X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=b4636bc523f0d453e0e55b241481ccdff87c2e14;hb=c6977851625f96831a95b45901aa1d84bd7774fe;hp=ec665dcc5be9db474d6ae1226ba3eaa415249dc1;hpb=acc9f3f5965575e9ccc7fc854544d97d5ca0425a;p=jalview.git diff --git a/build.gradle b/build.gradle index ec665dc..b4636bc 100644 --- a/build.gradle +++ b/build.gradle @@ -1,70 +1,136 @@ +/* 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 'org.openclover:clover:4.3.1' + 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 '7.0.9' - id 'com.dorongold.task-tree' version '1.4' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree + id 'com.install4j.gradle' version '9.0.6' + id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree + id 'com.palantir.git-version' version '0.13.0' apply false } 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.toString() + return o == null ? "" : o.toString() } - -ext { - jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() - - // local build environment properties - def localProps = "${jalviewDirAbsolutePath}/local.properties" - if (file(localProps).exists()) { +def overrideProperties(String propsFileName, boolean output = false) { + if (propsFileName == null) { + return + } + def propsFile = file(propsFileName) + if (propsFile != null && propsFile.exists()) { + println("Using properties from file '${propsFileName}'") try { def p = new Properties() - def localPropsFIS = new FileInputStream(localProps) + def localPropsFIS = new FileInputStream(propsFile) 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}'") + def oldval + if (project.hasProperty(key)) { + oldval = project.findProperty(key) + project.setProperty(key, val) + if (output) { + println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") + } + } else { + ext.setProperty(key, val) + if (output) { + println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'") + } } } } catch (Exception e) { - System.out.println("Exception reading local.properties") + println("Exception reading local.properties") + e.printStackTrace() } } +} - +ext { + jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() + jalviewDirRelativePath = jalviewDir + + getdownChannelName = CHANNEL.toLowerCase() + // default to "default". Currently only has different cosmetics for "develop", "release", "default" + propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default" + // Import channel_properties + channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}") + channelGradleProperties = string("${channelDir}/channel_gradle.properties") + channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}") + overrideProperties(channelGradleProperties, false) + // local build environment properties + // can be "projectDir/local.properties" + overrideProperties("${projectDir}/local.properties", true) + // or "../projectDir_local.properties" + overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true) + + //// + // 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 + 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 @@ -82,123 +148,232 @@ ext { } else { println("HEADLESS BUILD") } - /* + + J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable") + if (J2S_ENABLED) { + println("J2S ENABLED") + } + /* *-/ System.properties.sort { it.key }.each { key, val -> println("SYSTEM PROPERTY ${key}='${val}'") } + /-* *-/ + if (false && IN_ECLIPSE) { + jalviewDir = jalviewDirAbsolutePath + } */ - cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") - classes = string("${jalviewDir}/${classesDir}") - if (clover.equals("true")) { - use_clover = true - classes = string("${buildDir}/${cloverClassesDir}") - } else { - use_clover = false - classes = string("${jalviewDir}/${classesDir}") - } + // datestamp + buildDate = new Date().format("yyyyMMdd") + + // 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("${cloverBuildDir}/clover.db") + + testSourceDir = useClover ? cloverTestInstrDir : testDir + testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}" getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") - getdownDir = string("") - reportRsyncCmd = false buildDist = true - buildProperties = build_properties_file + buildProperties = null + + // the following values might be overridden by the CHANNEL switch + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}") + getdownAppDistDir = getdown_app_dir_alt + getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}") + getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application + reportRsyncCommand = false + jvlChannelName = CHANNEL.toLowerCase() + install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build + install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}" + install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}" + install4jInstallerName = "${jalview_name} Non-Release Installer" + install4jExecutableName = install4j_executable_name + install4jExtraScheme = "jalviewx" + install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}") + install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}") + install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}") + install4jBackground = string("${install4j_images_dir}/${install4j_background}") switch (CHANNEL) { case "BUILD": // TODO: get bamboo build artifact URL for getdown artifacts getdown_channel_base = bamboo_channelbase - getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}") - getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${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(testng_excluded_groups)) { + testng_excluded_groups = "Not-bamboo" + } + install4jExtraScheme = "jalviewb" break - case "RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_release - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + case [ "RELEASE", "JALVIEWJS-RELEASE" ]: + getdownAppDistDir = getdown_app_dir_release reportRsyncCommand = true + install4jSuffix = "" + install4jInstallerName = "${jalview_name} Installer" break case "ARCHIVE": - getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt - if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { - print "Must provide an ARCHIVEDIR value to produce an archive distribution" - exit + getdownChannelName = CHANNEL.toLowerCase()+"/${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 { - packageDir = string("${ARCHIVEDIR}/${packageDir}") - buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}") + package_dir = string("${ARCHIVEDIR}/${package_dir}") + buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true + install4jExtraScheme = "jalviewa" break case "ARCHIVELOCAL": - getdown_channel_name = string("archive/${JALVIEW_VERSION}") - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt - if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { - print "Must provide an ARCHIVEDIR value to produce an archive distribution" - exit + getdownChannelName = string("archive/${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 { - packageDir = string("${ARCHIVEDIR}/${packageDir}") - buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}") + package_dir = string("${ARCHIVEDIR}/${package_dir}") + buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jSuffix = "Archive" + install4jExtraScheme = "jalviewa" break case "DEVELOP": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") reportRsyncCommand = true + getdownSetAppBaseProperty = true + // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version + JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}" + + install4jSuffix = "Develop" + install4jExtraScheme = "jalviewd" + install4jInstallerName = "${jalview_name} Develop Installer" break case "TEST-RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") reportRsyncCommand = true + // Don't ignore transpile errors for release build + if (jalviewjs_ignore_transpile_errors.equals("true")) { + jalviewjs_ignore_transpile_errors = "false" + println("Setting jalviewjs_ignore_transpile_errors to 'false'") + } + JALVIEW_VERSION = JALVIEW_VERSION+"-test" + install4jSuffix = "Test" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" break case ~/^SCRATCH(|-[-\w]*)$/: - getdown_channel_name = CHANNEL - getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") - getdown_app_base = string("${getdown_channel_base}/${getdownDir}") - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + getdownChannelName = CHANNEL + JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL + + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") reportRsyncCommand = true + install4jSuffix = "Scratch" break - case "LOCAL": - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + case "TEST-LOCAL": + if (!file("${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" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" + break + + case [ "LOCAL", "JALVIEWJS" ]: + JALVIEW_VERSION = "TEST" + getdownAppBase = file(getdownWebsiteDir).toURI().toString() getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jExtraScheme = "jalviewl" 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 } - - getdownAppDir = string("${getdownWebsiteDir}/${getdown_app_dir}") + // override getdownAppBase if requested + if (findProperty("getdown_appbase_override") != null) { + // revert to LOCAL if empty string + if (string(getdown_appbase_override) == "") { + getdownAppBase = file(getdownWebsiteDir).toURI().toString() + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + } else if (string(getdown_appbase_override).startsWith("file://")) { + getdownAppBase = string(getdown_appbase_override) + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + } else { + getdownAppBase = string(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() + + getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local" + getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}") //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}") getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}") @@ -208,8 +383,21 @@ ext { modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) modules_runtimeClasspath = modules_compileClasspath */ - gitHash = string("") - gitBranch = string("") + + gitHash = "SOURCE" + gitBranch = "Source" + try { + apply plugin: "com.palantir.git-version" + def details = versionDetails() + gitHash = details.gitHash + gitBranch = details.branchName + } catch(org.gradle.api.internal.plugins.PluginApplicationException e) { + println("Not in a git repository. Using git values from RELEASE properties file.") + gitHash = releaseProps.getProperty("git.hash") + gitBranch = releaseProps.getProperty("git.branch") + } catch(java.lang.RuntimeException e1) { + throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.") + } println("Using a ${CHANNEL} profile.") @@ -223,38 +411,38 @@ ext { compile_source_compatibility = 1.8 compile_target_compatibility = 1.8 // these are getdown.txt properties defined dependent on the JAVA_VERSION - getdown_alt_java_min_version = getdown_alt_java8_min_version - getdown_alt_java_max_version = getdown_alt_java8_max_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 - getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location + getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location")) // this property is for the Java library used in eclipse - eclipse_java_runtime_name = string("JavaSE-1.8") + 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 - 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 = string("JavaSE-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 - 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 = string("JavaSE-11") + } else if (JAVA_VERSION.equals("17")) { + JAVA_INTEGER_VERSION = string("17") + libDir = j17libDir + libDistDir = j17libDir + compile_source_compatibility = 17 + compile_target_compatibility = 17 + 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-17") /* compile without modules -- using classpath libraries additional_compiler_args += [ '--module-path', modules_compileClasspath.asPath, @@ -267,17 +455,38 @@ ext { // for install4j - macosJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre") - macosJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz") - windowsJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre") - windowsJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz") - install4jDir = string("${jalviewDir}/${install4jResourceDir}") - install4jConfFileName = string("jalview-installers-java${JAVA_VERSION}.install4j") - install4jConfFile = string("${install4jDir}/${install4jConfFileName}") - - - buildingHTML = string("${jalviewDir}/${docDir}/building.html") - helpFile = string("${classes}/${helpDir}/help.jhm") + 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") + windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre") + linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre") + macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz") + windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz") + 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) + } + + resourceBuildDir = string("${buildDir}/resources") + resourcesBuildDir = string("${resourceBuildDir}/resources_build") + helpBuildDir = string("${resourceBuildDir}/help_build") + docBuildDir = string("${resourceBuildDir}/doc_build") + + if (buildProperties == null) { + buildProperties = string("${resourcesBuildDir}/${build_properties_file}") + } + buildingHTML = string("${jalviewDir}/${doc_dir}/building.html") + helpParentDir = string("${jalviewDir}/${help_parent_dir}") + helpSourceDir = string("${helpParentDir}/${help_dir}") + helpFile = string("${helpBuildDir}/${help_dir}/help.jhm") relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) @@ -293,7 +502,12 @@ ext { 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}") + jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}") + jalviewjsJ2sProps = null + jalviewjsJ2sPlugin = jalviewjs_j2s_plugin eclipseWorkspace = null eclipseBinary = string("") @@ -306,81 +520,62 @@ ext { sourceSets { main { java { - srcDirs "${jalviewDir}/${sourceDir}" - outputDir = file(project.classes) + srcDirs sourceDir + outputDir = file(classesDir) } resources { - srcDirs "${jalviewDir}/${resourceDir}" + srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ] } - jar.destinationDir = file("${jalviewDir}/${packageDir}") - compileClasspath = files(sourceSets.main.java.outputDir) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath + runtimeClasspath += files(sourceSets.main.resources.srcDirs) } clover { java { - srcDirs = [ cloverInstrDir ] - outputDir = file("${buildDir}/${cloverClassesDir}") + srcDirs cloverInstrDir + outputDir = cloverClassesDir } resources { srcDirs = sourceSets.main.resources.srcDirs } - compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir ) - compileClasspath += files(sourceSets.main.java.outputDir) - compileClasspath += sourceSets.main.compileClasspath - compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"]) + + 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 "${jalviewDir}/${testSourceDir}" - outputDir = file("${jalviewDir}/${testOutputDir}") + srcDirs testSourceDir + outputDir = file(testClassesDir) } resources { - srcDirs = sourceSets.main.resources.srcDirs + srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs } compileClasspath = files( sourceSets.test.java.outputDir ) - - if (use_clover) { - compileClasspath += sourceSets.clover.compileClasspath - } else { - compileClasspath += files(sourceSets.main.java.outputDir) - } - - compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) - compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"]) - compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"]) + compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath + compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath + runtimeClasspath += files(sourceSets.test.resources.srcDirs) } -} - -// clover bits -dependencies { - if (use_clover) { - cloverCompile 'org.openclover:clover:4.3.1' - testCompile 'org.openclover:clover:4.3.1' - } } -configurations { - cloverRuntime - cloverRuntime.extendsFrom cloverCompile -} - +// eclipse project and settings files creation, also used by buildship eclipse { project { name = eclipse_project_name @@ -395,14 +590,12 @@ eclipse { classpath { //defaultOutputDir = sourceSets.main.java.outputDir - def removeThese = [] - configurations.each{ - if (it.isCanBeResolved()) { - removeThese += it + configurations.each{ c-> + if (c.isCanBeResolved()) { + minusConfigurations += [c] } } - minusConfigurations += removeThese plusConfigurations = [ ] file { @@ -410,19 +603,21 @@ 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)) } @@ -432,11 +627,11 @@ 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("${jalviewDirAbsolutePath}/")) { @@ -452,7 +647,6 @@ eclipse { } } - //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each { sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //no longer want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { @@ -486,7 +680,7 @@ eclipse { // for the IDE, use java 11 compatibility sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility - javaRuntimeName = eclipse_java_runtime_name + javaRuntimeName = eclipseJavaRuntimeName // add in jalview project specific properties/preferences into eclipse core preferences file { @@ -500,6 +694,22 @@ eclipse { props.putAt(t, v) } } + // codestyle file -- overrides previous formatter prefs + def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}") + if (csFile.exists()) { + XmlParser parser = new XmlParser() + def profiles = parser.parse(csFile) + def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") } + if (profile != null) { + profile.'setting'.each { s -> + def id = s.'@id' + def value = s.'@value' + if (id != null && value != null) { + props.putAt(id, value) + } + } + } + } } } @@ -507,219 +717,474 @@ eclipse { if (IN_ECLIPSE) { // Don't want these to be activated if in headless build - //synchronizationTasks "eclipseConfiguration" - autoBuildTasks "eclipseAutoBuildTask" + synchronizationTasks "eclipseSynchronizationTask" + //autoBuildTasks "eclipseAutoBuildTask" + } } -task cloverInstr() { - // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) - outputs.dir cloverInstrDir +/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */ +// Class to allow updating arbitrary properties files +class PropertiesFile extends PropertiesPersistableConfigurationObject { + public PropertiesFile(PropertiesTransformer t) { super(t); } + @Override protected void load(Properties properties) { } + @Override protected void store(Properties properties) { } + @Override protected String getDefaultResourceName() { return ""; } + // This is necessary, because PropertiesPersistableConfigurationObject fails + // if no default properties file exists. + @Override public void loadDefaults() { load(new StringBufferInputStream("")); } +} - doFirst { - delete cloverInstrDir - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-d", "${buildDir}/${cloverSourcesInstrDir}"] - 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) +// 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 cloverReport { - group = "Verification" - description = "Createst the Clover report" - inputs.dir "${buildDir}/clover" - outputs.dir "${reportsDir}/clover" - onlyIf { - file("${buildDir}/clover/clover.db").exists() +task eclipseUIPreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.ui.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) } - doFirst { - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-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", "${reportsDir}/clover/clover.xml"].toArray() - com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) +task eclipseGroovyCorePreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.groovy.core.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) + } } } -// end clover bits +task eclipseAllPreferences { + dependsOn eclipseJdt + dependsOn eclipseUIPreferences + dependsOn eclipseGroovyCorePreferences +} -compileJava { +eclipseUIPreferences.mustRunAfter eclipseJdt +eclipseGroovyCorePreferences.mustRunAfter eclipseJdt - doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") - } +/* end of eclipse preferences hack */ -} +// clover bits -compileTestJava { - if (use_clover) { - dependsOn compileCloverJava - classpath += configurations.cloverRuntime - } else { - classpath += sourceSets.main.runtimeClasspath - } + +task cleanClover { doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") + delete cloverBuildDir + delete cloverReportDir } } -compileCloverJava { +task cloverInstrJava(type: JavaExec) { + group = "Verification" + description = "Create clover instrumented source java files" + + dependsOn cleanClover + + inputs.files(sourceSets.main.allJava) + outputs.dir(cloverInstrDir) + + //classpath = fileTree(dir: "${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 { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs += additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") + delete cloverInstrDir + println("Clover: About to instrument "+srcFiles.size() +" files") } - classpath += configurations.cloverRuntime } -clean { +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 sourceSets.main.java.outputDir + delete cloverTestInstrDir + println("Clover: About to instrument test files") } } -cleanTest { - doFirst { - delete sourceSets.test.java.outputDir - delete cloverInstrDir +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() } -// format is a string like date.format("dd MMMM yyyy") -def getDate(format) { - def date = new Date() - return date.format(format) +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 setGitVals { - def hashStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--short", "HEAD" - standardOutput = hashStdOut - ignoreExitValue true +task cloverXmlReport(type: JavaExec) { + group = "Verification" + description = "Creates clover XML report" + + onlyIf { + file(cloverDb).exists() } - def branchStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" - standardOutput = branchStdOut - ignoreExitValue true + 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 + ] - gitHash = hashStdOut.toString().trim() - gitBranch = branchStdOut.toString().trim() + if (cloverreport_xml_options.length() > 0) { + argsList += cloverreport_xml_options.split(" ") + } - outputs.upToDateWhen { false } + args argsList.toArray() } -task createBuildProperties(type: WriteProperties) { - dependsOn setGitVals - inputs.dir("${jalviewDir}/${sourceDir}") - inputs.dir("${jalviewDir}/${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) +task cloverReport { + group = "Verification" + description = "Creates clover reports" + + dependsOn cloverXmlReport + dependsOn cloverHtmlReport } -task