/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names. * For properties set within build.gradle, use camelCaseNoSpace. */ 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 import groovy.transform.ExternalizeMethods import groovy.util.XmlParser import groovy.xml.XmlUtil import com.vladsch.flexmark.util.ast.Node import com.vladsch.flexmark.html.HtmlRenderer import com.vladsch.flexmark.parser.Parser import com.vladsch.flexmark.util.data.MutableDataSet import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension import com.vladsch.flexmark.ext.tables.TablesExtension import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension import com.vladsch.flexmark.ext.autolink.AutolinkExtension import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension import com.vladsch.flexmark.ext.toc.TocExtension buildscript { repositories { mavenCentral() mavenLocal() } dependencies { classpath "com.vladsch.flexmark:flexmark-all:0.62.0" } } 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 '8.0.4' id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree } repositories { jcenter() mavenCentral() mavenLocal() } // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use def string(Object o) { return o == null ? "" : o.toString() } ext { jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() jalviewDirRelativePath = jalviewDir // local build environment properties // can be "projectDir/local.properties" def localProps = "${projectDir}/local.properties" def propsFile = null; if (file(localProps).exists()) { propsFile = localProps } // or "../projectDir_local.properties" def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties" if (file(dirLocalProps).exists()) { propsFile = dirLocalProps } if (propsFile != null) { try { def p = new Properties() def localPropsFIS = new FileInputStream(propsFile) p.load(localPropsFIS) localPropsFIS.close() p.each { key, val -> def oldval = findProperty(key) setProperty(key, val) if (oldval != null) { println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") } else { println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'") } } } catch (Exception e) { System.out.println("Exception reading local.properties") } } //// // Import releaseProps from the RELEASE file // or a file specified via JALVIEW_RELEASE_FILE if defined // Expect jalview.version and target release branch in jalview.release def releaseProps = new Properties(); def releasePropFile = findProperty("JALVIEW_RELEASE_FILE"); def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE"; try { (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { releaseProps.load(it) } } catch (Exception fileLoadError) { throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError); } //// // Set JALVIEW_VERSION if it is not already set if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) { JALVIEW_VERSION = releaseProps.get("jalview.version") } // this property set when running Eclipse headlessly j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild") // this property set by Eclipse eclipseApplicationProperty = string("eclipse.application") // CHECK IF RUNNING FROM WITHIN ECLIPSE def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty] IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.") // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET if (System.properties[j2sHeadlessBuildProperty].equals("true")) { println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'") IN_ECLIPSE = false } if (IN_ECLIPSE) { println("WITHIN ECLIPSE IDE") } 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}'") } /-* *-/ if (false && IN_ECLIPSE) { jalviewDir = jalviewDirAbsolutePath } */ // essentials bareSourceDir = string(source_dir) sourceDir = string("${jalviewDir}/${bareSourceDir}") resourceDir = string("${jalviewDir}/${resource_dir}") bareTestSourceDir = string(test_source_dir) testDir = string("${jalviewDir}/${bareTestSourceDir}") classesDir = string("${jalviewDir}/${classes_dir}") // clover useClover = clover.equals("true") cloverBuildDir = "${buildDir}/clover" cloverInstrDir = file("${cloverBuildDir}/clover-instr") cloverClassesDir = file("${cloverBuildDir}/clover-classes") cloverReportDir = file("${buildDir}/reports/clover") cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr") cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes") //cloverTestClassesDir = cloverClassesDir cloverDb = string("${cloverBuildDir}/clover.db") resourceClassesDir = useClover ? cloverClassesDir : classesDir testSourceDir = useClover ? cloverTestInstrDir : testDir testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}" getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") buildDist = true // the following values might be overridden by the CHANNEL switch getdownChannelName = CHANNEL.toLowerCase() getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = string("${getdown_channel_base}/${getdownDir}") getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}") getdownAppDistDir = getdown_app_dir_alt buildProperties = string("${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": // TODO: get bamboo build artifact URL for getdown artifacts getdown_channel_base = bamboo_channelbase getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}") getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") jvlChannelName += "_${getdownChannelName}" // automatically add the test group Not-bamboo for exclusion if ("".equals(testng_excluded_groups)) { testng_excluded_groups = "Not-bamboo" } install4jExtraScheme = "jalviewb" break case "RELEASE": getdownAppDistDir = getdown_app_dir_release reportRsyncCommand = true install4jSuffix = "" install4jDSStore = "DS_Store" install4jDMGBackgroundImage = "jalview_dmg_background.png" install4jInstallerName = "${jalview_name} Installer" break case "ARCHIVE": getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = string("${getdown_channel_base}/${getdownDir}") if (!file("${ARCHIVEDIR}/${package_dir}").exists()) { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { package_dir = string("${ARCHIVEDIR}/${package_dir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true install4jExtraScheme = "jalviewa" break case "ARCHIVELOCAL": getdownChannelName = string("archive/${JALVIEW_VERSION}") getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = file(getdownWebsiteDir).toURI().toString() if (!file("${ARCHIVEDIR}/${package_dir}").exists()) { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { package_dir = string("${ARCHIVEDIR}/${package_dir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") install4jSuffix = "Archive" install4jExtraScheme = "jalviewa" break case "DEVELOP": reportRsyncCommand = true // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version JALVIEW_VERSION=JALVIEW_VERSION+"-develop" install4jSuffix = "Develop" install4jDSStore = "DS_Store-DEVELOP" install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png" install4jExtraScheme = "jalviewd" install4jInstallerName = "${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 = JALVIEW_VERSION+"-test" install4jSuffix = "Test" install4jDSStore = "DS_Store-TEST-RELEASE" install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" install4jExtraScheme = "jalviewt" install4jInstallerName = "${jalview_name} Test Installer" break case ~/^SCRATCH(|-[-\w]*)$/: getdownChannelName = CHANNEL JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL 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": JALVIEW_VERSION = "TEST" getdownAppBase = file(getdownWebsiteDir).toURI().toString() getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") install4jExtraScheme = "jalviewl" break default: // something wrong specified throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") break } // override getdownAppBase if requested if (findProperty("getdown_appbase_override") != null) { getdownAppBase = string(getProperty("getdown_appbase_override")) println("Overriding getdown appbase with '${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}" getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}") getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}") getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/") getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}") /* compile without modules -- using classpath libraries modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) modules_runtimeClasspath = modules_compileClasspath */ gitHash = string("") gitBranch = string("") println("Using a ${CHANNEL} profile.") additional_compiler_args = [] // configure classpath/args for j8/j11 compilation if (JAVA_VERSION.equals("1.8")) { JAVA_INTEGER_VERSION = string("8") //libDir = j8libDir libDir = j11libDir libDistDir = j8libDir compile_source_compatibility = 1.8 compile_target_compatibility = 1.8 // these are getdown.txt properties defined dependent on the JAVA_VERSION getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version")) getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version")) // this property is assigned below and expanded to multiple lines in the getdown task getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location")) // this property is for the Java library used in eclipse eclipseJavaRuntimeName = string("JavaSE-1.8") } else if (JAVA_VERSION.equals("11")) { JAVA_INTEGER_VERSION = string("11") libDir = j11libDir libDistDir = j11libDir compile_source_compatibility = 11 compile_target_compatibility = 11 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version")) getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location")) eclipseJavaRuntimeName = string("JavaSE-11") /* compile without modules -- using classpath libraries additional_compiler_args += [ '--module-path', modules_compileClasspath.asPath, '--add-modules', j11modules ] */ } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) { JAVA_INTEGER_VERSION = JAVA_VERSION libDir = j11libDir libDistDir = j11libDir compile_source_compatibility = JAVA_VERSION compile_target_compatibility = JAVA_VERSION getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version")) getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location")) eclipseJavaRuntimeName = string("JavaSE-11") /* compile without modules -- using classpath libraries additional_compiler_args += [ '--module-path', modules_compileClasspath.asPath, '--add-modules', j11modules ] */ } else { throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview") } // for install4j JAVA_MIN_VERSION = JAVA_VERSION JAVA_MAX_VERSION = JAVA_VERSION def jreInstallsDir = string(jre_installs_dir) if (jreInstallsDir.startsWith("~/")) { jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1) } macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre") macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz") windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre") windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz") linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre") linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz") install4jDir = string("${jalviewDir}/${install4j_utils_dir}") install4jConfFileName = string("jalview-install4j-conf.install4j") install4jConfFile = file("${install4jDir}/${install4jConfFileName}") install4jHomeDir = install4j_home_dir if (install4jHomeDir.startsWith("~/")) { install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1) } buildingHTML = string("${jalviewDir}/${doc_dir}/building.html") helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm") helpParentDir = string("${jalviewDir}/${help_parent_dir}") helpSourceDir = string("${helpParentDir}/${help_dir}") relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs") jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}") if (IN_ECLIPSE) { jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir) } else { jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js") } jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib") jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs") jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core") jalviewjsJalviewCoreHtmlFile = string("") jalviewjsJalviewCoreName = string(jalviewjs_core_name) jalviewjsCoreClasslists = [] jalviewjsJalviewTemplateName = string(jalviewjs_name) jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}") jalviewjsJ2sProps = null jalviewjsJ2sPlugin = jalviewjs_j2s_plugin eclipseWorkspace = null eclipseBinary = string("") eclipseVersion = string("") eclipseDebug = false // ENDEXT } sourceSets { main { java { srcDirs sourceDir outputDir = file(classesDir) } resources { srcDirs resourceDir srcDirs += helpParentDir } jar.destinationDir = file("${jalviewDir}/${package_dir}") compileClasspath = files(sourceSets.main.java.outputDir) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath } clover { java { srcDirs cloverInstrDir outputDir = cloverClassesDir } resources { srcDirs = sourceSets.main.resources.srcDirs } compileClasspath = files( sourceSets.clover.java.outputDir ) //compileClasspath += files( testClassesDir ) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath } test { java { srcDirs testSourceDir outputDir = file(testClassesDir) } resources { srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs } compileClasspath = files( sourceSets.test.java.outputDir ) compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath } } // eclipse project and settings files creation, also used by buildship eclipse { project { name = eclipse_project_name natures 'org.eclipse.jdt.core.javanature', 'org.eclipse.jdt.groovy.core.groovyNature', 'org.eclipse.buildship.core.gradleprojectnature' buildCommand 'org.eclipse.jdt.core.javabuilder' buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder' } classpath { //defaultOutputDir = sourceSets.main.java.outputDir def removeThese = [] configurations.each{ if (it.isCanBeResolved()) { removeThese += it } } minusConfigurations += removeThese plusConfigurations = [ ] file { whenMerged { cp -> def removeTheseToo = [] HashMap alreadyAddedSrcPath = new HashMap<>(); cp.entries.each { entry -> // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test". // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover // we add the resources and help/help dirs in as libs afterwards (see below) if (entry.kind == 'src') { if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) { removeTheseToo += entry } else { alreadyAddedSrcPath.putAt(entry.path, true) } } } cp.entries.removeAll(removeTheseToo) //cp.entries += new Output("${eclipse_bin_dir}/main") if (file(helpParentDir).isDirectory()) { cp.entries += new Library(fileReference(helpParentDir)) } if (file(resourceDir).isDirectory()) { cp.entries += new Library(fileReference(resourceDir)) } HashMap alreadyAddedLibPath = new HashMap<>(); sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //don't want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath, especially if they don't exist return false // groovy "continue" in .any closure } def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { // make relative path itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) } if (alreadyAddedLibPath.get(itPath)) { //println("Not adding duplicate entry "+itPath) } else { //println("Adding entry "+itPath) cp.entries += new Library(fileReference(itPath)) alreadyAddedLibPath.put(itPath, true) } } sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //no longer want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath return false // groovy "continue" in .any closure } def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) } if (alreadyAddedLibPath.get(itPath)) { // don't duplicate } else { def lib = new Library(fileReference(itPath)) lib.entryAttributes["test"] = "true" cp.entries += lib alreadyAddedLibPath.put(itPath, true) } } } // whenMerged } // file containers 'org.eclipse.buildship.core.gradleclasspathcontainer' } // classpath jdt { // for the IDE, use java 11 compatibility sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility javaRuntimeName = eclipseJavaRuntimeName // add in