION,
1633 'Year-Rel': getDate("yyyy")
1640 exclude('**/*.html')
1645 inputs.dir(inputDir)
1646 outputs.dir(outputDir)
1649 task copyChannelResources(type: Copy) {
1650 dependsOn copyResources
1652 description = "Copy the channel resources dir to the build resources area"
1654 def inputDir = "${channelDir}/${resource_dir}"
1655 def outputDir = resourcesBuildDir
1657 include(channel_props)
1658 filter(ReplaceTokens,
1662 'SUFFIX': channelSuffix
1667 exclude(channel_props)
1671 inputs.dir(inputDir)
1672 outputs.dir(outputDir)
1675 task createBuildProperties(type: WriteProperties) {
1676 dependsOn copyResources
1678 description = "Create the ${buildProperties} file"
1680 inputs.dir(sourceDir)
1681 inputs.dir(resourcesBuildDir)
1682 outputFile (buildProperties)
1683 // taking time specific comment out to allow better incremental builds
1684 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1685 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1686 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1687 property "VERSION", JALVIEW_VERSION
1688 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1689 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1690 if (getdownSetAppBaseProperty) {
1691 property "GETDOWNAPPBASE", getdownAppBase
1692 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1694 outputs.file(outputFile)
1698 task buildIndices(type: JavaExec) {
1700 classpath = sourceSets.main.compileClasspath
1701 main = "com.sun.java.help.search.Indexer"
1702 workingDir = "${helpBuildDir}/${help_dir}"
1705 inputs.dir("${workingDir}/${argDir}")
1707 outputs.dir("${classesDir}/doc")
1708 outputs.dir("${classesDir}/help")
1709 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1710 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1711 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1712 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1713 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1714 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1717 task buildResources {
1718 dependsOn copyResources
1719 dependsOn copyChannelResources
1720 dependsOn createBuildProperties
1724 dependsOn buildResources
1727 dependsOn releasesTemplates
1728 dependsOn convertMdFiles
1729 dependsOn buildIndices
1733 compileJava.dependsOn prepare
1734 run.dependsOn compileJava
1735 compileTestJava.dependsOn compileJava
1740 group = "Verification"
1741 description = "Runs all testTaskN tasks)"
1744 dependsOn cloverClasses
1746 dependsOn testClasses
1749 // not running tests in this task
1753 /* testTask0 is the main test task */
1754 task testTask0(type: Test) {
1755 group = "Verification"
1756 description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
1758 includeGroups testng_groups.split(",")
1759 excludeGroups testng_excluded_groups.split(",")
1760 tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
1762 useDefaultListeners=true
1766 /* separated tests */
1767 task testTask1(type: Test) {
1768 group = "Verification"
1769 description = "Tests that need to be isolated from the main test run"
1772 excludeGroups testng_excluded_groups.split(",")
1774 useDefaultListeners=true
1778 /* insert more testTaskNs here -- change N to next digit or other string */
1780 task testTaskN(type: Test) {
1781 group = "Verification"
1782 description = "Tests that need to be isolated from the main test run"
1785 excludeGroups testng_excluded_groups.split(",")
1787 useDefaultListeners=true
1793 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
1794 * to summarise test results from all Test tasks
1796 /* START of test tasks results summary */
1797 import groovy.time.TimeCategory
1798 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
1799 import org.gradle.api.tasks.testing.logging.TestLogEvent
1800 rootProject.ext.testsResults = [] // Container for tests summaries
1802 tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
1804 // from original test task
1806 dependsOn cloverClasses
1808 dependsOn testClasses //?
1811 // run main tests first
1812 if (!testTask.name.equals("testTask0"))
1813 testTask.mustRunAfter "testTask0"
1815 testTask.testLogging { logging ->
1816 events TestLogEvent.FAILED,
1817 TestLogEvent.SKIPPED,
1818 TestLogEvent.STANDARD_OUT,
1819 TestLogEvent.STANDARD_ERROR
1821 exceptionFormat TestExceptionFormat.FULL
1824 showStackTraces true
1827 ignoreFailures = true // Always try to run all tests for all modules
1829 afterSuite { desc, result ->
1831 return // Only summarize results for whole modules
1833 def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
1835 rootProject.ext.testsResults.add(resultsInfo)
1838 // from original test task
1839 maxHeapSize = "1024m"
1841 workingDir = jalviewDir
1842 def testLaf = project.findProperty("test_laf")
1843 if (testLaf != null) {
1844 println("Setting Test LaF to '${testLaf}'")
1845 systemProperty "laf", testLaf
1847 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1848 if (testHiDPIScale != null) {
1849 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1850 systemProperty "sun.java2d.uiScale", testHiDPIScale
1852 sourceCompatibility = compile_source_compatibility
1853 targetCompatibility = compile_target_compatibility
1854 jvmArgs += additional_compiler_args
1857 // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
1858 // testTasks that include the tests, and exclude all from the others.
1859 // get --test argument
1860 filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
1863 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1867 /* ensure the "test" task dependsOn all the testTasks */
1868 test.dependsOn testTask
1871 gradle.buildFinished {
1872 def allResults = rootProject.ext.testsResults
1874 if (!allResults.isEmpty()) {
1875 printResults allResults
1876 allResults.each {r ->
1877 if (r[2].resultType == TestResult.ResultType.FAILURE)
1878 throw new GradleException("Failed tests!")
