X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=c3e89e588dad6f3018c376655becd2a32d094b48;hb=4728b1bd60655ad9f269438e505e70f23c9c83f3;hp=ba884a136dd5ff0fa5af7ef8935a827cd1849226;hpb=ca656d98cf6af805074a0e0f50f8b2f67d27fc0a;p=jalview.git diff --git a/build.gradle b/build.gradle index ba884a1..c3e89e5 100644 --- a/build.gradle +++ b/build.gradle @@ -1,305 +1,550 @@ +/* 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.apache.tools.ant.filters.ReplaceRegexp import org.gradle.internal.os.OperatingSystem -import org.gradle.plugins.ide.eclipse.model.* - - +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:4.4.1' - classpath 'org.apache.commons:commons-compress:1.18' + 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.install4j.gradle' version '8.0.4' + id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree + id 'com.palantir.git-version' version '0.12.3' } repositories { jcenter() mavenCentral() mavenLocal() - flatDir { - dirs gradlePluginsDir - } } -mainClassName = launcherClass -def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir") -def classes = "$jalviewDir/$classesDir" -if (clover.equals("true")) { - use_clover = true - classes = "$buildDir/$cloverClassesDir" -} else { - use_clover = false - classes = "$jalviewDir/$classesDir" +// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use +def string(Object o) { + return o == null ? "" : o.toString() } -// configure classpath/args for j8/j11 compilation - -def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() -def libDir -def libDistDir -def compile_source_compatibility -def compile_target_compatibility ext { - getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION - getdownDir = "" - reportRsyncCmd = false + jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() + jalviewDirRelativePath = jalviewDir + + // local build environment properties + // can be "projectDir/local.properties" + def localProps = "${projectDir}/local.properties" + def propsFile = null; + if (file(localProps).exists()) { + propsFile = localProps + } + // or "../projectDir_local.properties" + def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties" + if (file(dirLocalProps).exists()) { + propsFile = dirLocalProps + } + if (propsFile != null) { + try { + def p = new Properties() + def localPropsFIS = new FileInputStream(propsFile) + p.load(localPropsFIS) + localPropsFIS.close() + p.each { + key, val -> + def oldval = findProperty(key) + setProperty(key, val) + if (oldval != null) { + println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") + } else { + println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'") + } + } + } catch (Exception e) { + System.out.println("Exception reading local.properties") + } + } + + //// + // Import releaseProps from the RELEASE file + // or a file specified via JALVIEW_RELEASE_FILE if defined + // Expect jalview.version and target release branch in jalview.release + def releaseProps = new Properties(); + def releasePropFile = findProperty("JALVIEW_RELEASE_FILE"); + def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE"; + try { + (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { + releaseProps.load(it) + } + } catch (Exception fileLoadError) { + throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError); + } + //// + // Set JALVIEW_VERSION if it is not already set + if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) { + JALVIEW_VERSION = releaseProps.get("jalview.version") + } + + // this property set when running Eclipse headlessly + j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild") + // this property set by Eclipse + eclipseApplicationProperty = string("eclipse.application") + // CHECK IF RUNNING FROM WITHIN ECLIPSE + def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty] + IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.") + // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET + if (System.properties[j2sHeadlessBuildProperty].equals("true")) { + println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'") + IN_ECLIPSE = false + } + if (IN_ECLIPSE) { + println("WITHIN ECLIPSE IDE") + } else { + println("HEADLESS BUILD") + } + + J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable") + if (J2S_ENABLED) { + println("J2S ENABLED") + } + /* *-/ + System.properties.sort { it.key }.each { + key, val -> println("SYSTEM PROPERTY ${key}='${val}'") + } + /-* *-/ + if (false && IN_ECLIPSE) { + jalviewDir = jalviewDirAbsolutePath + } + */ + + // essentials + bareSourceDir = string(source_dir) + sourceDir = string("${jalviewDir}/${bareSourceDir}") + resourceDir = string("${jalviewDir}/${resource_dir}") + bareTestSourceDir = string(test_source_dir) + testDir = string("${jalviewDir}/${bareTestSourceDir}") + + classesDir = string("${jalviewDir}/${classes_dir}") + + // clover + useClover = clover.equals("true") + cloverBuildDir = "${buildDir}/clover" + cloverInstrDir = file("${cloverBuildDir}/clover-instr") + cloverClassesDir = file("${cloverBuildDir}/clover-classes") + cloverReportDir = file("${buildDir}/reports/clover") + cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr") + cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes") + //cloverTestClassesDir = cloverClassesDir + cloverDb = string("${cloverBuildDir}/clover.db") + + testSourceDir = useClover ? cloverTestInstrDir : testDir + testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}" + + getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") buildDist = true - buildProperties = buildPropertiesFile - getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher + + // the following values might be overridden by the CHANNEL switch + getdownChannelName = CHANNEL.toLowerCase() + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}") + getdownAppDistDir = getdown_app_dir_alt + reportRsyncCommand = false + jvlChannelName = CHANNEL.toLowerCase() + install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build + install4jDSStore = "DS_Store-NON-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png" + install4jInstallerName = "${jalview_name} Non-Release