cleanBuildingHTML(type: Delete) { +compileCloverJava { + doFirst { - delete buildingHTML + 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 -task convertBuildingMD(type: Exec) { - dependsOn cleanBuildingHTML - def buildingMD = "${jalviewDir}/${docDir}/building.md" - def css = "${jalviewDir}/${docDir}/github.css" +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") + } - def pandoc = null - pandoc_exec.split(",").each { - if (file(it.trim()).exists()) { - pandoc = it.trim() - return true - } +} + + +compileTestJava { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs = additional_compiler_args + doFirst { + print ("Setting target compatibility to "+targetCompatibility+"\n") } +} - def hostname = "hostname".execute().text.trim() - if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) { - pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" + +clean { + doFirst { + delete sourceSets.main.java.outputDir } +} + +cleanTest { + dependsOn cleanClover doFirst { - if (pandoc != null && file(pandoc).exists()) { - 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() - } + delete sourceSets.test.java.outputDir } +} - ignoreExitValue true - inputs.file(buildingMD) - inputs.file(css) - outputs.file(buildingHTML) +// format is a string like date.format("dd MMMM yyyy") +def getDate(format) { + def date = new Date() + return date.format(format) } -clean { - 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) + println("Creating ${htmlFilePath}") + htmlFile.text = htmlText + } +} + + +task copyDocs(type: Copy) { + def inputDir = "${jalviewDir}/${doc_dir}" + def outputDir = "${docBuildDir}/${doc_dir}" + from(inputDir) { + include('**/*.txt') + include('**/*.md') + include('**/*.html') + include('**/*.xml') + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) + } + from(inputDir) { + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.xml') } + into outputDir + + inputs.dir(inputDir) + outputs.dir(outputDir) } -task syncDocs(type: Sync) { - dependsOn convertBuildingMD - def syncDir = "${classes}/${docDir}" - from fileTree("${jalviewDir}/${docDir}") - into syncDir +task convertMdFiles { + dependsOn copyDocs + def mdFiles = fileTree(dir: docBuildDir, 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(/\..*?$/, ".html") + htmlFiles.add(file(htmlFilePath)) + } + outputs.files(htmlFiles) } task copyHelp(type: Copy) { - def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}" - def outputDir = "${classes}/${helpDir}" + def inputDir = helpSourceDir + def outputDir = "${helpBuildDir}/${help_dir}" from(inputDir) { - exclude '**/*.gif' - exclude '**/*.jpg' - exclude '**/*.png' + include('**/*.txt') + include('**/*.md') + include('**/*.html') + include('**/*.hs') + include('**/*.xml') + include('**/*.jhm') filter(ReplaceTokens, beginToken: '$$', endToken: '$$', @@ -730,9 +1195,12 @@ task copyHelp(type: Copy) { ) } from(inputDir) { - include '**/*.gif' - include '**/*.jpg' - include '**/*.png' + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.hs') + exclude('**/*.xml') + exclude('**/*.jhm') } into outputDir @@ -742,139 +1210,221 @@ task copyHelp(type: Copy) { } -task syncLib(type: Sync) { - def syncDir = "${classes}/${libDistDir}" - from fileTree("${jalviewDir}/${libDistDir}") - into syncDir +task copyResources(type: Copy) { + group = "build" + description = "Copy (and make text substitutions in) the resources dir to the build area" + + def inputDir = resourceDir + def outputDir = resourcesBuildDir + from(inputDir) { + include('**/*.txt') + include('**/*.md') + include('**/*.html') + include('**/*.xml') + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) + } + from(inputDir) { + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.xml') + } + into outputDir + + inputs.dir(inputDir) + outputs.dir(outputDir) } +task copyChannelResources(type: Copy) { + dependsOn copyResources + group = "build" + description = "Copy the channel resources dir to the build resources area" -task syncResources(type: Sync) { - from "${jalviewDir}/${resourceDir}" - include "**/*.*" - into "${classes}" - preserve { - include "**" + def inputDir = "${channelDir}/${resource_dir}" + def outputDir = resourcesBuildDir + from inputDir + into outputDir + + inputs.dir(inputDir) + outputs.dir(outputDir) +} + +task createBuildProperties(type: WriteProperties) { + dependsOn copyResources + group = "build" + description = "Create the ${buildProperties} file" + + inputs.dir(sourceDir) + inputs.dir(resourcesBuildDir) + outputFile (buildProperties) + // taking time specific comment out to allow better incremental builds + comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") + //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") + property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") + property "VERSION", JALVIEW_VERSION + property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" + if (getdownSetAppBaseProperty) { + property "GETDOWNAPPBASE", getdownAppBase + property "GETDOWNAPPDISTDIR", getdownAppDistDir } + outputs.file(outputFile) +} + + +task buildIndices(type: JavaExec) { + dependsOn copyHelp + classpath = sourceSets.main.compileClasspath + main = "com.sun.java.help.search.Indexer" + workingDir = "${helpBuildDir}/${help_dir}" + def argDir = "html" + args = [ argDir ] + inputs.dir("${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 buildResources { + dependsOn copyResources + dependsOn copyChannelResources + dependsOn createBuildProperties +} task prepare { - dependsOn syncResources - dependsOn syncDocs + dependsOn buildResources + dependsOn copyDocs dependsOn copyHelp + dependsOn convertMdFiles + dependsOn buildIndices } +compileJava.dependsOn prepare +run.dependsOn compileJava +//run.dependsOn prepare + + //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir test { dependsOn prepare - dependsOn compileJava - if (use_clover) { - dependsOn cloverInstr - } - if (use_clover) { - print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") + if (useClover) { + dependsOn cloverClasses + } else { //? + dependsOn compileJava //? } useTestNG() { - includeGroups testngGroups + includeGroups testng_groups + excludeGroups testng_excluded_groups preserveOrder true useDefaultListeners=true } + maxHeapSize = "1024m" + workingDir = jalviewDir - //systemProperties 'clover.jar' System.properties.clover.jar + def testLaf = project.findProperty("test_laf") + if (testLaf != null) { + println("Setting Test LaF to '${testLaf}'") + systemProperty "laf", testLaf + } + def testHiDPIScale = project.findProperty("test_HiDPIScale") + if (testHiDPIScale != null) { + println("Setting Test HiDPI Scale to '${testHiDPIScale}'") + systemProperty "sun.java2d.uiScale", testHiDPIScale + } sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility jvmArgs += additional_compiler_args -} - - -task buildIndices(type: JavaExec) { - dependsOn copyHelp - classpath = sourceSets.main.compileClasspath - main = "com.sun.java.help.search.Indexer" - workingDir = "${classes}/${helpDir}" - def argDir = "html" - args = [ argDir ] - inputs.dir("${workingDir}/${argDir}") - - outputs.dir("${classes}/doc") - outputs.dir("${classes}/help") - outputs.file("${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("${workingDir}/JavaHelpSearch/TMAP") + doFirst { + if (useClover) { + println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover") + } + } } task compileLinkCheck(type: JavaCompile) { options.fork = true - classpath = files("${jalviewDir}/${utilsDir}") - destinationDir = file("${jalviewDir}/${utilsDir}") - source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) + classpath = files("${jalviewDir}/${utils_dir}") + destinationDir = file("${jalviewDir}/${utils_dir}") + source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) - inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java") - inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java") - outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class") - outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class") + inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") + inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") + outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class") + outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class") } task linkCheck(type: JavaExec) { - dependsOn prepare, compileLinkCheck + dependsOn prepare + dependsOn compileLinkCheck - def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out") - classpath = files("${jalviewDir}/${utilsDir}") + def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out") + classpath = files("${jalviewDir}/${utils_dir}") main = "HelpLinksChecker" workingDir = jalviewDir - def help = "${classes}/${helpDir}" - args = [ "${classes}/${helpDir}", "-nointernet" ] + args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append - def errFOS = outFOS standardOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, - standardOutput) + System.out) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, - errorOutput) + System.err) - inputs.dir("${classes}/${helpDir}") + inputs.dir(helpBuildDir) outputs.file(helpLinksCheckerOutFile) } + // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" -ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}" -ant.importBuild "${utilsDir}/publishHelp.xml" +ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}" +ant.importBuild "${utils_dir}/publishHelp.xml" task cleanPackageDir(type: Delete) { doFirst { - delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar") + delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar") } } + jar { + dependsOn prepare dependsOn linkCheck - dependsOn buildIndices - dependsOn createBuildProperties manifest { - attributes "Main-Class": mainClass, + attributes "Main-Class": main_class, "Permissions": "all-permissions", - "Application-Name": "Jalview Desktop", - "Codebase": application_codebase + "Application-Name": install4jApplicationName, + "Codebase": application_codebase, + "Implementation-Version": JALVIEW_VERSION } - destinationDir = file("${jalviewDir}/${packageDir}") - archiveName = rootProject.name+".jar" + def outputDir = "${jalviewDir}/${package_dir}" + destinationDirectory = file(outputDir) + archiveFileName = rootProject.name+".jar" + duplicatesStrategy "EXCLUDE" + exclude "cache*/**" exclude "*.jar" @@ -882,23 +1432,27 @@ jar { exclude "**/*.jar" exclude "**/*.jar.*" - inputs.dir("${classes}") - outputs.file("${jalviewDir}/${packageDir}/${archiveName}") + inputs.dir(sourceSets.main.java.outputDir) + sourceSets.main.resources.srcDirs.each{ dir -> + inputs.dir(dir) + } + outputs.file("${outputDir}/${archiveFileName}") } task copyJars(type: Copy) { - from fileTree(dir: "${classes}", include: "**/*.jar").files - into "${jalviewDir}/${packageDir}" + 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) { + dependsOn jar from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files - into "${jalviewDir}/${packageDir}" + into "${jalviewDir}/${package_dir}" preserve { - include jar.archiveName + include jar.archiveFileName.getOrNull() } } @@ -912,7 +1466,7 @@ task makeDist { dependsOn cleanPackageDir dependsOn syncJars dependsOn jar - outputs.dir("${jalviewDir}/${packageDir}") + outputs.dir("${jalviewDir}/${package_dir}") } @@ -922,8 +1476,10 @@ task cleanDist { 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 } @@ -931,9 +1487,13 @@ shadowJar { include("*.jar") } manifest { - attributes 'Implementation-Version': JALVIEW_VERSION + attributes "Implementation-Version": JALVIEW_VERSION, + "Application-Name": install4jApplicationName } - mainClassName = shadowJarMainClass + + duplicatesStrategy "INCLUDE" + + mainClassName = shadow_jar_main_class mergeServiceFiles() classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION minimize() @@ -950,7 +1510,6 @@ task getdownWebsite() { def getdownWebsiteResourceFilenames = [] def getdownTextString = "" def getdownResourceDir = getdownResourceDir - def getdownAppDir = getdownAppDir def getdownResourceFilenames = [] doFirst { @@ -960,22 +1519,42 @@ task getdownWebsite() { copy { from buildProperties - rename(build_properties_file, getdown_build_properties) + rename(file(buildProperties).getName(), getdown_build_properties) into getdownAppDir } - getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}" + getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" + + copy { + from channelPropsFile + into getdownWebsiteDir + } + getdownWebsiteResourceFilenames += file(channelPropsFile).getName() - // go through properties looking for getdown_txt_... + // set some getdown_txt_ properties then go through all properties looking for getdown_txt_... def props = project.properties.sort { it.key } - if (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 (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) { + props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) } - if (getdown_alt_java_max_version.length() > 0) { - props.put("getdown_txt_java_max_version", getdown_alt_java_max_version) + if (getdownImagesDir != null && file(getdownImagesDir).exists()) { + props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}") + props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}") + props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}") + props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}") + props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}") + props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}") } - props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location) - props.put("getdown_txt_appbase", getdown_app_base) + props.put("getdown_txt_title", jalview_name) + props.put("getdown_txt_ui.name", install4jApplicationName) + + // start with appbase + getdownTextString += "appbase = ${getdownAppBase}\n" props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { if (prop.startsWith("getdown_txt_multi_")) { @@ -1018,9 +1597,21 @@ task getdownWebsite() { into getdownResourceDir } } + + def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ] + getdownWrapperScripts.each{ script -> + def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" ) + if (s.exists()) { + copy { + from s + into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}" + } + getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n" + } + } def codeFiles = [] - fileTree(file(packageDir)).each{ f -> + fileTree(file(package_dir)).each{ f -> if (f.isDirectory()) { def files = fileTree(dir: f, include: ["*"]).getFiles() codeFiles += files @@ -1028,9 +1619,11 @@ task getdownWebsite() { codeFiles += f } } - codeFiles.sort().each{f -> + def jalviewJar = jar.archiveFileName.getOrNull() + // put jalview.jar first for CLASSPATH and .properties files reasons + codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.