X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=dde96ea8be094e277acdbd758217f72bd0f5fe9a;hb=290d1c0638e869b08d5f2729472197873fa06af0;hp=76c1c4401ef6f9360c6d47c14013e1ec41eee071;hpb=6aec2dea780d21b874707b429964afa91558a6ff;p=jalview.git diff --git a/build.gradle b/build.gradle index 76c1c44..dde96ea 100644 --- a/build.gradle +++ b/build.gradle @@ -2,266 +2,388 @@ import org.apache.tools.ant.filters.ReplaceTokens import org.gradle.internal.os.OperatingSystem 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 + 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.github.johnrengelman.shadow' version '4.0.3' - id 'com.install4j.gradle' version '7.0.9' -} - -// local build environment properties -def localProps = "${jalviewDir}/local.properties" -if (file(localProps).exists()) { - try { - def p = new Properties() - def localPropsFIS = new FileInputStream(localProps) - p.load(localPropsFIS) - localPropsFIS.close() - p.each { - key, val -> - def over = getProperty(key) != null - setProperty(key, val) - if (over) { - println("Overriding property '${key}' with local.properties value '${val}'") - } - } - } catch (Exception e) { - System.out.println("Exception reading local.properties") - } + id 'com.install4j.gradle' version '8.0.4' + id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree } repositories { jcenter() mavenCentral() mavenLocal() - flatDir { - dirs gradlePluginsDir - } } -dependencies { - compile 'org.apache.commons:commons-compress:1.18' + +// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use +def string(Object o) { + return o == null ? "" : o.toString() } -mainClassName = launcherClass -def cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") -def classes = "${jalviewDir}/${classesDir}" -if (clover.equals("true")) { - use_clover = true - classes = "${buildDir}/${cloverClassesDir}" -} else { - use_clover = false - classes = "${jalviewDir}/${classesDir}" -} +ext { + jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() + jalviewDirRelativePath = jalviewDir + + // local build environment properties + // can be "projectDir/local.properties" + def localProps = "${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") + } + } -// configure classpath/args for j8/j11 compilation + // 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 + } + */ -def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() -def libDir -def libDistDir -def compile_source_compatibility -def compile_target_compatibility + // essentials + bareSourceDir = string(source_dir) + sourceDir = string("${jalviewDir}/${bareSourceDir}") + resourceDir = string("${jalviewDir}/${resource_dir}") + bareTestSourceDir = string(test_source_dir) + testSourceDir = string("${jalviewDir}/${bareTestSourceDir}") + + // clover + cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") + cloverDb = string("${buildDir}/clover/clover.db") + classesDir = string("${jalviewDir}/${classes_dir}") + if (clover.equals("true")) { + use_clover = true + classesDir = string("${buildDir}/${cloverClassesDir}") + } else { + use_clover = false + classesDir = string("${jalviewDir}/${classes_dir}") + } -ext { - getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}" - getdownDir = "" - reportRsyncCmd = false + classes = classesDir + + getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") buildDist = true - buildProperties = build_properties_file - getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}" + + // 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}/${build_properties_file}") + reportRsyncCommand = false + jvlChannelName = CHANNEL.toLowerCase() switch (CHANNEL) { case "BUILD": // TODO: get bamboo build artifact URL for getdown artifacts getdown_channel_base = bamboo_channelbase - getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}" - getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}" - getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}") + getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") + jvlChannelName += "_${getdownChannelName}" + // automatically add the test group Not-bamboo for exclusion + if ("".equals(testngExcludedGroups)) { + testngExcludedGroups = "Not-bamboo" + } break case "RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" - getdown_app_dir = getdown_app_dir_release - buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + 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'") + } break case "ARCHIVE": - getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" - getdown_app_dir = getdown_app_dir_alt + getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { - print "Must provide an ARCHIVEDIR value to produce an archive distribution" - exit + throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { - packageDir = "${ARCHIVEDIR}/${packageDir}" - buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}" + packageDir = string("${ARCHIVEDIR}/${packageDir}") + buildProperties = string("${buildDir}/archive/${build_properties_file}") buildDist = false } reportRsyncCommand = true break case "ARCHIVELOCAL": - getdown_channel_name = "archive/${JALVIEW_VERSION}" - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt + getdownChannelName = string("archive/${JALVIEW_VERSION}") + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = file(getdownWebsiteDir).toURI().toString() if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { - print "Must provide an ARCHIVEDIR value to produce an archive distribution" - exit + throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { - packageDir = "${ARCHIVEDIR}/${packageDir}" - buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}" + packageDir = string("${ARCHIVEDIR}/${packageDir}") + buildProperties = string("${buildDir}/archive/${build_properties_file}") buildDist = false } reportRsyncCommand = true - getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}" + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") break case "DEVELOP": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" - getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" reportRsyncCommand = true break case "TEST-RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" - getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" 