Installer" + install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase() + install4jExtraScheme = "jalviewx" switch (CHANNEL) { case "BUILD": // TODO: get bamboo build artifact URL for getdown artifacts getdown_channel_base = bamboo_channelbase - getdown_channel_name = bamboo_planKey + '/'+JAVA_VERSION - getdown_app_base = bamboo_channelbase + '/'+ bamboo_planKey + bamboo_getdown_channel_suffix + '/'+JAVA_VERSION - getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}") + getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") + jvlChannelName += "_${getdownChannelName}" + // automatically add the test group Not-bamboo for exclusion + if ("".equals(testng_excluded_groups)) { + testng_excluded_groups = "Not-bamboo" + } + install4jExtraScheme = "jalviewb" break case "RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_release - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + getdownAppDistDir = getdown_app_dir_release reportRsyncCommand = true + install4jSuffix = "" + install4jDSStore = "DS_Store" + install4jDMGBackgroundImage = "jalview_dmg_background.png" + install4jInstallerName = "${jalview_name} Installer" break case "ARCHIVE": - getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - 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}/${package_dir}").exists()) { + throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { - packageDir = ARCHIVEDIR + "/" + packageDir - buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile + package_dir = string("${ARCHIVEDIR}/${package_dir}") + buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true + install4jExtraScheme = "jalviewa" break case "ARCHIVELOCAL": - getdown_channel_name = "archive" + "/" + JALVIEW_VERSION - getdownDir = 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}/${package_dir}").exists()) { + throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { - packageDir = ARCHIVEDIR + "/" + packageDir - buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile + package_dir = string("${ARCHIVEDIR}/${package_dir}") + buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true - getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jSuffix = "Archive" + install4jExtraScheme = "jalviewa" break case "DEVELOP": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile reportRsyncCommand = true + + // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version + JALVIEW_VERSION=JALVIEW_VERSION+"-develop" + + channelPropertiesFile = string("${channel_properties_dir}/develop_properties") + getdownImagesDir = "${getdown_images_dir}/develop" + getdownBgColour = "000000" + getdownFgColour = "FFFFFF" + getdownLightFgColour = "CCCCFF" + install4jSuffix = "Develop" + install4jDSStore = "DS_Store-DEVELOP" + install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png" + install4jExtraScheme = "jalviewd" + install4jInstallerName = "${jalview_name} Develop Installer" + install4jMacIconsFile = string("${install4j_utils_dir}/develop/${install4j_mac_icons_file}") + install4jWindowsIconsFile = string("${install4j_utils_dir}/develop/${install4j_windows_icons_file}") + install4jPngIconFile = string("${install4j_utils_dir}/develop/${install4j_png_icon_file}") break case "TEST-RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile reportRsyncCommand = true + // Don't ignore transpile errors for release build + if (jalviewjs_ignore_transpile_errors.equals("true")) { + jalviewjs_ignore_transpile_errors = "false" + println("Setting jalviewjs_ignore_transpile_errors to 'false'") + } + JALVIEW_VERSION = JALVIEW_VERSION+"-test" + install4jSuffix = "Test" + install4jDSStore = "DS_Store-TEST-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" break case ~/^SCRATCH(|-[-\w]*)$/: - getdown_channel_name = CHANNEL - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + getdownChannelName = CHANNEL + JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL + + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") + getdownAppBase = string("${getdown_channel_base}/${getdownDir}") reportRsyncCommand = true + install4jSuffix = "Scratch" + break + + case "TEST-LOCAL": + if (!file("${LOCALDIR}").exists()) { + throw new GradleException("Must provide a LOCALDIR value to produce a local distribution") + } else { + getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString() + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + } + JALVIEW_VERSION = "TEST" + install4jSuffix = "Test-Local" + install4jDSStore = "DS_Store-TEST-RELEASE" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" + install4jExtraScheme = "jalviewt" + install4jInstallerName = "${jalview_name} Test Installer" break case "LOCAL": - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile - getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local + JALVIEW_VERSION = "TEST" + getdownAppBase = file(getdownWebsiteDir).toURI().toString() + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + install4jExtraScheme = "jalviewl" break default: // something wrong specified - print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") - exit + throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") break } - - println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base) - getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir - //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir - getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir - getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir - getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/' - getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir + // override getdownAppBase if requested + if (findProperty("getdown_appbase_override") != null) { + getdownAppBase = string(getProperty("getdown_appbase_override")) + println("Overriding getdown appbase with '${getdownAppBase}'") + } + // sanitise file name for jalview launcher file for this channel + jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_") + // install4j application and folder names + if (install4jSuffix == "") { + install4jApplicationName = "${jalview_name}" + install4jBundleId = "${install4j_bundle_id}" + install4jWinApplicationId = install4j_release_win_application_id + } else { + install4jApplicationName = "${jalview_name} ${install4jSuffix}" + install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase() + // add int hash of install4jSuffix to the last part of the application_id + def id = install4j_release_win_application_id + def idsplitreverse = id.split("-").reverse() + idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode() + install4jWinApplicationId = idsplitreverse.reverse().join("-") + } + // sanitise folder and id names + // install4jApplicationFolder = e.g. "Jalview Build" + install4jApplicationFolder = install4jApplicationName + .