X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=d955de332c6575cf33fbbe79689f639477167e68;hb=refs%2Fheads%2Fmerge%2FJalview-JS_develop_with_develop_build.gradle_gradle.properties_utils_install4j;hp=84c38db45b55018616f6ff30e89e4bdc40248342;hpb=1655b4dd264bcc756d2d08cfe786dd64d75e7d06;p=jalview.git diff --git a/build.gradle b/build.gradle index 84c38db..d955de3 100644 --- a/build.gradle +++ b/build.gradle @@ -1,5 +1,8 @@ import org.apache.tools.ant.filters.ReplaceTokens import org.gradle.internal.os.OperatingSystem +import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject +import org.gradle.api.internal.PropertiesTransformer +import org.gradle.util.ConfigureUtil import org.gradle.plugins.ide.eclipse.model.Output import org.gradle.plugins.ide.eclipse.model.Library import java.security.MessageDigest @@ -7,18 +10,25 @@ import groovy.transform.ExternalizeMethods import groovy.util.XmlParser import groovy.xml.XmlUtil + buildscript { + repositories { + mavenCentral() + mavenLocal() + } dependencies { - classpath 'org.openclover:clover:4.3.1' + classpath 'org.openclover:clover:4.4.1' } } + plugins { id 'java' id 'application' id 'eclipse' + id "com.diffplug.gradle.spotless" version "3.28.0" id 'com.github.johnrengelman.shadow' version '4.0.3' - id 'com.install4j.gradle' version '8.0.2' + id 'com.install4j.gradle' version '8.0.4' id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree } @@ -26,13 +36,6 @@ repositories { jcenter() mavenCentral() mavenLocal() - flatDir { - dirs gradlePluginsDir - } -} - -dependencies { - compile 'org.apache.commons:commons-compress:1.18' } @@ -47,11 +50,21 @@ ext { jalviewDirRelativePath = jalviewDir // local build environment properties - def localProps = "${jalviewDirAbsolutePath}/local.properties" + // can be "projectDir/local.properties" + def localProps = "${projectDir}/local.properties" + def propsFile = null; if (file(localProps).exists()) { + propsFile = localProps + } + // or "../projectDir_local.properties" + def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties" + if (file(dirLocalProps).exists()) { + propsFile = dirLocalProps + } + if (propsFile != null) { try { def p = new Properties() - def localPropsFIS = new FileInputStream(localProps) + def localPropsFIS = new FileInputStream(propsFile) p.load(localPropsFIS) localPropsFIS.close() p.each { @@ -59,9 +72,9 @@ ext { def oldval = findProperty(key) setProperty(key, val) if (oldval != null) { - println("Overriding property '${key}' ('${oldval}') with local.properties value '${val}'") + println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") } else { - println("Setting unknown property '${key}' with local.properties value '${val}'") + println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'") } } } catch (Exception e) { @@ -86,6 +99,12 @@ ext { } else { println("HEADLESS BUILD") } + + J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable") + if (J2S_ENABLED) { + println("J2S ENABLED") + } + /* *-/ System.properties.sort { it.key }.each { key, val -> println("SYSTEM PROPERTY ${key}='${val}'") @@ -105,6 +124,7 @@ ext { // clover cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") + cloverDb = string("${buildDir}/clover/clover.db") classesDir = string("${jalviewDir}/${classes_dir}") if (clover.equals("true")) { use_clover = true @@ -125,8 +145,15 @@ ext { getdownAppBase = string("${getdown_channel_base}/${getdownDir}") getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}") getdownAppDistDir = getdown_app_dir_alt - buildProperties = string("${classesDir}/${build_properties_file}") - reportRsyncCmd = false + buildProperties = string("${resourceDir}/${build_properties_file}") + reportRsyncCommand = false + jvlChannelName = CHANNEL.toLowerCase() + install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build + install4jDSStore = "DS_Store-NON-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png" + install4jInstallerName = "${jalview_name} Non-Release Installer" + install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase() + install4jExtraScheme = "jalviewx" switch (CHANNEL) { case "BUILD": @@ -134,11 +161,26 @@ ext { getdown_channel_base = bamboo_channelbase getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}") getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") + jvlChannelName += "_${getdownChannelName}" + // automatically add the test group Not-bamboo for exclusion + if ("".equals(testngExcludedGroups)) { + testngExcludedGroups = "Not-bamboo" + } + install4jExtraScheme = "jalviewb" break case "RELEASE": getdownAppDistDir = getdown_app_dir_release reportRsyncCommand = true + // Don't ignore transpile errors for release build + if (jalviewjs_ignore_transpile_errors.equals("true")) { + jalviewjs_ignore_transpile_errors = "false" + println("Setting jalviewjs_ignore_transpile_errors to 'false'") + } + install4jSuffix = "" + install4jDSStore = "DS_Store" + install4jDMGBackgroundImage = "jalview_dmg_background.png" + install4jInstallerName = "${jalview_name} Installer" break case "ARCHIVE": @@ -149,10 +191,11 @@ ext { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { packageDir = string("${ARCHIVEDIR}/${packageDir}") - buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") + buildProperties = string("${buildDir}/archive/${build_properties_file}") buildDist = false } reportRsyncCommand = true + install4jExtraScheme = "jalviewa" break case "ARCHIVELOCAL": @@ -163,19 +206,36 @@ ext { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { packageDir = string("${ARCHIVEDIR}/${packageDir}") - buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") + buildProperties = string("${buildDir}/archive/${build_properties_file}") buildDist = false } reportRsyncCommand = true getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jSuffix = "Archive" + install4jExtraScheme = "jalviewa" break case "DEVELOP": reportRsyncCommand = true + install4jDSStore = "DS_Store-DEVELOP" + install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png" + install4jExtraScheme = "jalviewd" + install4jInstallerName = "${jalview_name} Develop Installer" break case "TEST-RELEASE": reportRsyncCommand = true + // Don't ignore transpile errors for release build + if (jalviewjs_ignore_transpile_errors.equals("true")) { + jalviewjs_ignore_transpile_errors = "false" + println("Setting jalviewjs_ignore_transpile_errors to 'false'") + } + JALVIEW_VERSION = "TEST" + install4jSuffix = "Test" + install4jDSStore = "DS_Store-TEST-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" break case ~/^SCRATCH(|-[-\w]*)$/: @@ -183,11 +243,28 @@ ext { getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = string("${getdown_channel_base}/${getdownDir}") reportRsyncCommand = true + install4jSuffix = "Scratch" + break + + case "TEST-LOCAL": + if (!file("${LOCALDIR}").exists()) { + throw new GradleException("Must provide a LOCALDIR value to produce a local distribution") + } else { + getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString() + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + } + JALVIEW_VERSION = "TEST" + install4jSuffix = "Test-Local" + install4jDSStore = "DS_Store-TEST-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" break case "LOCAL": getdownAppBase = file(getdownWebsiteDir).toURI().toString() getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jExtraScheme = "jalviewl" break default: // something wrong specified @@ -200,6 +277,38 @@ ext { getdownAppBase = string(getProperty("getdown_appbase_override")) println("Overriding getdown appbase with '${getdownAppBase}'") } + // sanitise file name for jalview launcher file for this channel + jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_") + // install4j application and folder names + if (install4jSuffix == "") { + install4jApplicationName = "${jalview_name}" + install4jBundleId = "${install4j_bundle_id}" + install4jWinApplicationId = install4j_release_win_application_id + } else { + install4jApplicationName = "${jalview_name} ${install4jSuffix}" + install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase() + // add int hash of install4jSuffix to the last part of the application_id + def id = install4j_release_win_application_id + def idsplitreverse = id.split("-").reverse() + idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode() + install4jWinApplicationId = idsplitreverse.reverse().join("-") + } + // sanitise folder and id names + // install4jApplicationFolder = e.g. "Jalview Build" + install4jApplicationFolder = install4jApplicationName + .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \ + .replaceAll("_+", "_") // collapse __ + install4jInternalId = install4jApplicationName + .replaceAll(" ","_") + .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] + .replaceAll("_+", "") // collapse __ + //.replaceAll("_*-_*", "-") // collapse _-_ + install4jUnixApplicationFolder = install4jApplicationName + .replaceAll(" ","_") + .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] + .replaceAll("_+", "_") // collapse __ + .replaceAll("_*-_*", "-") // collapse _-_ + .toLowerCase() getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}") //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" @@ -315,6 +424,7 @@ ext { jalviewjsJalviewTemplateName = string(jalviewjs_name) jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}") jalviewjsJ2sProps = null + jalviewjsJ2sPlugin = jalviewjs_j2s_plugin eclipseWorkspace = null eclipseBinary = string("") @@ -376,7 +486,7 @@ sourceSets { compileClasspath = files( sourceSets.test.java.outputDir ) if (use_clover) { - compileClasspath += sourceSets.clover.compileClasspath + compileClasspath = sourceSets.clover.compileClasspath } else { compileClasspath += files(sourceSets.main.java.outputDir) } @@ -393,8 +503,8 @@ sourceSets { // clover bits dependencies { if (use_clover) { - cloverCompile 'org.openclover:clover:4.3.1' - testCompile 'org.openclover:clover:4.3.1' + cloverCompile 'org.openclover:clover:4.4.1' + testCompile 'org.openclover:clover:4.4.1' } } @@ -404,6 +514,8 @@ configurations { cloverRuntime.extendsFrom cloverCompile } + +// eclipse project and settings files creation, also used by buildship eclipse { project { name = eclipse_project_name @@ -513,6 +625,7 @@ eclipse { javaRuntimeName = eclipseJavaRuntimeName // add in jalview project specific properties/preferences into eclipse core preferences + // and also the codestyle XML file file { withProperties { props -> def jalview_prefs = new Properties() @@ -524,6 +637,22 @@ eclipse { props.putAt(t, v) } } + // codestyle file -- overrides previous formatter prefs + def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}") + if (csFile.exists()) { + XmlParser parser = new XmlParser() + def profiles = parser.parse(csFile) + def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") } + if (profile != null) { + profile.'setting'.each { s -> + def id = s.'@id' + def value = s.'@value' + if (id != null && value != null) { + props.putAt(id, value) + } + } + } + } } } @@ -532,24 +661,87 @@ eclipse { if (IN_ECLIPSE) { // Don't want these to be activated if in headless build synchronizationTasks "eclipseSynchronizationTask" - autoBuildTasks "eclipseAutoBuildTask" + //autoBuildTasks "eclipseAutoBuildTask" } } -task cloverInstr() { +/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */ +// Class to allow updating arbitrary properties files +class PropertiesFile extends PropertiesPersistableConfigurationObject { + public PropertiesFile(PropertiesTransformer t) { super(t); } + @Override protected void load(Properties properties) { } + @Override protected void store(Properties properties) { } + @Override protected String getDefaultResourceName() { return ""; } + // This is necessary, because PropertiesPersistableConfigurationObject fails + // if no default properties file exists. + @Override public void loadDefaults() { load(new StringBufferInputStream("")); } +} + +// Task to update arbitrary properties files (set outputFile) +class PropertiesFileTask extends PropertiesGeneratorTask { + private final PropertiesFileContentMerger file; + public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); } + protected PropertiesFile create() { return new PropertiesFile(getTransformer()); } + protected void configure(PropertiesFile props) { + file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props); + } + public void file(Closure closure) { ConfigureUtil.configure(closure, file); } +} + +task eclipseUIPreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.ui.