1883 private static String colString(styler, col, colour, text) {
1884 return col?"${styler[colour](text)}":text
1887 private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
1888 def colour = 'black'
1891 case TestResult.ResultType.SUCCESS:
1894 case TestResult.ResultType.FAILURE:
1901 StringBuilder sb = new StringBuilder()
1905 sb.append(" results: ")
1906 sb.append(colString(s, col && !nocol, colour, rt))
1908 sb.append("${rc} tests, ")
1909 sb.append(colString(s, col && rs > 0, 'green', rs))
1910 sb.append(" successes, ")
1911 sb.append(colString(s, col && rf > 0, 'red', rf))
1912 sb.append(" failures, ")
1913 sb.append("${rsk} skipped) in ${t}")
1914 return sb.toString()
1917 private static void printResults(allResults) {
1919 // styler from https://stackoverflow.com/a/56139852
1920 def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
1923 def failedTests = false
1924 def summaryLines = []
1926 def totalsuccess = 0
1929 def totaltime = TimeCategory.getSeconds(0)
1930 // sort on project name then task name
1931 allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
1932 def projectName = it[0]
1933 def taskName = it[1]
1937 def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
1938 def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
1939 def reportLine = "Report file: ${report}"
1940 def ls = summaryPlain.length()
1941 def lr = reportLine.length()
1942 def m = [ls, lr].max()
1945 def info = [ls, summaryCol, reportLine]
1946 summaryLines.add(info)
1947 failedTests |= result.resultType == TestResult.ResultType.FAILURE
1948 totalcount += result.testCount
1949 totalsuccess += result.successfulTestCount
1950 totalfail += result.failedTestCount
1951 totalskip += result.skippedTestCount
1954 def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
1955 def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
1956 def tls = totalSummaryPlain.length()
1957 if (tls > maxLength)
1959 def info = [tls, totalSummaryCol, null]
1960 summaryLines.add(info)
1962 def allSummaries = []
1963 for(sInfo : summaryLines) {
1965 def summary = sInfo[1]
1966 def report = sInfo[2]
1968 StringBuilder sb = new StringBuilder()
1969 sb.append("│" + summary + " " * (maxLength - ls) + "│")
1970 if (report != null) {
1971 sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
1973 allSummaries += sb.toString()
1976 println "┌${"${"─" * maxLength}"}┐"
1977 println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
1978 println "└${"${"─" * maxLength}"}┘"
1980 /* END of test tasks results summary */
1983 task compileLinkCheck(type: JavaCompile) {
1985 classpath = files("${jalviewDir}/${utils_dir}")
1986 destinationDir = file("${jalviewDir}/${utils_dir}")
1987 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1989 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1990 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1991 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1992 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1996 task linkCheck(type: JavaExec) {
1998 dependsOn compileLinkCheck
2000 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
2001 classpath = files("${jalviewDir}/${utils_dir}")
2002 main = "HelpLinksChecker"
2003 workingDir = "${helpBuildDir}"
2004 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
2006 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
2007 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
2010 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
2014 inputs.dir(helpBuildDir)
2015 outputs.file(helpLinksCheckerOutFile)
2019 // import the pubhtmlhelp target
2020 ant.properties.basedir = "${jalviewDir}"
2021 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
2022 ant.importBuild "${utils_dir}/publishHelp.xml"
2025 task cleanPackageDir(type: Delete) {
2027 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
2037 attributes "Main-Class": main_class,
2038 "Permissions": "all-permissions",
2039 "Application-Name": applicationName,
2040 "Codebase": application_codebase,
2041 "Implementation-Version": JALVIEW_VERSION
2044 def outputDir = "${jalviewDir}/${package_dir}"
2045 destinationDirectory = file(outputDir)
2046 archiveFileName = rootProject.name+".jar"
2047 duplicatesStrategy "EXCLUDE"
2054 exclude "**/*.jar.*"
2056 inputs.dir(sourceSets.main.java.outputDir)
2057 sourceSets.main.resources.srcDirs.each{ dir ->
2060 outputs.file("${outputDir}/${archiveFileName}")
2064 task copyJars(type: Copy) {
2065 from fileTree(dir: classesDir, include: "**/*.jar").files
2066 into "${jalviewDir}/${package_dir}"
2070 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
2071 task syncJars(type: Sync) {
2073 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
2074 into "${jalviewDir}/${package_dir}"
2076 include jar.archiveFileName.getOrNull()
2083 description = "Put all required libraries in dist"
2084 // order of "cleanPackageDir", "copyJars", "jar" important!
2085 jar.mustRunAfter cleanPackageDir
2086 syncJars.mustRunAfter cleanPackageDir
2087 dependsOn cleanPackageDir
2090 outputs.dir("${jalviewDir}/${package_dir}")
2095 dependsOn cleanPackageDir
2102 group = "distribution"
2103 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
2107 from ("${jalviewDir}/${libDistDir}") {
2111 attributes "Implementation-Version": JALVIEW_VERSION,
2112 "Application-Name": applicationName
2115 duplicatesStrategy "INCLUDE"
2117 mainClassName = shadow_jar_main_class
2119 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
2123 task getdownImagesCopy() {
2124 inputs.dir getdownImagesDir
2125 outputs.dir getdownImagesBuildDir
2129 from(getdownImagesDir) {
2130 include("*getdown*.png")
2132 into getdownImagesBuildDir
2137 task getdownImagesProcess() {
2138 dependsOn getdownImagesCopy
2141 if (backgroundImageText) {
2142 if (convertBinary == null) {
2143 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2145 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
2146 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2148 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
2150 executable convertBinary
2153 '-font', getdown_background_image_text_font,
2154 '-fill', getdown_background_image_text_colour,
2155 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
2156 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2157 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2166 task getdownImages() {
2167 dependsOn getdownImagesProcess
2170 task getdownWebsite() {
2171 group = "distribution"
2172 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
2174 dependsOn getdownImages
2179 def getdownWebsiteResourceFilenames = []
2180 def getdownResourceDir = getdownResourceDir
2181 def getdownResourceFilenames = []
2184 // clean the getdown website and files dir before creating getdown folders
2185 delete getdownAppBaseDir
2186 delete getdownFilesDir
2189 from buildProperties
2190 rename(file(buildProperties).getName(), getdown_build_properties)
2193 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2196 from channelPropsFile
2197 filter(ReplaceTokens,
2201 'SUFFIX': channelSuffix
2204 into getdownAppBaseDir
2206 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2208 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2209 def props = project.properties.sort { it.key }
2210 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2211 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2213 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2214 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2216 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2217 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2219 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2220 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2221 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2222 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2223 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2224 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2225 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2228 props.put("getdown_txt_title", jalview_name)
2229 props.put("getdown_txt_ui.name", applicationName)
2231 // start with appbase
2232 getdownTextLines += "appbase = ${getdownAppBase}"
2233 props.each{ prop, val ->
2234 if (prop.startsWith("getdown_txt_") && val != null) {
2235 if (prop.startsWith("getdown_txt_multi_")) {
2236 def key = prop.substring(18)
2237 val.split(",").each{ v ->
2238 def line = "${key} = ${v}"
2239 getdownTextLines += line
2242 // file values rationalised
2243 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2245 if (val.indexOf('/') == 0) {
2248 } else if (val.indexOf('/') > 0) {
2249 // relative path (relative to jalviewDir)
2250 r = file( "${jalviewDir}/${val}" )
2253 val = "${getdown_resource_dir}/" + r.getName()
2254 getdownWebsiteResourceFilenames += val
2255 getdownResourceFilenames += r.getPath()
2258 if (! prop.startsWith("getdown_txt_resource")) {
2259 def line = prop.substring(12) + " = ${val}"
2260 getdownTextLines += line
2266 getdownWebsiteResourceFilenames.each{ filename ->
2267 getdownTextLines += "resource = ${filename}"
2269 getdownResourceFilenames.each{ filename ->
2272 into getdownResourceDir
2276 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2277 getdownWrapperScripts.each{ script ->
2278 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2282 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2284 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2289 fileTree(file(package_dir)).each{ f ->
2290 if (f.isDirectory()) {
2291 def files = fileTree(dir: f, include: ["*"]).getFiles()
2293 } else if (f.exists()) {
2297 def jalviewJar = jar.archiveFileName.getOrNull()
2298 // put jalview.jar first for CLASSPATH and .properties files reasons
2299 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2300 def name = f.getName()
2301 def line = "code = ${getdownAppDistDir}/${name}"
2302 getdownTextLines += line
2309 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2311 if (JAVA_VERSION.equals("11")) {
2312 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2313 j11libFiles.sort().each{f ->
2314 def name = f.getName()
2315 def line = "code = ${getdown_j11lib_dir}/${name}"
2316 getdownTextLines += line
2319 into getdownJ11libDir
2325 // 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.