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \ + .replaceAll("_+", "_") // collapse __ + install4jInternalId = install4jApplicationName + .replaceAll(" ","_") + .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] + .replaceAll("_+", "") // collapse __ + //.replaceAll("_*-_*", "-") // collapse _-_ + install4jUnixApplicationFolder = install4jApplicationName + .replaceAll(" ","_") + .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] + .replaceAll("_+", "_") // collapse __ + .replaceAll("_*-_*", "-") // collapse _-_ + .toLowerCase() + + getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}") + //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" + getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}") + getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}") + getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/") + getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}") /* compile without modules -- using classpath libraries - modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"]) + modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) modules_runtimeClasspath = modules_compileClasspath */ - gitHash = "" - gitBranch = "" -} - -def JAVA_INTEGER_VERSION -def additional_compiler_args = [] -// these are getdown.txt properties defined dependent on the JAVA_VERSION -def getdown_alt_java_min_version -def getdown_alt_java_max_version -// this property is assigned below and expanded to multiple lines in the getdown task -def getdown_alt_multi_java_location -// this property is for the Java library used in eclipse -def eclipse_java_runtime_name -if (JAVA_VERSION.equals("1.8")) { - JAVA_INTEGER_VERSION = "8" - //libDir = j8libDir - libDir = j11libDir - libDistDir = j8libDir - compile_source_compatibility = 1.8 - compile_target_compatibility = 1.8 - getdown_alt_java_min_version = getdown_alt_java8_min_version - getdown_alt_java_max_version = getdown_alt_java8_max_version - getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-1.8" -} else if (JAVA_VERSION.equals("11")) { - JAVA_INTEGER_VERSION = "11" - libDir = j11libDir - libDistDir = j11libDir - compile_source_compatibility = 11 - compile_target_compatibility = 11 - getdown_alt_java_min_version = getdown_alt_java11_min_version - getdown_alt_java_max_version = getdown_alt_java11_max_version - getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-11" - /* compile without modules -- using classpath libraries - additional_compiler_args += [ - '--module-path', ext.modules_compileClasspath.asPath, - '--add-modules', j11modules - ] - */ -} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) { - JAVA_INTEGER_VERSION = JAVA_VERSION - libDir = j11libDir - libDistDir = j11libDir - compile_source_compatibility = JAVA_VERSION - compile_target_compatibility = JAVA_VERSION - getdown_alt_java_min_version = getdown_alt_java11_min_version - getdown_alt_java_max_version = getdown_alt_java11_max_version - getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-11" - /* compile without modules -- using classpath libraries - additional_compiler_args += [ - '--module-path', ext.modules_compileClasspath.asPath, - '--add-modules', j11modules - ] - */ -} else { - throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview") + def details = versionDetails() + gitHash = details.gitHash + gitBranch = details.branchName + + println("Using a ${CHANNEL} profile.") + + additional_compiler_args = [] + // configure classpath/args for j8/j11 compilation + if (JAVA_VERSION.equals("1.8")) { + JAVA_INTEGER_VERSION = string("8") + //libDir = j8libDir + libDir = j11libDir + libDistDir = j8libDir + compile_source_compatibility = 1.8 + compile_target_compatibility = 1.8 + // these are getdown.txt properties defined dependent on the JAVA_VERSION + getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version")) + getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version")) + // this property is assigned below and expanded to multiple lines in the getdown task + getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location")) + // this property is for the Java library used in eclipse + eclipseJavaRuntimeName = string("JavaSE-1.8") + } else if (JAVA_VERSION.equals("11")) { + JAVA_INTEGER_VERSION = string("11") + libDir = j11libDir + libDistDir = j11libDir + compile_source_compatibility = 11 + compile_target_compatibility = 11 + getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) + getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version")) + getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location")) + eclipseJavaRuntimeName = string("JavaSE-11") + /* compile without modules -- using classpath libraries + additional_compiler_args += [ + '--module-path', modules_compileClasspath.asPath, + '--add-modules', j11modules + ] + */ + } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) { + JAVA_INTEGER_VERSION = JAVA_VERSION + libDir = j11libDir + libDistDir = j11libDir + compile_source_compatibility = JAVA_VERSION + compile_target_compatibility = JAVA_VERSION + getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) + getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version")) + getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location")) + eclipseJavaRuntimeName = string("JavaSE-11") + /* compile without modules -- using classpath libraries + additional_compiler_args += [ + '--module-path', modules_compileClasspath.asPath, + '--add-modules', j11modules + ] + */ + } else { + throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview") + } + + + // for install4j + JAVA_MIN_VERSION = JAVA_VERSION + JAVA_MAX_VERSION = JAVA_VERSION + def jreInstallsDir = string(jre_installs_dir) + if (jreInstallsDir.startsWith("~/")) { + jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1) + } + macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre") + macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz") + windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre") + windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz") + linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre") + linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz") + install4jDir = string("${jalviewDir}/${install4j_utils_dir}") + install4jConfFileName = string("jalview-install4j-conf.install4j") + install4jConfFile = file("${install4jDir}/${install4jConfFileName}") + install4jHomeDir = install4j_home_dir + if (install4jHomeDir.startsWith("~/")) { + install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1) + } + + resourceBuildDir = string("${buildDir}/resources") + resourcesBuildDir = string("${resourceBuildDir}/resources_build") + helpBuildDir = string("${resourceBuildDir}/help_build") + docBuildDir = string("${resourceBuildDir}/doc_build") + + 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()) + jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs") + jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}") + if (IN_ECLIPSE) { + jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir) + } else { + jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js") + } + jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib") + jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs") + jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core") + jalviewjsJalviewCoreHtmlFile = string("") + jalviewjsJalviewCoreName = string(jalviewjs_core_name) + jalviewjsCoreClasslists = [] + jalviewjsJalviewTemplateName = string(jalviewjs_name) + jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}") + jalviewjsJ2sProps = null + jalviewjsJ2sPlugin = jalviewjs_j2s_plugin + + eclipseWorkspace = null + eclipseBinary = string("") + eclipseVersion = string("") + eclipseDebug = false + // ENDEXT } -sourceSets { +sourceSets { main { java { - srcDirs "$jalviewDir/$sourceDir" - outputDir = file("$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"]) + 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 += fileTree(dir: "$jalviewDir/$libDir", 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: "$jalviewDir/$utilsDir", include: ["**/*.jar"]) - compileClasspath += fileTree(dir: "$jalviewDir/$libDir", 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:4.4.1' - testCompile 'org.openclover:clover:4.4.1' - } } -configurations { - cloverRuntime - cloverRuntime.extendsFrom cloverCompile -} +// eclipse project and settings files creation, also used by buildship eclipse { project { - name = "Jalview with gradle build" + name = eclipse_project_name natures 'org.eclipse.jdt.core.javanature', 'org.eclipse.jdt.groovy.core.groovyNature', @@ -311,130 +556,103 @@ 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 { + plusConfigurations = [ ] + file { - whenMerged { cp -> - def removeTheseToo = [] - HashMap addedSrcPath = new HashMap<>(); - cp.entries.each { entry -> - if (entry.kind == 'src') { - if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) { - removeTheseToo += entry - } else { - addedSrcPath.putAt(entry.path, true) + whenMerged { cp -> + def removeTheseToo = [] + HashMap alreadyAddedSrcPath = new HashMap<>(); + cp.entries.each { entry -> + // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test". + // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover + // we add the resources and help/help dirs in as libs afterwards (see below) + if (entry.kind == 'src') { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) { + removeTheseToo += entry + } else { + alreadyAddedSrcPath.putAt(entry.path, true) + } } - } - } - cp.entries.removeAll(removeTheseToo) - - print ("CP="+cp.inspect()) - - cp.entries += new Output("bin/main") - cp.entries += new Library(fileReference(helpParentDir)) - cp.entries += new Library(fileReference(resourceDir)) - HashMap addedLibPath = new HashMap<>(); - - // changing from sourcesets.main.classpath to specific Java version lib - //sourceSets.main.compileClasspath.each{ - fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each { - //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 - } - def itPath = it.toString() - if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { - itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) - } - if (addedLibPath.get(itPath)) { - //println("Not adding duplicate entry "+itPath) - } else { - //println("Adding entry "+itPath) - cp.entries += new Library(fileReference(itPath)) - addedLibPath.put(itPath, true) } - } + cp.entries.removeAll(removeTheseToo) - // changing from sourcesets.main.classpath to specific Java version lib - //sourceSets.test.compileClasspath.each{ - fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each { - //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) { - //no longer want to add outputDir as eclipse is using its own output dir in bin/main - if (it.isDirectory() || ! it.exists()) { - // don't add dirs to classpath - return false // groovy "break" in .each loop - } - def itPath = it.toString() - if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { - itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) - } - if (addedLibPath.get(itPath)) { - // don't duplicate - } else { - def lib = new Library(fileReference(itPath)) - // this doesn't work... yet. Adding test=true attribute using withXml below - //def attrs = new Node(null, 'attributes', ["test":"true"]) - //lib.appendNode(attrs) // - cp.entries += lib - addedLibPath.put(itPath, true) + //cp.entries += new Output("${eclipse_bin_dir}/main") + if (file(helpParentDir).isDirectory()) { + cp.entries += new Library(fileReference(helpParentDir)) } + if (file(resourceDir).isDirectory()) { + cp.entries += new Library(fileReference(resourceDir)) } - } - // withXml