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) + } + } +} + +task eclipseGroovyCorePreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.groovy.core.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) + } + } +} + +task eclipseAllPreferences { + dependsOn eclipseJdt + dependsOn eclipseUIPreferences + dependsOn eclipseGroovyCorePreferences +} + +eclipseUIPreferences.mustRunAfter eclipseJdt +eclipseGroovyCorePreferences.mustRunAfter eclipseJdt + +/* end of eclipse preferences hack */ + + +task cloverInstr { // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"])) + inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) outputs.dir cloverInstrDir doFirst { delete cloverInstrDir - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-d", "${buildDir}/${cloverSourcesInstrDir}"] - argsList.addAll(inputs.files.files.collect({ file -> - file.absolutePath - })) + def argsList = [ + "--initstring", + cloverDb, + "-d", + cloverInstrDir.getPath(), + ] + argsList.addAll( + inputs.files.files.collect( + { file -> file.absolutePath } + ) + ) String[] args = argsList.toArray() println("About to instrument "+args.length +" files") com.atlassian.clover.CloverInstr.mainImpl(args) @@ -557,26 +749,57 @@ task cloverInstr() { } +cloverClasses.dependsOn cloverInstr + + task cloverReport { group = "Verification" - description = "Createst the Clover report" - inputs.dir "${buildDir}/clover" - outputs.dir "${reportsDir}/clover" - onlyIf { - file("${buildDir}/clover/clover.db").exists() - } + description = "Creates the Clover report" + inputs.dir "${buildDir}/clover" + outputs.dir "${reportsDir}/clover" + onlyIf { + file(cloverDb).exists() + } doFirst { - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover"] + def argsList = [ + "--initstring", + cloverDb, + "-o", + "${reportsDir}/clover" + ] String[] args = argsList.toArray() com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) // and generate ${reportsDir}/clover/clover.xml - args = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover/clover.xml"].toArray() + args = [ + "--initstring", + cloverDb, + "-o", + "${reportsDir}/clover/clover.xml" + ].toArray() com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) } } + + +compileCloverJava { + + doFirst { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs += additional_compiler_args + print ("Setting target compatibility to "+targetCompatibility+"\n") + } + classpath += configurations.cloverRuntime +} + + +task cleanClover { + doFirst { + delete cloverInstrDir + delete cloverDb + } +} // end clover bits @@ -608,18 +831,6 @@ compileTestJava { } -compileCloverJava { - - doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs += additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") - } - classpath += configurations.cloverRuntime -} - - clean { doFirst { delete sourceSets.main.java.outputDir @@ -628,9 +839,9 @@ clean { cleanTest { + dependsOn cleanClover doFirst { delete sourceSets.test.java.outputDir - delete cloverInstrDir } } @@ -665,6 +876,9 @@ task setGitVals { task createBuildProperties(type: WriteProperties) { + group = "build" + description = "Create the ${buildProperties} file" + dependsOn setGitVals inputs.dir(sourceDir) inputs.dir(resourceDir) @@ -680,6 +894,13 @@ task createBuildProperties(type: WriteProperties) { } +clean { + doFirst { + delete buildProperties + } +} + + task cleanBuildingHTML(type: Delete) { doFirst { delete buildingHTML @@ -700,7 +921,6 @@ task convertBuildingMD(type: Exec) { } } - def hostname = "hostname".execute().text.trim() def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) { pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" @@ -723,13 +943,6 @@ task convertBuildingMD(type: Exec) { } -clean { - doFirst { - delete buildingHTML - } -} - - task syncDocs(type: Sync) { dependsOn convertBuildingMD def syncDir = "${classesDir}/${docDir}" @@ -776,6 +989,7 @@ task syncLib(type: Sync) { task syncResources(type: Sync) { + dependsOn createBuildProperties from resourceDir include "**/*.*" into "${classesDir}" @@ -806,10 +1020,13 @@ test { useTestNG() { includeGroups testngGroups + excludeGroups testngExcludedGroups preserveOrder true useDefaultListeners=true } + maxHeapSize = "1024m" + workingDir = jalviewDir //systemProperties 'clover.jar' System.properties.clover.jar sourceCompatibility = compile_source_compatibility @@ -886,6 +1103,7 @@ task cleanPackageDir(type: Delete) { } } + jar { dependsOn linkCheck dependsOn buildIndices @@ -989,7 +1207,7 @@ task getdownWebsite() { } getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" - // go through properties looking for getdown_txt_... + // set some getdown_txt_ properties then go through all properties looking for getdown_txt_... def props = project.properties.sort { it.key } if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) { props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion) @@ -1001,7 +1219,11 @@ task getdownWebsite() { props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) } - props.put("getdown_txt_appbase", getdownAppBase) + props.put("getdown_txt_title", jalview_name) + props.put("getdown_txt_ui.name", install4jApplicationName) + + // start with appbase + getdownTextString += "appbase = ${getdownAppBase}\n" props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { if (prop.startsWith("getdown_txt_multi_")) { @@ -1088,9 +1310,9 @@ task getdownWebsite() { def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) - def getdownLaunchJvl = ( (getdownChannelName != null && getdownChannelName.length() > 0)?"