jalview project specific properties/preferences into eclipse core preferences file { withProperties { props -> def jalview_prefs = new Properties() def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}") jalview_prefs.load(ins) ins.close() jalview_prefs.forEach { t, v -> if (props.getAt(t) == null) { 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) } } } } } } } // jdt if (IN_ECLIPSE) { // Don't want these to be activated if in headless build synchronizationTasks "eclipseSynchronizationTask" //autoBuildTasks "eclipseAutoBuildTask" } } /* 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 */ // clover bits task cleanClover { doFirst { delete cloverBuildDir delete cloverReportDir } } task cloverInstrJava(type: JavaExec) { group = "Verification" description = "Create clover instrumented source java files" dependsOn cleanClover inputs.files(sourceSets.main.allJava) outputs.dir(cloverInstrDir) //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) classpath = sourceSets.clover.compileClasspath main = "com.atlassian.clover.CloverInstr" def argsList = [ "--encoding", "UTF-8", "--initstring", cloverDb, "--destdir", cloverInstrDir.getPath(), ] def srcFiles = sourceSets.main.allJava.files argsList.addAll( srcFiles.collect( { file -> file.absolutePath } ) ) args argsList.toArray() doFirst { delete cloverInstrDir println("Clover: About to instrument "+srcFiles.size() +" files") } } task cloverInstrTests(type: JavaExec) { group = "Verification" description = "Create clover instrumented source test files" dependsOn cleanClover inputs.files(testDir) outputs.dir(cloverTestInstrDir) classpath = sourceSets.clover.compileClasspath main = "com.atlassian.clover.CloverInstr" def argsList = [ "--encoding", "UTF-8", "--initstring", cloverDb, "--srcdir", testDir, "--destdir", cloverTestInstrDir.getPath(), ] args argsList.toArray() doFirst { delete cloverTestInstrDir println("Clover: About to instrument test files") } } task cloverInstr { group = "Verification" description = "Create clover instrumented all source files" dependsOn cloverInstrJava dependsOn cloverInstrTests } cloverClasses.dependsOn cloverInstr task cloverConsoleReport(type: JavaExec) { group = "Verification" description = "Creates clover console report" onlyIf { file(cloverDb).exists() } inputs.dir cloverClassesDir classpath = sourceSets.clover.runtimeClasspath main = "com.atlassian.clover.reporters.console.ConsoleReporter" if (cloverreport_mem.length() > 0) { maxHeapSize = cloverreport_mem } if (cloverreport_jvmargs.length() > 0) { jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } def argsList = [ "--alwaysreport", "--initstring", cloverDb, "--unittests" ] args argsList.toArray() } task cloverHtmlReport(type: JavaExec) { group = "Verification" description = "Creates clover HTML report" onlyIf { file(cloverDb).exists() } def cloverHtmlDir = cloverReportDir inputs.dir cloverClassesDir outputs.dir cloverHtmlDir classpath = sourceSets.clover.runtimeClasspath main = "com.atlassian.clover.reporters.html.HtmlReporter" if (cloverreport_mem.length() > 0) { maxHeapSize = cloverreport_mem } if (cloverreport_jvmargs.length() > 0) { jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } def argsList = [ "--alwaysreport", "--initstring", cloverDb, "--outputdir", cloverHtmlDir ] if (cloverreport_html_options.length() > 0) { argsList += cloverreport_html_options.split(" ") } args argsList.toArray() } task cloverXmlReport(type: JavaExec) { group = "Verification" description = "Creates clover XML report" onlyIf { file(cloverDb).exists() } def cloverXmlFile = "${cloverReportDir}/clover.xml" inputs.dir cloverClassesDir outputs.file cloverXmlFile classpath = sourceSets.clover.runtimeClasspath main = "com.atlassian.clover.reporters.xml.XMLReporter" if (cloverreport_mem.length() > 0) { maxHeapSize = cloverreport_mem } if (cloverreport_jvmargs.length() > 0) { jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } def argsList = [ "--alwaysreport", "--initstring", cloverDb, "--outfile", cloverXmlFile ] if (cloverreport_xml_options.length() > 0) { argsList += cloverreport_xml_options.split(" ") } args argsList.toArray() } task cloverReport { group = "Verification" description = "Creates clover reports" dependsOn cloverXmlReport dependsOn cloverHtmlReport } 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 } // end clover bits compileJava { // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ? sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility options.compilerArgs = additional_compiler_args options.encoding = "UTF-8" doFirst { print ("Setting target compatibility to "+compile_target_compatibility+"\n") } } compileTestJava { sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility options.compilerArgs = additional_compiler_args doFirst { print ("Setting target compatibility to "+targetCompatibility+"\n") } } clean { doFirst { delete sourceSets.main.java.outputDir } } cleanTest { dependsOn cleanClover doFirst { delete sourceSets.test.java.outputDir } } // format is a string like date.format("dd MMMM yyyy") def getDate(format) { def date = new Date() return date.format(format) } task setGitVals { doFirst { def hashStdOut = new ByteArrayOutputStream() def resultHash = exec { commandLine "git", "rev-parse", "--short", "HEAD" standardOutput = hashStdOut ignoreExitValue true } def branchStdOut = new ByteArrayOutputStream() def resultBranch = exec { commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" standardOutput = branchStdOut ignoreExitValue true } gitHash = resultHash.getExitValue() == 0 ? hashStdOut.toString().trim() : "NO_GIT_COMMITID_FOUND" gitBranch = resultBranch.getExitValue() == 0 ? branchStdOut.toString().trim() : "NO_GIT_BRANCH_FOUND" } outputs.upToDateWhen { false } } task createBuildProperties(type: WriteProperties) { group = "build" description = "Create the ${buildProperties} file" dependsOn setGitVals inputs.dir(sourceDir) inputs.dir(resourceDir) file(buildProperties).getParentFile().mkdirs() outputFile (buildProperties) // taking time specific comment out to allow better incremental builds comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") property "VERSION", JALVIEW_VERSION property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" outputs.file(outputFile) } clean { doFirst { delete buildProperties } } task cleanBuildingHTML(type: Delete) { doFirst { delete buildingHTML } } def convertMdToHtml (FileTree mdFiles, File cssFile) { MutableDataSet options = new MutableDataSet() def extensions = new ArrayList<>() extensions.add(AnchorLinkExtension.create()) extensions.add(AutolinkExtension.create()) extensions.add(StrikethroughExtension.create()) extensions.add(TaskListExtension.create()) extensions.add(TablesExtension.create()) extensions.add(TocExtension.create()) options.set(Parser.EXTENSIONS, extensions) // set GFM table parsing options options.set(TablesExtension.WITH_CAPTION, false) options.set(TablesExtension.COLUMN_SPANS, false) options.set(TablesExtension.MIN_HEADER_ROWS, 1) options.set(TablesExtension.MAX_HEADER_ROWS, 1) options.set(TablesExtension.APPEND_MISSING_COLUMNS, true) options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true) options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true) // GFM anchor links options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false) options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor") options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true) options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "") Parser parser = Parser.builder(options).build() HtmlRenderer renderer = HtmlRenderer.builder(options).build() mdFiles.each { mdFile -> // add table of contents def mdText = "[TOC]\n"+mdFile.text // grab the first top-level title def title = null def titleRegex = /(?m)^#(\s+|([^#]))(.*)/ def matcher = mdText =~ titleRegex if (matcher.size() > 0) { // matcher[0][2] is the first character of the title if there wasn't any whitespace after the # title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3] } // or use the filename if none found if (title == null) { title = mdFile.getName() } Node document = parser.parse(mdText) String htmlBody = renderer.render(document) def htmlText = ''' ''' htmlText += ((title != null) ? " ${title}" : '' ) htmlText += ''' ''' htmlText += ((cssFile != null) ? cssFile.text : '') htmlText += ''' ''' htmlText += htmlBody htmlText += ''' ''' def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html") def htmlFile = file(htmlFilePath) htmlFile.text = htmlText } } task convertMdFiles { dependsOn cleanBuildingHTML def mdFiles = fileTree(dir: "${jalviewDir}/${doc_dir}", include: "*.md") def cssFile = file("${jalviewDir}/${flexmark_css}") doLast { convertMdToHtml(mdFiles, cssFile) } inputs.files(mdFiles) inputs.file(cssFile) def htmlFiles = [] mdFiles.each { mdFile -> def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html") htmlFiles.add(file(htmlFilePath)) } outputs.files(htmlFiles) } task syncDocs(type: Sync) { dependsOn convertMdFiles def syncDir = "${classesDir}/${doc_dir}" from fileTree("${jalviewDir}/${doc_dir}") into syncDir } task copyHelp(type: Copy) { def inputDir = helpSourceDir def outputDir = "${resourceClassesDir}/${help_dir}" from(inputDir) { exclude '**/*.gif' exclude '**/*.jpg' exclude '**/*.png' filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: [ 'Version-Rel': JALVIEW_VERSION, 'Year-Rel': getDate("yyyy") ] ) } from(inputDir) { include '**/*.gif' include '**/*.jpg' include '**/*.png' } into outputDir inputs.dir(inputDir) outputs.files(helpFile) outputs.dir(outputDir) } task syncLib(type: Sync) { def syncDir = "${resourceClassesDir}/${libDistDir}" from fileTree("${jalviewDir}/${libDistDir}") into syncDir } task syncResources(type: Sync) { dependsOn createBuildProperties from resourceDir include "**/*.*" into "${resourceClassesDir}" preserve { include "**" } } task prepare { dependsOn syncResources dependsOn syncDocs dependsOn copyHelp } //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir test { dependsOn prepare //dependsOn compileJava ////? DELETE if (useClover) { dependsOn cloverClasses } else { //? dependsOn compileJava //? } useTestNG() { includeGroups testng_groups excludeGroups testng_excluded_groups preserveOrder true useDefaultListeners=true } maxHeapSize = "1024m" workingDir = jalviewDir //systemProperties 'clover.jar' System.properties.clover.jar sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility jvmArgs += additional_compiler_args doFirst { if (useClover) { println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover") } } } task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" workingDir = "${classesDir}/${help_dir}" def argDir = "html" args = [ argDir ] inputs.dir("${workingDir}/${argDir}") outputs.dir("${classesDir}/doc") outputs.dir("${classesDir}/help") outputs.file("${workingDir}/JavaHelpSearch/DOCS") outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") outputs.file("${workingDir}/JavaHelpSearch/POSITIONS") outputs.file("${workingDir}/JavaHelpSearch/SCHEMA") outputs.file("${workingDir}/JavaHelpSearch/TMAP") } task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utils_dir}") destinationDir = file("${jalviewDir}/${utils_dir}") source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class") outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class") } task linkCheck(type: JavaExec) { dependsOn prepare, compileLinkCheck def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out") classpath = files("${jalviewDir}/${utils_dir}") main = "HelpLinksChecker" workingDir = jalviewDir args = [ "${classesDir}/${help_dir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append def errFOS = outFOS standardOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, standardOutput) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, errorOutput) inputs.dir("${classesDir}/${help_dir}") outputs.file(helpLinksCheckerOutFile) } // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}" ant.importBuild "${utils_dir}/publishHelp.xml" task cleanPackageDir(type: Delete) { doFirst { delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar") } } jar { dependsOn linkCheck dependsOn buildIndices dependsOn createBuildProperties manifest { attributes "Main-Class": main_class, "Permissions": "all-permissions", "Application-Name": "Jalview Desktop", "Codebase": application_codebase } destinationDir = file("${jalviewDir}/${package_dir}") archiveName = rootProject.name+".jar" exclude "cache*/**" exclude "*.jar" exclude "*.jar.*" exclude "**/*.jar" exclude "**/*.jar.*" inputs.dir(classesDir) outputs.file("${jalviewDir}/${package_dir}/${archiveName}") } task copyJars(type: Copy) { from fileTree(dir: classesDir, include: "**/*.jar").files into "${jalviewDir}/${package_dir}" } // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well task syncJars(type: Sync) { from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files into "${jalviewDir}/${package_dir}" preserve { include jar.archiveName } } task makeDist { group = "build" description = "Put all required libraries in dist" // order of "cleanPackageDir", "copyJars", "jar" important! jar.mustRunAfter cleanPackageDir syncJars.mustRunAfter cleanPackageDir dependsOn cleanPackageDir dependsOn syncJars dependsOn jar outputs.dir("${jalviewDir}/${package_dir}") } task cleanDist { dependsOn cleanPackageDir dependsOn cleanTest dependsOn clean } shadowJar { group = "distribution" description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar" if (buildDist) { dependsOn makeDist } from ("${jalviewDir}/${libDistDir}") { include("*.jar") } manifest { attributes 'Implementation-Version': JALVIEW_VERSION } mainClassName = shadow_jar_main_class mergeServiceFiles() classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION minimize() } task getdownWebsite() { group = "distribution" description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer" if (buildDist) { dependsOn makeDist } def getdownWebsiteResourceFilenames = [] def getdownTextString = "" def getdownResourceDir = getdownResourceDir def getdownResourceFilenames = [] doFirst { // clean the getdown website and files dir before creating getdown folders delete getdownWebsiteDir delete getdownFilesDir copy { from buildProperties rename(build_properties_file, getdown_build_properties) into getdownAppDir } getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" // 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) } if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) { props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion) } if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) { props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) } props.put("getdown_txt_title", jalview_name) props.put("getdown_txt_ui.name", install4jApplicationName) // start with appbase getdownTextString += "appbase = ${getdownAppBase}\n" props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { if (prop.startsWith("getdown_txt_multi_")) { def key = prop.substring(18) val.split(",").each{ v -> def line = "${key} = ${v}\n" getdownTextString += line } } else { // file values rationalised if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) { def r = null if (val.indexOf('/') == 0) { // absolute path r = file(val) } else if (val.indexOf('/') > 0) { // relative path (relative to jalviewDir) r = file( "${jalviewDir}/${val}" ) } if (r.exists()) { val = "${getdown_resource_dir}/" + r.getName() getdownWebsiteResourceFilenames += val getdownResourceFilenames += r.getPath() } } if (! prop.startsWith("getdown_txt_resource")) { def line = prop.substring(12) + " = ${val}\n" getdownTextString += line } } } } getdownWebsiteResourceFilenames.each{ filename -> getdownTextString += "resource = ${filename}\n" } getdownResourceFilenames.each{ filename -> copy { from filename into getdownResourceDir } } def codeFiles = [] fileTree(file(package_dir)).each{ f -> if (f.isDirectory()) { def files = fileTree(dir: f, include: ["*"]).getFiles() codeFiles += files } else if (f.exists()) { codeFiles += f } } codeFiles.sort().each{f -> def name = f.getName() def line = "code = ${getdownAppDistDir}/${name}\n" getdownTextString += line copy { from f.getPath() into getdownAppDir } } // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist /* if (JAVA_VERSION.equals("11")) { def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles() j11libFiles.sort().each{f -> def name = f.getName() def line = "code = ${getdown_j11lib_dir}/${name}\n" getdownTextString += line copy { from f.getPath() into getdownJ11libDir } } } */ // 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. //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n" getdownTextString += "resource = ${getdown_launcher_new}\n" getdownTextString += "class = ${main_class}\n" def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) 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 rename(file(getdownLauncher).getName(), getdown_launcher_new) into getdownWebsiteDir } copy { from getdownLauncher if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownWebsiteDir } if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { copy { from getdown_txt from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownInstallDir } copy { from getdownInstallDir into getdownFilesInstallDir } } copy { from getdown_txt from launchJvl from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownFilesDir } copy { from getdownResourceDir into "${getdownFilesDir}/${getdown_resource_dir}" } } if (buildDist) { inputs.dir("${jalviewDir}/${package_dir}") } outputs.dir(getdownWebsiteDir) outputs.dir(getdownFilesDir) } // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir task getdownDigestDir(type: JavaExec) { group "Help" description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..." def digestDirPropertyName = "DIGESTDIR" 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" dependsOn getdownWebsite doFirst { classpath = files(getdownLauncher) } main = "com.threerings.getdown.tools.Digester" args getdownWebsiteDir inputs.dir(getdownWebsiteDir) outputs.file("${getdownWebsiteDir}/digest2.txt") } task getdown() { group = "distribution" description = "Create the minimal and full getdown app folder for installers and website and create digest file" dependsOn getdownDigest doLast { if (reportRsyncCommand) { def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/') def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/') println "LIKELY RSYNC COMMAND:" println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'" if (RUNRSYNC == "true") { exec { commandLine "mkdir", "-p", toDir } exec { commandLine "rsync", "-avh", "--delete", fromDir, toDir } } } } } tasks.withType(JavaCompile) { options.encoding = 'UTF-8' } clean { doFirst { delete getdownWebsiteDir delete getdownFilesDir } } install4j { if (file(install4jHomeDir).exists()) { // good to go! } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) { install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) { install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app" } installDir(file(install4jHomeDir)) mediaTypes = Arrays.asList(install4j_media_types.split(",")) } task copyInstall4jTemplate { def install4jTemplateFile = file("${install4jDir}/${install4j_template}") def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}") inputs.file(install4jTemplateFile) inputs.file(install4jFileAssociationsFile) inputs.property("CHANNEL", { CHANNEL }) outputs.file(install4jConfFile) doLast { def install4jConfigXml = new XmlParser().parse(install4jTemplateFile) // turn off code signing if no OSX_KEYPASS if (OSX_KEYPASS == "") { install4jConfigXml.'**'.codeSigning.each { codeSigning -> codeSigning.'@macEnabled' = "false" } install4jConfigXml.'**'.windows.each { windows -> windows.'@runPostProcessor' = "false" } } // 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 -> // .any{} stops after the first one that returns true if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') { def parent = a.parent() parent.remove(a) fileAssociationActions.each { faa -> parent.append(faa) } // don't need to continue in .any loop once replacements have been made return true } } // 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" // 2.11.1.0 NOT releasing with the Examples folder in the Program Group if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel 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) } } clean { doFirst { delete install4jConfFile } } task installers(type: com.install4j.gradle.Install4jTask) { group = "distribution" description = "Create the install4j installers" dependsOn setGitVals dependsOn getdown dependsOn copyInstall4jTemplate projectFile = install4jConfFile // create an md5 for the input files to use as version for install4j conf file def digest = MessageDigest.getInstance("MD5") digest.update( (file("${install4jDir}/${install4j_template}").text + file("${install4jDir}/${install4j_info_plist_file_associations}").text + file("${install4jDir}/${install4j_installer_file_associations}").text).bytes) def filesMd5 = new BigInteger(1, digest.digest()).toString(16) if (filesMd5.length() >= 8) { filesMd5 = filesMd5.substring(0,8) } def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}" // make install4jBuildDir relative to jalviewDir 