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 $jalviewDir
1743 dependsOn cloverClasses
1745 dependsOn compileJava //?
1749 includeGroups testng_groups
1750 excludeGroups testng_excluded_groups
1752 useDefaultListeners=true
1755 maxHeapSize = "4096m"
1756 jvmArgs '-Xmx4096m', '-Xms4096m'
1759 maxParallelForks = 1
1762 jvmArgs '-Xmx2048m', '-Xms2048m'
1765 workingDir = jalviewDir
1766 def testLaf = project.findProperty("test_laf")
1767 if (testLaf != null) {
1768 println("Setting Test LaF to '${testLaf}'")
1769 systemProperty "laf", testLaf
1771 def testHiDPIScale = project.findProperty("test_HiDPIScale")
1772 if (testHiDPIScale != null) {
1773 println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
1774 systemProperty "sun.java2d.uiScale", testHiDPIScale
1776 sourceCompatibility = compile_source_compatibility
1777 targetCompatibility = compile_target_compatibility
1778 jvmArgs += additional_compiler_args
1782 println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
1788 task compileLinkCheck(type: JavaCompile) {
1790 classpath = files("${jalviewDir}/${utils_dir}")
1791 destinationDir = file("${jalviewDir}/${utils_dir}")
1792 source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
1794 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1795 inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
1796 outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
1797 outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
1801 task linkCheck(type: JavaExec) {
1803 dependsOn compileLinkCheck
1805 def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
1806 classpath = files("${jalviewDir}/${utils_dir}")
1807 main = "HelpLinksChecker"
1808 workingDir = "${helpBuildDir}"
1809 args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
1811 def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
1812 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1815 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1819 inputs.dir(helpBuildDir)
1820 outputs.file(helpLinksCheckerOutFile)
1824 // import the pubhtmlhelp target
1825 ant.properties.basedir = "${jalviewDir}"
1826 ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
1827 ant.importBuild "${utils_dir}/publishHelp.xml"
1830 task cleanPackageDir(type: Delete) {
1832 delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
1842 attributes "Main-Class": main_class,
1843 "Permissions": "all-permissions",
1844 "Application-Name": applicationName,
1845 "Codebase": application_codebase,
1846 "Implementation-Version": JALVIEW_VERSION
1849 def outputDir = "${jalviewDir}/${package_dir}"
1850 destinationDirectory = file(outputDir)
1851 archiveFileName = rootProject.name+".jar"
1852 duplicatesStrategy "EXCLUDE"
1859 exclude "**/*.jar.*"
1861 inputs.dir(sourceSets.main.java.outputDir)
1862 sourceSets.main.resources.srcDirs.each{ dir ->
1865 outputs.file("${outputDir}/${archiveFileName}")
1869 task copyJars(type: Copy) {
1870 from fileTree(dir: classesDir, include: "**/*.jar").files
1871 into "${jalviewDir}/${package_dir}"
1875 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
1876 task syncJars(type: Sync) {
1878 from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
1879 into "${jalviewDir}/${package_dir}"
1881 include jar.archiveFileName.getOrNull()
1888 description = "Put all required libraries in dist"
1889 // order of "cleanPackageDir", "copyJars", "jar" important!
1890 jar.mustRunAfter cleanPackageDir
1891 syncJars.mustRunAfter cleanPackageDir
1892 dependsOn cleanPackageDir
1895 outputs.dir("${jalviewDir}/${package_dir}")
1900 dependsOn cleanPackageDir
1907 group = "distribution"
1908 description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
1912 from ("${jalviewDir}/${libDistDir}") {
1916 attributes "Implementation-Version": JALVIEW_VERSION,
1917 "Application-Name": applicationName
1920 duplicatesStrategy "INCLUDE"
1922 mainClassName = shadow_jar_main_class
1924 classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
1928 task getdownImagesCopy() {
1929 inputs.dir getdownImagesDir
1930 outputs.dir getdownImagesBuildDir
1934 from(getdownImagesDir) {
1935 include("*getdown*.png")
1937 into getdownImagesBuildDir
1942 task getdownImagesProcess() {
1943 dependsOn getdownImagesCopy
1946 if (backgroundImageText) {
1947 if (convertBinary == null) {
1948 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
1950 if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
1951 throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
1953 fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
1955 executable convertBinary
1958 '-font', getdown_background_image_text_font,
1959 '-fill', getdown_background_image_text_colour,
1960 '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
1961 '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
1962 '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
1971 task getdownImages() {
1972 dependsOn getdownImagesProcess
1975 task getdownWebsite() {
1976 group = "distribution"
1977 description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
1979 dependsOn getdownImages
1984 def getdownWebsiteResourceFilenames = []
1985 def getdownResourceDir = getdownResourceDir
1986 def getdownResourceFilenames = []
1989 // clean the getdown website and files dir before creating getdown folders
1990 delete getdownAppBaseDir
1991 delete getdownFilesDir
1994 from buildProperties
1995 rename(file(buildProperties).getName(), getdown_build_properties)
1998 getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
2001 from channelPropsFile
2002 filter(ReplaceTokens,
2006 'SUFFIX': channelSuffix
2009 into getdownAppBaseDir
2011 getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
2013 // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
2014 def props = project.properties.sort { it.key }
2015 if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
2016 props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
2018 if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
2019 props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
2021 if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
2022 props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
2024 if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
2025 props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
2026 props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
2027 props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
2028 props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
2029 props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
2030 props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
2033 props.put("getdown_txt_title", jalview_name)
2034 props.put("getdown_txt_ui.name", applicationName)
2036 // start with appbase
2037 getdownTextLines += "appbase = ${getdownAppBase}"
2038 props.each{ prop, val ->
2039 if (prop.startsWith("getdown_txt_") && val != null) {
2040 if (prop.startsWith("getdown_txt_multi_")) {
2041 def key = prop.substring(18)
2042 val.split(",").each{ v ->
2043 def line = "${key} = ${v}"
2044 getdownTextLines += line
2047 // file values rationalised
2048 if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
2050 if (val.indexOf('/') == 0) {
2053 } else if (val.indexOf('/') > 0) {
2054 // relative path (relative to jalviewDir)
2055 r = file( "${jalviewDir}/${val}" )
2058 val = "${getdown_resource_dir}/" + r.getName()
2059 getdownWebsiteResourceFilenames += val
2060 getdownResourceFilenames += r.getPath()
2063 if (! prop.startsWith("getdown_txt_resource")) {
2064 def line = prop.substring(12) + " = ${val}"
2065 getdownTextLines += line
2071 getdownWebsiteResourceFilenames.each{ filename ->
2072 getdownTextLines += "resource = ${filename}"
2074 getdownResourceFilenames.each{ filename ->
2077 into getdownResourceDir
2081 def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
2082 getdownWrapperScripts.each{ script ->
2083 def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
2087 into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
2089 getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
2094 fileTree(file(package_dir)).each{ f ->
2095 if (f.isDirectory()) {
2096 def files = fileTree(dir: f, include: ["*"]).getFiles()
2098 } else if (f.exists()) {
2102 def jalviewJar = jar.archiveFileName.getOrNull()
2103 // put jalview.jar first for CLASSPATH and .properties files reasons
2104 codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
2105 def name = f.getName()
2106 def line = "code = ${getdownAppDistDir}/${name}"
2107 getdownTextLines += line
2114 // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
2116 if (JAVA_VERSION.equals("11")) {
2117 def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
2118 j11libFiles.sort().each{f ->
2119 def name = f.getName()
2120 def line = "code = ${getdown_j11lib_dir}/${name}"
2121 getdownTextLines += line
2124 into getdownJ11libDir
2130 // 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.
