1 /* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
2 * For properties set within build.gradle, use camelCaseNoSpace.
4 import org.apache.tools.ant.filters.ReplaceTokens
5 import org.gradle.internal.os.OperatingSystem
6 import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
7 import org.gradle.api.internal.PropertiesTransformer
8 import org.gradle.util.ConfigureUtil
9 import org.gradle.plugins.ide.eclipse.model.Output
10 import org.gradle.plugins.ide.eclipse.model.Library
11 import java.security.MessageDigest
12 import java.util.regex.Matcher
13 import groovy.transform.ExternalizeMethods
14 import groovy.util.XmlParser
15 import groovy.xml.XmlUtil
16 import groovy.json.JsonBuilder
17 import com.vladsch.flexmark.util.ast.Node
18 import com.vladsch.flexmark.html.HtmlRenderer
19 import com.vladsch.flexmark.parser.Parser
20 import com.vladsch.flexmark.util.data.MutableDataSet
21 import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
22 import com.vladsch.flexmark.ext.tables.TablesExtension
23 import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
24 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
25 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
26 import com.vladsch.flexmark.ext.toc.TocExtension
27 import com.google.common.hash.HashCode
28 import com.google.common.hash.Hashing
29 import com.google.common.io.Files
30 import org.jsoup.Jsoup
31 import org.jsoup.nodes.Element
39 classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
40 classpath "org.jsoup:jsoup:1.14.3"
41 classpath "com.eowise:gradle-imagemagick:0.5.1"
50 id "com.diffplug.gradle.spotless" version "3.28.0"
51 id 'com.github.johnrengelman.shadow' version '4.0.3'
52 id 'com.install4j.gradle' version '10.0.3'
53 id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
54 id 'com.palantir.git-version' version '0.13.0' apply false
65 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
66 def string(Object o) {
67 return o == null ? "" : o.toString()
70 def overrideProperties(String propsFileName, boolean output = false) {
71 if (propsFileName == null) {
74 def propsFile = file(propsFileName)
75 if (propsFile != null && propsFile.exists()) {
76 println("Using properties from file '${propsFileName}'")
78 def p = new Properties()
79 def localPropsFIS = new FileInputStream(propsFile)
85 if (project.hasProperty(key)) {
86 oldval = project.findProperty(key)
87 project.setProperty(key, val)
89 println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
92 ext.setProperty(key, val)
94 println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
98 } catch (Exception e) {
99 println("Exception reading local.properties")
106 jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
107 jalviewDirRelativePath = jalviewDir
110 getdownChannelName = CHANNEL.toLowerCase()
111 // default to "default". Currently only has different cosmetics for "develop", "release", "default"
112 propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
113 channelDirName = propertiesChannelName
114 // Import channel_properties
115 if (getdownChannelName.startsWith("develop-")) {
116 channelDirName = "develop-SUFFIX"
118 channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
119 channelGradleProperties = string("${channelDir}/channel_gradle.properties")
120 channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
121 overrideProperties(channelGradleProperties, false)
122 // local build environment properties
123 // can be "projectDir/local.properties"
124 overrideProperties("${projectDir}/local.properties", true)
125 // or "../projectDir_local.properties"
126 overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
129 // Import releaseProps from the RELEASE file
130 // or a file specified via JALVIEW_RELEASE_FILE if defined
131 // Expect jalview.version and target release branch in jalview.release
132 releaseProps = new Properties();
133 def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
134 def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
136 (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
137 releaseProps.load(it)
139 } catch (Exception fileLoadError) {
140 throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
143 // Set JALVIEW_VERSION if it is not already set
144 if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
145 JALVIEW_VERSION = releaseProps.get("jalview.version")
147 println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
149 // this property set when running Eclipse headlessly
150 j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
151 // this property set by Eclipse
152 eclipseApplicationProperty = string("eclipse.application")
153 // CHECK IF RUNNING FROM WITHIN ECLIPSE
154 def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
155 IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
156 // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
157 if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
158 println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
162 println("WITHIN ECLIPSE IDE")
164 println("HEADLESS BUILD")
167 J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
169 println("J2S ENABLED")
172 System.properties.sort { it.key }.each {
173 key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
176 if (false && IN_ECLIPSE) {
177 jalviewDir = jalviewDirAbsolutePath
182 buildDate = new Date().format("yyyyMMdd")
185 bareSourceDir = string(source_dir)
186 sourceDir = string("${jalviewDir}/${bareSourceDir}")
187 resourceDir = string("${jalviewDir}/${resource_dir}")
188 bareTestSourceDir = string(test_source_dir)
189 testDir = string("${jalviewDir}/${bareTestSourceDir}")
191 classesDir = string("${jalviewDir}/${classes_dir}")
194 useClover = clover.equals("true")
195 cloverBuildDir = "${buildDir}/clover"
196 cloverInstrDir = file("${cloverBuildDir}/clover-instr")
197 cloverClassesDir = file("${cloverBuildDir}/clover-classes")
198 cloverReportDir = file("${buildDir}/reports/clover")
199 cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
200 cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
201 //cloverTestClassesDir = cloverClassesDir
202 cloverDb = string("${cloverBuildDir}/clover.db")
204 testSourceDir = useClover ? cloverTestInstrDir : testDir
205 testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
208 backgroundImageText = BACKGROUNDIMAGETEXT
209 getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
210 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
211 getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
212 getdownFullArchiveDir = null
213 getdownTextLines = []
214 getdownLaunchJvl = null
215 getdownVersionLaunchJvl = null
217 buildProperties = null
219 // the following values might be overridden by the CHANNEL switch
220 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
221 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
222 getdownArchiveAppBase = getdown_archive_base
223 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
224 getdownAppDistDir = getdown_app_dir_alt
225 getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
226 getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
227 getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
228 reportRsyncCommand = false
229 jvlChannelName = CHANNEL.toLowerCase()
230 install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
231 install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
232 install4jDMGBackgroundImageDir = "${install4j_images_dir}"
233 install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
234 install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
235 install4jInstallerName = "${jalview_name} Non-Release Installer"
236 install4jExecutableName = install4j_executable_name
237 install4jExtraScheme = "jalviewx"
238 install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
239 install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
240 install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
241 install4jBackground = string("${install4j_images_dir}/${install4j_background}")
242 install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
243 install4jCheckSums = true
245 applicationName = "${jalview_name}"
249 // TODO: get bamboo build artifact URL for getdown artifacts
250 getdown_channel_base = bamboo_channelbase
251 getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
252 getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
253 jvlChannelName += "_${getdownChannelName}"
254 // automatically add the test group Not-bamboo for exclusion
255 if ("".equals(testng_excluded_groups)) {
256 testng_excluded_groups = "Not-bamboo"
258 install4jExtraScheme = "jalviewb"
259 backgroundImageText = true
262 case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
263 getdownAppDistDir = getdown_app_dir_release
264 getdownSetAppBaseProperty = true
265 reportRsyncCommand = true
267 install4jInstallerName = "${jalview_name} Installer"
271 getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
272 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
273 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
274 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
275 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
277 package_dir = string("${ARCHIVEDIR}/${package_dir}")
278 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
281 reportRsyncCommand = true
282 install4jExtraScheme = "jalviewa"
286 getdownChannelName = string("archive/${JALVIEW_VERSION}")
287 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
288 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
289 if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
290 throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
292 package_dir = string("${ARCHIVEDIR}/${package_dir}")
293 buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
296 reportRsyncCommand = true
297 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
298 install4jSuffix = "Archive"
299 install4jExtraScheme = "jalviewa"
302 case ~/^DEVELOP-([\.\-\w]*)$/:
303 def suffix = Matcher.lastMatcher[0][1]
304 reportRsyncCommand = true
305 getdownSetAppBaseProperty = true
306 JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
307 install4jSuffix = "Develop ${suffix}"
308 install4jExtraScheme = "jalviewd"
309 install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
310 getdownChannelName = string("develop-${suffix}")
311 getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
312 getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
313 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
314 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
315 channelSuffix = string(suffix)
316 backgroundImageText = true
320 reportRsyncCommand = true
321 getdownSetAppBaseProperty = true
322 // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
323 JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
325 install4jSuffix = "Develop"
326 install4jExtraScheme = "jalviewd"
327 install4jInstallerName = "${jalview_name} Develop Installer"
328 backgroundImageText = true
332 reportRsyncCommand = true
333 getdownSetAppBaseProperty = true
334 // Don't ignore transpile errors for release build
335 if (jalviewjs_ignore_transpile_errors.equals("true")) {
336 jalviewjs_ignore_transpile_errors = "false"
337 println("Setting jalviewjs_ignore_transpile_errors to 'false'")
339 JALVIEW_VERSION = JALVIEW_VERSION+"-test"
340 install4jSuffix = "Test"
341 install4jExtraScheme = "jalviewt"
342 install4jInstallerName = "${jalview_name} Test Installer"
343 backgroundImageText = true
346 case ~/^SCRATCH(|-[-\w]*)$/:
347 getdownChannelName = CHANNEL
348 JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
350 getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
351 getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
352 reportRsyncCommand = true
353 install4jSuffix = "Scratch"
357 if (!file("${LOCALDIR}").exists()) {
358 throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
360 getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
361 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
363 JALVIEW_VERSION = "TEST"
364 install4jSuffix = "Test-Local"
365 install4jExtraScheme = "jalviewt"
366 install4jInstallerName = "${jalview_name} Test Installer"
367 backgroundImageText = true
370 case [ "LOCAL", "JALVIEWJS" ]:
371 JALVIEW_VERSION = "TEST"
372 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
373 getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
374 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
375 install4jExtraScheme = "jalviewl"
376 install4jCheckSums = false
379 default: // something wrong specified
380 throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
384 JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
385 hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
386 hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
387 // override getdownAppBase if requested
388 if (findProperty("getdown_appbase_override") != null) {
389 // revert to LOCAL if empty string
390 if (string(getdown_appbase_override) == "") {
391 getdownAppBase = file(getdownAppBaseDir).toURI().toString()
392 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
393 } else if (string(getdown_appbase_override).startsWith("file://")) {
394 getdownAppBase = string(getdown_appbase_override)
395 getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
397 getdownAppBase = string(getdown_appbase_override)
399 println("Overriding getdown appbase with '${getdownAppBase}'")
401 // sanitise file name for jalview launcher file for this channel
402 jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
403 // install4j application and folder names
404 if (install4jSuffix == "") {
405 install4jBundleId = "${install4j_bundle_id}"
406 install4jWinApplicationId = install4j_release_win_application_id
408 applicationName = "${jalview_name} ${install4jSuffix}"
409 install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
410 // add int hash of install4jSuffix to the last part of the application_id
411 def id = install4j_release_win_application_id
412 def idsplitreverse = id.split("-").reverse()
413 idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
414 install4jWinApplicationId = idsplitreverse.reverse().join("-")
416 // sanitise folder and id names
417 // install4jApplicationFolder = e.g. "Jalview Build"
418 install4jApplicationFolder = applicationName
419 .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
420 .replaceAll("_+", "_") // collapse __
421 install4jInternalId = applicationName
423 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
424 .replaceAll("_+", "") // collapse __
425 //.replaceAll("_*-_*", "-") // collapse _-_
426 install4jUnixApplicationFolder = applicationName
428 .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
429 .replaceAll("_+", "_") // collapse __
430 .replaceAll("_*-_*", "-") // collapse _-_
433 getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
434 getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
435 //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
436 getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
437 getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
438 getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
439 getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
440 /* compile without modules -- using classpath libraries
441 modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
442 modules_runtimeClasspath = modules_compileClasspath
448 apply plugin: "com.palantir.git-version"
449 def details = versionDetails()
450 gitHash = details.gitHash
451 gitBranch = details.branchName
452 } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
453 println("Not in a git repository. Using git values from RELEASE properties file.")