2326 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2327 getdownTextLines += "resource = ${getdown_launcher_new}"
2328 getdownTextLines += "class = ${main_class}"
2329 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2330 if (getdownSetAppBaseProperty) {
2331 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2332 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2335 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2336 getdownTxt.write(getdownTextLines.join("\n"))
2338 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2339 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2340 launchJvl.write("appbase=${getdownAppBase}")
2342 // files going into the getdown website dir: getdown-launcher.jar
2344 from getdownLauncher
2345 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2346 into getdownAppBaseDir
2349 // files going into the getdown website dir: getdown-launcher(-local).jar
2351 from getdownLauncher
2352 if (file(getdownLauncher).getName() != getdown_launcher) {
2353 rename(file(getdownLauncher).getName(), getdown_launcher)
2355 into getdownAppBaseDir
2358 // files going into the getdown website dir: ./install dir and files
2359 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2362 from getdownLauncher
2363 from "${getdownAppDir}/${getdown_build_properties}"
2364 if (file(getdownLauncher).getName() != getdown_launcher) {
2365 rename(file(getdownLauncher).getName(), getdown_launcher)
2367 into getdownInstallDir
2370 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2372 from getdownInstallDir
2373 into getdownFilesInstallDir
2377 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2381 from getdownLauncher
2382 from "${getdownAppBaseDir}/${getdown_build_properties}"
2383 from "${getdownAppBaseDir}/${channel_props}"
2384 if (file(getdownLauncher).getName() != getdown_launcher) {
2385 rename(file(getdownLauncher).getName(), getdown_launcher)
2387 into getdownFilesDir
2390 // and ./resource (not all downloaded by getdown)
2392 from getdownResourceDir
2393 into "${getdownFilesDir}/${getdown_resource_dir}"
2398 inputs.dir("${jalviewDir}/${package_dir}")
2400 outputs.dir(getdownAppBaseDir)
2401 outputs.dir(getdownFilesDir)
2405 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2406 task getdownDigestDir(type: JavaExec) {
2408 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2410 def digestDirPropertyName = "DIGESTDIR"
2412 classpath = files(getdownLauncher)
2413 def digestDir = findProperty(digestDirPropertyName)
2414 if (digestDir == null) {
2415 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2419 main = "com.threerings.getdown.tools.Digester"
2423 task getdownDigest(type: JavaExec) {
2424 group = "distribution"
2425 description = "Digest the getdown website folder"
2426 dependsOn getdownWebsite
2428 classpath = files(getdownLauncher)
2430 main = "com.threerings.getdown.tools.Digester"
2431 args getdownAppBaseDir
2432 inputs.dir(getdownAppBaseDir)
2433 outputs.file("${getdownAppBaseDir}/digest2.txt")
2438 group = "distribution"
2439 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2440 dependsOn getdownDigest
2442 if (reportRsyncCommand) {
2443 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2444 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2445 println "LIKELY RSYNC COMMAND:"
2446 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2447 if (RUNRSYNC == "true") {
2449 commandLine "mkdir", "-p", toDir
2452 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2460 task getdownArchiveBuild() {
2461 group = "distribution"
2462 description = "Put files in the archive dir to go on the website"
2464 dependsOn getdownWebsite
2466 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2467 def vDir = "${getdownArchiveDir}/${v}"
2468 getdownFullArchiveDir = "${vDir}/getdown"
2469 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2471 def vAltDir = "alt_${v}"
2472 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2475 // cleanup old "old" dir
2476 delete getdownArchiveDir
2478 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2479 getdownArchiveTxt.getParentFile().mkdirs()
2480 def getdownArchiveTextLines = []
2481 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2485 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2486 into "${getdownFullArchiveDir}/${vAltDir}"
2489 getdownTextLines.each { line ->
2490 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2491 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2492 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2493 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2494 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2495 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2496 // remove the existing resource = resource/ or bin/ lines
2497 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2498 getdownArchiveTextLines += line
2502 // the resource dir -- add these files as resource lines in getdown.txt
2504 from "${archiveImagesDir}"
2505 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2507 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2511 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2513 def vLaunchJvl = file(getdownVersionLaunchJvl)
2514 vLaunchJvl.getParentFile().mkdirs()
2515 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2516 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2517 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2518 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2519 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2520 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2522 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2524 from getdownLauncher
2525 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2526 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2527 from "${getdownAppBaseDir}/${channel_props}"
2528 if (file(getdownLauncher).getName() != getdown_launcher) {
2529 rename(file(getdownLauncher).getName(), getdown_launcher)
2531 into getdownFullArchiveDir
2537 task getdownArchiveDigest(type: JavaExec) {
2538 group = "distribution"
2539 description = "Digest the getdown archive folder"
2541 dependsOn getdownArchiveBuild
2544 classpath = files(getdownLauncher)
2545 args getdownFullArchiveDir
2547 main = "com.threerings.getdown.tools.Digester"
2548 inputs.dir(getdownFullArchiveDir)
2549 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2552 task getdownArchive() {
2553 group = "distribution"
2554 description = "Build the website archive dir with getdown digest"
2556 dependsOn getdownArchiveBuild
2557 dependsOn getdownArchiveDigest
2560 tasks.withType(JavaCompile) {
2561 options.encoding = 'UTF-8'
2567 delete getdownAppBaseDir
2568 delete getdownFilesDir
2569 delete getdownArchiveDir
2575 if (file(install4jHomeDir).exists()) {
2577 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2578 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2579 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2580 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2582 installDir(file(install4jHomeDir))
2584 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2588 task copyInstall4jTemplate {
2589 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2590 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2591 inputs.file(install4jTemplateFile)
2592 inputs.file(install4jFileAssociationsFile)
2593 inputs.property("CHANNEL", { CHANNEL })
2594 outputs.file(install4jConfFile)
2597 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2599 // turn off code signing if no OSX_KEYPASS
2600 if (OSX_KEYPASS == "") {
2601 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2602 codeSigning.'@macEnabled' = "false"
2604 install4jConfigXml.'**'.windows.each { windows ->
2605 windows.'@runPostProcessor' = "false"
2609 // disable install screen for OSX dmg (for 2.11.2.0)
2610 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2611 macosArchive.attributes().remove('executeSetupApp')
2612 macosArchive.attributes().remove('setupAppId')
2615 // turn off checksum creation for LOCAL channel
2616 def e = install4jConfigXml.application[0]
2617 e.'@createChecksums' = string(install4jCheckSums)
2619 // put file association actions where placeholder action is
2620 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2621 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2622 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2623 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2624 def parent = a.parent()
2626 fileAssociationActions.each { faa ->
2629 // don't need to continue in .any loop once replacements have been made
2634 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2635 // NB we're deleting the /other/ one!