${getdownChannelName}_":"" ) + getdown_launch_jvl - def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}") - launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) + def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl" + def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}") + launchJvl.write("appbase=${getdownAppBase}") copy { from getdownLauncher @@ -1125,7 +1347,7 @@ task getdownWebsite() { copy { from getdown_txt - from launch_jvl + from launchJvl from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { @@ -1148,6 +1370,22 @@ task getdownWebsite() { } +// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir +task getdownDigestDir(type: JavaExec) { + def digestDirPropertyName = "DIGESTDIR" + description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown" + doFirst { + classpath = files(getdownLauncher) + def digestDir = findProperty(digestDirPropertyName) + if (digestDir == null) { + throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest") + } + args digestDir + } + main = "com.threerings.getdown.tools.Digester" +} + + task getdownDigest(type: JavaExec) { group = "distribution" description = "Digest the getdown website folder" @@ -1212,6 +1450,7 @@ task copyInstall4jTemplate { def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}") inputs.file(install4jTemplateFile) inputs.file(install4jFileAssociationsFile) + inputs.property("CHANNEL", { CHANNEL }) outputs.file(install4jConfFile) doLast { @@ -1227,10 +1466,18 @@ task copyInstall4jTemplate { } } + // turn off checksum creation for LOCAL channel + def e = install4jConfigXml.application[0] + if (CHANNEL == "LOCAL") { + e.'@createChecksums' = "false" + } else { + e.'@createChecksums' = "true" + } + // put file association actions where placeholder action is def install4jFileAssociationsText = install4jFileAssociationsFile.text def fileAssociationActions = new XmlParser().parseText("${install4jFileAssociationsText}") - install4jConfigXml.'**'.action.any { a -> + install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') { def parent = a.parent() parent.remove(a) @@ -1242,6 +1489,35 @@ task copyInstall4jTemplate { } } + // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else + // NB we're deleting the /other/ one! + // Also remove the examples subdir from non-release versions + def customizedIdToDelete = "PROGRAM_GROUP_RELEASE" + if (CHANNEL=="RELEASE") { + customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE" + } else { + // remove the examples subdir from Full File Set + def files = install4jConfigXml.files[0] + def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" } + def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' } + def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' } + def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" } + dirEntry.parent().remove(dirEntry) + } + install4jConfigXml.'**'.action.any { a -> + if (a.'@customizedId' == customizedIdToDelete) { + def parent = a.parent() + parent.remove(a) + return true + } + } + + // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores + if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) { + def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" } + symlink.parent().remove(symlink) + } + // write install4j file install4jConfFile.text = XmlUtil.serialize(install4jConfigXml) } @@ -1279,6 +1555,8 @@ task installers(type: com.install4j.gradle.Install4jTask) { def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}" variables = [ + 'JALVIEW_NAME': jalview_name, + 'JALVIEW_APPLICATION_NAME': install4jApplicationName, 'JALVIEW_DIR': "../..", 'OSX_KEYSTORE': OSX_KEYSTORE, 'JSIGN_SH': JSIGN_SH, @@ -1297,7 +1575,12 @@ task installers(type: com.install4j.gradle.Install4jTask) { 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, 'COPYRIGHT_MESSAGE': install4j_copyright_message, - 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id, + 'BUNDLE_ID': install4jBundleId, + 'INTERNAL_ID': install4jInternalId, + 'WINDOWS_APPLICATION_ID': install4jWinApplicationId, + 'MACOS_DS_STORE': install4jDSStore, + 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage, + 'INSTALLER_NAME': install4jInstallerName, 'INSTALL4J_UTILS_DIR': install4j_utils_dir, 'GETDOWN_WEBSITE_DIR': getdown_website_dir, 'GETDOWN_FILES_DIR': getdown_files_dir, @@ -1307,13 +1590,20 @@ task installers(type: com.install4j.gradle.Install4jTask) { 'GETDOWN_INSTALL_DIR': getdown_install_dir, 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations, 'BUILD_DIR': install4jBuildDir, + 'APPLICATION_CATEGORIES': install4j_application_categories, + 'APPLICATION_FOLDER': install4jApplicationFolder, + 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder, + 'EXECUTABLE_NAME': install4jExecutableName, + 'EXTRA_SCHEME': install4jExtraScheme, ] + //println("INSTALL4J VARIABLES:") + //variables.each{k,v->println("${k}=${v}")} + destination = "${jalviewDir}/${install4jBuildDir}" buildSelected = true - if (install4j_faster.equals("true") || CHANNEL.startsWith("DEVELOP") || CHANNEL.startsWith("LOCAL")) { - // this doesn't seem to work + if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) { faster = true disableSigning = true } @@ -1335,6 +1625,13 @@ task installers(type: com.install4j.gradle.Install4jTask) { } +spotless { + java { + eclipse().configFile(eclipse_codestyle_file) + } +} + + task sourceDist(type: Tar) { def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") @@ -1350,33 +1647,47 @@ task sourceDist(type: Tar) { into project.name - def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*" - ,".*" - ,"benchmarking/*" - ,"**/.*" - ,"*.class" - ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales" - ,"*locales/**", - ,"utils/InstallAnywhere"] - def PROCESS_FILES=[ "AUTHORS", - "CITATION", - "FEATURETODO", - "JAVA-11-README", - "FEATURETODO", - "LICENSE", - "**/README", - "RELEASE", - "THIRDPARTYLIBS","TESTNG", - "build.gradle", - "gradle.properties", - "**/*.java", - "**/*.html", - "**/*.xml", - "**/*.gradle", - "**/*.groovy", - "**/*.properties", - "**/*.perl", - "**/*.sh"] + def EXCLUDE_FILES=[ + "build/*", + "bin/*", + "test-output/", + "test-reports", + "tests", + "clover*/*", + ".