454 gitHash = releaseProps.getProperty("git.hash")
455 gitBranch = releaseProps.getProperty("git.branch")
456 } catch(java.lang.RuntimeException e1) {
457 throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
460 println("Using a ${CHANNEL} profile.")
462 additional_compiler_args = []
463 // configure classpath/args for j8/j11 compilation
464 if (JAVA_VERSION.equals("1.8")) {
465 JAVA_INTEGER_VERSION = string("8")
468 libDistDir = j8libDir
469 compile_source_compatibility = 1.8
470 compile_target_compatibility = 1.8
471 // these are getdown.txt properties defined dependent on the JAVA_VERSION
472 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
473 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
474 // this property is assigned below and expanded to multiple lines in the getdown task
475 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
476 // this property is for the Java library used in eclipse
477 eclipseJavaRuntimeName = string("JavaSE-1.8")
478 } else if (JAVA_VERSION.equals("11")) {
479 JAVA_INTEGER_VERSION = string("11")
481 libDistDir = j11libDir
482 compile_source_compatibility = 11
483 compile_target_compatibility = 11
484 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
485 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
486 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
487 eclipseJavaRuntimeName = string("JavaSE-11")
488 /* compile without modules -- using classpath libraries
489 additional_compiler_args += [
490 '--module-path', modules_compileClasspath.asPath,
491 '--add-modules', j11modules
494 } else if (JAVA_VERSION.equals("17")) {
495 JAVA_INTEGER_VERSION = string("17")
497 libDistDir = j17libDir
498 compile_source_compatibility = 17
499 compile_target_compatibility = 17
500 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
501 getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
502 getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
503 eclipseJavaRuntimeName = string("JavaSE-17")
504 /* compile without modules -- using classpath libraries
505 additional_compiler_args += [
506 '--module-path', modules_compileClasspath.asPath,
507 '--add-modules', j11modules
511 throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
516 JAVA_MIN_VERSION = JAVA_VERSION
517 JAVA_MAX_VERSION = JAVA_VERSION
518 jreInstallsDir = string(jre_installs_dir)
519 if (jreInstallsDir.startsWith("~/")) {
520 jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
522 install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
523 install4jConfFileName = string("jalview-install4j-conf.install4j")
524 install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
525 install4jHomeDir = install4j_home_dir
526 if (install4jHomeDir.startsWith("~/")) {
527 install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
530 resourceBuildDir = string("${buildDir}/resources")
531 resourcesBuildDir = string("${resourceBuildDir}/resources_build")
532 helpBuildDir = string("${resourceBuildDir}/help_build")
533 docBuildDir = string("${resourceBuildDir}/doc_build")
535 if (buildProperties == null) {
536 buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
538 buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
539 helpParentDir = string("${jalviewDir}/${help_parent_dir}")
540 helpSourceDir = string("${helpParentDir}/${help_dir}")
541 helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
544 convertBinaryExpectedLocation = imagemagick_convert
545 if (convertBinaryExpectedLocation.startsWith("~/")) {
546 convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
548 if (file(convertBinaryExpectedLocation).exists()) {
549 convertBinary = convertBinaryExpectedLocation
552 relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
553 jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
554 jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
556 jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
558 jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
560 jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
561 jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
562 jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
563 jalviewjsJalviewCoreHtmlFile = string("")
564 jalviewjsJalviewCoreName = string(jalviewjs_core_name)
565 jalviewjsCoreClasslists = []
566 jalviewjsJalviewTemplateName = string(jalviewjs_name)
567 jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
568 jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
569 jalviewjsJ2sProps = null
570 jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
572 eclipseWorkspace = null
573 eclipseBinary = string("")
574 eclipseVersion = string("")
584 outputDir = file(classesDir)
588 srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
591 compileClasspath = files(sourceSets.main.java.outputDir)
592 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
594 runtimeClasspath = compileClasspath
595 runtimeClasspath += files(sourceSets.main.resources.srcDirs)
600 srcDirs cloverInstrDir
601 outputDir = cloverClassesDir
605 srcDirs = sourceSets.main.resources.srcDirs
608 compileClasspath = files( sourceSets.clover.java.outputDir )
609 //compileClasspath += files( testClassesDir )
610 compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
611 compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
612 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
614 runtimeClasspath = compileClasspath
619 srcDirs testSourceDir
620 outputDir = file(testClassesDir)
624 srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
627 compileClasspath = files( sourceSets.test.java.outputDir )
628 compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
629 compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
631 runtimeClasspath = compileClasspath
632 runtimeClasspath += files(sourceSets.test.resources.srcDirs)
638 // eclipse project and settings files creation, also used by buildship
641 name = eclipse_project_name
643 natures 'org.eclipse.jdt.core.javanature',
644 'org.eclipse.jdt.groovy.core.groovyNature',
645 'org.eclipse.buildship.core.gradleprojectnature'
647 buildCommand 'org.eclipse.jdt.core.javabuilder'
648 buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
652 //defaultOutputDir = sourceSets.main.java.outputDir
653 configurations.each{ c->
654 if (c.isCanBeResolved()) {
655 minusConfigurations += [c]
659 plusConfigurations = [ ]
663 def removeTheseToo = []
664 HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
665 cp.entries.each { entry ->
666 // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
667 // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
668 // we add the resources and help/help dirs in as libs afterwards (see below)
669 if (entry.kind == 'src') {
670 if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
671 removeTheseToo += entry
673 alreadyAddedSrcPath.putAt(entry.path, true)
678 cp.entries.removeAll(removeTheseToo)
680 //cp.entries += new Output("${eclipse_bin_dir}/main")
681 if (file(helpParentDir).isDirectory()) {
682 cp.entries += new Library(fileReference(helpParentDir))
684 if (file(resourceDir).isDirectory()) {
685 cp.entries += new Library(fileReference(resourceDir))
688 HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
690 sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
691 //don't want to add outputDir as eclipse is using its own output dir in bin/main
692 if (it.isDirectory() || ! it.exists()) {
693 // don't add dirs to classpath, especially if they don't exist
694 return false // groovy "continue" in .any closure
696 def itPath = it.toString()
697 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
698 // make relative path
699 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
701 if (alreadyAddedLibPath.get(itPath)) {
702 //println("Not adding duplicate entry "+itPath)
704 //println("Adding entry "+itPath)
705 cp.entries += new Library(fileReference(itPath))
706 alreadyAddedLibPath.put(itPath, true)
710 sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
711 //no longer want to add outputDir as eclipse is using its own output dir in bin/main
712 if (it.isDirectory() || ! it.exists()) {
713 // don't add dirs to classpath
714 return false // groovy "continue" in .any closure
717 def itPath = it.toString()
718 if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
719 itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
721 if (alreadyAddedLibPath.get(itPath)) {
724 def lib = new Library(fileReference(itPath))
725 lib.entryAttributes["test"] = "true"
727 alreadyAddedLibPath.put(itPath, true)
735 containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
740 // for the IDE, use java 11 compatibility
741 sourceCompatibility = compile_source_compatibility
742 targetCompatibility = compile_target_compatibility
743 javaRuntimeName = eclipseJavaRuntimeName
745 // add in jalview project specific properties/preferences into eclipse core preferences
747 withProperties { props ->
748 def jalview_prefs = new Properties()
749 def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
750 jalview_prefs.load(ins)
752 jalview_prefs.forEach { t, v ->
753 if (props.getAt(t) == null) {
757 // codestyle file -- overrides previous formatter prefs
758 def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
759 if (csFile.exists()) {
760 XmlParser parser = new XmlParser()
761 def profiles = parser.parse(csFile)
762 def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
763 if (profile != null) {
764 profile.'setting'.each { s ->
766 def value = s.'@value'
767 if (id != null && value != null) {
768 props.putAt(id, value)
779 // Don't want these to be activated if in headless build
780 synchronizationTasks "eclipseSynchronizationTask"
781 //autoBuildTasks "eclipseAutoBuildTask"
787 /* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
788 // Class to allow updating arbitrary properties files
789 class PropertiesFile extends PropertiesPersistableConfigurationObject {
790 public PropertiesFile(PropertiesTransformer t) { super(t); }
791 @Override protected void load(Properties properties) { }
792 @Override protected void store(Properties properties) { }
793 @Override protected String getDefaultResourceName() { return ""; }
794 // This is necessary, because PropertiesPersistableConfigurationObject fails
795 // if no default properties file exists.