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() @@ -1057,20 +1650,28 @@ task getdownWebsite() { // 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 = ${mainClass}\n" + getdownTextString += "class = ${main_class}\n" + // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache + if (getdownSetAppBaseProperty) { + getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n" + getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n" + } def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) - def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}") - launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) + def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl" + def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}") + launchJvl.write("appbase=${getdownAppBase}") + // files going into the getdown website dir: getdown-launcher.jar copy { from getdownLauncher rename(file(getdownLauncher).getName(), getdown_launcher_new) into getdownWebsiteDir } + // files going into the getdown website dir: getdown-launcher(-local).jar copy { from getdownLauncher if (file(getdownLauncher).getName() != getdown_launcher) { @@ -1079,34 +1680,39 @@ task getdownWebsite() { into getdownWebsiteDir } + // files going into the getdown website dir: ./install dir and files if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { copy { from getdown_txt from getdownLauncher - from "${getdownWebsiteDir}/${getdown_build_properties}" + from "${getdownAppDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownInstallDir } + // and make a copy in the getdown files dir (these are not downloaded by getdown) copy { from getdownInstallDir into getdownFilesInstallDir } } + // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties copy { from getdown_txt - from launch_jvl + from launchJvl from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" + from "${getdownWebsiteDir}/${channel_props}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownFilesDir } + // and ./resources (not all downloaded by getdown) copy { from getdownResourceDir into "${getdownFilesDir}/${getdown_resource_dir}" @@ -1114,19 +1720,37 @@ task getdownWebsite() { } if (buildDist) { - inputs.dir("${jalviewDir}/${packageDir}") + 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("${getdownWebsiteDir}/${getdown_launcher}") + classpath = files(getdownLauncher) } main = "com.threerings.getdown.tools.Digester" args getdownWebsiteDir @@ -1158,6 +1782,11 @@ task getdown() { } +tasks.withType(JavaCompile) { + options.encoding = 'UTF-8' +} + + clean { doFirst { delete getdownWebsiteDir @@ -1167,98 +1796,95 @@ clean { 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(",")) } -task copyInstall4jTemplate(type: Copy) { - from (install4jDir) { - include install4jTemplate - rename (install4jTemplate, install4jConfFileName) - 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' - ] - ) - } - } - into install4jDir - outputs.files(install4jConfFile) +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 { - // include file associations in installer - def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerFileAssociationsXml, - file: install4jConfFile - ) - /* - // include uninstaller applescript app files in dmg - def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerDMGUninstallerXml, - file: install4jConfFile - ) - */ + 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" + } + } + + // disable install screen for OSX dmg (for 2.11.2.0) + install4jConfigXml.'**'.macosArchive.each { macosArchive -> + macosArchive.attributes().remove('executeSetupApp') + macosArchive.attributes().remove('setupAppId') + } + + // 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 + } + } + + // write install4j file + install4jConfFile.text = XmlUtil.serialize(install4jConfigXml) } } @@ -1275,76 +1901,199 @@ task installers(type: com.install4j.gradle.Install4jTask) { description = "Create the install4j installers" dependsOn getdown dependsOn copyInstall4jTemplate - projectFile = file(install4jConfFile) - 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': jalview_name, + 'JALVIEW_APPLICATION_NAME': install4jApplicationName, + 'JALVIEW_DIR': "../..", + 'OSX_KEYSTORE': OSX_KEYSTORE, + 'OSX_APPLEID': OSX_APPLEID, + 'OSX_ALTOOLPASS': OSX_ALTOOLPASS, + '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_DMG_DS_STORE': install4jDMGDSStore, + 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage, + 'WRAPPER_LINK': getdownWrapperLink, + 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script, + 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script, + 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir, + '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, + 'MAC_ICONS_FILE': install4jMacIconsFile, + 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile, + 'PNG_ICON_FILE': install4jPngIconFile, + 'BACKGROUND': install4jBackground, + + ] + + //println("INSTALL4J VARIABLES:") + //variables.each{k,v->println("${k}=${v}")} + + destination = "${jalviewDir}/${install4jBuildDir}" buildSelected = true + if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) { + faster = true + disableSigning = true + disableNotarization = true + } + if (OSX_KEYPASS) { - macKeystorePassword=OSX_KEYPASS + macKeystorePassword = OSX_KEYPASS + } + + if (OSX_ALTOOLPASS) { + appleIdPassword = OSX_ALTOOLPASS + disableNotarization = false + } else { + disableNotarization = true } doFirst { println("Using projectFile "+projectFile) + if (!disableNotarization) { println("Will notarize OSX App DMG") } } + //verbose=true inputs.dir(getdownWebsiteDir) inputs.file(install4jConfFile) + inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") inputs.dir(macosJavaVMDir) inputs.dir(windowsJavaVMDir) - outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}") + outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}") } -clean { +spotless { + java { + eclipse().configFile(eclipse_codestyle_file) + } +} + +task createSourceReleaseProperties(type: WriteProperties) { + group = "distribution" + description = "Create the source RELEASE properties file" + + def sourceTarBuildDir = "${buildDir}/sourceTar" + def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE" + outputFile (sourceReleasePropertiesFile) + doFirst { - delete install4jConfFile + releaseProps.each{ key, val -> property key, val } + property "git.branch", gitBranch + property "git.hash", gitHash } + + outputs.file(outputFile) } +task sourceDist(type: Tar) { + group "distribution" + description "Create a source .tar.gz file for distribution" + + dependsOn createBuildProperties + dependsOn convertMdFiles + dependsOn eclipseAllPreferences + dependsOn createSourceReleaseProperties + -task sourceDist (type: Tar) { - def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" - // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09] - try { - archiveFileName = outputFileName - } catch (Exception e) { - archiveName = outputFileName - } + archiveFileName = outputFileName compression Compression.GZIP into project.name - def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*" - ,".*" - ,"benchmarking/*" - ,"**/.