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'") + } break case ~/^SCRATCH(|-[-\w]*)$/: - getdown_channel_name = CHANNEL - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" - getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + getdownChannelName = CHANNEL + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") reportRsyncCommand = true 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}/${getdown_launcher_local}") + } + break + case "LOCAL": - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" - getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}" + getdownAppBase = file(getdownWebsiteDir).toURI().toString() + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") break default: // something wrong specified - print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") - exit + 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 '${getdownAppBase}'") + } + // sanitise file name for jalview launcher file for this channel + jvlChannelName = jvlChannelName.replaceAll(/[^\w\-]/,"_") - getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}" + getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}") //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" - getdownResourceDir = "${getdownWebsiteDir}/${getdown_resource_dir}" - getdownInstallDir = "${getdownWebsiteDir}/${getdown_install_dir}" - getdownFilesDir = "${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/" - getdownFilesInstallDir = "${getdownFilesDir}/${getdown_install_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 = "" - gitBranch = "" + gitHash = string("") + gitBranch = string("") println("Using a ${CHANNEL} profile.") -} -def JAVA_INTEGER_VERSION -def additional_compiler_args = [] -// these are getdown.txt properties defined dependent on the JAVA_VERSION -def getdown_alt_java_min_version -def getdown_alt_java_max_version -// this property is assigned below and expanded to multiple lines in the getdown task -def getdown_alt_multi_java_location -// this property is for the Java library used in eclipse -def eclipse_java_runtime_name -if (JAVA_VERSION.equals("1.8")) { - JAVA_INTEGER_VERSION = "8" - //libDir = j8libDir - libDir = j11libDir - libDistDir = j8libDir - compile_source_compatibility = 1.8 - compile_target_compatibility = 1.8 - getdown_alt_java_min_version = getdown_alt_java8_min_version - getdown_alt_java_max_version = getdown_alt_java8_max_version - getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-1.8" -} else if (JAVA_VERSION.equals("11")) { - JAVA_INTEGER_VERSION = "11" - libDir = j11libDir - libDistDir = j11libDir - compile_source_compatibility = 11 - compile_target_compatibility = 11 - getdown_alt_java_min_version = getdown_alt_java11_min_version - getdown_alt_java_max_version = getdown_alt_java11_max_version - getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-11" - /* compile without modules -- using classpath libraries - additional_compiler_args += [ - '--module-path', ext.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 - getdown_alt_java_min_version = getdown_alt_java11_min_version - getdown_alt_java_max_version = getdown_alt_java11_max_version - getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-11" - /* compile without modules -- using classpath libraries - additional_compiler_args += [ - '--module-path', ext.modules_compileClasspath.asPath, - '--add-modules', j11modules - ] - */ -} else { - throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview") + 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}/${docDir}/building.html") + helpFile = string("${classesDir}/${help_dir}/help.jhm") + helpParentDir = string("${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 "${jalviewDir}/${sourceDir}" - outputDir = file("${classes}") + srcDirs sourceDir + outputDir = file(classesDir) } resources { - srcDirs "${jalviewDir}/${resourceDir}" + srcDirs resourceDir + srcDirs += helpParentDir } jar.destinationDir = file("${jalviewDir}/${packageDir}") compileClasspath = files(sourceSets.main.java.outputDir) + //compileClasspath += files(sourceSets.main.resources.srcDirs) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath @@ -287,7 +409,7 @@ sourceSets { test { java { - srcDirs "${jalviewDir}/${testSourceDir}" + srcDirs testSourceDir outputDir = file("${jalviewDir}/${testOutputDir}") } @@ -298,7 +420,7 @@ sourceSets { compileClasspath = files( sourceSets.test.java.outputDir ) if (use_clover) { - compileClasspath += sourceSets.clover.compileClasspath + compileClasspath = sourceSets.clover.compileClasspath } else { compileClasspath += files(sourceSets.main.java.outputDir) } @@ -315,8 +437,8 @@ sourceSets { // clover bits dependencies { if (use_clover) { - cloverCompile 'org.openclover:clover:4.3.1' - testCompile 'org.openclover:clover:4.3.1' + cloverCompile 'org.openclover:clover:4.4.1' + testCompile 'org.openclover:clover:4.4.1' } } @@ -327,6 +449,7 @@ configurations { } +// eclipse project and settings files creation, also used by buildship eclipse { project { name = eclipse_project_name @@ -356,19 +479,21 @@ eclipse { def removeTheseToo = [] HashMap alreadyAddedSrcPath = new HashMap<>(); cp.entries.each { entry -> + // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test". + // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover + // we add the resources and help/help dirs in as libs afterwards (see below) if (entry.kind == 'src') { - if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) { removeTheseToo += entry } else { alreadyAddedSrcPath.putAt(entry.path, true) } } + } cp.entries.removeAll(removeTheseToo) - if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) { - cp.entries += new Output("${eclipse_bin_dir}/main") - } + //cp.entries += new Output("${eclipse_bin_dir}/main") if (file(helpParentDir).isDirectory()) { cp.entries += new Library(fileReference(helpParentDir)) } @@ -378,11 +503,11 @@ eclipse { HashMap alreadyAddedLibPath = new HashMap<>(); - sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each { + sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //don't