2636 // Also remove the examples subdir from non-release versions
2637 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2638 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2639 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2640 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2642 // remove the examples subdir from Full File Set
2643 def files = install4jConfigXml.files[0]
2644 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2645 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2646 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2647 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2648 dirEntry.parent().remove(dirEntry)
2650 install4jConfigXml.'**'.action.any { a ->
2651 if (a.'@customizedId' == customizedIdToDelete) {
2652 def parent = a.parent()
2658 // write install4j file
2659 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2666 delete install4jConfFile
2670 task cleanInstallersDataFiles {
2671 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2672 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2673 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2675 delete installersOutputTxt
2676 delete installersSha256
2677 delete hugoDataJsonFile
2681 task install4jDMGBackgroundImageCopy {
2682 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2683 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2686 from(install4jDMGBackgroundImageDir) {
2687 include(install4jDMGBackgroundImageFile)
2689 into install4jDMGBackgroundImageBuildDir
2694 task install4jDMGBackgroundImageProcess {
2695 dependsOn install4jDMGBackgroundImageCopy
2698 if (backgroundImageText) {
2699 if (convertBinary == null) {
2700 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2702 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2703 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2705 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2707 executable convertBinary
2710 '-font', install4j_background_image_text_font,
2711 '-fill', install4j_background_image_text_colour,
2712 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2713 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2714 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2723 task install4jDMGBackgroundImage {
2724 dependsOn install4jDMGBackgroundImageProcess
2727 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2728 group = "distribution"
2729 description = "Create the install4j installers"
2731 dependsOn copyInstall4jTemplate
2732 dependsOn cleanInstallersDataFiles
2733 dependsOn install4jDMGBackgroundImage
2735 projectFile = install4jConfFile
2737 // create an md5 for the input files to use as version for install4j conf file
2738 def digest = MessageDigest.getInstance("MD5")
2740 (file("${install4jDir}/${install4j_template}").text +
2741 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2742 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2743 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2744 if (filesMd5.length() >= 8) {
2745 filesMd5 = filesMd5.substring(0,8)
2747 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2750 'JALVIEW_NAME': jalview_name,
2751 'JALVIEW_APPLICATION_NAME': applicationName,
2752 'JALVIEW_DIR': "../..",
2753 'OSX_KEYSTORE': OSX_KEYSTORE,
2754 'OSX_APPLEID': OSX_APPLEID,
2755 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2756 'JSIGN_SH': JSIGN_SH,
2757 'JRE_DIR': getdown_app_dir_java,
2758 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2759 'JALVIEW_VERSION': JALVIEW_VERSION,
2760 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2761 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2762 'JAVA_VERSION': JAVA_VERSION,
2763 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2764 'VERSION': JALVIEW_VERSION,
2765 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2766 'BUNDLE_ID': install4jBundleId,
2767 'INTERNAL_ID': install4jInternalId,
2768 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2769 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2770 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2771 'WRAPPER_LINK': getdownWrapperLink,
2772 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2773 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2774 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2775 'INSTALLER_NAME': install4jInstallerName,
2776 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2777 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2778 'GETDOWN_FILES_DIR': getdown_files_dir,
2779 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2780 'GETDOWN_DIST_DIR': getdownAppDistDir,
2781 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2782 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2783 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2784 'BUILD_DIR': install4jBuildDir,
2785 'APPLICATION_CATEGORIES': install4j_application_categories,
2786 'APPLICATION_FOLDER': install4jApplicationFolder,
2787 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2788 'EXECUTABLE_NAME': install4jExecutableName,
2789 'EXTRA_SCHEME': install4jExtraScheme,
2790 'MAC_ICONS_FILE': install4jMacIconsFile,
2791 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2792 'PNG_ICON_FILE': install4jPngIconFile,
2793 'BACKGROUND': install4jBackground,
2798 'windows': 'WINDOWS',
2802 // these are the bundled OS/architecture VMs needed by install4j
2805 [ "mac", "aarch64" ],
2806 [ "windows", "x64" ],
2808 [ "linux", "aarch64" ]
2810 osArch.forEach { os, arch ->
2811 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)
2812 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2813 // otherwise running `gradle installers` generates a non-useful error:
2814 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2815 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)
2818 //println("INSTALL4J VARIABLES:")
2819 //variables.each{k,v->println("${k}=${v}")}
2821 destination = "${jalviewDir}/${install4jBuildDir}"
2822 buildSelected = true
2824 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2826 disableSigning = true
2827 disableNotarization = true
2831 macKeystorePassword = OSX_KEYPASS
2834 if (OSX_ALTOOLPASS) {
2835 appleIdPassword = OSX_ALTOOLPASS
2836 disableNotarization = false
2838 disableNotarization = true
2842 println("Using projectFile "+projectFile)
2843 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2847 inputs.dir(getdownAppBaseDir)
2848 inputs.file(install4jConfFile)
2849 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2850 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2853 def getDataHash(File myFile) {
2854 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2855 return myFile.exists()
2857 "file" : myFile.getName(),
2858 "filesize" : myFile.length(),
2859 "sha256" : hash.toString()
2864 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2866 "channel" : getdownChannelName,
2867 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2868 "git-commit" : "${gitHash} [${gitBranch}]",
2869 "version" : JALVIEW_VERSION
2871 // install4j installer files
2872 if (installersOutputTxt.exists()) {
2874 installersOutputTxt.readLines().each { def line ->
2875 if (line.startsWith("#")) {
2878 line.replaceAll("\n","")
2879 def vals = line.split("\t")
2880 def filename = vals[3]
2881 def filesize = file(filename).length()
2882 filename = filename.replaceAll(/^.*\//, "")
2883 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2884 idHash."${filename}" = vals[0]
2886 if (install4jCheckSums && installersSha256.exists()) {
2887 installersSha256.readLines().each { def line ->
2888 if (line.startsWith("#")) {
2891 line.replaceAll("\n","")
2892 def vals = line.split(/\s+\*?/)
2893 def filename = vals[1]
2894 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2900 "JAR": shadowJar.archiveFile, // executable JAR
2901 "JVL": getdownVersionLaunchJvl, // version JVL
2902 "SOURCE": sourceDist.archiveFile // source TGZ
2903 ].each { key, value ->
2904 def file = file(value)
2905 if (file.exists()) {
2906 def fileHash = getDataHash(file)
2907 if (fileHash != null) {
2908 hash."${key}" = fileHash;