796 @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
799 // Task to update arbitrary properties files (set outputFile)
800 class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
801 private final PropertiesFileContentMerger file;
802 public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
803 protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
804 protected void configure(PropertiesFile props) {
805 file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
807 public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
810 task eclipseUIPreferences(type: PropertiesFileTask) {
811 description = "Generate Eclipse additional settings"
812 def filename = "org.eclipse.jdt.ui.prefs"
813 outputFile = "$projectDir/.settings/${filename}" as File
816 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
821 task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
822 description = "Generate Eclipse additional settings"
823 def filename = "org.eclipse.jdt.groovy.core.prefs"
824 outputFile = "$projectDir/.settings/${filename}" as File
827 it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
832 task eclipseAllPreferences {
834 dependsOn eclipseUIPreferences
835 dependsOn eclipseGroovyCorePreferences
838 eclipseUIPreferences.mustRunAfter eclipseJdt
839 eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
841 /* end of eclipse preferences hack */
849 delete cloverBuildDir
850 delete cloverReportDir
855 task cloverInstrJava(type: JavaExec) {
856 group = "Verification"
857 description = "Create clover instrumented source java files"
859 dependsOn cleanClover
861 inputs.files(sourceSets.main.allJava)
862 outputs.dir(cloverInstrDir)
864 //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
865 classpath = sourceSets.clover.compileClasspath
866 main = "com.atlassian.clover.CloverInstr"
874 cloverInstrDir.getPath(),
876 def srcFiles = sourceSets.main.allJava.files
879 { file -> file.absolutePath }
882 args argsList.toArray()
885 delete cloverInstrDir
886 println("Clover: About to instrument "+srcFiles.size() +" files")
891 task cloverInstrTests(type: JavaExec) {
892 group = "Verification"
893 description = "Create clover instrumented source test files"
895 dependsOn cleanClover
897 inputs.files(testDir)
898 outputs.dir(cloverTestInstrDir)
900 classpath = sourceSets.clover.compileClasspath
901 main = "com.atlassian.clover.CloverInstr"
911 cloverTestInstrDir.getPath(),
913 args argsList.toArray()
916 delete cloverTestInstrDir
917 println("Clover: About to instrument test files")
923 group = "Verification"
924 description = "Create clover instrumented all source files"
926 dependsOn cloverInstrJava
927 dependsOn cloverInstrTests
931 cloverClasses.dependsOn cloverInstr
934 task cloverConsoleReport(type: JavaExec) {
935 group = "Verification"
936 description = "Creates clover console report"
939 file(cloverDb).exists()
942 inputs.dir cloverClassesDir
944 classpath = sourceSets.clover.runtimeClasspath
945 main = "com.atlassian.clover.reporters.console.ConsoleReporter"
947 if (cloverreport_mem.length() > 0) {
948 maxHeapSize = cloverreport_mem
950 if (cloverreport_jvmargs.length() > 0) {
951 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
961 args argsList.toArray()
965 task cloverHtmlReport(type: JavaExec) {
966 group = "Verification"
967 description = "Creates clover HTML report"
970 file(cloverDb).exists()
973 def cloverHtmlDir = cloverReportDir
974 inputs.dir cloverClassesDir
975 outputs.dir cloverHtmlDir
977 classpath = sourceSets.clover.runtimeClasspath
978 main = "com.atlassian.clover.reporters.html.HtmlReporter"
980 if (cloverreport_mem.length() > 0) {
981 maxHeapSize = cloverreport_mem
983 if (cloverreport_jvmargs.length() > 0) {
984 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
995 if (cloverreport_html_options.length() > 0) {
996 argsList += cloverreport_html_options.split(" ")
999 args argsList.toArray()
1003 task cloverXmlReport(type: JavaExec) {
1004 group = "Verification"
1005 description = "Creates clover XML report"
1008 file(cloverDb).exists()
1011 def cloverXmlFile = "${cloverReportDir}/clover.xml"
1012 inputs.dir cloverClassesDir
1013 outputs.file cloverXmlFile
1015 classpath = sourceSets.clover.runtimeClasspath
1016 main = "com.atlassian.clover.reporters.xml.XMLReporter"
1018 if (cloverreport_mem.length() > 0) {
1019 maxHeapSize = cloverreport_mem
1021 if (cloverreport_jvmargs.length() > 0) {
1022 jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
1033 if (cloverreport_xml_options.length() > 0) {
1034 argsList += cloverreport_xml_options.split(" ")
1037 args argsList.toArray()
1042 group = "Verification"
1043 description = "Creates clover reports"
1045 dependsOn cloverXmlReport
1046 dependsOn cloverHtmlReport
1053 sourceCompatibility = compile_source_compatibility
1054 targetCompatibility = compile_target_compatibility
1055 options.compilerArgs += additional_compiler_args
1056 print ("Setting target compatibility to "+targetCompatibility+"\n")
1058 //classpath += configurations.cloverRuntime
1064 // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
1065 sourceCompatibility = compile_source_compatibility
1066 targetCompatibility = compile_target_compatibility
1067 options.compilerArgs = additional_compiler_args
1068 options.encoding = "UTF-8"
1070 print ("Setting target compatibility to "+compile_target_compatibility+"\n")
1077 sourceCompatibility = compile_source_compatibility
1078 targetCompatibility = compile_target_compatibility
1079 options.compilerArgs = additional_compiler_args
1081 print ("Setting target compatibility to "+targetCompatibility+"\n")
1088 delete sourceSets.main.java.outputDir
1094 dependsOn cleanClover
1096 delete sourceSets.test.java.outputDir
1101 // format is a string like date.format("dd MMMM yyyy")
1102 def getDate(format) {
1103 return date.format(format)
1107 def convertMdToHtml (FileTree mdFiles, File cssFile) {
1108 MutableDataSet options = new MutableDataSet()
1110 def extensions = new ArrayList<>()
1111 extensions.add(AnchorLinkExtension.create())
1112 extensions.add(AutolinkExtension.create())
1113 extensions.add(StrikethroughExtension.create())
1114 extensions.add(TaskListExtension.create())
1115 extensions.add(TablesExtension.create())
1116 extensions.add(TocExtension.create())
1118 options.set(Parser.EXTENSIONS, extensions)
1120 // set GFM table parsing options
1121 options.set(TablesExtension.WITH_CAPTION, false)
1122 options.set(TablesExtension.COLUMN_SPANS, false)
1123 options.set(TablesExtension.MIN_HEADER_ROWS, 1)
1124 options.set(TablesExtension.MAX_HEADER_ROWS, 1)
1125 options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
1126 options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
1127 options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
1129 options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
1130 options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
1131 options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
1132 options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
1134 Parser parser = Parser.builder(options).build()
1135 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1137 mdFiles.each { mdFile ->
1138 // add table of contents
1139 def mdText = "[TOC]\n"+mdFile.text
1141 // grab the first top-level title
1143 def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
1144 def matcher = mdText =~ titleRegex
1145 if (matcher.size() > 0) {
1146 // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
1147 title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
1149 // or use the filename if none found
1150 if (title == null) {
1151 title = mdFile.getName()
1154 Node document = parser.parse(mdText)
1155 String htmlBody = renderer.render(document)
1156 def htmlText = '''<html>
1157 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1158 <html xmlns="http://www.w3.org/1999/xhtml">
1160 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1161 <meta http-equiv="Content-Style-Type" content="text/css" />
1162 <meta name="generator" content="flexmark" />
1164 htmlText += ((title != null) ? " <title>${title}</title>" : '' )
1166 <style type="text/css">code{white-space: pre;}</style>
1168 htmlText += ((cssFile != null) ? cssFile.text : '')
1169 htmlText += '''</head>
1172 htmlText += htmlBody
1178 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1179 def htmlFile = file(htmlFilePath)
1180 println("Creating ${htmlFilePath}")
1181 htmlFile.text = htmlText
1186 task copyDocs(type: Copy) {
1187 def inputDir = "${jalviewDir}/${doc_dir}"
1188 def outputDir = "${docBuildDir}/${doc_dir}"
1192 include('**/*.html')
1194 filter(ReplaceTokens,
1198 'Version-Rel': JALVIEW_VERSION,
1199 'Year-Rel': getDate("yyyy")
1206 exclude('**/*.html')
1211 inputs.dir(inputDir)
1212 outputs.dir(outputDir)
1216 task convertMdFiles {
1218 def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
1219 def cssFile = file("${jalviewDir}/${flexmark_css}")
1222 convertMdToHtml(mdFiles, cssFile)
1225 inputs.files(mdFiles)
1226 inputs.file(cssFile)
1229 mdFiles.each { mdFile ->
1230 def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
1231 htmlFiles.add(file(htmlFilePath))
1233 outputs.files(htmlFiles)
1237 def hugoTemplateSubstitutions(String input, Map extras=null) {
1238 def replacements = [
1239 DATE: getDate("yyyy-MM-dd"),
1240 CHANNEL: propertiesChannelName,
1241 APPLICATION_NAME: applicationName,
1243 GIT_BRANCH: gitBranch,
1244 VERSION: JALVIEW_VERSION,
1245 JAVA_VERSION: JAVA_VERSION,
1246 VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
1251 if (extras != null) {
1252 extras.each{ k, v ->
1253 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1256 replacements.each{ k, v ->
1257 output = output.replaceAll("__${k}__", ((v == null)?"":v))
1262 def mdFileComponents(File mdFile, def dateOnly=false) {
1265 if (mdFile.exists()) {
1266 def inFrontMatter = false
1267 def firstLine = true
1268 mdFile.eachLine { line ->
1269 if (line.matches("---")) {
1270 def prev = inFrontMatter
1271 inFrontMatter = firstLine
1272 if (inFrontMatter != prev)
1275 if (inFrontMatter) {
1277 if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
1278 map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
1279 } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
1280 map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
1281 } else if (m = line =~ /^channel:\s*(\S+)/) {
1282 map["channel"] = m[0][1]
1283 } else if (m = line =~ /^version:\s*(\S+)/) {
1284 map["version"] = m[0][1]
1285 } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
1286 map[ m[0][1] ] = m[0][2]
1288 if (dateOnly && map["date"] != null) {
1294 content += line+"\n"
1299 return dateOnly ? map["date"] : [map, content]
1302 task hugoTemplates {
1304 description "Create partially populated md pages for hugo website build"
1306 def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
1307 def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
1308 def templateFiles = fileTree(dir: hugoTemplatesDir)
1309 def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1310 def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1311 def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
1312 def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
1315 // specific release template for version archive
1318 def givenDate = null
1319 def givenChannel = null
1320 def givenVersion = null
1321 if (CHANNEL == "RELEASE") {
1322 def (map, content) = mdFileComponents(releaseMdFile)
1323 givenDate = map.date
1324 givenChannel = map.channel
1325 givenVersion = map.version
1327 if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
1328 throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
1331 if (whatsnewMdFile.exists())
1332 whatsnew = whatsnewMdFile.text
1335 def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
1336 def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
1338 def changesHugo = null
1339 if (changes != null) {
1340 changesHugo = '<div class="release_notes">\n\n'
1341 def inSection = false
1342 changes.eachLine { line ->
1344 if (m = line =~ /^##([^#].*)$/) {
1346 changesHugo += "</div>\n\n"
1348 def section = m[0][1].trim()
1349 section = section.toLowerCase()
1350 section = section.replaceAll(/ +/, "_")
1351 section = section.replaceAll(/[^a-z0-9_\-]/, "")
1352 changesHugo += "<div class=\"${section}\">\n\n"
1354 } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
1355 def comment = m[0][2].trim()
1356 if (comment != "") {
1357 comment = comment.replaceAll('"', """)
1359 comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
1360 def newline = m[0][1]