want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { - // don't add dirs to classpath - return + // don't add dirs to classpath, especially if they don't exist + return false // groovy "continue" in .any closure } def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { @@ -398,7 +523,6 @@ eclipse { } } - //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each { 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()) { @@ -432,9 +556,10 @@ eclipse { // for the IDE, use java 11 compatibility sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility - javaRuntimeName = eclipse_java_runtime_name + 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() @@ -446,29 +571,54 @@ 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) + } + } + } + } } } } // jdt - - synchronizationTasks "eclipseSynchronizationTask" - autoBuildTasks "eclipseAutoBuildTask" + if (IN_ECLIPSE) { + // Don't want these to be activated if in headless build + synchronizationTasks "eclipseSynchronizationTask" + //autoBuildTasks "eclipseAutoBuildTask" + + } } -task cloverInstr() { +task cloverInstr { // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$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}/${cloverSourcesInstrDir}"] - argsList.addAll(inputs.files.files.collect({ file -> - file.absolutePath - })) + def argsList = [ + "--initstring", + cloverDb, + "-d", + cloverInstrDir.getPath(), + ] + argsList.addAll( + inputs.files.files.collect( + { file -> file.absolutePath } + ) + ) String[] args = argsList.toArray() println("About to instrument "+args.length +" files") com.atlassian.clover.CloverInstr.mainImpl(args) @@ -476,26 +626,57 @@ task cloverInstr() { } +cloverClasses.dependsOn cloverInstr + + task cloverReport { group = "Verification" - description = "Createst the Clover report" - inputs.dir "${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 @@ -527,18 +708,6 @@ 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 @@ -547,9 +716,9 @@ clean { cleanTest { + dependsOn cleanClover doFirst { delete sourceSets.test.java.outputDir - delete cloverInstrDir } } @@ -576,17 +745,19 @@ task setGitVals { ignoreExitValue true } - project.ext.gitHash = hashStdOut.toString().trim() - project.ext.gitBranch = branchStdOut.toString().trim() + gitHash = hashStdOut.toString().trim() + gitBranch = branchStdOut.toString().trim() outputs.upToDateWhen { false } } task createBuildProperties(type: WriteProperties) { + group = "build" + description = "Create the ${buildProperties} file" dependsOn setGitVals - inputs.dir("${jalviewDir}/${sourceDir}") - inputs.dir("${jalviewDir}/${resourceDir}") + inputs.dir(sourceDir) + inputs.dir(resourceDir) file(buildProperties).getParentFile().mkdirs() outputFile (buildProperties) // taking time specific comment out to allow better incremental builds @@ -594,12 +765,18 @@ task createBuildProperties(type: WriteProperties) { //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") property "VERSION", JALVIEW_VERSION - property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]" + property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" outputs.file(outputFile) } -def buildingHTML = "${jalviewDir}/${docDir}/building.html" +clean { + doFirst { + delete buildProperties + } +} + + task cleanBuildingHTML(type: Delete) { doFirst { delete buildingHTML @@ -620,8 +797,8 @@ task convertBuildingMD(type: Exec) { } } - def hostname = "hostname".execute().text.trim() - if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) { + def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" + if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) { pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" } @@ -630,7 +807,7 @@ task convertBuildingMD(type: Exec) { commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD } else { println("Cannot find pandoc. Skipping convert building.md to HTML") - throw new StopExecutionException() + throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML") } } @@ -651,22 +828,28 @@ clean { task syncDocs(type: Sync) { dependsOn convertBuildingMD - def syncDir = "${classes}/${docDir}" + def syncDir = "${classesDir}/${docDir}" from fileTree("${jalviewDir}/${docDir}") into syncDir } -def helpFile = "${classes}/${helpDir}/help.jhm" task copyHelp(type: Copy) { - def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}" - def outputDir = "${classes}/${helpDir}" + def inputDir = helpSourceDir + def outputDir = "${classesDir}/${help_dir}" from(inputDir) { exclude '**/*.gif' exclude '**/*.jpg' exclude '**/*.png' - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) } from(inputDir) { include '**/*.gif' @@ -682,16 +865,17 @@ task copyHelp(type: Copy) { task syncLib(type: Sync) { - def syncDir = "${classes}/${libDistDir}" + def syncDir = "${classesDir}/${libDistDir}" from fileTree("${jalviewDir}/${libDistDir}") into syncDir } task syncResources(type: Sync) { - from "${jalviewDir}/${resourceDir}" + dependsOn createBuildProperties + from resourceDir include "**/*.*" - into "${classes}" + into "${classesDir}" preserve { include "**" } @@ -719,10 +903,13 @@ 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 @@ -736,13 +923,13 @@ task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" - workingDir = "${classes}/${helpDir}" + workingDir = "${classesDir}/${help_dir}" def argDir = "html" args = [ argDir ] inputs.dir("${workingDir}/${argDir}") - outputs.dir("${classes}/doc") - outputs.dir("${classes}/help") + outputs.dir("${classesDir}/doc") + outputs.dir("${classesDir}/help") outputs.file("${workingDir}/JavaHelpSearch/DOCS") outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") @@ -772,8 +959,7 @@ task linkCheck(type: JavaExec) { classpath = files("${jalviewDir}/${utilsDir}") main = "HelpLinksChecker" workingDir = jalviewDir - def help = "${classes}/${helpDir}" - args = [ "${classes}/${helpDir}", "-nointernet" ] + args = [ "${classesDir}/${help_dir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append def errFOS = outFOS @@ -784,13 +970,13 @@ task linkCheck(type: JavaExec) { outFOS, errorOutput) - inputs.dir("${classes}/${helpDir}") + inputs.dir("${classesDir}/${help_dir}") outputs.file(helpLinksCheckerOutFile) } // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" -ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}" +ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}" ant.importBuild "${utilsDir}/publishHelp.xml" @@ -800,6 +986,7 @@ task cleanPackageDir(type: Delete) { } } + jar { dependsOn linkCheck dependsOn buildIndices @@ -821,13 +1008,13 @@ jar { exclude "**/*.jar" exclude "**/*.jar.