changes ignored by buildship, these add the "test=true" attribute - withXml { - def node = it.asNode() + HashMap alreadyAddedLibPath = new HashMap<>(); - def srcTestAttributes - node.children().each{ cpe -> - def attributes = cpe.attributes() - if (attributes.get("kind") == "src" && attributes.get("path") == "test") { - srcTestAttributes = cpe.find { a -> a.name() == "attributes" } - return + sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any { + //don't want to add outputDir as eclipse is using its own output dir in bin/main + if (it.isDirectory() || ! it.exists()) { + // don't add dirs to classpath, especially if they don't exist + return false // groovy "continue" in .any closure } - } - def addTestAttribute = true - srcTestAttributes.each{a -> - if (a.name() == "attribute" && a.attributes().getAt("name") == "test") { - addTestAttribute = false + def itPath = it.toString() + if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { + // make relative path + itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) + } + if (alreadyAddedLibPath.get(itPath)) { + //println("Not adding duplicate entry "+itPath) + } else { + //println("Adding entry "+itPath) + cp.entries += new Library(fileReference(itPath)) + alreadyAddedLibPath.put(itPath, true) } } - if (addTestAttribute) { - srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"])) - } - node.children().each{ cpe -> - def attributes = cpe.attributes() - if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) { - cpe.appendNode('attributes') - .appendNode('attribute', [name:"test", value:"true"]) + sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { + //no longer want to add outputDir as eclipse is using its own output dir in bin/main + if (it.isDirectory() || ! it.exists()) { + // don't add dirs to classpath + return false // groovy "continue" in .any closure + } + + def itPath = it.toString() + if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { + itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) + } + if (alreadyAddedLibPath.get(itPath)) { + // don't duplicate + } else { + def lib = new Library(fileReference(itPath)) + lib.entryAttributes["test"] = "true" + cp.entries += lib + alreadyAddedLibPath.put(itPath, true) } } - } // withXML + + } // whenMerged + } // file containers 'org.eclipse.buildship.core.gradleclasspathcontainer' + } // classpath jdt { // for the IDE, use java 11 compatibility sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility - javaRuntimeName = eclipse_java_runtime_name + javaRuntimeName = eclipseJavaRuntimeName + // add in jalview project specific properties/preferences into eclipse core preferences file { withProperties { props -> def jalview_prefs = new Properties() - def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file) + def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}") jalview_prefs.load(ins) ins.close() jalview_prefs.forEach { t, v -> @@ -442,340 +660,706 @@ eclipse { props.putAt(t, v) } } + // codestyle file -- overrides previous formatter prefs + def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}") + if (csFile.exists()) { + XmlParser parser = new XmlParser() + def profiles = parser.parse(csFile) + def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") } + if (profile != null) { + profile.'setting'.each { s -> + def id = s.'@id' + def value = s.'@value' + if (id != null && value != null) { + props.putAt(id, value) + } + } + } + } } } - } - //synchronizationTasks eclipseClasspath - //autoBuildTasks eclipseClasspath -} + } // jdt -task cloverInstr() { - // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) - outputs.dir cloverInstrDir + if (IN_ECLIPSE) { + // Don't want these to be activated if in headless build + synchronizationTasks "eclipseSynchronizationTask" + //autoBuildTasks "eclipseAutoBuildTask" - doFirst { - delete cloverInstrDir - def argsList = ["--initstring", "${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 cloverReport { - group = "Verification" - description = "Createst the Clover report" - inputs.dir "${buildDir}/clover" - outputs.dir "${reportsDir}/clover" - onlyIf { - file("${buildDir}/clover/clover.db").exists() - } - doFirst { - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover"] - String[] args = argsList.toArray() - com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) +/* 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("")); } +} - // and generate ${reportsDir}/clover/clover.xml - args = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover/clover.xml"].toArray() - com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) +// Task to update arbitrary properties files (set outputFile) +class PropertiesFileTask extends PropertiesGeneratorTask { + private final PropertiesFileContentMerger file; + public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); } + protected PropertiesFile create() { return new PropertiesFile(getTransformer()); } + protected void configure(PropertiesFile props) { + file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props); } + public void file(Closure closure) { ConfigureUtil.configure(closure, file); } } -// end clover bits - - -compileJava { - - doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") +task eclipseUIPreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.ui.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) + } } - } -compileTestJava { - if (use_clover) { - dependsOn compileCloverJava - classpath += configurations.cloverRuntime - } else { - classpath += sourceSets.main.runtimeClasspath - } - doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") +task eclipseGroovyCorePreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.groovy.core.