*", + "benchmarking/*", + "**/.*", + "*.class", + "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales", + "*locales/**", + "utils/InstallAnywhere", + "**/*.log", + ] + def PROCESS_FILES=[ + "AUTHORS", + "CITATION", + "FEATURETODO", + "JAVA-11-README", + "FEATURETODO", + "LICENSE", + "**/README", + "RELEASE", + "THIRDPARTYLIBS", + "TESTNG", + "build.gradle", + "gradle.properties", + "**/*.java", + "**/*.html", + "**/*.xml", + "**/*.gradle", + "**/*.groovy", + "**/*.properties", + "**/*.perl", + "**/*.sh", + ] + def INCLUDE_FILES=[ + ".settings/org.eclipse.jdt.core.jalview.prefs", + ] from(jalviewDir) { exclude (EXCLUDE_FILES) @@ -1404,12 +1715,15 @@ task sourceDist(type: Tar) { // exluding these as not using jars as modules yet exclude ("${j11modDir}/**/*.jar") } - // from (jalviewDir) { - // // explicit includes for stuff that seemed to not get included - // include(fileTree("test/**/*.")) - // exclude(EXCLUDE_FILES) - // exclude(PROCESS_FILES) - // } + from(jalviewDir) { + include(INCLUDE_FILES) + } +// from (jalviewDir) { +// // explicit includes for stuff that seemed to not get included +// include(fileTree("test/**/*.")) +// exclude(EXCLUDE_FILES) +// exclude(PROCESS_FILES) +// } } @@ -1421,6 +1735,1023 @@ task helppages { outputs.dir("${buildDir}/distributions/${help_dir}") } -// LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE -task eclipseAutoBuildTask {} -task eclipseSynchronizationTask {} + +task j2sSetHeadlessBuild { + doFirst { + IN_ECLIPSE = false + } +} + + +task jalviewjsSetEclipseWorkspace { + def propKey = "jalviewjs_eclipse_workspace" + def propVal = null + if (project.hasProperty(propKey)) { + propVal = project.getProperty(propKey) + if (propVal.startsWith("~/")) { + propVal = System.getProperty("user.home") + propVal.substring(1) + } + } + def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}" + def propsFile = file(propsFileName) + def eclipseWsDir = propVal + def props = new Properties() + + def writeProps = true + if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) { + def ins = new FileInputStream(propsFileName) + props.load(ins) + ins.close() + if (props.getProperty(propKey, null) != null) { + eclipseWsDir = props.getProperty(propKey) + writeProps = false + } + } + + if (eclipseWsDir == null || !file(eclipseWsDir).exists()) { + def tempDir = File.createTempDir() + eclipseWsDir = tempDir.getAbsolutePath() + writeProps = true + } + eclipseWorkspace = file(eclipseWsDir) + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + + if (writeProps) { + props.setProperty(propKey, eclipseWsDir) + propsFile.parentFile.mkdirs() + def bytes = new ByteArrayOutputStream() + props.store(bytes, null) + def propertiesString = bytes.toString() + propsFile.text = propertiesString + print("NEW ") + } else { + print("EXISTING ") + } + + println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) + } + + //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date + outputs.file(propsFileName) + outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() } +} + + +task jalviewjsEclipsePaths { + def eclipseProduct + + def eclipseRoot = jalviewjs_eclipse_root + if (eclipseRoot.startsWith("~/")) { + eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1) + } + if (OperatingSystem.current().isMacOsX()) { + eclipseRoot += "/Eclipse.app" + eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse" + eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" + } else if (OperatingSystem.current().isWindows()) { // check these paths!! + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { + eclipseRoot += "/eclipse.exe" + } + eclipseBinary = "${eclipseRoot}/eclipse" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" + } else { // linux or unix + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { + eclipseRoot += "/eclipse" + } + eclipseBinary = "${eclipseRoot}/eclipse" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" + } + + eclipseVersion = "4.13" // default + def assumedVersion = true + if (file(eclipseProduct).exists()) { + def fis = new FileInputStream(eclipseProduct) + def props = new Properties() + props.load(fis) + eclipseVersion = props.getProperty("version") + fis.close() + assumedVersion = false + } + + def propKey = "eclipse_debug" + eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true")) + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + + if (!assumedVersion) { + println("ECLIPSE VERSION=${eclipseVersion}") + } + } +} + + +task printProperties { + group "Debug" + description "Output to console all System.properties" + doFirst { + System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") } + } +} + + +task eclipseSetup { + dependsOn eclipseProject + dependsOn eclipseClasspath + dependsOn eclipseJdt +} + + +// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir +task jalviewjsEclipseCopyDropins(type: Copy) { + dependsOn jalviewjsEclipsePaths + + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") + inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}") + def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" + + from inputFiles + into outputDir +} + + +// this eclipse -clean doesn't actually work +task jalviewjsCleanEclipse(type: Exec) { + dependsOn eclipseSetup + dependsOn jalviewjsEclipsePaths + dependsOn jalviewjsEclipseCopyDropins + + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"]) + if (eclipseDebug) { + args += "-debug" + } + args += "-l" + + def inputString = """exit +y +""" + def inputByteStream = new ByteArrayInputStream(inputString.getBytes()) + standardInput = inputByteStream +} + +/* not really working yet +jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse +*/ + + +task jalviewjsTransferUnzipSwingJs { + def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}" + + doLast { + copy { + from zipTree(file_zip) + into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" + } + } + + inputs.file file_zip + outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" +} + + +task jalviewjsTransferUnzipLib { + def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip") + + doLast { + zipFiles.each { file_zip -> + copy { + from zipTree(file_zip) + into "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + } + } + } + + inputs.files zipFiles + outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}" +} + + +task jalviewjsTransferUnzipAllLibs { + dependsOn jalviewjsTransferUnzipSwingJs + dependsOn jalviewjsTransferUnzipLib +} + + +task jalviewjsCreateJ2sSettings(type: WriteProperties) { + group "JalviewJS" + description "Create the .j2s file from the j2s.