*" - inputs.dir("${classes}") + inputs.dir(classesDir) outputs.file("${jalviewDir}/${packageDir}/${archiveName}") } task copyJars(type: Copy) { - from fileTree(dir: "${classes}", include: "**/*.jar").files + from fileTree(dir: classesDir, include: "**/*.jar").files into "${jalviewDir}/${packageDir}" } @@ -888,33 +1075,34 @@ task getdownWebsite() { def getdownWebsiteResourceFilenames = [] def getdownTextString = "" - def getdownResourceDir = project.ext.getdownResourceDir - def getdownAppDir = project.ext.getdownAppDir + def getdownResourceDir = getdownResourceDir def getdownResourceFilenames = [] doFirst { // clean the getdown website and files dir before creating getdown folders - delete project.ext.getdownWebsiteDir - delete project.ext.getdownFilesDir + delete getdownWebsiteDir + delete getdownFilesDir copy { from buildProperties rename(build_properties_file, getdown_build_properties) - into project.ext.getdownAppDir + into getdownAppDir } - getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}" + getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" // go through properties looking for getdown_txt_... def props = project.properties.sort { it.key } - if (getdown_alt_java_min_version.length() > 0) { - props.put("getdown_txt_java_min_version", getdown_alt_java_min_version) + 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 (getdown_alt_java_max_version.length() > 0) { - props.put("getdown_txt_java_max_version", getdown_alt_java_max_version) + if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) { + props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) } - props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location) - props.put("getdown_txt_appbase", getdown_app_base) + props.put("getdown_txt_appbase", getdownAppBase) props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { if (prop.startsWith("getdown_txt_multi_")) { @@ -954,7 +1142,7 @@ task getdownWebsite() { getdownResourceFilenames.each{ filename -> copy { from filename - into project.ext.getdownResourceDir + into getdownResourceDir } } @@ -969,11 +1157,11 @@ task getdownWebsite() { } codeFiles.sort().each{f -> def name = f.getName() - def line = "code = ${getdown_app_dir}/${name}\n" + def line = "code = ${getdownAppDistDir}/${name}\n" getdownTextString += line copy { from f.getPath() - into project.ext.getdownAppDir + into getdownAppDir } } @@ -987,7 +1175,7 @@ task getdownWebsite() { getdownTextString += line copy { from f.getPath() - into project.ext.getdownJ11libDir + into getdownJ11libDir } } } @@ -998,16 +1186,17 @@ task getdownWebsite() { getdownTextString += "resource = ${getdown_launcher_new}\n" getdownTextString += "class = ${mainClass}\n" - def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt") + def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) - def launch_jvl = file("${project.ext.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="+props.get("getdown_txt_appbase")) copy { from getdownLauncher rename(file(getdownLauncher).getName(), getdown_launcher_new) - into project.ext.getdownWebsiteDir + into getdownWebsiteDir } copy { @@ -1015,7 +1204,7 @@ task getdownWebsite() { if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } - into project.ext.getdownWebsiteDir + into getdownWebsiteDir } if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { @@ -1037,7 +1226,7 @@ task getdownWebsite() { copy { from getdown_txt - from launch_jvl + from launchJvl from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { @@ -1048,15 +1237,31 @@ task getdownWebsite() { copy { from getdownResourceDir - into "${project.ext.getdownFilesDir}/${getdown_resource_dir}" + into "${getdownFilesDir}/${getdown_resource_dir}" } } if (buildDist) { inputs.dir("${jalviewDir}/${packageDir}") } - outputs.dir(project.ext.getdownWebsiteDir) - outputs.dir(project.ext.getdownFilesDir) + 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) { + def digestDirPropertyName = "DIGESTDIR" + description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown" + doFirst { + classpath = files(getdownLauncher) + def digestDir = findProperty(digestDirPropertyName) + if (digestDir == null) { + throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest") + } + args digestDir + } + main = "com.threerings.getdown.tools.Digester" } @@ -1065,12 +1270,12 @@ task getdownDigest(type: JavaExec) { description = "Digest the getdown website folder" dependsOn getdownWebsite doFirst { - classpath = files("${getdownWebsiteDir}/${getdown_launcher}") + classpath = files(getdownLauncher) } main = "com.threerings.getdown.tools.Digester" - args project.ext.getdownWebsiteDir - inputs.dir(project.ext.getdownWebsiteDir) - outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt") + args getdownWebsiteDir + inputs.dir(getdownWebsiteDir) + outputs.file("${getdownWebsiteDir}/digest2.txt") } @@ -1099,98 +1304,78 @@ task getdown() { clean { doFirst { - delete project.ext.getdownWebsiteDir - delete project.ext.getdownFilesDir + delete getdownWebsiteDir + delete getdownFilesDir } } install4j { - def install4jHomeDir = "/opt/install4j" - def hostname = "hostname".execute().text.trim() - if (hostname.equals("jv-bamboo")) { + if (file(install4jHomeDir).exists()) { + // good to go! + } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) { install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" - } else if (OperatingSystem.current().isMacOsX()) { - install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app' - if (! file(install4jHomeDir).exists()) { - install4jHomeDir = System.getProperty("user.home")+install4jHomeDir - } - } else if (OperatingSystem.current().isLinux()) { - install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" - } - installDir = file(install4jHomeDir) - mediaTypes = Arrays.asList(install4jMediaTypes.split(",")) - if (install4jFaster.equals("true")) { - faster = true + } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) { + install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app" } + installDir(file(install4jHomeDir)) + + mediaTypes = Arrays.asList(install4j_media_types.split(",")) } -def install4jConf -def macosJavaVMDir -def macosJavaVMTgz -def windowsJavaVMDir -def windowsJavaVMTgz -def install4jDir = "${jalviewDir}/${install4jResourceDir}" -def install4jConfFile = "jalview-installers-java${JAVA_VERSION}.install4j" -install4jConf = "${install4jDir}/${install4jConfFile}" - -task copyInstall4jTemplate(type: Copy) { - macosJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre" - macosJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz" - windowsJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre" - windowsJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz" - from (install4jDir) { - include install4jTemplate - rename (install4jTemplate, install4jConfFile) - filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION]) - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', - tokens: [ - 'JAVA_VERSION': JAVA_VERSION, - 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, - 'VERSION': JALVIEW_VERSION, - 'MACOS_JAVA_VM_DIR': macosJavaVMDir, - 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, - 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, - 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, - 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations, - 'COPYRIGHT_MESSAGE': install4jCopyrightMessage, - 'MACOS_BUNDLE_ID': install4jMacOSBundleId, - 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, - 'GETDOWN_DIST_DIR': getdown_app_dir, - 'GETDOWN_ALT_DIR': getdown_app_dir_alt, - 'GETDOWN_INSTALL_DIR': getdown_install_dir - ] - ) - if (OSX_KEYPASS=="") { - filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"']) - filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor']) +task copyInstall4jTemplate { + def install4jTemplateFile = file("${install4jDir}/${install4j_template}") + def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}") + inputs.file(install4jTemplateFile) + inputs.file(install4jFileAssociationsFile) + 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("${install4jFileAssociationsText}") + install4jConfigXml.'**'.action.any { a -> + if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') { + def parent = a.parent() + parent.remove(a) + fileAssociationActions.each { faa -> + parent.append(faa) + } + // don't need to continue in .any loop once replacements have been made + return true + } + } + + // write install4j file + install4jConfFile.text = XmlUtil.serialize(install4jConfigXml) } - into install4jDir - outputs.files(install4jConf) +} - doLast { - // include file associations in installer - def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerFileAssociationsXml, - file: install4jConf - ) - /* - // include uninstaller applescript app files in dmg - def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerDMGUninstallerXml, - file: install4jConf - ) - */ + +clean { + doFirst { + delete install4jConfFile } } @@ -1198,37 +1383,85 @@ task copyInstall4jTemplate(type: Copy) { task installers(type: com.install4j.gradle.Install4jTask) { group = "distribution" description = "Create the install4j installers" + dependsOn setGitVals dependsOn getdown dependsOn copyInstall4jTemplate - projectFile = file(install4jConf) - variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH] - destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}" + + 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}/${JAVA_VERSION}" + + variables = [ + 'JALVIEW_NAME': getdown_txt_title, + 'JALVIEW_DIR': "../..", + 'OSX_KEYSTORE': OSX_KEYSTORE, + 'JSIGN_SH': JSIGN_SH, + 'JRE_DIR': getdown_app_dir_java, + 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion, + 'JALVIEW_VERSION': JALVIEW_VERSION, + 'JAVA_MIN_VERSION': JAVA_MIN_VERSION, + 'JAVA_MAX_VERSION': JAVA_MAX_VERSION, + 'JAVA_VERSION': JAVA_VERSION, + 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, + 'VERSION': JALVIEW_VERSION, + 'MACOS_JAVA_VM_DIR': macosJavaVMDir, + 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, + 'LINUX_JAVA_VM_DIR': linuxJavaVMDir, + 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, + 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, + 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, + 'COPYRIGHT_MESSAGE': install4j_copyright_message, + 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id, + 'INSTALLER_NAME': install4j_installer_name, + 'INSTALL4J_UTILS_DIR': install4j_utils_dir, + 'GETDOWN_WEBSITE_DIR': getdown_website_dir, + 'GETDOWN_FILES_DIR': getdown_files_dir, + 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, + 'GETDOWN_DIST_DIR': getdownAppDistDir, + 'GETDOWN_ALT_DIR': getdown_app_dir_alt, + 'GETDOWN_INSTALL_DIR': getdown_install_dir, + 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations, + 'BUILD_DIR': install4jBuildDir, + ] + + destination = "${jalviewDir}/${install4jBuildDir}" buildSelected = true + if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) { + faster = true + disableSigning = true + } + if (OSX_KEYPASS) { - macKeystorePassword=OSX_KEYPASS + macKeystorePassword = OSX_KEYPASS } doFirst { println("Using projectFile "+projectFile) } - inputs.dir(project.ext.getdownWebsiteDir) - inputs.file(install4jConf) + inputs.dir(getdownWebsiteDir) + inputs.file(install4jConfFile) + inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") inputs.dir(macosJavaVMDir) inputs.dir(windowsJavaVMDir) - outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}") + outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}") } -clean { - doFirst { - delete install4jConf - } -} - - -task sourceDist (type: Tar) { +task sourceDist(type: Tar) { def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" @@ -1243,53 +1476,77 @@ task sourceDist (type: Tar) { into project.name - def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*" - ,".*" - ,"benchmarking/*" - ,"**/.