2912 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2915 task staticMakeInstallersJsonFile {
2917 def output = findProperty("i4j_output")
2918 def sha256 = findProperty("i4j_sha256")
2919 def json = findProperty("i4j_json")
2920 if (output == null || sha256 == null || json == null) {
2921 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2923 writeDataJsonFile(file(output), file(sha256), file(json))
2928 dependsOn installerFiles
2934 eclipse().configFile(eclipse_codestyle_file)
2938 task createSourceReleaseProperties(type: WriteProperties) {
2939 group = "distribution"
2940 description = "Create the source RELEASE properties file"
2942 def sourceTarBuildDir = "${buildDir}/sourceTar"
2943 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2944 outputFile (sourceReleasePropertiesFile)
2947 releaseProps.each{ key, val -> property key, val }
2948 property "git.branch", gitBranch
2949 property "git.hash", gitHash
2952 outputs.file(outputFile)
2955 task sourceDist(type: Tar) {
2956 group "distribution"
2957 description "Create a source .tar.gz file for distribution"
2959 dependsOn createBuildProperties
2960 dependsOn convertMdFiles
2961 dependsOn eclipseAllPreferences
2962 dependsOn createSourceReleaseProperties
2965 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2966 archiveFileName = outputFileName
2968 compression Compression.GZIP
2983 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2985 "utils/InstallAnywhere",
3000 "gradle.properties",
3012 ".settings/org.eclipse.buildship.core.prefs",
3013 ".settings/org.eclipse.jdt.core.prefs"
3017 exclude (EXCLUDE_FILES)
3018 include (PROCESS_FILES)
3019 filter(ReplaceTokens,
3023 'Version-Rel': JALVIEW_VERSION,
3024 'Year-Rel': getDate("yyyy")
3029 exclude (EXCLUDE_FILES)
3030 exclude (PROCESS_FILES)
3031 exclude ("appletlib")
3032 exclude ("**/*locales")
3033 exclude ("*locales/**")
3034 exclude ("utils/InstallAnywhere")
3036 exclude (getdown_files_dir)
3037 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
3038 //exclude (getdown_website_dir)
3039 //exclude (getdown_archive_dir)
3041 // exluding these as not using jars as modules yet
3042 exclude ("${j11modDir}/**/*.jar")
3045 include(INCLUDE_FILES)
3047 // from (jalviewDir) {
3048 // // explicit includes for stuff that seemed to not get included
3049 // include(fileTree("test/**/*."))
3050 // exclude(EXCLUDE_FILES)
3051 // exclude(PROCESS_FILES)
3054 from(file(buildProperties).getParent()) {
3055 include(file(buildProperties).getName())
3056 rename(file(buildProperties).getName(), "build_properties")
3058 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
3062 def sourceTarBuildDir = "${buildDir}/sourceTar"
3063 from(sourceTarBuildDir) {
3064 // this includes the appended RELEASE properties file
3068 task dataInstallersJson {
3070 description "Create the installers-VERSION.json data file for installer files created"
3072 mustRunAfter installers
3073 mustRunAfter shadowJar
3074 mustRunAfter sourceDist
3075 mustRunAfter getdownArchive
3077 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
3078 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
3080 if (installersOutputTxt.exists()) {
3081 inputs.file(installersOutputTxt)
3083 if (install4jCheckSums && installersSha256.exists()) {
3084 inputs.file(installersSha256)
3087 shadowJar.archiveFile, // executable JAR
3088 getdownVersionLaunchJvl, // version JVL
3089 sourceDist.archiveFile // source TGZ
3090 ].each { fileName ->
3091 if (file(fileName).exists()) {
3092 inputs.file(fileName)
3096 outputs.file(hugoDataJsonFile)
3099 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
3105 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
3108 dependsOn pubhtmlhelp
3110 inputs.dir("${helpBuildDir}/${help_dir}")
3111 outputs.dir("${buildDir}/distributions/${help_dir}")
3115 task j2sSetHeadlessBuild {
3122 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
3124 description "Enable the alternative J2S Config file for headless build"
3126 outputFile = jalviewjsJ2sSettingsFileName
3127 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
3128 def j2sProps = new Properties()
3129 if (j2sPropsFile.exists()) {
3131 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
3132 j2sProps.load(j2sPropsFileFIS)
3133 j2sPropsFileFIS.close()
3135 j2sProps.each { prop, val ->
3138 } catch (Exception e) {
3139 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
3143 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
3144 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
3149 task jalviewjsSetEclipseWorkspace {
3150 def propKey = "jalviewjs_eclipse_workspace"
3152 if (project.hasProperty(propKey)) {
3153 propVal = project.getProperty(propKey)
3154 if (propVal.startsWith("~/")) {
3155 propVal = System.getProperty("user.home") + propVal.substring(1)
3158 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
3159 def propsFile = file(propsFileName)
3160 def eclipseWsDir = propVal
3161 def props = new Properties()
3163 def writeProps = true
3164 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
3165 def ins = new FileInputStream(propsFileName)
3168 if (props.getProperty(propKey, null) != null) {
3169 eclipseWsDir = props.getProperty(propKey)
3174 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
3175 def tempDir = File.createTempDir()
3176 eclipseWsDir = tempDir.getAbsolutePath()
3179 eclipseWorkspace = file(eclipseWsDir)
3182 // do not run a headless transpile when we claim to be in Eclipse
3184 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3185 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3187 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3191 props.setProperty(propKey, eclipseWsDir)
3192 propsFile.parentFile.mkdirs()
3193 def bytes = new ByteArrayOutputStream()
3194 props.store(bytes, null)
3195 def propertiesString = bytes.toString()
3196 propsFile.text = propertiesString
3202 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3205 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3206 outputs.file(propsFileName)
3207 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3211 task jalviewjsEclipsePaths {
3214 def eclipseRoot = jalviewjs_eclipse_root
3215 if (eclipseRoot.startsWith("~/")) {
3216 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3218 if (OperatingSystem.current().isMacOsX()) {
3219 eclipseRoot += "/Eclipse.app"
3220 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3221 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3222 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3223 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3224 eclipseRoot += "/eclipse"
3226 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3227 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3228 } else { // linux or unix
3229 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3230 eclipseRoot += "/eclipse"
3231 println("eclipseDir exists")
3233 eclipseBinary = "${eclipseRoot}/eclipse"
3234 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3237 eclipseVersion = "4.13" // default
3238 def assumedVersion = true
3239 if (file(eclipseProduct).exists()) {
3240 def fis = new FileInputStream(eclipseProduct)
3241 def props = new Properties()
3243 eclipseVersion = props.getProperty("version")
3245 assumedVersion = false
3248 def propKey = "eclipse_debug"
3249 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3252 // do not run a headless transpile when we claim to be in Eclipse
3254 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3255 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3257 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3260 if (!assumedVersion) {
3261 println("ECLIPSE VERSION=${eclipseVersion}")
3267 task printProperties {
3269 description "Output to console all System.properties"
3271 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3277 dependsOn eclipseProject
3278 dependsOn eclipseClasspath
3279 dependsOn eclipseJdt
3283 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3284 task jalviewjsEclipseCopyDropins(type: Copy) {
3285 dependsOn jalviewjsEclipsePaths