2131 //getdownTextLines += "class = " + file(getdownLauncher).getName()
2132 getdownTextLines += "resource = ${getdown_launcher_new}"
2133 getdownTextLines += "class = ${main_class}"
2134 // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
2135 if (getdownSetAppBaseProperty) {
2136 getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
2137 getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
2140 def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
2141 getdownTxt.write(getdownTextLines.join("\n"))
2143 getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
2144 def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
2145 launchJvl.write("appbase=${getdownAppBase}")
2147 // files going into the getdown website dir: getdown-launcher.jar
2149 from getdownLauncher
2150 rename(file(getdownLauncher).getName(), getdown_launcher_new)
2151 into getdownAppBaseDir
2154 // files going into the getdown website dir: getdown-launcher(-local).jar
2156 from getdownLauncher
2157 if (file(getdownLauncher).getName() != getdown_launcher) {
2158 rename(file(getdownLauncher).getName(), getdown_launcher)
2160 into getdownAppBaseDir
2163 // files going into the getdown website dir: ./install dir and files
2164 if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
2167 from getdownLauncher
2168 from "${getdownAppDir}/${getdown_build_properties}"
2169 if (file(getdownLauncher).getName() != getdown_launcher) {
2170 rename(file(getdownLauncher).getName(), getdown_launcher)
2172 into getdownInstallDir
2175 // and make a copy in the getdown files dir (these are not downloaded by getdown)
2177 from getdownInstallDir
2178 into getdownFilesInstallDir
2182 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2186 from getdownLauncher
2187 from "${getdownAppBaseDir}/${getdown_build_properties}"
2188 from "${getdownAppBaseDir}/${channel_props}"
2189 if (file(getdownLauncher).getName() != getdown_launcher) {
2190 rename(file(getdownLauncher).getName(), getdown_launcher)
2192 into getdownFilesDir
2195 // and ./resource (not all downloaded by getdown)
2197 from getdownResourceDir
2198 into "${getdownFilesDir}/${getdown_resource_dir}"
2203 inputs.dir("${jalviewDir}/${package_dir}")
2205 outputs.dir(getdownAppBaseDir)
2206 outputs.dir(getdownFilesDir)
2210 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
2211 task getdownDigestDir(type: JavaExec) {
2213 description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
2215 def digestDirPropertyName = "DIGESTDIR"
2217 classpath = files(getdownLauncher)
2218 def digestDir = findProperty(digestDirPropertyName)
2219 if (digestDir == null) {
2220 throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
2224 main = "com.threerings.getdown.tools.Digester"
2228 task getdownDigest(type: JavaExec) {
2229 group = "distribution"
2230 description = "Digest the getdown website folder"
2231 dependsOn getdownWebsite
2233 classpath = files(getdownLauncher)
2235 main = "com.threerings.getdown.tools.Digester"
2236 args getdownAppBaseDir
2237 inputs.dir(getdownAppBaseDir)
2238 outputs.file("${getdownAppBaseDir}/digest2.txt")
2243 group = "distribution"
2244 description = "Create the minimal and full getdown app folder for installers and website and create digest file"
2245 dependsOn getdownDigest
2247 if (reportRsyncCommand) {
2248 def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
2249 def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
2250 println "LIKELY RSYNC COMMAND:"
2251 println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
2252 if (RUNRSYNC == "true") {
2254 commandLine "mkdir", "-p", toDir
2257 commandLine "rsync", "-avh", "--delete", fromDir, toDir
2265 task getdownArchiveBuild() {
2266 group = "distribution"
2267 description = "Put files in the archive dir to go on the website"
2269 dependsOn getdownWebsite
2271 def v = "v${JALVIEW_VERSION_UNDERSCORES}"
2272 def vDir = "${getdownArchiveDir}/${v}"
2273 getdownFullArchiveDir = "${vDir}/getdown"
2274 getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
2276 def vAltDir = "alt_${v}"
2277 def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
2280 // cleanup old "old" dir
2281 delete getdownArchiveDir
2283 def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
2284 getdownArchiveTxt.getParentFile().mkdirs()
2285 def getdownArchiveTextLines = []
2286 def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
2290 from "${getdownAppBaseDir}/${getdownAppDistDir}"
2291 into "${getdownFullArchiveDir}/${vAltDir}"
2294 getdownTextLines.each { line ->
2295 line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
2296 line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
2297 line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
2298 line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
2299 line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
2300 line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
2301 // remove the existing resource = resource/ or bin/ lines
2302 if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
2303 getdownArchiveTextLines += line
2307 // the resource dir -- add these files as resource lines in getdown.txt
2309 from "${archiveImagesDir}"
2310 into "${getdownFullArchiveDir}/${getdown_resource_dir}"
2312 getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
2316 getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
2318 def vLaunchJvl = file(getdownVersionLaunchJvl)
2319 vLaunchJvl.getParentFile().mkdirs()
2320 vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
2321 def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
2322 def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
2323 // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
2324 //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
2325 java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
2327 // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
2329 from getdownLauncher
2330 from "${getdownAppBaseDir}/${getdownLaunchJvl}"
2331 from "${getdownAppBaseDir}/${getdown_launcher_new}"
2332 from "${getdownAppBaseDir}/${channel_props}"
2333 if (file(getdownLauncher).getName() != getdown_launcher) {
2334 rename(file(getdownLauncher).getName(), getdown_launcher)
2336 into getdownFullArchiveDir
2342 task getdownArchiveDigest(type: JavaExec) {
2343 group = "distribution"
2344 description = "Digest the getdown archive folder"
2346 dependsOn getdownArchiveBuild
2349 classpath = files(getdownLauncher)
2350 args getdownFullArchiveDir
2352 main = "com.threerings.getdown.tools.Digester"