* properties" + + jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } + def siteDirProperty = "j2s.site.directory" + def setSiteDir = false + jalviewjsJ2sProps.each { prop, val -> + if (val != null) { + if (prop == siteDirProperty) { + if (!(val.startsWith('/') || val.startsWith("file://") )) { + val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}" + } + setSiteDir = true + } + property(prop,val) + } + if (!setSiteDir) { // default site location, don't override specifically set property + property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}") + } + } + outputFile = jalviewjsJ2sSettingsFileName + + if (! IN_ECLIPSE) { + inputs.properties(jalviewjsJ2sProps) + outputs.file(jalviewjsJ2sSettingsFileName) + } +} + + +task jalviewjsEclipseSetup { + dependsOn jalviewjsEclipseCopyDropins + dependsOn jalviewjsSetEclipseWorkspace + dependsOn jalviewjsCreateJ2sSettings +} + + +task jalviewjsSyncAllLibs (type: Sync) { + dependsOn jalviewjsTransferUnzipAllLibs + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}") + inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncResources (type: Sync) { + def inputFiles = fileTree(dir: resourceDir) + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncSiteResources (type: Sync) { + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncBuildProperties (type: Sync) { + dependsOn createBuildProperties + def inputFiles = [file(buildProperties)] + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsProjectImport(type: Exec) { + dependsOn eclipseSetup + dependsOn jalviewjsEclipsePaths + dependsOn jalviewjsEclipseSetup + + doFirst { + // do not run a headless import when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + } + + //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" + def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview" + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath]) + if (eclipseDebug) { + args += "-debug" + } + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] + if (!IN_ECLIPSE) { + args += [ "-D${j2sHeadlessBuildProperty}=true" ] + } + + inputs.file("${jalviewDir}/.project") + outputs.upToDateWhen { + file(projdir).exists() + } +} + + +task jalviewjsTranspile(type: Exec) { + dependsOn jalviewjsEclipseSetup + dependsOn jalviewjsProjectImport + dependsOn jalviewjsEclipsePaths + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + } + + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ]) + if (eclipseDebug) { + args += "-debug" + } + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] + if (!IN_ECLIPSE) { + args += [ "-D${j2sHeadlessBuildProperty}=true" ] + } + + def stdout + def stderr + doFirst { + stdout = new ByteArrayOutputStream() + stderr = new ByteArrayOutputStream() + + def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}" + def logOutFile = file(logOutFileName) + logOutFile.createNewFile() + logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} +BINARY: ${eclipseBinary} +VERSION: ${eclipseVersion} +WORKSPACE: ${eclipseWorkspace} +DEBUG: ${eclipseDebug} +---- +""" + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + // combine stdout and stderr + def logErrFOS = logOutFOS + + if (jalviewjs_j2s_to_console.equals("true")) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr), + errorOutput) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr) + } + } + + doLast { + if (stdout.toString().contains("Error processing ")) { + // j2s did not complete transpile + //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + if (jalviewjs_ignore_transpile_errors.equals("true")) { + println("IGNORING TRANSPILE ERRORS") + println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + } else { + throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + } + } + } + + inputs.dir("${jalviewDir}/${sourceDir}") + outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}") + outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } ) +} + + +def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) { + + def stdout = new ByteArrayOutputStream() + def stderr = new ByteArrayOutputStream() + + def coreFile = file(jsfile) + def msg = "" + msg = "Creating core for ${name}...\nGenerating ${jsfile}" + println(msg) + logOutFile.createNewFile() + logOutFile.append(msg+"\n") + + def coreTop = file(prefixFile) + def coreBottom = file(suffixFile) + coreFile.getParentFile().mkdirs() + coreFile.createNewFile() + coreFile.write( coreTop.text ) + list.each { + f -> + if (f.exists()) { + def t = f.text + t.replaceAll("Clazz\\.([^_])","Clazz_${1}") + coreFile.append( t ) + } else { + msg = "...file '"+f.getPath()+"' does not exist, skipping" + println(msg) + logOutFile.append(msg+"\n") + } + } + coreFile.append( coreBottom.text ) + + msg = "Generating ${zjsfile}" + println(msg) + logOutFile.append(msg+"\n") + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + def logErrFOS = logOutFOS + + javaexec { + classpath = files(["${jalviewDir}/tools/closure_compiler.jar"]) + args = [ "--js", jsfile, "--js_output_file", zjsfile ] + maxHeapSize = "2g" + + msg = "\nRunning '"+commandLine.join(' ')+"'\n" + println(msg) + logOutFile.append(msg+"\n") + + if (logOutConsole) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr), + errorOutput) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr) + } + } + msg = "--" + println(msg) + logOutFile.append(msg+"\n") +} + + +task jalviewjsBuildAllCores { + group "JalviewJS" + description "Build the core js lib closures listed in the classlists dir" + dependsOn jalviewjsTranspile + dependsOn