3287 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3288 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3289 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3296 // this eclipse -clean doesn't actually work
3297 task jalviewjsCleanEclipse(type: Exec) {
3298 dependsOn eclipseSetup
3299 dependsOn jalviewjsEclipsePaths
3300 dependsOn jalviewjsEclipseCopyDropins
3302 executable(eclipseBinary)
3303 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3309 def inputString = """exit
3312 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3313 standardInput = inputByteStream
3316 /* not really working yet
3317 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3321 task jalviewjsTransferUnzipSwingJs {
3322 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3326 from zipTree(file_zip)
3327 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3331 inputs.file file_zip
3332 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3336 task jalviewjsTransferUnzipLib {
3337 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3340 zipFiles.each { file_zip ->
3342 from zipTree(file_zip)
3343 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3348 inputs.files zipFiles
3349 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3353 task jalviewjsTransferUnzipAllLibs {
3354 dependsOn jalviewjsTransferUnzipSwingJs
3355 dependsOn jalviewjsTransferUnzipLib
3359 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3361 description "Create the alternative j2s file from the j2s.* properties"
3363 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3364 def siteDirProperty = "j2s.site.directory"
3365 def setSiteDir = false
3366 jalviewjsJ2sProps.each { prop, val ->
3368 if (prop == siteDirProperty) {
3369 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3370 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3376 if (!setSiteDir) { // default site location, don't override specifically set property
3377 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3380 outputFile = jalviewjsJ2sAltSettingsFileName
3383 inputs.properties(jalviewjsJ2sProps)
3384 outputs.file(jalviewjsJ2sAltSettingsFileName)
3389 task jalviewjsEclipseSetup {
3390 dependsOn jalviewjsEclipseCopyDropins
3391 dependsOn jalviewjsSetEclipseWorkspace
3392 dependsOn jalviewjsCreateJ2sSettings
3396 task jalviewjsSyncAllLibs (type: Sync) {
3397 dependsOn jalviewjsTransferUnzipAllLibs
3398 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3399 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3400 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3404 def outputFiles = []
3405 rename { filename ->
3406 outputFiles += "${outputDir}/${filename}"
3413 // should this be exclude really ?
3414 duplicatesStrategy "INCLUDE"
3416 outputs.files outputFiles
3417 inputs.files inputFiles
3421 task jalviewjsSyncResources (type: Sync) {
3422 dependsOn buildResources
3424 def inputFiles = fileTree(dir: resourcesBuildDir)
3425 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3429 def outputFiles = []
3430 rename { filename ->
3431 outputFiles += "${outputDir}/${filename}"
3437 outputs.files outputFiles
3438 inputs.files inputFiles
3442 task jalviewjsSyncSiteResources (type: Sync) {
3443 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3444 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3448 def outputFiles = []
3449 rename { filename ->
3450 outputFiles += "${outputDir}/${filename}"
3456 outputs.files outputFiles
3457 inputs.files inputFiles
3461 task jalviewjsSyncBuildProperties (type: Sync) {
3462 dependsOn createBuildProperties
3463 def inputFiles = [file(buildProperties)]
3464 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3468 def outputFiles = []
3469 rename { filename ->
3470 outputFiles += "${outputDir}/${filename}"
3476 outputs.files outputFiles
3477 inputs.files inputFiles
3481 task jalviewjsProjectImport(type: Exec) {
3482 dependsOn eclipseSetup
3483 dependsOn jalviewjsEclipsePaths
3484 dependsOn jalviewjsEclipseSetup
3487 // do not run a headless import when we claim to be in Eclipse
3489 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3490 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3492 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3496 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3497 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3498 executable(eclipseBinary)
3499 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3503 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3505 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3506 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3509 inputs.file("${jalviewDir}/.project")
3510 outputs.upToDateWhen {
3511 file(projdir).exists()
3516 task jalviewjsTranspile(type: Exec) {
3517 dependsOn jalviewjsEclipseSetup
3518 dependsOn jalviewjsProjectImport
3519 dependsOn jalviewjsEclipsePaths
3521 dependsOn jalviewjsEnableAltFileProperty
3525 // do not run a headless transpile when we claim to be in Eclipse
3527 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3528 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3530 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3534 executable(eclipseBinary)
3535 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3539 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3541 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3542 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3548 stdout = new ByteArrayOutputStream()
3549 stderr = new ByteArrayOutputStream()
3551 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3552 def logOutFile = file(logOutFileName)
3553 logOutFile.createNewFile()
3554 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3555 BINARY: ${eclipseBinary}
3556 VERSION: ${eclipseVersion}
3557 WORKSPACE: ${eclipseWorkspace}
3558 DEBUG: ${eclipseDebug}
3561 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3562 // combine stdout and stderr
3563 def logErrFOS = logOutFOS
3565 if (jalviewjs_j2s_to_console.equals("true")) {
3566 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3567 new org.apache.tools.ant.util.TeeOutputStream(
3571 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3572 new org.apache.tools.ant.util.TeeOutputStream(
3577 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3580 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3587 if (stdout.toString().contains("Error processing ")) {
3588 // j2s did not complete transpile
3589 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3590 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3591 println("IGNORING TRANSPILE ERRORS")
3592 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3594 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3599 inputs.dir("${jalviewDir}/${sourceDir}")
3600 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3601 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3605 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3607 def stdout = new ByteArrayOutputStream()
3608 def stderr = new ByteArrayOutputStream()
3610 def coreFile = file(jsfile)
3612 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3614 logOutFile.createNewFile()
3615 logOutFile.append(msg+"\n")
3617 def coreTop = file(prefixFile)
3618 def coreBottom = file(suffixFile)
3619 coreFile.getParentFile().mkdirs()
3620 coreFile.createNewFile()
3621 coreFile.write( coreTop.getText("UTF-8") )
3625 def t = f.getText("UTF-8")
3626 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3627 coreFile.append( t )
3629 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3631 logOutFile.append(msg+"\n")
3634 coreFile.append( coreBottom.getText("UTF-8") )
3636 msg = "Generating ${zjsfile}"
3638 logOutFile.append(msg+"\n")
3639 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3640 def logErrFOS = logOutFOS
3643 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3644 main = "com.google.javascript.jscomp.CommandLineRunner"
3645 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3646 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3649 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3651 logOutFile.append(msg+"\n")