1361 if (comment.trim() != "")
1362 newline += "{{<comment>}}${comment}{{</comment>}} "
1363 newline += m[0][3].trim()
1364 if (issuekeys.size() > 0)
1365 newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
1366 if (m[0][4] != null)
1371 changesHugo += line+"\n"
1374 changesHugo += "\n</div>\n\n"
1376 changesHugo += '</div>'
1379 templateFiles.each{ templateFile ->
1380 def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
1381 def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
1382 def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
1384 def outPathName = string("${hugoBuildDir}/$newRelPathName")
1388 rename(templateFile.getName(), newFileName)
1392 def newFile = file("${outPathName}/${newFileName}".toString())
1393 def content = newFile.text
1394 newFile.text = hugoTemplateSubstitutions(content,
1397 CHANGES: changesHugo,
1398 DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
1399 DRAFT: givenDate == null ? "true" : "false",
1400 JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
1401 JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
1408 inputs.file(oldJvlFile)
1409 inputs.dir(hugoTemplatesDir)
1410 inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
1411 inputs.property("CHANNEL", { CHANNEL })
1414 def getMdDate(File mdFile) {
1415 return mdFileComponents(mdFile, true)
1418 def getMdSections(String content) {
1420 def sectionContent = ""
1421 def sectionName = null
1422 content.eachLine { line ->
1424 if (m = line =~ /^##([^#].*)$/) {
1425 if (sectionName != null) {
1426 sections[sectionName] = sectionContent
1430 sectionName = m[0][1].trim()
1431 sectionName = sectionName.toLowerCase()
1432 sectionName = sectionName.replaceAll(/ +/, "_")
1433 sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
1434 } else if (sectionName != null) {
1435 sectionContent += line+"\n"
1438 if (sectionContent != null) {
1439 sections[sectionName] = sectionContent
1445 task copyHelp(type: Copy) {
1446 def inputDir = helpSourceDir
1447 def outputDir = "${helpBuildDir}/${help_dir}"
1451 include('**/*.html')
1455 filter(ReplaceTokens,
1459 'Version-Rel': JALVIEW_VERSION,
1460 'Year-Rel': getDate("yyyy")
1467 exclude('**/*.html')
1474 inputs.dir(inputDir)
1475 outputs.files(helpFile)
1476 outputs.dir(outputDir)
1480 task releasesTemplates {
1482 description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
1486 def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
1487 def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
1488 def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
1489 def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
1490 def releasesMdDir = "${jalviewDir}/${releases_dir}"
1491 def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
1494 def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
1495 def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
1497 if (CHANNEL == "RELEASE") {
1498 if (!releaseMdFile.exists()) {
1499 throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
1501 if (!whatsnewMdFile.exists()) {
1502 throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
1506 def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
1507 def releaseFilesDates = releaseFiles.collectEntries {
1508 [(it): getMdDate(it)]
1510 releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
1512 def releasesTemplate = releasesTemplateFile.text
1513 def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
1514 def versionTemplate = m[0][1]
1516 MutableDataSet options = new MutableDataSet()
1518 def extensions = new ArrayList<>()
1519 options.set(Parser.EXTENSIONS, extensions)
1520 options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
1522 Parser parser = Parser.builder(options).build()
1523 HtmlRenderer renderer = HtmlRenderer.builder(options).build()
1525 def actualVersions = releaseFiles.collect { rf ->
1526 def (rfMap, rfContent) = mdFileComponents(rf)
1527 return rfMap.version
1529 def versionsHtml = ""
1530 def linkedVersions = []
1531 releaseFiles.reverse().each { rFile ->
1532 def (rMap, rContent) = mdFileComponents(rFile)
1534 def versionLink = ""
1535 def partialVersion = ""
1536 def firstPart = true
1537 rMap.version.split("\\.").each { part ->
1538 def displayPart = ( firstPart ? "" : "." ) + part
1539 partialVersion += displayPart
1541 linkedVersions.contains(partialVersion)
1542 || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
1544 versionLink += displayPart
1546 versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
1547 linkedVersions += partialVersion
1551 def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
1554 def rContentProcessed = ""
1555 rContent.eachLine { line ->
1556 if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
1557 line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
1558 } else if (lm = line =~ /^###([^#]+.*)$/) {
1559 line = "_${lm[0][1].trim()}_"
1561 rContentProcessed += line + "\n"
1564 def rContentSections = getMdSections(rContentProcessed)
1565 def rVersion = versionTemplate
1566 if (rVersion != "") {
1567 def rNewFeatures = rContentSections["new_features"]
1568 def rIssuesResolved = rContentSections["issues_resolved"]
1569 Node newFeaturesNode = parser.parse(rNewFeatures)
1570 String newFeaturesHtml = renderer.render(newFeaturesNode)
1571 Node issuesResolvedNode = parser.parse(rIssuesResolved)
1572 String issuesResolvedHtml = renderer.render(issuesResolvedNode)
1573 rVersion = hugoTemplateSubstitutions(rVersion,
1575 VERSION: rMap.version,
1576 VERSION_LINK: versionLink,
1577 DISPLAY_DATE: displayDate,
1578 NEW_FEATURES: newFeaturesHtml,
1579 ISSUES_RESOLVED: issuesResolvedHtml
1582 versionsHtml += rVersion
1586 releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
1587 releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
1588 releasesHtmlFile.text = releasesTemplate
1590 if (whatsnewMdFile.exists()) {
1591 def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
1592 def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
1593 Node whatsnewNode = parser.parse(whatsnewMd)
1594 String whatsnewHtml = renderer.render(whatsnewNode)
1595 whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
1596 whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
1598 VERSION: JALVIEW_VERSION,
1599 DISPLAY_DATE: wnDisplayDate
1602 } else if (gradle.taskGraph.hasTask(":linkCheck")) {
1603 whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
1608 inputs.file(releasesTemplateFile)
1609 inputs.file(whatsnewTemplateFile)
1610 inputs.dir(releasesMdDir)
1611 inputs.dir(whatsnewMdDir)
1612 outputs.file(releasesHtmlFile)
1613 outputs.file(whatsnewHtmlFile)
1617 task copyResources(type: Copy) {
1619 description = "Copy (and make text substitutions in) the resources dir to the build area"
1621 def inputDir = resourceDir
1622 def outputDir = resourcesBuildDir
1626 include('**/*.html')
1628 filter(ReplaceTokens,
1632 'Version-Rel': JALVIEW_VERSION,
1633 'Year-Rel': getDate("yyyy")
1640 exclude('**/*.html')
1645 inputs.dir(inputDir)
1646 outputs.dir(outputDir)
1649 task copyChannelResources(type: Copy) {
1650 dependsOn copyResources
1652 description = "Copy the channel resources dir to the build resources area"
1654 def inputDir = "${channelDir}/${resource_dir}"
1655 def outputDir = resourcesBuildDir
1657 include(channel_props)
1658 filter(ReplaceTokens,
1662 'SUFFIX': channelSuffix
1667 exclude(channel_props)
1671 inputs.dir(inputDir)
1672 outputs.dir(outputDir)
1675 task createBuildProperties(type: WriteProperties) {
1676 dependsOn copyResources
1678 description = "Create the ${buildProperties} file"
1680 inputs.dir(sourceDir)
1681 inputs.dir(resourcesBuildDir)
1682 outputFile (buildProperties)
1683 // taking time specific comment out to allow better incremental builds
1684 comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
1685 //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
1686 property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
1687 property "VERSION", JALVIEW_VERSION
1688 property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
1689 property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
1690 if (getdownSetAppBaseProperty) {
1691 property "GETDOWNAPPBASE", getdownAppBase
1692 property "GETDOWNAPPDISTDIR", getdownAppDistDir
1694 outputs.file(outputFile)
1698 task buildIndices(type: JavaExec) {
1700 classpath = sourceSets.main.compileClasspath
1701 main = "com.sun.java.help.search.Indexer"
1702 workingDir = "${helpBuildDir}/${help_dir}"
1705 inputs.dir("${workingDir}/${argDir}")
1707 outputs.dir("${classesDir}/doc")
1708 outputs.dir("${classesDir}/help")
1709 outputs.file("${workingDir}/JavaHelpSearch/DOCS")
1710 outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
1711 outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
1712 outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
1713 outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
1714 outputs.file("${workingDir}/JavaHelpSearch/TMAP")
1717 task buildResources {
1718 dependsOn copyResources
1719 dependsOn copyChannelResources
1720 dependsOn createBuildProperties
1724 dependsOn buildResources
1727 dependsOn releasesTemplates
1728 dependsOn convertMdFiles
1729 dependsOn buildIndices
1733 compileJava.dependsOn prepare
1734 run.dependsOn compileJava
1735 //run.dependsOn prepare
1738 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
1743 dependsOn cloverClasses
1745 dependsOn compileJava //?
1749 includeGroups testng_groups
1750 excludeGroups testng_excluded_groups
1752 useDefaultListeners=true
1755 maxHeapSize = "4096m"
1756 jvmArgs '-Xmx4096m', '-Xms4096m'
1760 maxParallelForks = 1
1763 jvmArgs '-Xmx2048m', '-Xms2048m'
1766 workingDir = jalviewDir
1767 def testLaf = project.findProperty("test_laf")
1768 if (testLaf != null) {
1769 println("Setting Test LaF to '${testLaf}'")
1770 systemProperty "laf", testLaf
1772 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1773 if (testHiDPIScale != null) {
1774 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1775 systemProperty "sun.java2d.uiScale", testHiDPIScale
1777 sourceCompatibility = compile_source_compatibility
1778 targetCompatibility = compile_target_compatibility
1779 jvmArgs += additional_compiler_args
1783 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1789 task compileLinkCheck(type: JavaCompile) {
1791 classpath = files("${jalviewDir}/${utils_dir}")
1792 destinationDir = file("${jalviewDir}/${utils_dir}")
1793 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1795 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1796 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1797 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1798 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1802 task linkCheck(type: JavaExec) {
1804 dependsOn compileLinkCheck
1806 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1807 classpath = files("${jalviewDir}/${utils_dir}")
1808 main = "HelpLinksChecker"
1809 workingDir = "${helpBuildDir}"
1810 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1812 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1813 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1816 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1820 inputs.dir(helpBuildDir)
1821 outputs.file(helpLinksCheckerOutFile)
1825 // import the pubhtmlhelp target
1826 ant.properties.basedir = "${jalviewDir}"
1827 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1828 ant.importBuild "${utils_dir}/publishHelp.xml"
1831 task cleanPackageDir(type: Delete) {
1833 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1843 attributes "Main-Class": main_class,
1844 "Permissions": "all-permissions",
1845 "Application-Name": applicationName,
1846 "Codebase": application_codebase,
1847 "Implementation-Version": JALVIEW_VERSION
1850 def outputDir = "${jalviewDir}/${package_dir}"
1851 destinationDirectory = file(outputDir)
1852 archiveFileName = rootProject.name+".jar"
1853 duplicatesStrategy "EXCLUDE"
1860 exclude "**/*.jar.*"
1862 inputs.dir(sourceSets.main.java.outputDir)
1863 sourceSets.main.resources.srcDirs.each{ dir ->
1866 outputs.file("${outputDir}/${archiveFileName}")
1870 task copyJars(type: Copy) {
1871 from fileTree(dir: classesDir, include: "**/*.jar").files
1872 into "${jalviewDir}/${package_dir}"
1876 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1877 task syncJars(type: Sync) {
1879 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1880 into "${jalviewDir}/${package_dir}"
1882 include jar.archiveFileName.getOrNull()
1889 description = "Put all required libraries in dist"
1890 // order of "cleanPackageDir", "copyJars", "jar" important!