2353 inputs.dir(getdownFullArchiveDir)
2354 outputs.file("${getdownFullArchiveDir}/digest2.txt")
2357 task getdownArchive() {
2358 group = "distribution"
2359 description = "Build the website archive dir with getdown digest"
2361 dependsOn getdownArchiveBuild
2362 dependsOn getdownArchiveDigest
2365 tasks.withType(JavaCompile) {
2366 options.encoding = 'UTF-8'
2372 delete getdownAppBaseDir
2373 delete getdownFilesDir
2374 delete getdownArchiveDir
2380 if (file(install4jHomeDir).exists()) {
2382 } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
2383 install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
2384 } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
2385 install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
2387 installDir(file(install4jHomeDir))
2389 mediaTypes = Arrays.asList(install4j_media_types.split(","))
2393 task copyInstall4jTemplate {
2394 def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
2395 def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
2396 inputs.file(install4jTemplateFile)
2397 inputs.file(install4jFileAssociationsFile)
2398 inputs.property("CHANNEL", { CHANNEL })
2399 outputs.file(install4jConfFile)
2402 def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
2404 // turn off code signing if no OSX_KEYPASS
2405 if (OSX_KEYPASS == "") {
2406 install4jConfigXml.'**'.codeSigning.each { codeSigning ->
2407 codeSigning.'@macEnabled' = "false"
2409 install4jConfigXml.'**'.windows.each { windows ->
2410 windows.'@runPostProcessor' = "false"
2414 // disable install screen for OSX dmg (for 2.11.2.0)
2415 install4jConfigXml.'**'.macosArchive.each { macosArchive ->
2416 macosArchive.attributes().remove('executeSetupApp')
2417 macosArchive.attributes().remove('setupAppId')
2420 // turn off checksum creation for LOCAL channel
2421 def e = install4jConfigXml.application[0]
2422 e.'@createChecksums' = string(install4jCheckSums)
2424 // put file association actions where placeholder action is
2425 def install4jFileAssociationsText = install4jFileAssociationsFile.text
2426 def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
2427 install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
2428 if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
2429 def parent = a.parent()
2431 fileAssociationActions.each { faa ->
2434 // don't need to continue in .any loop once replacements have been made
2439 // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
2440 // NB we're deleting the /other/ one!
2441 // Also remove the examples subdir from non-release versions
2442 def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
2443 // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
2444 if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
2445 customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
2447 // remove the examples subdir from Full File Set
2448 def files = install4jConfigXml.files[0]
2449 def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
2450 def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
2451 def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
2452 def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
2453 dirEntry.parent().remove(dirEntry)
2455 install4jConfigXml.'**'.action.any { a ->
2456 if (a.'@customizedId' == customizedIdToDelete) {
2457 def parent = a.parent()
2463 // write install4j file
2464 install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
2471 delete install4jConfFile
2475 task cleanInstallersDataFiles {
2476 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2477 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2478 def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
2480 delete installersOutputTxt
2481 delete installersSha256
2482 delete hugoDataJsonFile
2486 task install4jDMGBackgroundImageCopy {
2487 inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
2488 outputs.dir "${install4jDMGBackgroundImageBuildDir}"
2491 from(install4jDMGBackgroundImageDir) {
2492 include(install4jDMGBackgroundImageFile)
2494 into install4jDMGBackgroundImageBuildDir
2499 task install4jDMGBackgroundImageProcess {
2500 dependsOn install4jDMGBackgroundImageCopy
2503 if (backgroundImageText) {
2504 if (convertBinary == null) {
2505 throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
2507 if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
2508 throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
2510 fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
2512 executable convertBinary
2515 '-font', install4j_background_image_text_font,
2516 '-fill', install4j_background_image_text_colour,
2517 '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
2518 '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
2519 '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
2528 task install4jDMGBackgroundImage {
2529 dependsOn install4jDMGBackgroundImageProcess
2532 task installerFiles(type: com.install4j.gradle.Install4jTask) {
2533 group = "distribution"
2534 description = "Create the install4j installers"
2536 dependsOn copyInstall4jTemplate
2537 dependsOn cleanInstallersDataFiles
2538 dependsOn install4jDMGBackgroundImage
2540 projectFile = install4jConfFile
2542 // create an md5 for the input files to use as version for install4j conf file
2543 def digest = MessageDigest.getInstance("MD5")
2545 (file("${install4jDir}/${install4j_template}").text +
2546 file("${install4jDir}/${install4j_info_plist_file_associations}").text +
2547 file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
2548 def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
2549 if (filesMd5.length() >= 8) {
2550 filesMd5 = filesMd5.substring(0,8)
2552 def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
2555 'JALVIEW_NAME': jalview_name,
2556 'JALVIEW_APPLICATION_NAME': applicationName,
2557 'JALVIEW_DIR': "../..",
2558 'OSX_KEYSTORE': OSX_KEYSTORE,
2559 'OSX_APPLEID': OSX_APPLEID,
2560 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
2561 'JSIGN_SH': JSIGN_SH,
2562 'JRE_DIR': getdown_app_dir_java,
2563 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
2564 'JALVIEW_VERSION': JALVIEW_VERSION,
2565 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
2566 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
2567 'JAVA_VERSION': JAVA_VERSION,
2568 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
2569 'VERSION': JALVIEW_VERSION,
2570 'COPYRIGHT_MESSAGE': install4j_copyright_message,
2571 'BUNDLE_ID': install4jBundleId,
2572 'INTERNAL_ID': install4jInternalId,
2573 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