jalviewjsTransferUnzipSwingJs + + def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}" + def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}" + def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}" + def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}" + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core" + def prefixFile = "${jsDir}/core/coretop2.js" + def suffixFile = "${jsDir}/core/corebottom2.js" + + inputs.file prefixFile + inputs.file suffixFile + + def classlistFiles = [] + // add the classlists found int the jalviewjs_classlists_dir + fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each { + file -> + def name = file.getName() - ".txt" + classlistFiles += [ + 'file': file, + 'name': name + ] + } + + // _jmol and _jalview cores. Add any other peculiar classlist.txt files here + //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ] + classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ] + + jalviewjsCoreClasslists = [] + + classlistFiles.each { + hash -> + + def file = hash['file'] + if (! file.exists()) { + //println("...classlist file '"+file.getPath()+"' does not exist, skipping") + return false // this is a "continue" in groovy .each closure + } + def name = hash['name'] + if (name == null) { + name = file.getName() - ".txt" + } + + def filelist = [] + file.eachLine { + line -> + filelist += line + } + def list = fileTree(dir: j2sDir, includes: filelist) + + def jsfile = "${outputDir}/core${name}.js" + def zjsfile = "${outputDir}/core${name}.z.js" + + jalviewjsCoreClasslists += [ + 'jsfile': jsfile, + 'zjsfile': zjsfile, + 'list': list, + 'name': name + ] + + inputs.file(file) + inputs.files(list) + outputs.file(jsfile) + outputs.file(zjsfile) + } + + // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) + def stevesoftClasslistName = "_stevesoft" + def stevesoftClasslist = [ + 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js", + 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js", + 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"), + 'name': stevesoftClasslistName + ] + jalviewjsCoreClasslists += stevesoftClasslist + inputs.files(stevesoftClasslist['list']) + outputs.file(stevesoftClasslist['jsfile']) + outputs.file(stevesoftClasslist['zjsfile']) + + // _all core + def allClasslistName = "_all" + def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js") + allJsFiles += fileTree( + dir: libJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js", + "**/org/jmol/export/JSExporter.js" + ] + ) + allJsFiles += fileTree( + dir: swingJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/sun/misc/Unsafe.js", + "**/swingjs/jquery/jquery-editable-select.js", + "**/swingjs/jquery/j2sComboBox.js", + "**/sun/misc/FloatingDecimal.js" + ] + ) + def allClasslist = [ + 'jsfile': "${outputDir}/core${allClasslistName}.js", + 'zjsfile': "${outputDir}/core${allClasslistName}.z.js", + 'list': allJsFiles, + 'name': allClasslistName + ] + // not including this version of "all" core at the moment + //jalviewjsCoreClasslists += allClasslist + inputs.files(allClasslist['list']) + outputs.file(allClasslist['jsfile']) + outputs.file(allClasslist['zjsfile']) + + doFirst { + def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}") + logOutFile.getParentFile().mkdirs() + logOutFile.createNewFile() + logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n") + + jalviewjsCoreClasslists.each { + jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true")) + } + } + +} + + +def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) { + copy { + from inputFile + into file(outputFile).getParentFile() + rename { filename -> + if (filename.equals(inputFile.getName())) { + return file(outputFile).getName() + } + return null + } + filter(ReplaceTokens, + beginToken: '_', + endToken: '_', + tokens: [ + 'MAIN': '"'+mainClass+'"', + 'CODE': "null", + 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]", + 'COREKEY': jalviewjs_core_key, + 'CORENAME': coreName + ] + ) + } +} + + +task jalviewjsPublishCoreTemplates { + dependsOn jalviewjsBuildAllCores + def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}" + def inputFile = file(inputFileName) + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + + def outputFiles = [] + jalviewjsCoreClasslists.each { cl -> + def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html" + cl['outputfile'] = outputFile + outputFiles += outputFile + } + + doFirst { + jalviewjsCoreClasslists.each { cl -> + jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile) + } + } + inputs.file(inputFile) + outputs.files(outputFiles) +} + + +task jalviewjsSyncCore (type: Sync) { + dependsOn jalviewjsBuildAllCores + dependsOn jalviewjsPublishCoreTemplates + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +// this Copy version of TransferSiteJs will delete anything else in the target dir +task jalviewjsCopyTransferSiteJs(type: Copy) { + dependsOn jalviewjsTranspile + from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + into "${jalviewDir}/${jalviewjsSiteDir}" +} + + +// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes +task jalviewjsSyncTransferSiteJs(type: Sync) { + from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + include "**/*.