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) + } } } +task eclipseAllPreferences { + dependsOn eclipseJdt + dependsOn eclipseUIPreferences + dependsOn eclipseGroovyCorePreferences +} + +eclipseUIPreferences.mustRunAfter eclipseJdt +eclipseGroovyCorePreferences.mustRunAfter eclipseJdt + +/* end of eclipse preferences hack */ + + +// clover bits -compileCloverJava { +task cleanClover { doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs += additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") + delete cloverBuildDir + delete cloverReportDir } - classpath += configurations.cloverRuntime } -clean { - delete sourceSets.main.java.outputDir -} -cleanTest { - delete sourceSets.test.java.outputDir - delete cloverInstrDir -} +task cloverInstrJava(type: JavaExec) { + group = "Verification" + description = "Create clover instrumented source java files" -// format is a string like date.format("dd MMMM yyyy") -def getDate(format) { - def date = new Date() - return date.format(format) -} + dependsOn cleanClover -task setGitVals { - def hashStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--short", "HEAD" - standardOutput = hashStdOut - ignoreExitValue true - } + inputs.files(sourceSets.main.allJava) + outputs.dir(cloverInstrDir) - def branchStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" - standardOutput = branchStdOut - ignoreExitValue true - } + //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) + classpath = sourceSets.clover.compileClasspath + main = "com.atlassian.clover.CloverInstr" - project.ext.gitHash = hashStdOut.toString().trim() - project.ext.gitBranch = branchStdOut.toString().trim() + def argsList = [ + "--encoding", + "UTF-8", + "--initstring", + cloverDb, + "--destdir", + cloverInstrDir.getPath(), + ] + def srcFiles = sourceSets.main.allJava.files + argsList.addAll( + srcFiles.collect( + { file -> file.absolutePath } + ) + ) + args argsList.toArray() - outputs.upToDateWhen { false } + doFirst { + delete cloverInstrDir + println("Clover: About to instrument "+srcFiles.size() +" files") + } } -task createBuildProperties(type: WriteProperties) { - dependsOn setGitVals - inputs.dir("$jalviewDir/$sourceDir") - inputs.dir("$classes") - inputs.dir("$jalviewDir/$resourceDir") - 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:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]" - outputs.file(outputFile) -} -def buildingHTML = "$jalviewDir/$docDir/building.html" -task deleteBuildingHTML(type: Delete) { - delete buildingHTML -} +task cloverInstrTests(type: JavaExec) { + group = "Verification" + description = "Create clover instrumented source test files" -task convertBuildingMD(type: Exec) { - dependsOn deleteBuildingHTML - def buildingMD = "$jalviewDir/$docDir/building.md" - def css = "$jalviewDir/$docDir/github.css" + dependsOn cleanClover - def pandoc = null - pandoc_exec.split(",").each { - if (file(it.trim()).exists()) { - pandoc = it.trim() - return true - } - } + inputs.files(testDir) + outputs.dir(cloverTestInstrDir) - 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" - } + 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 { - 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 cloverTestInstrDir + println("Clover: About to instrument test files") } +} - ignoreExitValue true - inputs.file(buildingMD) - inputs.file(css) - outputs.file(buildingHTML) -} -clean { - delete buildingHTML +task cloverInstr { + group = "Verification" + description = "Create clover instrumented all source files" + + dependsOn cloverInstrJava + dependsOn cloverInstrTests } -task syncDocs(type: Sync) { - dependsOn convertBuildingMD - def syncDir = "$classes/$docDir" - from fileTree("$jalviewDir/$docDir") - into syncDir -} +cloverClasses.dependsOn cloverInstr -def helpFile = "$classes/$helpDir/help.jhm" -task copyHelp(type: Copy) { - def inputDir = "$jalviewDir/$helpParentDir/$helpDir" - def outputDir = "$classes/$helpDir" - from(inputDir) { - exclude '**/*.gif' - exclude '**/*.jpg' - exclude '**/*.png' - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) - } - from(inputDir) { - include '**/*.gif' - include '**/*.jpg' - include '**/*.png' +task cloverConsoleReport(type: JavaExec) { + group = "Verification" + description = "Creates clover console report" + + onlyIf { + file(cloverDb).exists() } - into outputDir - inputs.dir(inputDir) - outputs.files(helpFile) - outputs.dir(outputDir) -} + inputs.dir cloverClassesDir -task syncLib(type: Sync) { - def syncDir = "$classes/$libDistDir" - from fileTree("$jalviewDir/$libDistDir") - into syncDir -} + classpath = sourceSets.clover.runtimeClasspath + main = "com.atlassian.clover.reporters.console.ConsoleReporter" -task syncResources(type: Sync) { - from "$jalviewDir/$resourceDir" - include "**/*.*" - exclude "install4j" - into "$classes" - preserve { - include "**" + if (cloverreport_mem.length() > 0) { + maxHeapSize = cloverreport_mem + } + if (cloverreport_jvmargs.length() > 0) { + jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } -} -task prepare { - dependsOn syncResources - dependsOn syncDocs - dependsOn copyHelp + def argsList = [ + "--alwaysreport", + "--initstring", + cloverDb, + "--unittests" + ] + + args argsList.toArray() } -//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir -test { - dependsOn prepare - dependsOn compileJava - if (use_clover) { - dependsOn cloverInstr +task cloverHtmlReport(type: JavaExec) { + group = "Verification" + description = "Creates clover HTML report" + + onlyIf { + file(cloverDb).exists() } - if (use_clover) { - print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") + def cloverHtmlDir = cloverReportDir + inputs.dir cloverClassesDir + outputs.dir cloverHtmlDir + + classpath = sourceSets.clover.runtimeClasspath + main = "com.atlassian.clover.reporters.html.HtmlReporter" + + if (cloverreport_mem.length() > 0) { + maxHeapSize = cloverreport_mem + } + if (cloverreport_jvmargs.length() > 0) { + jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) } - useTestNG() { - includeGroups testngGroups - preserveOrder true - useDefaultListeners=true + def argsList = [ + "--alwaysreport", + "--initstring", + cloverDb, + "--outputdir", + cloverHtmlDir + ] + + if (cloverreport_html_options.length() > 0) { + argsList += cloverreport_html_options.split(" ") } - workingDir = jalviewDir - //systemProperties 'clover.jar' System.properties.clover.jar - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - jvmArgs += additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") + args