2574 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
2575 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
2576 'WRAPPER_LINK': getdownWrapperLink,
2577 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
2578 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
2579 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
2580 'INSTALLER_NAME': install4jInstallerName,
2581 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
2582 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
2583 'GETDOWN_FILES_DIR': getdown_files_dir,
2584 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
2585 'GETDOWN_DIST_DIR': getdownAppDistDir,
2586 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
2587 'GETDOWN_INSTALL_DIR': getdown_install_dir,
2588 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
2589 'BUILD_DIR': install4jBuildDir,
2590 'APPLICATION_CATEGORIES': install4j_application_categories,
2591 'APPLICATION_FOLDER': install4jApplicationFolder,
2592 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
2593 'EXECUTABLE_NAME': install4jExecutableName,
2594 'EXTRA_SCHEME': install4jExtraScheme,
2595 'MAC_ICONS_FILE': install4jMacIconsFile,
2596 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
2597 'PNG_ICON_FILE': install4jPngIconFile,
2598 'BACKGROUND': install4jBackground,
2603 'windows': 'WINDOWS',
2607 // these are the bundled OS/architecture VMs needed by install4j
2610 [ "mac", "aarch64" ],
2611 [ "windows", "x64" ],
2613 [ "linux", "aarch64" ]
2615 osArch.forEach { os, arch ->
2616 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)
2617 // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
2618 // otherwise running `gradle installers` generates a non-useful error:
2619 // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
2620 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)
2623 //println("INSTALL4J VARIABLES:")
2624 //variables.each{k,v->println("${k}=${v}")}
2626 destination = "${jalviewDir}/${install4jBuildDir}"
2627 buildSelected = true
2629 if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
2631 disableSigning = true
2632 disableNotarization = true
2636 macKeystorePassword = OSX_KEYPASS
2639 if (OSX_ALTOOLPASS) {
2640 appleIdPassword = OSX_ALTOOLPASS
2641 disableNotarization = false
2643 disableNotarization = true
2647 println("Using projectFile "+projectFile)
2648 if (!disableNotarization) { println("Will notarize OSX App DMG") }
2652 inputs.dir(getdownAppBaseDir)
2653 inputs.file(install4jConfFile)
2654 inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
2655 outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
2658 def getDataHash(File myFile) {
2659 HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
2660 return myFile.exists()
2662 "file" : myFile.getName(),
2663 "filesize" : myFile.length(),
2664 "sha256" : hash.toString()
2669 def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
2671 "channel" : getdownChannelName,
2672 "date" : getDate("yyyy-MM-dd HH:mm:ss"),
2673 "git-commit" : "${gitHash} [${gitBranch}]",
2674 "version" : JALVIEW_VERSION
2676 // install4j installer files
2677 if (installersOutputTxt.exists()) {
2679 installersOutputTxt.readLines().each { def line ->
2680 if (line.startsWith("#")) {
2683 line.replaceAll("\n","")
2684 def vals = line.split("\t")
2685 def filename = vals[3]
2686 def filesize = file(filename).length()
2687 filename = filename.replaceAll(/^.*\//, "")
2688 hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
2689 idHash."${filename}" = vals[0]
2691 if (install4jCheckSums && installersSha256.exists()) {
2692 installersSha256.readLines().each { def line ->
2693 if (line.startsWith("#")) {
2696 line.replaceAll("\n","")
2697 def vals = line.split(/\s+\*?/)
2698 def filename = vals[1]
2699 def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
2705 "JAR": shadowJar.archiveFile, // executable JAR
2706 "JVL": getdownVersionLaunchJvl, // version JVL
2707 "SOURCE": sourceDist.archiveFile // source TGZ
2708 ].each { key, value ->
2709 def file = file(value)
2710 if (file.exists()) {
2711 def fileHash = getDataHash(file)
2712 if (fileHash != null) {
2713 hash."${key}" = fileHash;
2717 return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
2720 task staticMakeInstallersJsonFile {
2722 def output = findProperty("i4j_output")
2723 def sha256 = findProperty("i4j_sha256")
2724 def json = findProperty("i4j_json")
2725 if (output == null || sha256 == null || json == null) {
2726 throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
2728 writeDataJsonFile(file(output), file(sha256), file(json))
2733 dependsOn installerFiles
2739 eclipse().configFile(eclipse_codestyle_file)
2743 task createSourceReleaseProperties(type: WriteProperties) {
2744 group = "distribution"
2745 description = "Create the source RELEASE properties file"
2747 def sourceTarBuildDir = "${buildDir}/sourceTar"
2748 def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
2749 outputFile (sourceReleasePropertiesFile)
2752 releaseProps.each{ key, val -> property key, val }
2753 property "git.branch", gitBranch
2754 property "git.hash", gitHash
2757 outputs.file(outputFile)
2760 task sourceDist(type: Tar) {
2761 group "distribution"
2762 description "Create a source .tar.gz file for distribution"
2764 dependsOn createBuildProperties
2765 dependsOn convertMdFiles
2766 dependsOn eclipseAllPreferences
2767 dependsOn createSourceReleaseProperties
2770 def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
2771 archiveFileName = outputFileName
2773 compression Compression.GZIP
2788 "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
2790 "utils/InstallAnywhere",
2805 "gradle.properties",
2817 ".settings/org.eclipse.buildship.core.prefs",
2818 ".settings/org.eclipse.jdt.core.prefs"
2822 exclude (EXCLUDE_FILES)
2823 include (PROCESS_FILES)
2824 filter(ReplaceTokens,
2828 'Version-Rel': JALVIEW_VERSION,
2829 'Year-Rel': getDate("yyyy")
2834 exclude (EXCLUDE_FILES)
2835 exclude (PROCESS_FILES)
2836 exclude ("appletlib")
2837 exclude ("**/*locales")
2838 exclude ("*locales/**")
2839 exclude ("utils/InstallAnywhere")
2841 exclude (getdown_files_dir)
2842 // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
2843 //exclude (getdown_website_dir)
2844 //exclude (getdown_archive_dir)
2846 // exluding these as not using jars as modules yet
2847 exclude ("${j11modDir}/**/*.jar")
2850 include(INCLUDE_FILES)
2852 // from (jalviewDir) {
2853 // // explicit includes for stuff that seemed to not get included
2854 // include(fileTree("test/**/*."))