*" - ,"*.class" - ,"**/*.class","${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) include (PROCESS_FILES) - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) + 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 ("appletlib") + exclude ("**/*locales") + exclude ("*locales/**") + exclude ("utils/InstallAnywhere") exclude (getdown_files_dir) - exclude (getdown_website_dir) + exclude (getdown_website_dir) - // exluding these as not using jars as modules yet - exclude ("${j11modDir}/**/*.jar") -} + // exluding these as not using jars as modules yet + exclude ("${j11modDir}/**/*.jar") + } + from(jalviewDir) { + include(INCLUDE_FILES) + } // from (jalviewDir) { // // explicit includes for stuff that seemed to not get included // include(fileTree("test/**/*.")) @@ -1299,33 +1556,22 @@ task sourceDist (type: Tar) { } -task helppages { +task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("${classes}/${helpDir}") - outputs.dir("${helpOutputDir}") + inputs.dir("${classesDir}/${help_dir}") + outputs.dir("${buildDir}/distributions/${help_dir}") } -def jalviewjsBuildDir -def jalviewjsSiteDir -def jalviewjsTransferSiteJsDir -def jalviewjsTransferSiteLibDir -def jalviewjsTransferSiteSwingJsDir -def jalviewjsTransferSiteCoreDir -task jalviewjsSitePath { - def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) - jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs" - jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}" - jalviewjsTransferSiteJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js" - jalviewjsTransferSiteLibDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib" - jalviewjsTransferSiteSwingJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs" - jalviewjsTransferSiteCoreDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core" +task j2sSetHeadlessBuild { + doFirst { + IN_ECLIPSE = false + } } -def eclipseWorkspace task jalviewjsSetEclipseWorkspace { def propKey = "jalviewjs_eclipse_workspace" def propVal = null @@ -1340,16 +1586,17 @@ task jalviewjsSetEclipseWorkspace { 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 } } - def writeProps = false if (eclipseWsDir == null || !file(eclipseWsDir).exists()) { def tempDir = File.createTempDir() eclipseWsDir = tempDir.getAbsolutePath() @@ -1358,6 +1605,14 @@ task jalviewjsSetEclipseWorkspace { 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() @@ -1365,6 +1620,9 @@ task jalviewjsSetEclipseWorkspace { props.store(bytes, null) def propertiesString = bytes.toString() propsFile.text = propertiesString + print("NEW ") + } else { + print("EXISTING ") } println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) @@ -1372,14 +1630,10 @@ task jalviewjsSetEclipseWorkspace { //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() } + outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() } } -def eclipseBinary -def eclipseVersion -def eclipseDebug = false -def eclipseVersionSuffix = "" task jalviewjsEclipsePaths { def eclipseProduct @@ -1420,6 +1674,14 @@ task jalviewjsEclipsePaths { 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}") } @@ -1427,6 +1689,15 @@ task jalviewjsEclipsePaths { } +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 @@ -1439,7 +1710,7 @@ task jalviewjsEclipseCopyDropins(type: Copy) { dependsOn jalviewjsEclipsePaths def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") - inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}") + inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}") def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" from inputFiles @@ -1473,8 +1744,6 @@ jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse task jalviewjsTransferUnzipSwingJs { - dependsOn jalviewjsSitePath - def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}" doLast { @@ -1490,8 +1759,6 @@ task jalviewjsTransferUnzipSwingJs { task jalviewjsTransferUnzipLib { - dependsOn jalviewjsSitePath - def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip") doLast { @@ -1518,13 +1785,10 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { group "JalviewJS" description "Create the .j2s file from the j2s.* properties" - dependsOn jalviewjsSitePath - - outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}") - def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } + jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } def siteDirProperty = "j2s.site.directory" def setSiteDir = false - j2s_props.each { prop, val -> + jalviewjsJ2sProps.each { prop, val -> if (val != null) { if (prop == siteDirProperty) { if (!(val.startsWith('/') || val.startsWith("file://") )) { @@ -1535,11 +1799,15 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { property(prop,val) } if (!setSiteDir) { // default site location, don't override specifically set property - property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}") + property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}") } } - inputs.properties(j2s_props) - outputs.file(outputFile) + outputFile = jalviewjsJ2sSettingsFileName + + if (! IN_ECLIPSE) { + inputs.properties(jalviewjsJ2sProps) + outputs.file(jalviewjsJ2sSettingsFileName) + } } @@ -1551,7 +1819,6 @@ task jalviewjsEclipseSetup { task jalviewjsSyncAllLibs (type: Sync) { - dependsOn jalviewjsSitePath dependsOn jalviewjsTransferUnzipAllLibs def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}") inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") @@ -1573,8 +1840,7 @@ task jalviewjsSyncAllLibs (type: Sync) { task jalviewjsSyncResources (type: Sync) { - dependsOn jalviewjsSitePath - def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}") + def inputFiles = fileTree(dir: resourceDir) def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" from inputFiles @@ -1593,7 +1859,6 @@ task jalviewjsSyncResources (type: Sync) { task jalviewjsSyncSiteResources (type: Sync) { - dependsOn jalviewjsSitePath def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}") def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" @@ -1613,7 +1878,6 @@ task jalviewjsSyncSiteResources (type: Sync) { task jalviewjsSyncBuildProperties (type: Sync) { - dependsOn jalviewjsSitePath dependsOn createBuildProperties def inputFiles = [file(buildProperties)] def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" @@ -1640,8 +1904,11 @@ task jalviewjsProjectImport(type: Exec) { doFirst { // do not run a headless import when we claim to be in Eclipse - if (ECLIPSE_IDE_DEVELOPER.equals("true")) { - throw new StopExecutionException("Not running headless import whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'") + 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}") } } @@ -1653,6 +1920,9 @@ task jalviewjsProjectImport(type: Exec) { 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 { @@ -1668,8 +1938,11 @@ task jalviewjsTranspile(type: Exec) { doFirst { // do not run a headless transpile when we claim to be in Eclipse - if (ECLIPSE_IDE_DEVELOPER.equals("true")) { - throw new StopExecutionException("Not running headless transpile whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'") + 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}") } } @@ -1679,6 +1952,9 @@ task jalviewjsTranspile(type: Exec) { 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 @@ -1725,7 +2001,12 @@ DEBUG: ${eclipseDebug} if (stdout.toString().contains("Error processing ")) { // j2s did not complete transpile //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") - throw new GradleException("Error during transpilation:\n${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}'") + } } } @@ -1735,14 +2016,14 @@ DEBUG: ${eclipseDebug} } -def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) { +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 = "Generating ${jsfile}" + msg = "Creating core for ${name}...\nGenerating ${jsfile}" println(msg) logOutFile.createNewFile() logOutFile.append(msg+"\n") @@ -1756,8 +2037,7 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, f -> if (f.exists()) { def t = f.text - t.replaceAll("Clazz\\.","Clazz_") - t.replaceAll("Class__","Clazz._") + t.replaceAll("Clazz\\.([^_])","Clazz_${1}") coreFile.append( t ) } else { msg = "...file '"+f.getPath()+"' does not exist, skipping" @@ -1776,6 +2056,7 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, javaexec { classpath = files(["${jalviewDir}/tools/closure_compiler.jar"]) args = [ "--js", jsfile, "--js_output_file", zjsfile ] + maxHeapSize = "2g" msg = "\nRunning '"+commandLine.join(' ')+"'\n" println(msg) @@ -1807,11 +2088,15 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, } -task jalviewjsNoTranspileBuildAllCores { - dependsOn jalviewjsSitePath +task jalviewjsBuildAllCores { + group "JalviewJS" + description "Build the core js lib closures listed in the classlists dir" + dependsOn jalviewjsTranspile dependsOn jalviewjsTransferUnzipSwingJs def j2sDir = "${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 = "${jsDir}/core/coretop2.js" @@ -1832,17 +2117,17 @@ task jalviewjsNoTranspileBuildAllCores { } // _jmol and _jalview cores. Add any other peculiar classlist.txt files here - classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ] - classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': "_jalview" ] + //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ] + classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ] - def classlists = [] + jalviewjsCoreClasslists = [] classlistFiles.each { hash -> def file = hash['file'] if (! file.exists()) { - println("...classlist file '"+file.getPath()+"' does not exist, skipping") + //println("...classlist file '"+file.getPath()+"' does not exist, skipping") return false // this is a "continue" in groovy .each closure } def name = hash['name'] @@ -1860,10 +2145,11 @@ task jalviewjsNoTranspileBuildAllCores { def jsfile = "${outputDir}/core${name}.js" def zjsfile = "${outputDir}/core${name}.z.js" - classlists += [ - 'jsfile': jsfile, - 'zjsfile': zjsfile, - 'list': list + jalviewjsCoreClasslists += [ + 'jsfile': jsfile, + 'zjsfile': zjsfile, + 'list': list, + 'name': name ] inputs.file(file) @@ -1873,77 +2159,118 @@ task jalviewjsNoTranspileBuildAllCores { } // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) + def stevesoftClasslistName = "_stevesoft" def stevesoftClasslist = [ - 'jsfile': "${outputDir}/core_stevesoft.js", - 'zjsfile': "${outputDir}/core_stevesoft.z.js", - 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js") + 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js", + 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js", + 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"), + 'name': stevesoftClasslistName ] - classlists += stevesoftClasslist + jalviewjsCoreClasslists += stevesoftClasslist inputs.files(stevesoftClasslist['list']) outputs.file(stevesoftClasslist['jsfile']) outputs.file(stevesoftClasslist['zjsfile']) + // _all core + def allClasslistName = "_all" + def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js") + allJsFiles += fileTree( + dir: libJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js", + "**/org/jmol/export/JSExporter.js" + ] + ) + allJsFiles += fileTree( + dir: swingJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/sun/misc/Unsafe.js", + "**/swingjs/jquery/jquery-editable-select.js", + "**/swingjs/jquery/j2sComboBox.js", + "**/sun/misc/FloatingDecimal.js" + ] + ) + def allClasslist = [ + 'jsfile': "${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")+" jalviewjsNoTranspileBuildAllCores\n----\n") + logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n") - classlists.each { - jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true")) + jalviewjsCoreClasslists.each { + jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true")) } } } -jalviewjsNoTranspileBuildAllCores.mustRunAfter jalviewjsTranspile - - -task jalviewjsBuildAllCores { - group "JalviewJS" - description "Build the core js lib closures listed in the classlists dir" - dependsOn jalviewjsTranspile - dependsOn jalviewjsNoTranspileBuildAllCores +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 ${coreName}]", + 'COREKEY': jalviewjs_core_key, + 'CORENAME': coreName + ] + ) + } } -task jalviewjsPublishCoreTemplate(type: Sync) { - dependsOn jalviewjsSitePath +task jalviewjsPublishCoreTemplates { dependsOn jalviewjsBuildAllCores - -// clean this up - def inputFile = file("${jalviewDir}/${j2s_template_html}") + def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}" + def inputFile = file(inputFileName) def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" -// clean this up - def jalviewTemplateName = "JalviewJS" - def jalviewCoreName = "_jalview" - - from inputFile - into outputDir def outputFiles = [] - rename { filename -> - outputFiles += "${outputDir}/${filename}" - if (filename.equals(inputFile.getName())) { - return "${jalviewTemplateName}_${jalviewCoreName}.html" - } - return null + jalviewjsCoreClasslists.each { cl -> + def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html" + cl['outputfile'] = outputFile + outputFiles += outputFile } - filter(ReplaceTokens, beginToken: '_', endToken: '_', tokens: ['MAIN': mainClass, 'CODE': "null", 'NAME': jalviewTemplateName]) - filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['NONE': jalviewCoreName]) - preserve { - include "**" + + doFirst { + jalviewjsCoreClasslists.each { cl -> + jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile) + } } - outputs.files outputFiles - inputs.files inputFile + inputs.file(inputFile) + outputs.files(outputFiles) } -task jalviewjsNoTranspileSyncCore (type: Sync) { - dependsOn jalviewjsSitePath - dependsOn jalviewjsNoTranspileBuildAllCores - dependsOn jalviewjsPublishCoreTemplate +task jalviewjsSyncCore (type: Sync) { + dependsOn jalviewjsBuildAllCores + dependsOn jalviewjsPublishCoreTemplates def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}") def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" @@ -1962,13 +2289,6 @@ task jalviewjsNoTranspileSyncCore (type: Sync) { } -task jalviewjsSyncCore (type: Sync) { - dependsOn jalviewjsTranspile - dependsOn jalviewjsNoTranspileSyncCore - dependsOn "jalviewjsBuildAllCores" -} - - // this Copy version of TransferSiteJs will delete anything else in the target dir task jalviewjsCopyTransferSiteJs(type: Copy) { dependsOn jalviewjsTranspile @@ -1978,7 +2298,7 @@ task jalviewjsCopyTransferSiteJs(type: Copy) { // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes -task jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) { +task jalviewjsSyncTransferSiteJs(type: Sync) { from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" include "**/*.*" into "${jalviewDir}/${jalviewjsSiteDir}" @@ -1987,24 +2307,16 @@ task jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) { } } + jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs -jalviewjsSyncAllLibs.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs -jalviewjsSyncResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs -jalviewjsSyncSiteResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs -jalviewjsSyncBuildProperties.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs - - -task jalviewjsNoTranspilePrepareSite { - dependsOn jalviewjsSyncAllLibs - dependsOn jalviewjsSyncResources - dependsOn jalviewjsSyncSiteResources - dependsOn jalviewjsSyncBuildProperties - dependsOn jalviewjsNoTranspileSyncCore -} +jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs task jalviewjsPrepareSite { @@ -2026,12 +2338,19 @@ task jalviewjsBuildSite { } -task cleanJalviewjsSite { +task cleanJalviewjsTransferSite { doFirst { delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}" delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}" delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + } +} + + +task cleanJalviewjsSite { + dependsOn cleanJalviewjsTransferSite + doFirst { delete "${jalviewDir}/${jalviewjsSiteDir}" } } @@ -2061,7 +2380,6 @@ task jalviewjsServer { group "JalviewJS" def filename = "jalviewjsTest.html" description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port." - dependsOn jalviewjsSitePath def htmlFile = "${jalviewDirAbsolutePath}/${filename}" doLast { @@ -2070,26 +2388,35 @@ task jalviewjsServer { def start = port def running = false def url + def jalviewjsServer while(port < start+1000 && !running) { try { def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") - def jalviewjsServer = factory.start(doc_root, port) + 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") - - file(htmlFile).text = """ -

Jalview JS Test. <${url}>

-

Jalview JS Test with 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 ${cl.name}: "+urlcore) + } + file(htmlFile).text = htmlText } outputs.file(htmlFile) @@ -2116,10 +2443,65 @@ task cleanJalviewjsAll { } +task jalviewjsIDE_checkJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)" -task jalviewjsIDE_CopyTransferSiteJs(type: Copy) { - from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" - into "${jalviewDir}/${jalviewjsSiteDir}" + doFirst { + def j2sPlugin = string("${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() + } + } } @@ -2130,18 +2512,37 @@ task jalviewjsIDE_j2sFile { } -task jalviewjsIDE_BuildAllCores { +task jalviewjsIDE_SyncCore { group "00 JalviewJS in Eclipse" - description "Build the core js lib closures listed in the classlists dir" - dependsOn jalviewjsNoTranspileBuildAllCores + 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 the Eclipse transpiled site and unzips supporting zipfiles" - dependsOn jalviewjsIDE_CopyTransferSiteJs - dependsOn jalviewjsNoTranspilePrepareSite + description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site" + dependsOn jalviewjsPrepareSite } @@ -2159,26 +2560,25 @@ task jalviewjsIDE_Server { } -// buildship runs this at import +// buildship runs this at import or gradle refresh task eclipseSynchronizationTask { - dependsOn eclipseSetup - dependsOn jalviewjsIDE_j2sFile + //dependsOn eclipseSetup + dependsOn createBuildProperties + if (J2S_ENABLED) { + dependsOn jalviewjsIDE_j2sFile + dependsOn jalviewjsIDE_checkJ2sPlugin + dependsOn jalviewjsIDE_PrepareSite + } } -// buildship runs this at build time +// buildship runs this at build time or project refresh task eclipseAutoBuildTask { - dependsOn jalviewjsNoTranspileSyncTransferSiteJs - dependsOn jalviewjsNoTranspilePrepareSite + //dependsOn jalviewjsIDE_checkJ2sPlugin + //dependsOn jalviewjsIDE_PrepareSite } - - - - - - task jalviewjs { group "JalviewJS" description "Build the site"