*" + into "${jalviewDir}/${jalviewjsSiteDir}" + preserve { + include "**" + } +} + + +jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs +jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs +jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs + +jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs + + +task jalviewjsPrepareSite { + group "JalviewJS" + description "Prepares the website folder including unzipping files and copying resources" + dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncResources + dependsOn jalviewjsSyncSiteResources + dependsOn jalviewjsSyncBuildProperties + dependsOn jalviewjsSyncCore +} + + +task jalviewjsBuildSite { + group "JalviewJS" + description "Builds the whole website including transpiled code" + dependsOn jalviewjsCopyTransferSiteJs + dependsOn jalviewjsPrepareSite +} + + +task cleanJalviewjsTransferSite { + doFirst { + delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + } +} + + +task cleanJalviewjsSite { + dependsOn cleanJalviewjsTransferSite + doFirst { + delete "${jalviewDir}/${jalviewjsSiteDir}" + } +} + + +task jalviewjsSiteTar(type: Tar) { + group "JalviewJS" + description "Creates a tar.gz file for the website" + dependsOn jalviewjsBuildSite + def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz" + try { + archiveFileName = outputFilename + } catch (Exception e) { + archiveName = outputFilename + } + + compression Compression.GZIP + + from "${jalviewDir}/${jalviewjsSiteDir}" + into jalviewjs_site_dir // this is inside the tar file + + inputs.dir("${jalviewDir}/${jalviewjsSiteDir}") +} + + +task jalviewjsServer { + group "JalviewJS" + def filename = "jalviewjsTest.html" + description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port." + def htmlFile = "${jalviewDirAbsolutePath}/${filename}" + doLast { + + SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory() + def port = Integer.valueOf(jalviewjs_server_port) + def start = port + def running = false + def url + def jalviewjsServer + while(port < start+1000 && !running) { + try { + def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") + jalviewjsServer = factory.start(doc_root, port) + running = true + url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource) + println("SERVER STARTED with document root ${doc_root}.") + println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).") + println("For debug: "+url+"?j2sdebug") + println("For verbose: "+url+"?j2sverbose") + } catch (Exception e) { + port++; + } + } + def htmlText = """ +

JalviewJS Test. <${url}>

+

JalviewJS Test with debug. <${url}?j2sdebug>

+

JalviewJS Test with verbose. <${url}?j2sdebug>

+ """ + jalviewjsCoreClasslists.each { cl -> + def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName()) + htmlText += """ +

${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}>

+ """ + println("For core ${cl.name}: "+urlcore) + } + + file(htmlFile).text = htmlText + } + + outputs.file(htmlFile) + outputs.upToDateWhen({false}) +} + + +task cleanJalviewjsAll { + group "JalviewJS" + description "Delete all configuration and build artifacts to do with JalviewJS build" + dependsOn cleanJalviewjsSite + dependsOn jalviewjsEclipsePaths + + doFirst { + delete "${jalviewDir}/${jalviewjsBuildDir}" + delete "${jalviewDir}/${eclipse_bin_dir}" + if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) { + delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") + } + delete "${jalviewDir}/${jalviewjs_j2s_settings}" + } + + outputs.upToDateWhen( { false } ) +} + + +task jalviewjsIDE_checkJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)" + + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.") + } + def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}" + def eclipseJ2sPluginFile = file(eclipseJ2sPlugin) + if (!eclipseJ2sPluginFile.exists()) { + def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin" + System.err.println(msg) + throw new StopExecutionException(msg) + } + + def digest = MessageDigest.getInstance("MD5") + + digest.update(j2sPluginFile.text.bytes) + def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + digest.update(eclipseJ2sPluginFile.text.bytes) + def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + if (j2sPluginMd5 != eclipseJ2sPluginMd5) { + def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'" + System.err.println(msg) + throw new StopExecutionException(msg) + } else { + def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)" + println(msg) + } + } +} + +task jalviewjsIDE_copyJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir" + + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.") + } + def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}" + def eclipseJ2sPluginFile = file(eclipseJ2sPlugin) + def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart" + System.err.println(msg) + copy { + from j2sPlugin + eclipseJ2sPluginFile.getParentFile().mkdirs() + into eclipseJ2sPluginFile.getParent() + } + } +} + + +task jalviewjsIDE_j2sFile { + group "00 JalviewJS in Eclipse" + description "Creates the .j2s file" + dependsOn jalviewjsCreateJ2sSettings +} + + +task jalviewjsIDE_SyncCore { + group "00 JalviewJS in Eclipse" + description "Build the core js lib closures listed in the classlists dir and publish core html from template" + dependsOn jalviewjsSyncCore +} + + +task jalviewjsIDE_SyncSiteAll { + dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncResources + dependsOn jalviewjsSyncSiteResources + dependsOn jalviewjsSyncBuildProperties +} + + +cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll + + +task jalviewjsIDE_PrepareSite { + group "00 JalviewJS in Eclipse" + description "Sync libs and resources to site dir, but not closure cores" + + dependsOn jalviewjsIDE_SyncSiteAll + dependsOn cleanJalviewjsTransferSite +} + + +task jalviewjsIDE_AssembleSite { + group "00 JalviewJS in Eclipse" + description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site" + dependsOn jalviewjsPrepareSite +} + + +task jalviewjsIDE_SiteClean { + group "00 JalviewJS in Eclipse" + description "Deletes the Eclipse transpiled site" + dependsOn cleanJalviewjsSite +} + + +task jalviewjsIDE_Server { + group "00 JalviewJS in Eclipse" + description "Starts a webserver on localhost to test the website" + dependsOn jalviewjsServer +} + + +// buildship runs this at import or gradle refresh +task eclipseSynchronizationTask { + //dependsOn eclipseSetup + dependsOn createBuildProperties + if (J2S_ENABLED) { + dependsOn jalviewjsIDE_j2sFile + dependsOn jalviewjsIDE_checkJ2sPlugin + dependsOn jalviewjsIDE_PrepareSite + } +} + + +// buildship runs this at build time or project refresh +task eclipseAutoBuildTask { + //dependsOn jalviewjsIDE_checkJ2sPlugin + //dependsOn jalviewjsIDE_PrepareSite +} + + +task jalviewjs { + group "JalviewJS" + description "Build the site" + dependsOn jalviewjsBuildSite +}