2855 // exclude(EXCLUDE_FILES)
2856 // exclude(PROCESS_FILES)
2859 from(file(buildProperties).getParent()) {
2860 include(file(buildProperties).getName())
2861 rename(file(buildProperties).getName(), "build_properties")
2863 line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
2867 def sourceTarBuildDir = "${buildDir}/sourceTar"
2868 from(sourceTarBuildDir) {
2869 // this includes the appended RELEASE properties file
2873 task dataInstallersJson {
2875 description "Create the installers-VERSION.json data file for installer files created"
2877 mustRunAfter installers
2878 mustRunAfter shadowJar
2879 mustRunAfter sourceDist
2880 mustRunAfter getdownArchive
2882 def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
2883 def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
2885 if (installersOutputTxt.exists()) {
2886 inputs.file(installersOutputTxt)
2888 if (install4jCheckSums && installersSha256.exists()) {
2889 inputs.file(installersSha256)
2892 shadowJar.archiveFile, // executable JAR
2893 getdownVersionLaunchJvl, // version JVL
2894 sourceDist.archiveFile // source TGZ
2895 ].each { fileName ->
2896 if (file(fileName).exists()) {
2897 inputs.file(fileName)
2901 outputs.file(hugoDataJsonFile)
2904 writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
2910 description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
2913 dependsOn pubhtmlhelp
2915 inputs.dir("${helpBuildDir}/${help_dir}")
2916 outputs.dir("${buildDir}/distributions/${help_dir}")
2920 task j2sSetHeadlessBuild {
2927 task jalviewjsEnableAltFileProperty(type: WriteProperties) {
2929 description "Enable the alternative J2S Config file for headless build"
2931 outputFile = jalviewjsJ2sSettingsFileName
2932 def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
2933 def j2sProps = new Properties()
2934 if (j2sPropsFile.exists()) {
2936 def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
2937 j2sProps.load(j2sPropsFileFIS)
2938 j2sPropsFileFIS.close()
2940 j2sProps.each { prop, val ->
2943 } catch (Exception e) {
2944 println("Exception reading ${jalviewjsJ2sSettingsFileName}")
2948 if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
2949 property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
2954 task jalviewjsSetEclipseWorkspace {
2955 def propKey = "jalviewjs_eclipse_workspace"
2957 if (project.hasProperty(propKey)) {
2958 propVal = project.getProperty(propKey)
2959 if (propVal.startsWith("~/")) {
2960 propVal = System.getProperty("user.home") + propVal.substring(1)
2963 def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
2964 def propsFile = file(propsFileName)
2965 def eclipseWsDir = propVal
2966 def props = new Properties()
2968 def writeProps = true
2969 if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
2970 def ins = new FileInputStream(propsFileName)
2973 if (props.getProperty(propKey, null) != null) {
2974 eclipseWsDir = props.getProperty(propKey)
2979 if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
2980 def tempDir = File.createTempDir()
2981 eclipseWsDir = tempDir.getAbsolutePath()
2984 eclipseWorkspace = file(eclipseWsDir)
2987 // do not run a headless transpile when we claim to be in Eclipse
2989 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2990 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
2992 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
2996 props.setProperty(propKey, eclipseWsDir)
2997 propsFile.parentFile.mkdirs()
2998 def bytes = new ByteArrayOutputStream()
2999 props.store(bytes, null)
3000 def propertiesString = bytes.toString()
3001 propsFile.text = propertiesString
3007 println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
3010 //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
3011 outputs.file(propsFileName)
3012 outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
3016 task jalviewjsEclipsePaths {
3019 def eclipseRoot = jalviewjs_eclipse_root
3020 if (eclipseRoot.startsWith("~/")) {
3021 eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
3023 if (OperatingSystem.current().isMacOsX()) {
3024 eclipseRoot += "/Eclipse.app"
3025 eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
3026 eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
3027 } else if (OperatingSystem.current().isWindows()) { // check these paths!!
3028 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3029 eclipseRoot += "/eclipse"
3031 eclipseBinary = "${eclipseRoot}/eclipse.exe"
3032 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3033 } else { // linux or unix
3034 if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
3035 eclipseRoot += "/eclipse"
3036 println("eclipseDir exists")
3038 eclipseBinary = "${eclipseRoot}/eclipse"
3039 eclipseProduct = "${eclipseRoot}/.eclipseproduct"
3042 eclipseVersion = "4.13" // default
3043 def assumedVersion = true
3044 if (file(eclipseProduct).exists()) {
3045 def fis = new FileInputStream(eclipseProduct)
3046 def props = new Properties()
3048 eclipseVersion = props.getProperty("version")
3050 assumedVersion = false
3053 def propKey = "eclipse_debug"
3054 eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
3057 // do not run a headless transpile when we claim to be in Eclipse
3059 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3060 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3062 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3065 if (!assumedVersion) {
3066 println("ECLIPSE VERSION=${eclipseVersion}")
3072 task printProperties {
3074 description "Output to console all System.properties"
3076 System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
3082 dependsOn eclipseProject
3083 dependsOn eclipseClasspath
3084 dependsOn eclipseJdt
3088 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
3089 task jalviewjsEclipseCopyDropins(type: Copy) {
3090 dependsOn jalviewjsEclipsePaths
3092 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
3093 inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
3094 def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
3101 // this eclipse -clean doesn't actually work
3102 task jalviewjsCleanEclipse(type: Exec) {
3103 dependsOn eclipseSetup
3104 dependsOn jalviewjsEclipsePaths
3105 dependsOn jalviewjsEclipseCopyDropins
3107 executable(eclipseBinary)
3108 args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
3114 def inputString = """exit
3117 def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
3118 standardInput = inputByteStream
3121 /* not really working yet
3122 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
3126 task jalviewjsTransferUnzipSwingJs {
3127 def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
3131 from zipTree(file_zip)
3132 into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3136 inputs.file file_zip
3137 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3141 task jalviewjsTransferUnzipLib {
3142 def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
3145 zipFiles.each { file_zip ->
3147 from zipTree(file_zip)
3148 into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3153 inputs.files zipFiles
3154 outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3158 task jalviewjsTransferUnzipAllLibs {
3159 dependsOn jalviewjsTransferUnzipSwingJs
3160 dependsOn jalviewjsTransferUnzipLib
3164 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
3166 description "Create the alternative j2s file from the j2s.* properties"
3168 jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
3169 def siteDirProperty = "j2s.site.directory"
3170 def setSiteDir = false
3171 jalviewjsJ2sProps.each { prop, val ->
3173 if (prop == siteDirProperty) {
3174 if (!(val.startsWith('/') || val.startsWith("file://") )) {
3175 val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
3181 if (!setSiteDir) { // default site location, don't override specifically set property
3182 property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
3185 outputFile = jalviewjsJ2sAltSettingsFileName
3188 inputs.properties(jalviewjsJ2sProps)
3189 outputs.file(jalviewjsJ2sAltSettingsFileName)
3194 task jalviewjsEclipseSetup {
3195 dependsOn jalviewjsEclipseCopyDropins
3196 dependsOn jalviewjsSetEclipseWorkspace
3197 dependsOn jalviewjsCreateJ2sSettings
3201 task jalviewjsSyncAllLibs (type: Sync) {
3202 dependsOn jalviewjsTransferUnzipAllLibs
3203 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
3204 inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
3205 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3209 def outputFiles = []
3210 rename { filename ->
3211 outputFiles += "${outputDir}/${filename}"
3218 // should this be exclude really ?