1891 jar.mustRunAfter cleanPackageDir
1892 syncJars.mustRunAfter cleanPackageDir
1893 dependsOn cleanPackageDir
1896 outputs.dir("${jalviewDir}/${package_dir}")
1901 dependsOn cleanPackageDir
1908 group = "distribution"
1909 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1913 from ("${jalviewDir}/${libDistDir}") {
1917 attributes "Implementation-Version": JALVIEW_VERSION,
1918 "Application-Name": applicationName
1921 duplicatesStrategy "INCLUDE"
1923 mainClassName = shadow_jar_main_class
1925 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1929 task getdownImagesCopy() {
1930 inputs.dir getdownImagesDir
1931 outputs.dir getdownImagesBuildDir
1935 from(getdownImagesDir) {
1936 include("*getdown*.png")
1938 into getdownImagesBuildDir
1943 task getdownImagesProcess() {
1944 dependsOn getdownImagesCopy
1947 if (backgroundImageText) {
1948 if (convertBinary == null) {
1949 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
1951 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
1952 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
1954 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
1956 executable convertBinary
1959 '-font', getdown_background_image_text_font,
1960 '-fill', getdown_background_image_text_colour,
1961 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
1962 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
1963 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
1972 task getdownImages() {
1973 dependsOn getdownImagesProcess
1976 task getdownWebsite() {
1977 group = "distribution"
1978 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1980 dependsOn getdownImages
1985 def getdownWebsiteResourceFilenames = []
1986 def getdownResourceDir = getdownResourceDir
1987 def getdownResourceFilenames = []
1990 // clean the getdown website and files dir before creating getdown folders
1991 delete getdownAppBaseDir
1992 delete getdownFilesDir
1995 from buildProperties
1996 rename(file(buildProperties).getName(), getdown_build_properties)
1999 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2002 from channelPropsFile
2003 filter(ReplaceTokens,
2007 'SUFFIX': channelSuffix
2010 into getdownAppBaseDir
2012 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2014 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2015 def props = project.properties.sort { it.key }
2016 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2017 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2019 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2020 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2022 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2023 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2025 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2026 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2027 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2028 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2029 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2030 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2031 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2034 props.put("getdown_txt_title", jalview_name)
2035 props.put("getdown_txt_ui.name", applicationName)
2037 // start with appbase
2038 getdownTextLines += "appbase = ${getdownAppBase}"
2039 props.each{ prop, val ->
2040 if (prop.startsWith("getdown_txt_") && val != null) {
2041 if (prop.startsWith("getdown_txt_multi_")) {
2042 def key = prop.substring(18)
2043 val.split(",").each{ v ->
2044 def line = "${key} = ${v}"
2045 getdownTextLines += line
2048 // file values rationalised
2049 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2051 if (val.indexOf('/') == 0) {
2054 } else if (val.indexOf('/') > 0) {
2055 // relative path (relative to jalviewDir)
2056 r = file( "${jalviewDir}/${val}" )
2059 val = "${getdown_resource_dir}/" + r.getName()
2060 getdownWebsiteResourceFilenames += val
2061 getdownResourceFilenames += r.getPath()
2064 if (! prop.startsWith("getdown_txt_resource")) {
2065 def line = prop.substring(12) + " = ${val}"
2066 getdownTextLines += line
2072 getdownWebsiteResourceFilenames.each{ filename ->
2073 getdownTextLines += "resource = ${filename}"
2075 getdownResourceFilenames.each{ filename ->
2078 into getdownResourceDir
2082 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2083 getdownWrapperScripts.each{ script ->
2084 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2088 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2090 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2095 fileTree(file(package_dir)).each{ f ->
2096 if (f.isDirectory()) {
2097 def files = fileTree(dir: f, include: ["*"]).getFiles()
2099 } else if (f.exists()) {
2103 def jalviewJar = jar.archiveFileName.getOrNull()
2104 // put jalview.jar first for CLASSPATH and .properties files reasons
2105 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2106 def name = f.getName()
2107 def line = "code = ${getdownAppDistDir}/${name}"
2108 getdownTextLines += line
2115 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2117 if (JAVA_VERSION.equals("11")) {
2118 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2119 j11libFiles.sort().each{f ->
2120 def name = f.getName()
2121 def line = "code = ${getdown_j11lib_dir}/${name}"
2122 getdownTextLines += line
2125 into getdownJ11libDir
2131 // 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.
2132 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2133 getdownTextLines += "resource = ${getdown_launcher_new}"
2134 getdownTextLines += "class = ${main_class}"
2135 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2136 if (getdownSetAppBaseProperty) {
2137 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2138 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2141 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2142 getdownTxt.write(getdownTextLines.join("\n"))
2144 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2145 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2146 launchJvl.write("appbase=${getdownAppBase}")
2148 // files going into the getdown website dir: getdown-launcher.jar
2150 from getdownLauncher
2151 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2152 into getdownAppBaseDir
2155 // files going into the getdown website dir: getdown-launcher(-local).jar
2157 from getdownLauncher
2158 if (file(getdownLauncher).getName() != getdown_launcher) {
2159 rename(file(getdownLauncher).getName(), getdown_launcher)
2161 into getdownAppBaseDir
2164 // files going into the getdown website dir: ./install dir and files
2165 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2168 from getdownLauncher
2169 from "${getdownAppDir}/${getdown_build_properties}"
2170 if (file(getdownLauncher).getName() != getdown_launcher) {
2171 rename(file(getdownLauncher).getName(), getdown_launcher)
2173 into getdownInstallDir
2176 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2178 from getdownInstallDir
2179 into getdownFilesInstallDir
2183 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2187 from getdownLauncher
2188 from "${getdownAppBaseDir}/${getdown_build_properties}"
2189 from "${getdownAppBaseDir}/${channel_props}"
2190 if (file(getdownLauncher).getName() != getdown_launcher) {
2191 rename(file(getdownLauncher).getName(), getdown_launcher)
2193 into getdownFilesDir
2196 // and ./resource (not all downloaded by getdown)
2198 from getdownResourceDir
2199 into "${getdownFilesDir}/${getdown_resource_dir}"
2204 inputs.dir("${jalviewDir}/${package_dir}")
2206 outputs.dir(getdownAppBaseDir)
2207 outputs.dir(getdownFilesDir)
2211 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2212 task getdownDigestDir(type: JavaExec) {
2214 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2216 def digestDirPropertyName = "DIGESTDIR"
2218 classpath = files(getdownLauncher)
2219 def digestDir = findProperty(digestDirPropertyName)
2220 if (digestDir == null) {
2221 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2225 main = "com.threerings.getdown.tools.Digester"
2229 task getdownDigest(type: JavaExec) {
2230 group = "distribution"
2231 description = "Digest the getdown website folder"
2232 dependsOn getdownWebsite
2234 classpath = files(getdownLauncher)
2236 main = "com.threerings.getdown.tools.Digester"
2237 args getdownAppBaseDir
2238 inputs.dir(getdownAppBaseDir)
2239 outputs.file("${getdownAppBaseDir}/digest2.txt")
2244 group = "distribution"
2245 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2246 dependsOn getdownDigest
2248 if (reportRsyncCommand) {
2249 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2250 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2251 println "LIKELY RSYNC COMMAND:"
2252 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2253 if (RUNRSYNC == "true") {
2255 commandLine "mkdir", "-p", toDir
2258 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2266 task getdownArchiveBuild() {
2267 group = "distribution"
2268 description = "Put files in the archive dir to go on the website"
2270 dependsOn getdownWebsite
2272 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2273 def vDir = "${getdownArchiveDir}/${v}"
2274 getdownFullArchiveDir = "${vDir}/getdown"
2275 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2277 def vAltDir = "alt_${v}"
2278 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2281 // cleanup old "old" dir
2282 delete getdownArchiveDir
2284 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2285 getdownArchiveTxt.getParentFile().mkdirs()
2286 def getdownArchiveTextLines = []
2287 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2291 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2292 into "${getdownFullArchiveDir}/${vAltDir}"
2295 getdownTextLines.each { line ->
2296 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2297 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2298 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2299 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2300 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2301 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2302 // remove the existing resource = resource/ or bin/ lines
2303 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2304 getdownArchiveTextLines += line
2308 // the resource dir -- add these files as resource lines in getdown.txt
2310 from "${archiveImagesDir}"
2311 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2313 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2317 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2319 def vLaunchJvl = file(getdownVersionLaunchJvl)
2320 vLaunchJvl.getParentFile().mkdirs()
2321 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2322 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2323 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2324 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2325 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2326 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2328 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2330 from getdownLauncher
2331 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2332 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2333 from "${getdownAppBaseDir}/${channel_props}"
2334 if (file(getdownLauncher).getName() != getdown_launcher) {
2335 rename(file(getdownLauncher).getName(), getdown_launcher)
2337 into getdownFullArchiveDir
2343 task getdownArchiveDigest(type: JavaExec) {
2344 group = "distribution"
2345 description = "Digest the getdown archive folder"
2347 dependsOn getdownArchiveBuild
2350 classpath = files(getdownLauncher)
2351 args getdownFullArchiveDir
2353 main = "com.threerings.getdown.tools.Digester"
2354 inputs.dir(getdownFullArchiveDir)
2355 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2358 task getdownArchive() {
2359 group = "distribution"
2360 description = "Build the website archive dir with getdown digest"
2362 dependsOn getdownArchiveBuild
2363 dependsOn getdownArchiveDigest
2366 tasks.withType(JavaCompile) {
2367 options.encoding = 'UTF-8'
2373 delete getdownAppBaseDir
2374 delete getdownFilesDir
2375 delete getdownArchiveDir
2381 if (file(install4jHomeDir).exists()) {
2383 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2384 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2385 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2386 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2388 installDir(file(install4jHomeDir))
2390 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2394 task copyInstall4jTemplate {
2395 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2396 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2397 inputs.file(install4jTemplateFile)
2398 inputs.file(install4jFileAssociationsFile)
2399 inputs.property("CHANNEL", { CHANNEL })
2400 outputs.file(install4jConfFile)
2403 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2405 // turn off code signing if no OSX_KEYPASS
2406 if (OSX_KEYPASS == "") {
2407 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2408 codeSigning.'@macEnabled' = "false"
2410 install4jConfigXml.'**'.windows.each { windows ->
2411 windows.'@runPostProcessor' = "false"
2415 // disable install screen for OSX dmg (for 2.11.2.0)
2416 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2417 macosArchive.attributes().remove('executeSetupApp')
2418 macosArchive.attributes().remove('setupAppId')
2421 // turn off checksum creation for LOCAL channel
2422 def e = install4jConfigXml.application[0]
2423 e.'@createChecksums' = string(install4jCheckSums)
2425 // put file association actions where placeholder action is
2426 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2427 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2428 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2429 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2430 def parent = a.parent()
2432 fileAssociationActions.each { faa ->
2435 // don't need to continue in .any loop once replacements have been made
2440 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2441 // NB we're deleting the /other/ one!