*" - ,"*.class" - ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales" - ,"*locales/**", - ,"utils/InstallAnywhere"] - 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","$j11modDir/**/*.jar","appletlib","**/*locales", + "*locales/**", + "utils/InstallAnywhere", + "**/*.log", + "RELEASE", + ] + def PROCESS_FILES=[ + "AUTHORS", + "CITATION", + "FEATURETODO", + "JAVA-11-README", + "FEATURETODO", + "LICENSE", + "**/README", + "THIRDPARTYLIBS", + "TESTNG", + "build.gradle", + "gradle.properties", + "**/*.java", + "**/*.html", + "**/*.xml", + "**/*.gradle", + "**/*.groovy", + "**/*.properties", + "**/*.perl", + "**/*.sh", + ] + def INCLUDE_FILES=[ + ".classpath", + ".settings/org.eclipse.buildship.core.prefs", + ".settings/org.eclipse.jdt.core.prefs" + ] from(jalviewDir) { exclude (EXCLUDE_FILES) @@ -1372,21 +2121,37 @@ task sourceDist (type: Tar) { // exluding these as not using jars as modules yet exclude ("${j11modDir}/**/*.jar") } - // from (jalviewDir) { - // // explicit includes for stuff that seemed to not get included - // include(fileTree("test/**/*.")) - // exclude(EXCLUDE_FILES) - // exclude(PROCESS_FILES) - // } + from(jalviewDir) { + include(INCLUDE_FILES) + } +// from (jalviewDir) { +// // explicit includes for stuff that seemed to not get included +// include(fileTree("test/**/*.")) +// exclude(EXCLUDE_FILES) +// exclude(PROCESS_FILES) +// } + + from(file(buildProperties).getParent()) { + include(file(buildProperties).getName()) + rename(file(buildProperties).getName(), "build_properties") + filter({ line -> + line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]") + }) + } + + def sourceTarBuildDir = "${buildDir}/sourceTar" + from(sourceTarBuildDir) { + // this includes the appended RELEASE properties file + } } -task helppages { +task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("${classes}/${helpDir}") - outputs.dir("${helpOutputDir}") + inputs.dir("${helpBuildDir}/${help_dir}") + outputs.dir("${buildDir}/distributions/${help_dir}") } @@ -1397,6 +2162,33 @@ task j2sSetHeadlessBuild { } +task jalviewjsEnableAltFileProperty(type: WriteProperties) { + group "jalviewjs" + description "Enable the alternative J2S Config file for headless build" + + outputFile = jalviewjsJ2sSettingsFileName + def j2sPropsFile = file(jalviewjsJ2sSettingsFileName) + def j2sProps = new Properties() + if (j2sPropsFile.exists()) { + try { + def j2sPropsFileFIS = new FileInputStream(j2sPropsFile) + j2sProps.load(j2sPropsFileFIS) + j2sPropsFileFIS.close() + + j2sProps.each { prop, val -> + property(prop, val) + } + } catch (Exception e) { + println("Exception reading ${jalviewjsJ2sSettingsFileName}") + e.printStackTrace() + } + } + if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) { + property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property) + } +} + + task jalviewjsSetEclipseWorkspace { def propKey = "jalviewjs_eclipse_workspace" def propVal = null @@ -1411,16 +2203,17 @@ task jalviewjsSetEclipseWorkspace { def eclipseWsDir = propVal def props = new Properties() + def writeProps = true if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) { def ins = new FileInputStream(propsFileName) props.load(ins) ins.close() if (props.getProperty(propKey, null) != null) { eclipseWsDir = props.getProperty(propKey) + writeProps = false } } - def writeProps = false if (eclipseWsDir == null || !file(eclipseWsDir).exists()) { def tempDir = File.createTempDir() eclipseWsDir = tempDir.getAbsolutePath() @@ -1444,6 +2237,9 @@ task jalviewjsSetEclipseWorkspace { props.store(bytes, null) def propertiesString = bytes.toString() propsFile.text = propertiesString + print("NEW ") + } else { + print("EXISTING ") } println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) @@ -1451,7 +2247,7 @@ task jalviewjsSetEclipseWorkspace { //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date outputs.file(propsFileName) - outputs.upToDateWhen { eclipseWorkspace.exists() } + outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() } } @@ -1468,13 +2264,14 @@ task jalviewjsEclipsePaths { eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" } else if (OperatingSystem.current().isWindows()) { // check these paths!! if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { - eclipseRoot += "/eclipse.exe" + eclipseRoot += "/eclipse" } - eclipseBinary = "${eclipseRoot}/eclipse" + eclipseBinary = "${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" @@ -1510,6 +2307,15 @@ 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 @@ -1522,7 +2328,7 @@ 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}/${jalviewjs_eclipse_tmp_dropins_dir}" from inputFiles @@ -1595,13 +2401,12 @@ task jalviewjsTransferUnzipAllLibs { task jalviewjsCreateJ2sSettings(type: WriteProperties) { group "JalviewJS" - description "Create the .j2s file from the j2s.* properties" + description "Create the alternative j2s file from the j2s.* properties" - outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}") - def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } + jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } def siteDirProperty = "j2s.site.directory" def setSiteDir = false - j2s_props.each { prop, val -> + jalviewjsJ2sProps.each { prop, val -> if (val != null) { if (prop == siteDirProperty) { if (!(val.startsWith('/') || val.startsWith("file://") )) { @@ -1612,11 +2417,15 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { property(prop,val) } if (!setSiteDir) { // default site location, don't override specifically set property - property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}") + property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}") } } - inputs.properties(j2s_props) - outputs.file(outputFile) + outputFile = jalviewjsJ2sAltSettingsFileName + + if (! IN_ECLIPSE) { + inputs.properties(jalviewjsJ2sProps) + outputs.file(jalviewjsJ2sAltSettingsFileName) + } } @@ -1643,13 +2452,19 @@ task jalviewjsSyncAllLibs (type: Sync) { preserve { include "**" } + + // should this be exclude really ? + duplicatesStrategy "INCLUDE" + outputs.files outputFiles inputs.files inputFiles } task jalviewjsSyncResources (type: Sync) { - def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}") + dependsOn buildResources + + def inputFiles = fileTree(dir: resourcesBuildDir) def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" from inputFiles @@ -1731,6 +2546,7 @@ task jalviewjsProjectImport(type: Exec) { 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" ] + args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ] } inputs.file("${jalviewDir}/.project") @@ -1744,6 +2560,9 @@ task jalviewjsTranspile(type: Exec) { dependsOn jalviewjsEclipseSetup dependsOn jalviewjsProjectImport dependsOn jalviewjsEclipsePaths + if (!IN_ECLIPSE) { + dependsOn jalviewjsEnableAltFileProperty + } doFirst { // do not run a headless transpile when we claim to be in Eclipse @@ -1763,6 +2582,7 @@ task jalviewjsTranspile(type: Exec) { args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] if (!IN_ECLIPSE) { args += [ "-D${j2sHeadlessBuildProperty}=true" ] + args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ] } def stdout @@ -1790,12 +2610,12 @@ DEBUG: ${eclipseDebug} new org.apache.tools.ant.util.TeeOutputStream( logOutFOS, stdout), - standardOutput) + System.out) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( new org.apache.tools.ant.util.TeeOutputStream( logErrFOS, stderr), - errorOutput) + System.err) } else { standardOutput = new org.apache.tools.ant.util.TeeOutputStream( logOutFOS, @@ -1810,7 +2630,12 @@ 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}'") + } } } @@ -1820,14 +2645,14 @@ 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 ${jsfile}" println(msg) logOutFile.createNewFile() logOutFile.append(msg+"\n") @@ -1836,13 +2661,12 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, def coreBottom = file(suffixFile) coreFile.getParentFile().mkdirs() coreFile.createNewFile() - coreFile.write( coreTop.text ) + coreFile.write( coreTop.getText("UTF-8") ) list.each { f -> if (f.exists()) { - def t = f.text - t.replaceAll("Clazz\\.","Clazz_") - t.replaceAll("Class__","Clazz._") + def t = f.getText("UTF-8") + t.replaceAll("Clazz\\.