3219 duplicatesStrategy "INCLUDE"
3221 outputs.files outputFiles
3222 inputs.files inputFiles
3226 task jalviewjsSyncResources (type: Sync) {
3227 dependsOn buildResources
3229 def inputFiles = fileTree(dir: resourcesBuildDir)
3230 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3234 def outputFiles = []
3235 rename { filename ->
3236 outputFiles += "${outputDir}/${filename}"
3242 outputs.files outputFiles
3243 inputs.files inputFiles
3247 task jalviewjsSyncSiteResources (type: Sync) {
3248 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
3249 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3253 def outputFiles = []
3254 rename { filename ->
3255 outputFiles += "${outputDir}/${filename}"
3261 outputs.files outputFiles
3262 inputs.files inputFiles
3266 task jalviewjsSyncBuildProperties (type: Sync) {
3267 dependsOn createBuildProperties
3268 def inputFiles = [file(buildProperties)]
3269 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
3273 def outputFiles = []
3274 rename { filename ->
3275 outputFiles += "${outputDir}/${filename}"
3281 outputs.files outputFiles
3282 inputs.files inputFiles
3286 task jalviewjsProjectImport(type: Exec) {
3287 dependsOn eclipseSetup
3288 dependsOn jalviewjsEclipsePaths
3289 dependsOn jalviewjsEclipseSetup
3292 // do not run a headless import when we claim to be in Eclipse
3294 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3295 throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3297 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3301 //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
3302 def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
3303 executable(eclipseBinary)
3304 args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
3308 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3310 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3311 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3314 inputs.file("${jalviewDir}/.project")
3315 outputs.upToDateWhen {
3316 file(projdir).exists()
3321 task jalviewjsTranspile(type: Exec) {
3322 dependsOn jalviewjsEclipseSetup
3323 dependsOn jalviewjsProjectImport
3324 dependsOn jalviewjsEclipsePaths
3326 dependsOn jalviewjsEnableAltFileProperty
3330 // do not run a headless transpile when we claim to be in Eclipse
3332 println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3333 throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
3335 println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
3339 executable(eclipseBinary)
3340 args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
3344 args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
3346 args += [ "-D${j2sHeadlessBuildProperty}=true" ]
3347 args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
3353 stdout = new ByteArrayOutputStream()
3354 stderr = new ByteArrayOutputStream()
3356 def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
3357 def logOutFile = file(logOutFileName)
3358 logOutFile.createNewFile()
3359 logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
3360 BINARY: ${eclipseBinary}
3361 VERSION: ${eclipseVersion}
3362 WORKSPACE: ${eclipseWorkspace}
3363 DEBUG: ${eclipseDebug}
3366 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3367 // combine stdout and stderr
3368 def logErrFOS = logOutFOS
3370 if (jalviewjs_j2s_to_console.equals("true")) {
3371 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3372 new org.apache.tools.ant.util.TeeOutputStream(
3376 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3377 new org.apache.tools.ant.util.TeeOutputStream(
3382 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3385 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3392 if (stdout.toString().contains("Error processing ")) {
3393 // j2s did not complete transpile
3394 //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3395 if (jalviewjs_ignore_transpile_errors.equals("true")) {
3396 println("IGNORING TRANSPILE ERRORS")
3397 println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3399 throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
3404 inputs.dir("${jalviewDir}/${sourceDir}")
3405 outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
3406 outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
3410 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
3412 def stdout = new ByteArrayOutputStream()
3413 def stderr = new ByteArrayOutputStream()
3415 def coreFile = file(jsfile)
3417 msg = "Creating core for ${name}...\nGenerating ${jsfile}"
3419 logOutFile.createNewFile()
3420 logOutFile.append(msg+"\n")
3422 def coreTop = file(prefixFile)
3423 def coreBottom = file(suffixFile)
3424 coreFile.getParentFile().mkdirs()
3425 coreFile.createNewFile()
3426 coreFile.write( coreTop.getText("UTF-8") )
3430 def t = f.getText("UTF-8")
3431 t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
3432 coreFile.append( t )
3434 msg = "...file '"+f.getPath()+"' does not exist, skipping"
3436 logOutFile.append(msg+"\n")
3439 coreFile.append( coreBottom.getText("UTF-8") )
3441 msg = "Generating ${zjsfile}"
3443 logOutFile.append(msg+"\n")
3444 def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
3445 def logErrFOS = logOutFOS
3448 classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
3449 main = "com.google.javascript.jscomp.CommandLineRunner"
3450 jvmArgs = [ "-Dfile.encoding=UTF-8" ]
3451 args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
3454 msg = "\nRunning '"+commandLine.join(' ')+"'\n"
3456 logOutFile.append(msg+"\n")
3458 if (logOutConsole) {
3459 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3460 new org.apache.tools.ant.util.TeeOutputStream(
3464 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3465 new org.apache.tools.ant.util.TeeOutputStream(
3470 standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
3473 errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
3480 logOutFile.append(msg+"\n")
3484 task jalviewjsBuildAllCores {
3486 description "Build the core js lib closures listed in the classlists dir"
3487 dependsOn jalviewjsTranspile
3488 dependsOn jalviewjsTransferUnzipSwingJs
3490 def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
3491 def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
3492 def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
3493 def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
3494 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
3495 def prefixFile = "${jsDir}/core/coretop2.js"
3496 def suffixFile = "${jsDir}/core/corebottom2.js"
3498 inputs.file prefixFile
3499 inputs.file suffixFile
3501 def classlistFiles = []
3502 // add the classlists found int the jalviewjs_classlists_dir
3503 fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
3505 def name = file.getName() - ".txt"
3512 // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
3513 //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