2442 // Also remove the examples subdir from non-release versions
2443 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2444 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2445 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2446 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2448 // remove the examples subdir from Full File Set
2449 def files = install4jConfigXml.files[0]
2450 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2451 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2452 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2453 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2454 dirEntry.parent().remove(dirEntry)
2456 install4jConfigXml.'**'.action.any { a ->
2457 if (a.'@customizedId' == customizedIdToDelete) {
2458 def parent = a.parent()
2464 // write install4j file
2465 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2472 delete install4jConfFile
2476 task cleanInstallersDataFiles {
2477 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2478 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2479 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2481 delete installersOutputTxt
2482 delete installersSha256
2483 delete hugoDataJsonFile
2487 task install4jDMGBackgroundImageCopy {
2488 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2489 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2492 from(install4jDMGBackgroundImageDir) {
2493 include(install4jDMGBackgroundImageFile)
2495 into install4jDMGBackgroundImageBuildDir
2500 task install4jDMGBackgroundImageProcess {
2501 dependsOn install4jDMGBackgroundImageCopy
2504 if (backgroundImageText) {
2505 if (convertBinary == null) {
2506 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2508 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2509 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2511 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2513 executable convertBinary
2516 '-font', install4j_background_image_text_font,
2517 '-fill', install4j_background_image_text_colour,
2518 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2519 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2520 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2529 task install4jDMGBackgroundImage {
2530 dependsOn install4jDMGBackgroundImageProcess
2533 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2534 group = "distribution"
2535 description = "Create the install4j installers"
2537 dependsOn copyInstall4jTemplate
2538 dependsOn cleanInstallersDataFiles
2539 dependsOn install4jDMGBackgroundImage
2541 projectFile = install4jConfFile
2543 // create an md5 for the input files to use as version for install4j conf file
2544 def digest = MessageDigest.getInstance("MD5")
2546 (file("${install4jDir}/${install4j_template}").text +
2547 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2548 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2549 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2550 if (filesMd5.length() >= 8) {
2551 filesMd5 = filesMd5.substring(0,8)
2553 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2556 'JALVIEW_NAME': jalview_name,
2557 'JALVIEW_APPLICATION_NAME': applicationName,
2558 'JALVIEW_DIR': "../..",
2559 'OSX_KEYSTORE': OSX_KEYSTORE,
2560 'OSX_APPLEID': OSX_APPLEID,
2561 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2562 'JSIGN_SH': JSIGN_SH,
2563 'JRE_DIR': getdown_app_dir_java,
2564 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2565 'JALVIEW_VERSION': JALVIEW_VERSION,
2566 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2567 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2568 'JAVA_VERSION': JAVA_VERSION,
2569 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2570 'VERSION': JALVIEW_VERSION,
2571 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2572 'BUNDLE_ID': install4jBundleId,
2573 'INTERNAL_ID': install4jInternalId,
2574 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2575 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2576 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2577 'WRAPPER_LINK': getdownWrapperLink,
2578 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2579 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2580 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2581 'INSTALLER_NAME': install4jInstallerName,
2582 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2583 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2584 'GETDOWN_FILES_DIR': getdown_files_dir,
2585 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2586 'GETDOWN_DIST_DIR': getdownAppDistDir,
2587 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2588 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2589 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2590 'BUILD_DIR': install4jBuildDir,
2591 'APPLICATION_CATEGORIES': install4j_application_categories,
2592 'APPLICATION_FOLDER': install4jApplicationFolder,
2593 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2594 'EXECUTABLE_NAME': install4jExecutableName,
2595 'EXTRA_SCHEME': install4jExtraScheme,
2596 'MAC_ICONS_FILE': install4jMacIconsFile,
2597 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2598 'PNG_ICON_FILE': install4jPngIconFile,
2599 'BACKGROUND': install4jBackground,
2604 'windows': 'WINDOWS',
2608 // these are the bundled OS/architecture VMs needed by install4j
2611 [ "mac", "aarch64" ],
2612 [ "windows", "x64" ],
2614 [ "linux", "aarch64" ]
2616 osArch.forEach { os, arch ->
2617 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)
2618 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2619 // otherwise running `gradle installers` generates a non-useful error:
2620 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2621 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)
2624 //println("INSTALL4J VARIABLES:")
2625 //variables.each{k,v->println("${k}=${v}")}
2627 destination = "${jalviewDir}/${install4jBuildDir}"
2628 buildSelected = true
2630 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2632 disableSigning = true
2633 disableNotarization = true
2637 macKeystorePassword = OSX_KEYPASS
2640 if (OSX_ALTOOLPASS) {
2641 appleIdPassword = OSX_ALTOOLPASS
2642 disableNotarization = false
2644 disableNotarization = true
2648 println("Using projectFile "+projectFile)
2649 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2653 inputs.dir(getdownAppBaseDir)
2654 inputs.file(install4jConfFile)
2655 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2656 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2659 def getDataHash(File myFile) {
2660 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2661 return myFile.exists()
2663 "file" : myFile.getName(),
2664 "filesize" : myFile.length(),
2665 "sha256" : hash.toString()
2670 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2672 "channel" : getdownChannelName,
2673 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2674 "git-commit" : "${gitHash} [${gitBranch}]",
2675 "version" : JALVIEW_VERSION
2677 // install4j installer files
2678 if (installersOutputTxt.exists()) {
2680 installersOutputTxt.readLines().each { def line ->
2681 if (line.startsWith("#")) {
2684 line.replaceAll("\n","")
2685 def vals = line.split("\t")
2686 def filename = vals[3]
2687 def filesize = file(filename).length()
2688 filename = filename.replaceAll(/^.*\//, "")
2689 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2690 idHash."${filename}" = vals[0]
2692 if (install4jCheckSums && installersSha256.exists()) {
2693 installersSha256.readLines().each { def line ->
2694 if (line.startsWith("#")) {
2697 line.replaceAll("\n","")
2698 def vals = line.split(/\s+\*?/)
2699 def filename = vals[1]
2700 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2706 "JAR": shadowJar.archiveFile, // executable JAR
2707 "JVL": getdownVersionLaunchJvl, // version JVL
2708 "SOURCE": sourceDist.archiveFile // source TGZ
2709 ].each { key, value ->
2710 def file = file(value)
2711 if (file.exists()) {
2712 def fileHash = getDataHash(file)
2713 if (fileHash != null) {
2714 hash."${key}" = fileHash;
2718 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2721 task staticMakeInstallersJsonFile {
2723 def output = findProperty("i4j_output")
2724 def sha256 = findProperty("i4j_sha256")
2725 def json = findProperty("i4j_json")
2726 if (output == null || sha256 == null || json == null) {
2727 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2729 writeDataJsonFile(file(output), file(sha256), file(json))
2734 dependsOn installerFiles
2740 eclipse().configFile(eclipse_codestyle_file)
2744 task createSourceReleaseProperties(type: WriteProperties) {
2745 group = "distribution"
2746 description = "Create the source RELEASE properties file"
2748 def sourceTarBuildDir = "${buildDir}/sourceTar"
2749 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2750 outputFile (sourceReleasePropertiesFile)
2753 releaseProps.each{ key, val -> property key, val }
2754 property "git.branch", gitBranch
2755 property "git.hash", gitHash
2758 outputs.file(outputFile)
2761 task sourceDist(type: Tar) {
2762 group "distribution"
2763 description "Create a source .tar.gz file for distribution"
2765 dependsOn createBuildProperties
2766 dependsOn convertMdFiles
2767 dependsOn eclipseAllPreferences
2768 dependsOn createSourceReleaseProperties
2771 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2772 archiveFileName = outputFileName
2774 compression Compression.GZIP
2789 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2791 "utils/InstallAnywhere",
2806 "gradle.properties",
2818 ".settings/org.eclipse.buildship.core.prefs",
2819 ".settings/org.eclipse.jdt.core.prefs"
2823 exclude (EXCLUDE_FILES)
2824 include (PROCESS_FILES)
2825 filter(ReplaceTokens,
2829 'Version-Rel': JALVIEW_VERSION,
2830 'Year-Rel': getDate("yyyy")
2835 exclude (EXCLUDE_FILES)
2836 exclude (PROCESS_FILES)
2837 exclude ("appletlib")
2838 exclude ("**/*locales")
2839 exclude ("*locales/**")
2840 exclude ("utils/InstallAnywhere")
2842 exclude (getdown_files_dir)
2843 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2844 //exclude (getdown_website_dir)
2845 //exclude (getdown_archive_dir)
2847 // exluding these as not using jars as modules yet
2848 exclude ("${j11modDir}/**/*.jar")
2851 include(INCLUDE_FILES)
2853 // from (jalviewDir) {
2854 // // explicit includes for stuff that seemed to not get included
2855 // include(fileTree("test/**/*."))