3653 if (logOutConsole) {
3654 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3655 new org.apache.tools.ant.util.TeeOutputStream(
3659 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3660 new org.apache.tools.ant.util.TeeOutputStream(
3665 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3668 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3675 logOutFile.append(msg+"\n")
3679 task jalviewjsBuildAllCores {
3681 description "Build the core js lib closures listed in the classlists dir"
3682 dependsOn jalviewjsTranspile
3683 dependsOn jalviewjsTransferUnzipSwingJs
3685 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3686 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3687 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3688 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3689 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3690 def prefixFile = "${jsDir}/core/coretop2.js"
3691 def suffixFile = "${jsDir}/core/corebottom2.js"
3693 inputs.file prefixFile
3694 inputs.file suffixFile
3696 def classlistFiles = []
3697 // add the classlists found int the jalviewjs_classlists_dir
3698 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3700 def name = file.getName() - ".txt"
3707 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3708 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3709 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3711 jalviewjsCoreClasslists = []
3713 classlistFiles.each {
3716 def file = hash['file']
3717 if (! file.exists()) {
3718 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3719 return false // this is a "continue" in groovy .each closure
3721 def name = hash['name']
3723 name = file.getName() - ".txt"
3731 def list = fileTree(dir: j2sDir, includes: filelist)
3733 def jsfile = "${outputDir}/core${name}.js"
3734 def zjsfile = "${outputDir}/core${name}.z.js"
3736 jalviewjsCoreClasslists += [
3745 outputs.file(jsfile)
3746 outputs.file(zjsfile)
3749 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3750 def stevesoftClasslistName = "_stevesoft"
3751 def stevesoftClasslist = [
3752 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3753 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3754 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3755 'name': stevesoftClasslistName
3757 jalviewjsCoreClasslists += stevesoftClasslist
3758 inputs.files(stevesoftClasslist['list'])
3759 outputs.file(stevesoftClasslist['jsfile'])
3760 outputs.file(stevesoftClasslist['zjsfile'])
3763 def allClasslistName = "_all"
3764 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3765 allJsFiles += fileTree(
3769 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3770 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3771 "**/org/jmol/export/JSExporter.js"
3774 allJsFiles += fileTree(
3778 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3779 "**/sun/misc/Unsafe.js",
3780 "**/swingjs/jquery/jquery-editable-select.js",
3781 "**/swingjs/jquery/j2sComboBox.js",
3782 "**/sun/misc/FloatingDecimal.js"
3785 def allClasslist = [
3786 'jsfile': "${outputDir}/core${allClasslistName}.js",
3787 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3789 'name': allClasslistName
3791 // not including this version of "all" core at the moment
3792 //jalviewjsCoreClasslists += allClasslist
3793 inputs.files(allClasslist['list'])
3794 outputs.file(allClasslist['jsfile'])
3795 outputs.file(allClasslist['zjsfile'])
3798 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3799 logOutFile.getParentFile().mkdirs()
3800 logOutFile.createNewFile()
3801 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3803 jalviewjsCoreClasslists.each {
3804 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3811 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3814 into file(outputFile).getParentFile()
3815 rename { filename ->
3816 if (filename.equals(inputFile.getName())) {
3817 return file(outputFile).getName()
3821 filter(ReplaceTokens,
3825 'MAIN': '"'+main_class+'"',
3827 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3828 'COREKEY': jalviewjs_core_key,
3829 'CORENAME': coreName
3836 task jalviewjsPublishCoreTemplates {
3837 dependsOn jalviewjsBuildAllCores
3838 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3839 def inputFile = file(inputFileName)
3840 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3842 def outputFiles = []
3843 jalviewjsCoreClasslists.each { cl ->
3844 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3845 cl['outputfile'] = outputFile
3846 outputFiles += outputFile
3850 jalviewjsCoreClasslists.each { cl ->
3851 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3854 inputs.file(inputFile)
3855 outputs.files(outputFiles)
3859 task jalviewjsSyncCore (type: Sync) {
3860 dependsOn jalviewjsBuildAllCores
3861 dependsOn jalviewjsPublishCoreTemplates
3862 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3863 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3867 def outputFiles = []
3868 rename { filename ->
3869 outputFiles += "${outputDir}/${filename}"
3875 outputs.files outputFiles
3876 inputs.files inputFiles
3880 // this Copy version of TransferSiteJs will delete anything else in the target dir
3881 task jalviewjsCopyTransferSiteJs(type: Copy) {
3882 dependsOn jalviewjsTranspile
3883 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3884 into "${jalviewDir}/${jalviewjsSiteDir}"
3888 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3889 task jalviewjsSyncTransferSiteJs(type: Sync) {
3890 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3892 into "${jalviewDir}/${jalviewjsSiteDir}"
3899 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3900 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3901 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3902 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3904 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3905 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3906 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3907 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3910 task jalviewjsPrepareSite {
3912 description "Prepares the website folder including unzipping files and copying resources"
3913 dependsOn jalviewjsSyncAllLibs
3914 dependsOn jalviewjsSyncResources
3915 dependsOn jalviewjsSyncSiteResources
3916 dependsOn jalviewjsSyncBuildProperties
3917 dependsOn jalviewjsSyncCore
3921 task jalviewjsBuildSite {
3923 description "Builds the whole website including transpiled code"
3924 dependsOn jalviewjsCopyTransferSiteJs
3925 dependsOn jalviewjsPrepareSite
3929 task cleanJalviewjsTransferSite {
3931 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3932 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3933 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3934 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3939 task cleanJalviewjsSite {
3940 dependsOn cleanJalviewjsTransferSite
3942 delete "${jalviewDir}/${jalviewjsSiteDir}"
3947 task jalviewjsSiteTar(type: Tar) {
3949 description "Creates a tar.gz file for the website"
3950 dependsOn jalviewjsBuildSite
3951 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3952 archiveFileName = outputFilename
3954 compression Compression.GZIP
3956 from "${jalviewDir}/${jalviewjsSiteDir}"
3957 into jalviewjs_site_dir // this is inside the tar file
3959 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3963 task jalviewjsServer {
3965 def filename = "jalviewjsTest.html"
3966 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3967 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3972 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3973 factory = f.newInstance()
3974 } catch (ClassNotFoundException e) {
3975 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3977 def port = Integer.valueOf(jalviewjs_server_port)
3982 while(port < start+1000 && !running) {
3984 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3985 jalviewjsServer = factory.start(doc_root, port)
3987 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3988 println("SERVER STARTED with document root ${doc_root}.")