3514 classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
3516 jalviewjsCoreClasslists = []
3518 classlistFiles.each {
3521 def file = hash['file']
3522 if (! file.exists()) {
3523 //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
3524 return false // this is a "continue" in groovy .each closure
3526 def name = hash['name']
3528 name = file.getName() - ".txt"
3536 def list = fileTree(dir: j2sDir, includes: filelist)
3538 def jsfile = "${outputDir}/core${name}.js"
3539 def zjsfile = "${outputDir}/core${name}.z.js"
3541 jalviewjsCoreClasslists += [
3550 outputs.file(jsfile)
3551 outputs.file(zjsfile)
3554 // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
3555 def stevesoftClasslistName = "_stevesoft"
3556 def stevesoftClasslist = [
3557 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
3558 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
3559 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
3560 'name': stevesoftClasslistName
3562 jalviewjsCoreClasslists += stevesoftClasslist
3563 inputs.files(stevesoftClasslist['list'])
3564 outputs.file(stevesoftClasslist['jsfile'])
3565 outputs.file(stevesoftClasslist['zjsfile'])
3568 def allClasslistName = "_all"
3569 def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
3570 allJsFiles += fileTree(
3574 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3575 "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
3576 "**/org/jmol/export/JSExporter.js"
3579 allJsFiles += fileTree(
3583 // these exlusions are files that the closure-compiler produces errors for. Should fix them
3584 "**/sun/misc/Unsafe.js",
3585 "**/swingjs/jquery/jquery-editable-select.js",
3586 "**/swingjs/jquery/j2sComboBox.js",
3587 "**/sun/misc/FloatingDecimal.js"
3590 def allClasslist = [
3591 'jsfile': "${outputDir}/core${allClasslistName}.js",
3592 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
3594 'name': allClasslistName
3596 // not including this version of "all" core at the moment
3597 //jalviewjsCoreClasslists += allClasslist
3598 inputs.files(allClasslist['list'])
3599 outputs.file(allClasslist['jsfile'])
3600 outputs.file(allClasslist['zjsfile'])
3603 def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
3604 logOutFile.getParentFile().mkdirs()
3605 logOutFile.createNewFile()
3606 logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
3608 jalviewjsCoreClasslists.each {
3609 jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
3616 def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
3619 into file(outputFile).getParentFile()
3620 rename { filename ->
3621 if (filename.equals(inputFile.getName())) {
3622 return file(outputFile).getName()
3626 filter(ReplaceTokens,
3630 'MAIN': '"'+main_class+'"',
3632 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
3633 'COREKEY': jalviewjs_core_key,
3634 'CORENAME': coreName
3641 task jalviewjsPublishCoreTemplates {
3642 dependsOn jalviewjsBuildAllCores
3643 def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
3644 def inputFile = file(inputFileName)
3645 def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3647 def outputFiles = []
3648 jalviewjsCoreClasslists.each { cl ->
3649 def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
3650 cl['outputfile'] = outputFile
3651 outputFiles += outputFile
3655 jalviewjsCoreClasslists.each { cl ->
3656 jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
3659 inputs.file(inputFile)
3660 outputs.files(outputFiles)
3664 task jalviewjsSyncCore (type: Sync) {
3665 dependsOn jalviewjsBuildAllCores
3666 dependsOn jalviewjsPublishCoreTemplates
3667 def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
3668 def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
3672 def outputFiles = []
3673 rename { filename ->
3674 outputFiles += "${outputDir}/${filename}"
3680 outputs.files outputFiles
3681 inputs.files inputFiles
3685 // this Copy version of TransferSiteJs will delete anything else in the target dir
3686 task jalviewjsCopyTransferSiteJs(type: Copy) {
3687 dependsOn jalviewjsTranspile
3688 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3689 into "${jalviewDir}/${jalviewjsSiteDir}"
3693 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
3694 task jalviewjsSyncTransferSiteJs(type: Sync) {
3695 from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3697 into "${jalviewDir}/${jalviewjsSiteDir}"
3704 jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
3705 jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
3706 jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
3707 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
3709 jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
3710 jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
3711 jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
3712 jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
3715 task jalviewjsPrepareSite {
3717 description "Prepares the website folder including unzipping files and copying resources"
3718 dependsOn jalviewjsSyncAllLibs
3719 dependsOn jalviewjsSyncResources
3720 dependsOn jalviewjsSyncSiteResources
3721 dependsOn jalviewjsSyncBuildProperties
3722 dependsOn jalviewjsSyncCore
3726 task jalviewjsBuildSite {
3728 description "Builds the whole website including transpiled code"
3729 dependsOn jalviewjsCopyTransferSiteJs
3730 dependsOn jalviewjsPrepareSite
3734 task cleanJalviewjsTransferSite {
3736 delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
3737 delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
3738 delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
3739 delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
3744 task cleanJalviewjsSite {
3745 dependsOn cleanJalviewjsTransferSite
3747 delete "${jalviewDir}/${jalviewjsSiteDir}"
3752 task jalviewjsSiteTar(type: Tar) {
3754 description "Creates a tar.gz file for the website"
3755 dependsOn jalviewjsBuildSite
3756 def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
3757 archiveFileName = outputFilename
3759 compression Compression.GZIP
3761 from "${jalviewDir}/${jalviewjsSiteDir}"
3762 into jalviewjs_site_dir // this is inside the tar file
3764 inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
3768 task jalviewjsServer {
3770 def filename = "jalviewjsTest.html"
3771 description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
3772 def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
3777 def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
3778 factory = f.newInstance()
3779 } catch (ClassNotFoundException e) {
3780 throw new GradleException("Unable to create SimpleHttpFileServerFactory")
3782 def port = Integer.valueOf(jalviewjs_server_port)
3787 while(port < start+1000 && !running) {
3789 def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
3790 jalviewjsServer = factory.start(doc_root, port)
3792 url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
3793 println("SERVER STARTED with document root ${doc_root}.")