([^_])","Clazz_${1}") coreFile.append( t ) } else { msg = "...file '"+f.getPath()+"' does not exist, skipping" @@ -1850,7 +2674,7 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, logOutFile.append(msg+"\n") } } - coreFile.append( coreBottom.text ) + coreFile.append( coreBottom.getText("UTF-8") ) msg = "Generating ${zjsfile}" println(msg) @@ -1859,8 +2683,11 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, def logErrFOS = logOutFOS javaexec { - classpath = files(["${jalviewDir}/tools/closure_compiler.jar"]) - args = [ "--js", jsfile, "--js_output_file", zjsfile ] + 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) @@ -1876,7 +2703,7 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, new org.apache.tools.ant.util.TeeOutputStream( logErrFOS, stderr), - errorOutput) + System.err) } else { standardOutput = new org.apache.tools.ant.util.TeeOutputStream( logOutFOS, @@ -1899,6 +2726,8 @@ task jalviewjsBuildAllCores { 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" @@ -1919,17 +2748,17 @@ task jalviewjsBuildAllCores { } // _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_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'] @@ -1947,10 +2776,11 @@ task jalviewjsBuildAllCores { 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) @@ -1960,74 +2790,118 @@ task jalviewjsBuildAllCores { } // _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")+" 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")) } } } -task jalviewjsPublishCoreTemplate(type: Sync) { - dependsOn jalviewjsBuildAllCores +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 ${coreName}]", + 'COREKEY': jalviewjs_core_key, + 'CORENAME': coreName + ] + ) + } +} + - def inputFile = file("${jalviewDir}/${j2s_template_html}") +task jalviewjsPublishCoreTemplates { + dependsOn jalviewjsBuildAllCores + def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}" + def inputFile = file(inputFileName) def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" - from inputFile - into outputDir def outputFiles = [] - jalviewjsJalviewCoreHtmlFile = "${jalviewjsJalviewTemplateName}_${jalviewjsJalviewCoreName}.html" - rename { filename -> - outputFiles += "${outputDir}/${filename}" - if (filename.equals(inputFile.getName())) { - return jalviewjsJalviewCoreHtmlFile - } - return null - } - filter(ReplaceTokens, - beginToken: '_', - endToken: '_', - tokens: [ - 'MAIN': '"'+mainClass+'"', - 'CODE': "null", - 'NAME': jalviewjsJalviewTemplateName - ] - ) - filter(ReplaceTokens, - beginToken: '', - endToken: '', - tokens: [ - 'NONE': jalviewjsJalviewCoreName - ] - ) - preserve { - include "**" + jalviewjsCoreClasslists.each { cl -> + def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html" + cl['outputfile'] = outputFile + outputFiles += outputFile } - outputs.files outputFiles - inputs.files inputFile + + doFirst { + jalviewjsCoreClasslists.each { cl -> + jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile) + } + } + inputs.file(inputFile) + outputs.files(outputFiles) } task jalviewjsSyncCore (type: Sync) { dependsOn jalviewjsBuildAllCores - dependsOn jalviewjsPublishCoreTemplate + dependsOn jalviewjsPublishCoreTemplates def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}") def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" @@ -2095,12 +2969,19 @@ 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}" } } @@ -2111,11 +2992,7 @@ task jalviewjsSiteTar(type: Tar) { description "Creates a tar.gz file for the website" dependsOn jalviewjsBuildSite def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz" - try { - archiveFileName = outputFilename - } catch (Exception e) { - archiveName = outputFilename - } + archiveFileName = outputFilename compression Compression.GZIP @@ -2133,35 +3010,46 @@ task jalviewjsServer { def htmlFile = "${jalviewDirAbsolutePath}/${filename}" doLast { - SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory() + def factory + try { + def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory") + factory = f.newInstance() + } catch (ClassNotFoundException e) { + throw new GradleException("Unable to create SimpleHttpFileServerFactory") + } def port = Integer.valueOf(jalviewjs_server_port) def start = port def running = false def url - def urlcore + def jalviewjsServer while(port < start+1000 && !running) { try { def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") - def jalviewjsServer = factory.start(doc_root, port) + jalviewjsServer = factory.start(doc_root, port) running = true url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource) - urlcore = jalviewjsServer.getResourceUrl(jalviewjsJalviewCoreHtmlFile) 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 core: "+urlcore) - - file(htmlFile).text = """ -

JalviewJS Test. <${url}>

-

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

-

${jalviewjsJalviewTemplateName} Core Test. <${urlcore}>

- """ - + 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 ${cl.name}: "+urlcore) + } + file(htmlFile).text = htmlText } outputs.file(htmlFile) @@ -2181,13 +3069,89 @@ task cleanJalviewjsAll { if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) { delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") } - delete "${jalviewDir}/${jalviewjs_j2s_settings}" + delete jalviewjsJ2sAltSettingsFileName } outputs.upToDateWhen( { false } ) } +task jalviewjsIDE_checkJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)" + + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.") + } + def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ] + def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"] + if (altPluginsDir != null && file(altPluginsDir).exists()) { + eclipseJ2sPluginDirs += altPluginsDir + } + def foundPlugin = false + def j2sPluginFileName = j2sPluginFile.getName() + def eclipseJ2sPlugin + def eclipseJ2sPluginFile + eclipseJ2sPluginDirs.any { dir -> + eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}" + eclipseJ2sPluginFile = file(eclipseJ2sPlugin) + if (eclipseJ2sPluginFile.exists()) { + foundPlugin = true + return true + } + } + if (!foundPlugin) { + def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin" + System.err.println(msg) + throw new StopExecutionException(msg) + } + + def digest = MessageDigest.getInstance("MD5") + + digest.update(j2sPluginFile.text.bytes) + def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + digest.update(eclipseJ2sPluginFile.text.bytes) + def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + if (j2sPluginMd5 != eclipseJ2sPluginMd5) { + def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'" + System.err.println(msg) + throw new StopExecutionException(msg) + } else { + def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' 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" @@ -2203,9 +3167,7 @@ task jalviewjsIDE_SyncCore { } -task jalviewjsIDE_PrepareSite { - group "00 JalviewJS in Eclipse" - description "Sync libs and resources to site dir, but not closure cores" +task jalviewjsIDE_SyncSiteAll { dependsOn jalviewjsSyncAllLibs dependsOn jalviewjsSyncResources dependsOn jalviewjsSyncSiteResources @@ -2213,6 +3175,18 @@ task jalviewjsIDE_PrepareSite { } +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" @@ -2234,25 +3208,25 @@ task jalviewjsIDE_Server { } -// buildship runs this at import -task eclipseConfiguration { - dependsOn eclipseSetup - dependsOn jalviewjsIDE_j2sFile +// 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 +// buildship runs this at build time or project refresh task eclipseAutoBuildTask { - dependsOn jalviewjsIDE_PrepareSite + //dependsOn jalviewjsIDE_checkJ2sPlugin + //dependsOn jalviewjsIDE_PrepareSite } - - - - - - task jalviewjs { group "JalviewJS" description "Build the site"