3989 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3990 println("For debug: "+url+"?j2sdebug")
3991 println("For verbose: "+url+"?j2sverbose")
3992 } catch (Exception e) {
3997 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3998 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3999 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
4001 jalviewjsCoreClasslists.each { cl ->
4002 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
4004 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
4006 println("For core ${cl.name}: "+urlcore)
4009 file(htmlFile).text = htmlText
4012 outputs.file(htmlFile)
4013 outputs.upToDateWhen({false})
4017 task cleanJalviewjsAll {
4019 description "Delete all configuration and build artifacts to do with JalviewJS build"
4020 dependsOn cleanJalviewjsSite
4021 dependsOn jalviewjsEclipsePaths
4024 delete "${jalviewDir}/${jalviewjsBuildDir}"
4025 delete "${jalviewDir}/${eclipse_bin_dir}"
4026 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
4027 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
4029 delete jalviewjsJ2sAltSettingsFileName
4032 outputs.upToDateWhen( { false } )
4036 task jalviewjsIDE_checkJ2sPlugin {
4037 group "00 JalviewJS in Eclipse"
4038 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
4041 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4042 def j2sPluginFile = file(j2sPlugin)
4043 def eclipseHome = System.properties["eclipse.home.location"]
4044 if (eclipseHome == null || ! IN_ECLIPSE) {
4045 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
4047 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
4048 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
4049 if (altPluginsDir != null && file(altPluginsDir).exists()) {
4050 eclipseJ2sPluginDirs += altPluginsDir
4052 def foundPlugin = false
4053 def j2sPluginFileName = j2sPluginFile.getName()
4054 def eclipseJ2sPlugin
4055 def eclipseJ2sPluginFile
4056 eclipseJ2sPluginDirs.any { dir ->
4057 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
4058 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4059 if (eclipseJ2sPluginFile.exists()) {
4065 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
4066 System.err.println(msg)
4067 throw new StopExecutionException(msg)
4070 def digest = MessageDigest.getInstance("MD5")
4072 digest.update(j2sPluginFile.text.bytes)
4073 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4075 digest.update(eclipseJ2sPluginFile.text.bytes)
4076 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
4078 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
4079 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
4080 System.err.println(msg)
4081 throw new StopExecutionException(msg)
4083 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
4089 task jalviewjsIDE_copyJ2sPlugin {
4090 group "00 JalviewJS in Eclipse"
4091 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
4094 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
4095 def j2sPluginFile = file(j2sPlugin)
4096 def eclipseHome = System.properties["eclipse.home.location"]
4097 if (eclipseHome == null || ! IN_ECLIPSE) {
4098 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
4100 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
4101 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
4102 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
4103 System.err.println(msg)
4106 eclipseJ2sPluginFile.getParentFile().mkdirs()
4107 into eclipseJ2sPluginFile.getParent()
4113 task jalviewjsIDE_j2sFile {
4114 group "00 JalviewJS in Eclipse"
4115 description "Creates the .j2s file"
4116 dependsOn jalviewjsCreateJ2sSettings
4120 task jalviewjsIDE_SyncCore {
4121 group "00 JalviewJS in Eclipse"
4122 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
4123 dependsOn jalviewjsSyncCore
4127 task jalviewjsIDE_SyncSiteAll {
4128 dependsOn jalviewjsSyncAllLibs
4129 dependsOn jalviewjsSyncResources
4130 dependsOn jalviewjsSyncSiteResources
4131 dependsOn jalviewjsSyncBuildProperties
4135 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
4138 task jalviewjsIDE_PrepareSite {
4139 group "00 JalviewJS in Eclipse"
4140 description "Sync libs and resources to site dir, but not closure cores"
4142 dependsOn jalviewjsIDE_SyncSiteAll
4143 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
4147 task jalviewjsIDE_AssembleSite {
4148 group "00 JalviewJS in Eclipse"
4149 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
4150 dependsOn jalviewjsPrepareSite
4154 task jalviewjsIDE_SiteClean {
4155 group "00 JalviewJS in Eclipse"
4156 description "Deletes the Eclipse transpiled site"
4157 dependsOn cleanJalviewjsSite
4161 task jalviewjsIDE_Server {
4162 group "00 JalviewJS in Eclipse"
4163 description "Starts a webserver on localhost to test the website"
4164 dependsOn jalviewjsServer
4168 // buildship runs this at import or gradle refresh
4169 task eclipseSynchronizationTask {
4170 //dependsOn eclipseSetup
4171 dependsOn createBuildProperties
4173 dependsOn jalviewjsIDE_j2sFile
4174 dependsOn jalviewjsIDE_checkJ2sPlugin
4175 dependsOn jalviewjsIDE_PrepareSite
4180 // buildship runs this at build time or project refresh
4181 task eclipseAutoBuildTask {
4182 //dependsOn jalviewjsIDE_checkJ2sPlugin
4183 //dependsOn jalviewjsIDE_PrepareSite
4189 description "Build the site"
4190 dependsOn jalviewjsBuildSite