3794 println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
3795 println("For debug: "+url+"?j2sdebug")
3796 println("For verbose: "+url+"?j2sverbose")
3797 } catch (Exception e) {
3802 <p><a href="${url}">JalviewJS Test. <${url}></a></p>
3803 <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
3804 <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
3806 jalviewjsCoreClasslists.each { cl ->
3807 def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
3809 <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
3811 println("For core ${cl.name}: "+urlcore)
3814 file(htmlFile).text = htmlText
3817 outputs.file(htmlFile)
3818 outputs.upToDateWhen({false})
3822 task cleanJalviewjsAll {
3824 description "Delete all configuration and build artifacts to do with JalviewJS build"
3825 dependsOn cleanJalviewjsSite
3826 dependsOn jalviewjsEclipsePaths
3829 delete "${jalviewDir}/${jalviewjsBuildDir}"
3830 delete "${jalviewDir}/${eclipse_bin_dir}"
3831 if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
3832 delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
3834 delete jalviewjsJ2sAltSettingsFileName
3837 outputs.upToDateWhen( { false } )
3841 task jalviewjsIDE_checkJ2sPlugin {
3842 group "00 JalviewJS in Eclipse"
3843 description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
3846 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3847 def j2sPluginFile = file(j2sPlugin)
3848 def eclipseHome = System.properties["eclipse.home.location"]
3849 if (eclipseHome == null || ! IN_ECLIPSE) {
3850 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
3852 def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
3853 def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
3854 if (altPluginsDir != null && file(altPluginsDir).exists()) {
3855 eclipseJ2sPluginDirs += altPluginsDir
3857 def foundPlugin = false
3858 def j2sPluginFileName = j2sPluginFile.getName()
3859 def eclipseJ2sPlugin
3860 def eclipseJ2sPluginFile
3861 eclipseJ2sPluginDirs.any { dir ->
3862 eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
3863 eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3864 if (eclipseJ2sPluginFile.exists()) {
3870 def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
3871 System.err.println(msg)
3872 throw new StopExecutionException(msg)
3875 def digest = MessageDigest.getInstance("MD5")
3877 digest.update(j2sPluginFile.text.bytes)
3878 def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3880 digest.update(eclipseJ2sPluginFile.text.bytes)
3881 def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
3883 if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
3884 def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
3885 System.err.println(msg)
3886 throw new StopExecutionException(msg)
3888 def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
3894 task jalviewjsIDE_copyJ2sPlugin {
3895 group "00 JalviewJS in Eclipse"
3896 description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
3899 def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
3900 def j2sPluginFile = file(j2sPlugin)
3901 def eclipseHome = System.properties["eclipse.home.location"]
3902 if (eclipseHome == null || ! IN_ECLIPSE) {
3903 throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
3905 def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
3906 def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
3907 def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
3908 System.err.println(msg)
3911 eclipseJ2sPluginFile.getParentFile().mkdirs()
3912 into eclipseJ2sPluginFile.getParent()
3918 task jalviewjsIDE_j2sFile {
3919 group "00 JalviewJS in Eclipse"
3920 description "Creates the .j2s file"
3921 dependsOn jalviewjsCreateJ2sSettings
3925 task jalviewjsIDE_SyncCore {
3926 group "00 JalviewJS in Eclipse"
3927 description "Build the core js lib closures listed in the classlists dir and publish core html from template"
3928 dependsOn jalviewjsSyncCore
3932 task jalviewjsIDE_SyncSiteAll {
3933 dependsOn jalviewjsSyncAllLibs
3934 dependsOn jalviewjsSyncResources
3935 dependsOn jalviewjsSyncSiteResources
3936 dependsOn jalviewjsSyncBuildProperties
3940 cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
3943 task jalviewjsIDE_PrepareSite {
3944 group "00 JalviewJS in Eclipse"
3945 description "Sync libs and resources to site dir, but not closure cores"
3947 dependsOn jalviewjsIDE_SyncSiteAll
3948 //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
3952 task jalviewjsIDE_AssembleSite {
3953 group "00 JalviewJS in Eclipse"
3954 description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
3955 dependsOn jalviewjsPrepareSite
3959 task jalviewjsIDE_SiteClean {
3960 group "00 JalviewJS in Eclipse"
3961 description "Deletes the Eclipse transpiled site"
3962 dependsOn cleanJalviewjsSite
3966 task jalviewjsIDE_Server {
3967 group "00 JalviewJS in Eclipse"
3968 description "Starts a webserver on localhost to test the website"
3969 dependsOn jalviewjsServer
3973 // buildship runs this at import or gradle refresh
3974 task eclipseSynchronizationTask {
3975 //dependsOn eclipseSetup
3976 dependsOn createBuildProperties
3978 dependsOn jalviewjsIDE_j2sFile
3979 dependsOn jalviewjsIDE_checkJ2sPlugin
3980 dependsOn jalviewjsIDE_PrepareSite
3985 // buildship runs this at build time or project refresh
3986 task eclipseAutoBuildTask {
3987 //dependsOn jalviewjsIDE_checkJ2sPlugin
3988 //dependsOn jalviewjsIDE_PrepareSite
3994 description "Build the site"
3995 dependsOn jalviewjsBuildSite