2856 // exclude(EXCLUDE_FILES)
2857 // exclude(PROCESS_FILES)
2860 from(file(buildProperties).getParent()) {
2861 include(file(buildProperties).getName())
2862 rename(file(buildProperties).getName(), "build_properties")
2864 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2868 def sourceTarBuildDir = "${buildDir}/sourceTar"
2869 from(sourceTarBuildDir) {
2870 // this includes the appended RELEASE properties file
2874 task dataInstallersJson {
2876 description "Create the installers-VERSION.json data file for installer files created"
2878 mustRunAfter installers
2879 mustRunAfter shadowJar
2880 mustRunAfter sourceDist
2881 mustRunAfter getdownArchive
2883 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2884 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2886 if (installersOutputTxt.exists()) {
2887 inputs.file(installersOutputTxt)
2889 if (install4jCheckSums && installersSha256.exists()) {
2890 inputs.file(installersSha256)
2893 shadowJar.archiveFile, // executable JAR
2894 getdownVersionLaunchJvl, // version JVL
2895 sourceDist.archiveFile // source TGZ
2896 ].each { fileName ->
2897 if (file(fileName).exists()) {
2898 inputs.file(fileName)
2902 outputs.file(hugoDataJsonFile)
2905 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
2911 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
2914 dependsOn pubhtmlhelp
2916 inputs.dir("${helpBuildDir}/${help_dir}")
2917 outputs.dir("${buildDir}/distributions/${help_dir}")
2921 task j2sSetHeadlessBuild {
2928 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2930 description "Enable the alternative J2S Config file for headless build"
2932 outputFile = jalviewjsJ2sSettingsFileName
2933 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2934 def j2sProps = new Properties()
2935 if (j2sPropsFile.exists()) {
2937 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2938 j2sProps.load(j2sPropsFileFIS)
2939 j2sPropsFileFIS.close()
2941 j2sProps.each { prop, val ->
2944 } catch (Exception e) {
2945 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2949 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2950 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2955 task jalviewjsSetEclipseWorkspace {
2956 def propKey = "jalviewjs_eclipse_workspace"
2958 if (project.hasProperty(propKey)) {
2959 propVal = project.getProperty(propKey)
2960 if (propVal.startsWith("~/")) {
2961 propVal = System.getProperty("user.home") + propVal.substring(1)
2964 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2965 def propsFile = file(propsFileName)
2966 def eclipseWsDir = propVal
2967 def props = new Properties()
2969 def writeProps = true
2970 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2971 def ins = new FileInputStream(propsFileName)
2974 if (props.getProperty(propKey, null) != null) {
2975 eclipseWsDir = props.getProperty(propKey)
2980 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2981 def tempDir = File.createTempDir()
2982 eclipseWsDir = tempDir.getAbsolutePath()
2985 eclipseWorkspace = file(eclipseWsDir)
2988 // do not run a headless transpile when we claim to be in Eclipse
2990 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2991 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2993 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2997 props.setProperty(propKey, eclipseWsDir)
2998 propsFile.parentFile.mkdirs()
2999 def bytes = new ByteArrayOutputStream()
3000 props.store(bytes, null)
3001 def propertiesString = bytes.toString()
3002 propsFile.text = propertiesString
3008 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3011 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3012 outputs.file(propsFileName)
3013 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3017 task jalviewjsEclipsePaths {
3020 def eclipseRoot = jalviewjs_eclipse_root
3021 if (eclipseRoot.startsWith("~/")) {
3022 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3024 if (OperatingSystem.current().isMacOsX()) {
3025 eclipseRoot += "/Eclipse.app"
3026 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3027 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3028 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3029 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3030 eclipseRoot += "/eclipse"
3032 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3033 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3034 } else { // linux or unix
3035 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3036 eclipseRoot += "/eclipse"
3037 println("eclipseDir exists")
3039 eclipseBinary = "${eclipseRoot}/eclipse"
3040 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3043 eclipseVersion = "4.13" // default
3044 def assumedVersion = true
3045 if (file(eclipseProduct).exists()) {
3046 def fis = new FileInputStream(eclipseProduct)
3047 def props = new Properties()
3049 eclipseVersion = props.getProperty("version")
3051 assumedVersion = false
3054 def propKey = "eclipse_debug"
3055 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3058 // do not run a headless transpile when we claim to be in Eclipse
3060 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3061 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3063 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3066 if (!assumedVersion) {
3067 println("ECLIPSE VERSION=${eclipseVersion}")
3073 task printProperties {
3075 description "Output to console all System.properties"
3077 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3083 dependsOn eclipseProject
3084 dependsOn eclipseClasspath
3085 dependsOn eclipseJdt
3089 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3090 task jalviewjsEclipseCopyDropins(type: Copy) {
3091 dependsOn jalviewjsEclipsePaths
3093 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3094 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3095 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3102 // this eclipse -clean doesn't actually work
3103 task jalviewjsCleanEclipse(type: Exec) {
3104 dependsOn eclipseSetup
3105 dependsOn jalviewjsEclipsePaths
3106 dependsOn jalviewjsEclipseCopyDropins
3108 executable(eclipseBinary)
3109 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3115 def inputString = """exit
3118 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3119 standardInput = inputByteStream
3122 /* not really working yet
3123 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3127 task jalviewjsTransferUnzipSwingJs {
3128 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3132 from zipTree(file_zip)
3133 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3137 inputs.file file_zip
3138 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3142 task jalviewjsTransferUnzipLib {
3143 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3146 zipFiles.each { file_zip ->
3148 from zipTree(file_zip)
3149 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3154 inputs.files zipFiles
3155 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3159 task jalviewjsTransferUnzipAllLibs {
3160 dependsOn jalviewjsTransferUnzipSwingJs
3161 dependsOn jalviewjsTransferUnzipLib
3165 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3167 description "Create the alternative j2s file from the j2s.* properties"
3169 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3170 def siteDirProperty = "j2s.site.directory"
3171 def setSiteDir = false
3172 jalviewjsJ2sProps.each { prop, val ->
3174 if (prop == siteDirProperty) {
3175 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3176 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3182 if (!setSiteDir) { // default site location, don't override specifically set property
3183 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3186 outputFile = jalviewjsJ2sAltSettingsFileName
3189 inputs.properties(jalviewjsJ2sProps)
3190 outputs.file(jalviewjsJ2sAltSettingsFileName)
3195 task jalviewjsEclipseSetup {
3196 dependsOn jalviewjsEclipseCopyDropins
3197 dependsOn jalviewjsSetEclipseWorkspace
3198 dependsOn jalviewjsCreateJ2sSettings
3202 task jalviewjsSyncAllLibs (type: Sync) {
3203 dependsOn jalviewjsTransferUnzipAllLibs
3204 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3205 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3206 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3210 def outputFiles = []
3211 rename { filename ->
3212 outputFiles += "${outputDir}/${filename}"
3219 // should this be exclude really ?
3220 duplicatesStrategy "INCLUDE"
3222 outputs.files outputFiles
3223 inputs.files inputFiles
3227 task jalviewjsSyncResources (type: Sync) {
3228 dependsOn buildResources
3230 def inputFiles = fileTree(dir: resourcesBuildDir)
3231 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3235 def outputFiles = []
3236 rename { filename ->
3237 outputFiles += "${outputDir}/${filename}"
3243 outputs.files outputFiles
3244 inputs.files inputFiles
3248 task jalviewjsSyncSiteResources (type: Sync) {
3249 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3250 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3254 def outputFiles = []
3255 rename { filename ->
3256 outputFiles += "${outputDir}/${filename}"
3262 outputs.files outputFiles
3263 inputs.files inputFiles
3267 task jalviewjsSyncBuildProperties (type: Sync) {
3268 dependsOn createBuildProperties
3269 def inputFiles = [file(buildProperties)]
3270 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3274 def outputFiles = []
3275 rename { filename ->
3276 outputFiles += "${outputDir}/${filename}"
3282 outputs.files outputFiles
3283 inputs.files inputFiles
3287 task jalviewjsProjectImport(type: Exec) {
3288 dependsOn eclipseSetup
3289 dependsOn jalviewjsEclipsePaths
3290 dependsOn jalviewjsEclipseSetup
3293 // do not run a headless import when we claim to be in Eclipse
3295 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3296 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3298 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3302 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3303 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3304 executable(eclipseBinary)
3305 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3309 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3311 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3312 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3315 inputs.file("${jalviewDir}/.project")
3316 outputs.upToDateWhen {
3317 file(projdir).exists()
3322 task jalviewjsTranspile(type: Exec) {
3323 dependsOn jalviewjsEclipseSetup
3324 dependsOn jalviewjsProjectImport
3325 dependsOn jalviewjsEclipsePaths
3327 dependsOn jalviewjsEnableAltFileProperty
3331 // do not run a headless transpile when we claim to be in Eclipse
3333 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3334 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3336 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3340 executable(eclipseBinary)
3341 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3345 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3347 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3348 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3354 stdout = new ByteArrayOutputStream()
3355 stderr = new ByteArrayOutputStream()
3357 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3358 def logOutFile = file(logOutFileName)
3359 logOutFile.createNewFile()
3360 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3361 BINARY: ${eclipseBinary}
3362 VERSION: ${eclipseVersion}
3363 WORKSPACE: ${eclipseWorkspace}
3364 DEBUG: ${eclipseDebug}
3367 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3368 // combine stdout and stderr
3369 def logErrFOS = logOutFOS
3371 if (jalviewjs_j2s_to_console.equals("true")) {
3372 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3373 new org.apache.tools.ant.util.TeeOutputStream(
3377 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3378 new org.apache.tools.ant.util.TeeOutputStream(
3383 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3386 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3393 if (stdout.toString().contains("Error processing ")) {
3394 // j2s did not complete transpile
3395 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3396 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3397 println("IGNORING TRANSPILE ERRORS")
3398 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3400 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3405 inputs.dir("${jalviewDir}/${sourceDir}")
3406 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3407 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3411 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3413 def stdout = new ByteArrayOutputStream()
3414 def stderr = new ByteArrayOutputStream()
3416 def coreFile = file(jsfile)
3418 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3420 logOutFile.createNewFile()
3421 logOutFile.append(msg+"\n")
3423 def coreTop = file(prefixFile)
3424 def coreBottom = file(suffixFile)
3425 coreFile.getParentFile().mkdirs()
3426 coreFile.createNewFile()
3427 coreFile.write( coreTop.getText("UTF-8") )
3431 def t = f.getText("UTF-8")
3432 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3433 coreFile.append( t )
3435 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3437 logOutFile.append(msg+"\n")
3440 coreFile.append( coreBottom.getText("UTF-8") )
3442 msg = "Generating ${zjsfile}"
3444 logOutFile.append(msg+"\n")
3445 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3446 def logErrFOS = logOutFOS
3449 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3450 main = "com.google.javascript.jscomp.CommandLineRunner"