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, 'JRE_DIR': getdown_app_dir_java, 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion, 'JALVIEW_VERSION': JALVIEW_VERSION, 'JAVA_MIN_VERSION': JAVA_MIN_VERSION, 'JAVA_MAX_VERSION': JAVA_MAX_VERSION, 'JAVA_VERSION': JAVA_VERSION, 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, 'VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, 'LINUX_JAVA_VM_DIR': linuxJavaVMDir, 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, 'COPYRIGHT_MESSAGE': install4j_copyright_message, '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, 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, 'GETDOWN_DIST_DIR': getdownAppDistDir, 'GETDOWN_ALT_DIR': getdown_app_dir_alt, '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("LOCAL")) { faster = true disableSigning = true } if (OSX_KEYPASS) { macKeystorePassword = OSX_KEYPASS } doFirst { println("Using projectFile "+projectFile) } inputs.dir(getdownWebsiteDir) inputs.file(install4jConfFile) inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") inputs.dir(macosJavaVMDir) inputs.dir(windowsJavaVMDir) outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}") } spotless { java { eclipse().configFile(eclipse_codestyle_file) } } task sourceDist(type: Tar) { group "distribution" description "Create a source .tar.gz file for distribution" dependsOn convertMdFiles def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09] try { archiveFileName = outputFileName } catch (Exception e) { archiveName = outputFileName } compression Compression.GZIP into project.name def EXCLUDE_FILES=[ "build/*", "bin/*", "test-output/", "test-reports", "tests", "clover*/*", ".*", "benchmarking/*", "**/.*", "*.class", "**/*.class","$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) include (PROCESS_FILES) filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: [ 'Version-Rel': JALVIEW_VERSION, 'Year-Rel': getDate("yyyy") ] ) } from(jalviewDir) { exclude (EXCLUDE_FILES) exclude (PROCESS_FILES) exclude ("appletlib") exclude ("**/*locales") exclude ("*locales/**") exclude ("utils/InstallAnywhere") exclude (getdown_files_dir) exclude (getdown_website_dir) // exluding these as not using jars as modules yet exclude ("${j11modDir}/**/*.jar") } from(jalviewDir) { include(INCLUDE_FILES) } // from (jalviewDir) { // // explicit includes for stuff that seemed to not get included // include(fileTree("test/**/*.")) // exclude(EXCLUDE_FILES) // exclude(PROCESS_FILES) // } } task helppages { dependsOn copyHelp dependsOn pubhtmlhelp inputs.dir("${classesDir}/${help_dir}") outputs.dir("${buildDir}/distributions/${help_dir}") } task j2sSetHeadlessBuild { doFirst { IN_ECLIPSE = false } } task jalviewjsSetEclipseWorkspace { def propKey = "jalviewjs_eclipse_workspace" def propVal = null if (project.hasProperty(propKey)) { propVal = project.getProperty(propKey) if (propVal.startsWith("~/")) { propVal = System.getProperty("user.home") + propVal.substring(1) } } def propsFileName = "${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" } eclipseBinary = "${eclipseRoot}/eclipse.exe" eclipseProduct = "${eclipseRoot}/.eclipseproduct" } else { // linux or unix if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" println("eclipseDir exists") } 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 ${jsfile}" println(msg) logOutFile.createNewFile() logOutFile.append(msg+"\n") def coreTop = file(prefixFile) def coreBottom = file(suffixFile) coreFile.getParentFile().mkdirs() coreFile.createNewFile() coreFile.write( coreTop.getText("UTF-8") ) list.each { f -> if (f.exists()) { def t = f.getText("UTF-8") t.replaceAll("Clazz\\.([^_])","Clazz_${1}") coreFile.append( t ) } else { msg = "...file '"+f.getPath()+"' does not exist, skipping" println(msg) logOutFile.append(msg+"\n") } } coreFile.append( coreBottom.getText("UTF-8") ) msg = "Generating ${zjsfile}" println(msg) logOutFile.append(msg+"\n") def logOutFOS = new FileOutputStream(logOutFile, true) // true == append def logErrFOS = logOutFOS javaexec { classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"]) main = "com.google.javascript.jscomp.CommandLineRunner" jvmArgs = [ "-Dfile.encoding=UTF-8" ] args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ] maxHeapSize = "2g" msg = "\nRunning '"+commandLine.join(' ')+"'\n" println(msg) logOutFile.append(msg+"\n") if (logOutConsole) { standardOutput = new org.apache.tools.ant.util.TeeOutputStream( new org.apache.tools.ant.util.TeeOutputStream( logOutFOS, stdout), standardOutput) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( new org.apache.tools.ant.util.TeeOutputStream( logErrFOS, stderr), errorOutput) } else { standardOutput = new org.apache.tools.ant.util.TeeOutputStream( logOutFOS, stdout) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( logErrFOS, stderr) } } msg = "--" println(msg) logOutFile.append(msg+"\n") } task jalviewjsBuildAllCores { group "JalviewJS" description "Build the core js lib closures listed in the classlists dir" dependsOn jalviewjsTranspile dependsOn jalviewjsTransferUnzipSwingJs def j2sDir = "${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': '"'+main_class+'"', '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 // not sure why this clean is here -- will slow down a re-run of this task } 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 }