3451 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3452 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3455 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3457 logOutFile.append(msg+"\n")
3459 if (logOutConsole) {
3460 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3461 new org.apache.tools.ant.util.TeeOutputStream(
3465 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3466 new org.apache.tools.ant.util.TeeOutputStream(
3471 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3474 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3481 logOutFile.append(msg+"\n")
3485 task jalviewjsBuildAllCores {
3487 description "Build the core js lib closures listed in the classlists dir"
3488 dependsOn jalviewjsTranspile
3489 dependsOn jalviewjsTransferUnzipSwingJs
3491 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3492 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3493 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3494 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3495 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3496 def prefixFile = "${jsDir}/core/coretop2.js"
3497 def suffixFile = "${jsDir}/core/corebottom2.js"
3499 inputs.file prefixFile
3500 inputs.file suffixFile
3502 def classlistFiles = []
3503 // add the classlists found int the jalviewjs_classlists_dir
3504 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3506 def name = file.getName() - ".txt"
3513 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3514 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3515 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3517 jalviewjsCoreClasslists = []
3519 classlistFiles.each {
3522 def file = hash['file']
3523 if (! file.exists()) {
3524 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3525 return false // this is a "continue" in groovy .each closure
3527 def name = hash['name']
3529 name = file.getName() - ".txt"
3537 def list = fileTree(dir: j2sDir, includes: filelist)
3539 def jsfile = "${outputDir}/core${name}.js"
3540 def zjsfile = "${outputDir}/core${name}.z.js"
3542 jalviewjsCoreClasslists += [
3551 outputs.file(jsfile)
3552 outputs.file(zjsfile)
3555 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3556 def stevesoftClasslistName = "_stevesoft"
3557 def stevesoftClasslist = [
3558 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3559 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3560 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3561 'name': stevesoftClasslistName
3563 jalviewjsCoreClasslists += stevesoftClasslist
3564 inputs.files(stevesoftClasslist['list'])
3565 outputs.file(stevesoftClasslist['jsfile'])
3566 outputs.file(stevesoftClasslist['zjsfile'])
3569 def allClasslistName = "_all"
3570 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3571 allJsFiles += fileTree(
3575 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3576 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3577 "**/org/jmol/export/JSExporter.js"
3580 allJsFiles += fileTree(
3584 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3585 "**/sun/misc/Unsafe.js",
3586 "**/swingjs/jquery/jquery-editable-select.js",
3587 "**/swingjs/jquery/j2sComboBox.js",
3588 "**/sun/misc/FloatingDecimal.js"
3591 def allClasslist = [
3592 'jsfile': "${outputDir}/core${allClasslistName}.js",
3593 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3595 'name': allClasslistName
3597 // not including this version of "all" core at the moment
3598 //jalviewjsCoreClasslists += allClasslist
3599 inputs.files(allClasslist['list'])
3600 outputs.file(allClasslist['jsfile'])
3601 outputs.file(allClasslist['zjsfile'])
3604 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3605 logOutFile.getParentFile().mkdirs()
3606 logOutFile.createNewFile()
3607 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3609 jalviewjsCoreClasslists.each {
3610 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3617 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3620 into file(outputFile).getParentFile()
3621 rename { filename ->
3622 if (filename.equals(inputFile.getName())) {
3623 return file(outputFile).getName()
3627 filter(ReplaceTokens,
3631 'MAIN': '"'+main_class+'"',
3633 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3634 'COREKEY': jalviewjs_core_key,
3635 'CORENAME': coreName
3642 task jalviewjsPublishCoreTemplates {
3643 dependsOn jalviewjsBuildAllCores
3644 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3645 def inputFile = file(inputFileName)
3646 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3648 def outputFiles = []
3649 jalviewjsCoreClasslists.each { cl ->
3650 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3651 cl['outputfile'] = outputFile
3652 outputFiles += outputFile
3656 jalviewjsCoreClasslists.each { cl ->
3657 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3660 inputs.file(inputFile)
3661 outputs.files(outputFiles)
3665 task jalviewjsSyncCore (type: Sync) {
3666 dependsOn jalviewjsBuildAllCores
3667 dependsOn jalviewjsPublishCoreTemplates
3668 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3669 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3673 def outputFiles = []
3674 rename { filename ->
3675 outputFiles += "${outputDir}/${filename}"
3681 outputs.files outputFiles
3682 inputs.files inputFiles
3686 // this Copy version of TransferSiteJs will delete anything else in the target dir
3687 task jalviewjsCopyTransferSiteJs(type: Copy) {
3688 dependsOn jalviewjsTranspile
3689 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3690 into "${jalviewDir}/${jalviewjsSiteDir}"
3694 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3695 task jalviewjsSyncTransferSiteJs(type: Sync) {
3696 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3698 into "${jalviewDir}/${jalviewjsSiteDir}"
3705 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3706 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3707 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3708 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3710 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3711 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3712 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3713 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3716 task jalviewjsPrepareSite {
3718 description "Prepares the website folder including unzipping files and copying resources"
3719 dependsOn jalviewjsSyncAllLibs
3720 dependsOn jalviewjsSyncResources
3721 dependsOn jalviewjsSyncSiteResources
3722 dependsOn jalviewjsSyncBuildProperties
3723 dependsOn jalviewjsSyncCore
3727 task jalviewjsBuildSite {
3729 description "Builds the whole website including transpiled code"
3730 dependsOn jalviewjsCopyTransferSiteJs
3731 dependsOn jalviewjsPrepareSite
3735 task cleanJalviewjsTransferSite {
3737 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3738 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3739 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3740 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3745 task cleanJalviewjsSite {
3746 dependsOn cleanJalviewjsTransferSite
3748 delete "${jalviewDir}/${jalviewjsSiteDir}"
3753 task jalviewjsSiteTar(type: Tar) {
3755 description "Creates a tar.gz file for the website"
3756 dependsOn jalviewjsBuildSite
3757 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3758 archiveFileName = outputFilename
3760 compression Compression.GZIP
3762 from "${jalviewDir}/${jalviewjsSiteDir}"
3763 into jalviewjs_site_dir // this is inside the tar file
3765 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3769 task jalviewjsServer {
3771 def filename = "jalviewjsTest.html"
3772 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3773 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3778 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3779 factory = f.newInstance()
3780 } catch (ClassNotFoundException e) {
3781 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3783 def port = Integer.valueOf(jalviewjs_server_port)
3788 while(port < start+1000 && !running) {
3790 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3791 jalviewjsServer = factory.start(doc_root, port)
3793 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3794 println("SERVER STARTED with document root ${doc_root}.")
3795 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3796 println("For debug: "+url+"?j2sdebug")
3797 println("For verbose: "+url+"?j2sverbose")
3798 } catch (Exception e) {
3803 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3804 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3805 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3807 jalviewjsCoreClasslists.each { cl ->
3808 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3810 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3812 println("For core ${cl.name}: "+urlcore)
3815 file(htmlFile).text = htmlText
3818 outputs.file(htmlFile)
3819 outputs.upToDateWhen({false})
3823 task cleanJalviewjsAll {
3825 description "Delete all configuration and build artifacts to do with JalviewJS build"
3826 dependsOn cleanJalviewjsSite
3827 dependsOn jalviewjsEclipsePaths
3830 delete "${jalviewDir}/${jalviewjsBuildDir}"
3831 delete "${jalviewDir}/${eclipse_bin_dir}"
3832 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3833 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3835 delete jalviewjsJ2sAltSettingsFileName
3838 outputs.upToDateWhen( { false } )
3842 task jalviewjsIDE_checkJ2sPlugin {
3843 group "00 JalviewJS in Eclipse"
3844 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3847 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3848 def j2sPluginFile = file(j2sPlugin)
3849 def eclipseHome = System.properties["eclipse.home.location"]
3850 if (eclipseHome == null || ! IN_ECLIPSE) {
3851 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3853 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3854 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3855 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3856 eclipseJ2sPluginDirs += altPluginsDir
3858 def foundPlugin = false
3859 def j2sPluginFileName = j2sPluginFile.getName()
3860 def eclipseJ2sPlugin
3861 def eclipseJ2sPluginFile
3862 eclipseJ2sPluginDirs.any { dir ->
3863 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3864 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3865 if (eclipseJ2sPluginFile.exists()) {
3871 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3872 System.err.println(msg)
3873 throw new StopExecutionException(msg)
3876 def digest = MessageDigest.getInstance("MD5")
3878 digest.update(j2sPluginFile.text.bytes)
3879 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3881 digest.update(eclipseJ2sPluginFile.text.bytes)
3882 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3884 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3885 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3886 System.err.println(msg)
3887 throw new StopExecutionException(msg)
3889 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3895 task jalviewjsIDE_copyJ2sPlugin {
3896 group "00 JalviewJS in Eclipse"
3897 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3900 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3901 def j2sPluginFile = file(j2sPlugin)
3902 def eclipseHome = System.properties["eclipse.home.location"]
3903 if (eclipseHome == null || ! IN_ECLIPSE) {
3904 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3906 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3907 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3908 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3909 System.err.println(msg)
3912 eclipseJ2sPluginFile.getParentFile().mkdirs()
3913 into eclipseJ2sPluginFile.getParent()
3919 task jalviewjsIDE_j2sFile {
3920 group "00 JalviewJS in Eclipse"
3921 description "Creates the .j2s file"
3922 dependsOn jalviewjsCreateJ2sSettings
3926 task jalviewjsIDE_SyncCore {
3927 group "00 JalviewJS in Eclipse"
3928 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3929 dependsOn jalviewjsSyncCore
3933 task jalviewjsIDE_SyncSiteAll {
3934 dependsOn jalviewjsSyncAllLibs
3935 dependsOn jalviewjsSyncResources
3936 dependsOn jalviewjsSyncSiteResources
3937 dependsOn jalviewjsSyncBuildProperties
3941 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3944 task jalviewjsIDE_PrepareSite {
3945 group "00 JalviewJS in Eclipse"
3946 description "Sync libs and resources to site dir, but not closure cores"
3948 dependsOn jalviewjsIDE_SyncSiteAll
3949 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3953 task jalviewjsIDE_AssembleSite {
3954 group "00 JalviewJS in Eclipse"
3955 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3956 dependsOn jalviewjsPrepareSite
3960 task jalviewjsIDE_SiteClean {
3961 group "00 JalviewJS in Eclipse"
3962 description "Deletes the Eclipse transpiled site"
3963 dependsOn cleanJalviewjsSite
3967 task jalviewjsIDE_Server {
3968 group "00 JalviewJS in Eclipse"
3969 description "Starts a webserver on localhost to test the website"
3970 dependsOn jalviewjsServer
3974 // buildship runs this at import or gradle refresh
3975 task eclipseSynchronizationTask {
3976 //dependsOn eclipseSetup
3977 dependsOn createBuildProperties
3979 dependsOn jalviewjsIDE_j2sFile
3980 dependsOn jalviewjsIDE_checkJ2sPlugin
3981 dependsOn jalviewjsIDE_PrepareSite
3986 // buildship runs this at build time or project refresh
3987 task eclipseAutoBuildTask {
3988 //dependsOn jalviewjsIDE_checkJ2sPlugin
3989 //dependsOn jalviewjsIDE_PrepareSite
3995 description "Build the site"
3996 dependsOn jalviewjsBuildSite