argsList.toArray() } -task buildIndices(type: JavaExec) { - dependsOn copyHelp - classpath = sourceSets.main.compileClasspath - main = "com.sun.java.help.search.Indexer" - workingDir = "$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("$workingDir/JavaHelpSearch/TMAP") -} +task cloverXmlReport(type: JavaExec) { + group = "Verification" + description = "Creates clover XML report" -task compileLinkCheck(type: JavaCompile) { - options.fork = true - classpath = files("$jalviewDir/$utilsDir") - destinationDir = file("$jalviewDir/$utilsDir") - source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) + onlyIf { + file(cloverDb).exists() + } - inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java") - inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java") - outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class") - outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class") -} + def cloverXmlFile = "${cloverReportDir}/clover.xml" + inputs.dir cloverClassesDir + outputs.file cloverXmlFile -def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch") -task linkCheck(type: JavaExec) { - dependsOn prepare, compileLinkCheck - classpath = files("$jalviewDir/$utilsDir") - main = "HelpLinksChecker" - workingDir = jalviewDir - def help = "$classes/$helpDir" - args = [ "$classes/$helpDir", "-nointernet" ] + classpath = sourceSets.clover.runtimeClasspath + main = "com.atlassian.clover.reporters.xml.XMLReporter" - doLast { - helplinkscheckertouchfile.createNewFile() + if (cloverreport_mem.length() > 0) { + maxHeapSize = cloverreport_mem + } + if (cloverreport_jvmargs.length() > 0) { + jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) + } + + def argsList = [ + "--alwaysreport", + "--initstring", + cloverDb, + "--outfile", + cloverXmlFile + ] + + if (cloverreport_xml_options.length() > 0) { + argsList += cloverreport_xml_options.split(" ") } - inputs.dir("$classes/$helpDir") - outputs.file(helplinkscheckertouchfile) + args argsList.toArray() } -// import the pubhtmlhelp target -ant.properties.basedir = "$jalviewDir" -ant.properties.helpBuildDir = jalviewDirAbsolutePath+"/$classes/$helpDir" -ant.importBuild "$utilsDir/publishHelp.xml" +task cloverReport { + group = "Verification" + description = "Creates clover reports" -task cleanPackageDir(type: Delete) { - delete fileTree("$jalviewDir/$packageDir").include("*.jar") + dependsOn cloverXmlReport + dependsOn cloverHtmlReport } -jar { - dependsOn linkCheck - dependsOn buildIndices - dependsOn createBuildProperties + +compileCloverJava { + + doFirst { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs += additional_compiler_args + print ("Setting target compatibility to "+targetCompatibility+"\n") + } + //classpath += configurations.cloverRuntime +} +// end clover bits + + +compileJava { + // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ? + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs = additional_compiler_args + options.encoding = "UTF-8" + doFirst { + print ("Setting target compatibility to "+compile_target_compatibility+"\n") + } + +} + + +compileTestJava { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs = additional_compiler_args + doFirst { + print ("Setting target compatibility to "+targetCompatibility+"\n") + } +} + + +clean { + doFirst { + delete sourceSets.main.java.outputDir + } +} + + +cleanTest { + dependsOn cleanClover + doFirst { + delete sourceSets.test.java.outputDir + } +} + + +// format is a string like date.format("dd MMMM yyyy") +def getDate(format) { + def date = new Date() + return date.format(format) +} + + +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 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(/\..*?$/, ".html") + htmlFiles.add(file(htmlFilePath)) + } + outputs.files(htmlFiles) +} + + +task copyHelp(type: Copy) { + def inputDir = helpSourceDir + def outputDir = "${helpBuildDir}/${help_dir}" + from(inputDir) { + include('**/*.txt') + include('**/*.md') + include('**/*.html') + include('**/*.hs') + include('**/*.xml') + include('**/*.jhm') + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) + } + from(inputDir) { + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.hs') + exclude('**/*.xml') + exclude('**/*.jhm') + } + into outputDir + + inputs.dir(inputDir) + outputs.files(helpFile) + outputs.dir(outputDir) +} + + +task copyResources(type: Copy) { + 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 createBuildProperties(type: WriteProperties) { + dependsOn copyResources + group = "build" + description = "Create the ${buildProperties} file" + + inputs.dir(sourceDir) + inputs.dir(resourcesBuildDir) + outputFile (buildProperties) + // taking time specific comment out to allow better incremental builds + comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") + //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") + property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") + property "VERSION", JALVIEW_VERSION + property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" + outputs.file(outputFile) +} + + +task buildIndices(type: JavaExec) { + dependsOn copyHelp + classpath = sourceSets.main.compileClasspath + main = "com.sun.java.help.search.Indexer" + workingDir = "${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 prepare { + dependsOn copyResources + dependsOn copyDocs + dependsOn copyHelp + dependsOn createBuildProperties + dependsOn convertMdFiles + dependsOn buildIndices +} + + +compileJava.dependsOn prepare +run.dependsOn compileJava +//run.dependsOn prepare + + +//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir +test { + dependsOn prepare + + if (useClover) { + dependsOn cloverClasses + } else { //? + dependsOn compileJava //? + } + + useTestNG() { + includeGroups testng_groups + excludeGroups testng_excluded_groups + preserveOrder true + useDefaultListeners=true + } + + maxHeapSize = "1024m" + + workingDir = jalviewDir + def testLaf = project.findProperty("test_laf") + if (testLaf != null) { + println("Setting Test LaF to '${testLaf}'") + systemProperty "laf", testLaf + } + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + jvmArgs += additional_compiler_args + + doFirst { + if (useClover) { + println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover") + } + } +} + + +task compileLinkCheck(type: JavaCompile) { + options.fork = true + classpath = files("${jalviewDir}/${utils_dir}") + destinationDir = file("${jalviewDir}/${utils_dir}") + source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) + + inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") + inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") + outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class") + outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class") +} + + +task linkCheck(type: JavaExec) { + dependsOn prepare + dependsOn compileLinkCheck + + def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out") + classpath = files("${jalviewDir}/${utils_dir}") + main = "HelpLinksChecker" + workingDir = jalviewDir + 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) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + outFOS, + errorOutput) + + inputs.dir(helpBuildDir) + outputs.file(helpLinksCheckerOutFile) +} + + +// import the pubhtmlhelp target +ant.properties.basedir = "${jalviewDir}" +ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}" +ant.importBuild "${utils_dir}/publishHelp.xml" + + +task cleanPackageDir(type: Delete) { + doFirst { + delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar") + } +} + + +jar { + dependsOn prepare + dependsOn linkCheck 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" + destinationDirectory = file("${jalviewDir}/${package_dir}") + archiveFileName = rootProject.name+".jar" exclude "cache*/**" exclude "*.jar" @@ -783,24 +1367,31 @@ 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("${destinationDirectory}/${archiveFileName}") } + task copyJars(type: Copy) { - from fileTree("$classes").include("**/*.jar").include("*.jar").files - into "$jalviewDir/$packageDir" + from fileTree(dir: classesDir, include: "**/*.jar").files + into "${jalviewDir}/${package_dir}" } + // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well task syncJars(type: Sync) { - from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files - into "$jalviewDir/$packageDir" + dependsOn jar + from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files + into "${jalviewDir}/${package_dir}" preserve { - include jar.archiveName + include jar.archiveFileName.getOrNull() } } + task makeDist { group = "build" description = "Put all required libraries in dist" @@ -810,32 +1401,37 @@ task makeDist { dependsOn cleanPackageDir dependsOn syncJars dependsOn jar - outputs.dir("$jalviewDir/$packageDir") + outputs.dir("${jalviewDir}/${package_dir}") } + task cleanDist { dependsOn cleanPackageDir dependsOn cleanTest dependsOn clean } + shadowJar { group = "distribution" + description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar" if (buildDist) { dependsOn makeDist } - from ("$jalviewDir/$libDistDir") { + from ("${jalviewDir}/${libDistDir}") { include("*.jar") } manifest { - attributes 'Implementation-Version': JALVIEW_VERSION + attributes "Implementation-Version": JALVIEW_VERSION, + "Application-Name": install4jApplicationName } - mainClassName = shadowJarMainClass + mainClassName = shadow_jar_main_class mergeServiceFiles() classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION minimize() } + task getdownWebsite() { group = "distribution" description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer" @@ -843,41 +1439,46 @@ task getdownWebsite() { dependsOn makeDist } - // clean the getdown website and files dir before creating getdown folders - delete project.ext.getdownWebsiteDir - delete project.ext.getdownFilesDir - def getdownWebsiteResourceFilenames = [] def getdownTextString = "" - def getdownResourceDir = project.ext.getdownResourceDir - def getdownAppDir = project.ext.getdownAppDir + def getdownResourceDir = getdownResourceDir def getdownResourceFilenames = [] doFirst { + // clean the getdown website and files dir before creating getdown folders + delete getdownWebsiteDir + delete getdownFilesDir + copy { from buildProperties - rename(buildPropertiesFile, getdown_build_properties) - into project.ext.getdownAppDir + rename(build_properties_file, getdown_build_properties) + into getdownAppDir } - getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties + getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" - // go through properties looking for getdown_txt_... + // set some getdown_txt_ properties then go through all properties looking for getdown_txt_... def props = project.properties.sort { it.key } - if (getdown_alt_java_min_version.length() > 0) { - props.put("getdown_txt_java_min_version", getdown_alt_java_min_version) - } - if (getdown_alt_java_max_version.length() > 0) { - props.put("getdown_txt_java_max_version", getdown_alt_java_max_version) - } - props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location) - - props.put("getdown_txt_appbase", getdown_app_base) + if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) { + props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion) + } + if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) { + props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion) + } + if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) { + props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) + } + + props.put("getdown_txt_title", jalview_name) + props.put("getdown_txt_ui.name", install4jApplicationName) + + // start with appbase + getdownTextString += "appbase = ${getdownAppBase}\n" props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { if (prop.startsWith("getdown_txt_multi_")) { def key = prop.substring(18) val.split(",").each{ v -> - def line = key + " = " + v + "\n" + def line = "${key} = ${v}\n" getdownTextString += line } } else { @@ -889,16 +1490,16 @@ task getdownWebsite() { r = file(val) } else if (val.indexOf('/') > 0) { // relative path (relative to jalviewDir) - r = file( jalviewDir + '/' + val ) + r = file( "${jalviewDir}/${val}" ) } if (r.exists()) { - val = getdown_resource_dir + '/' + r.getName() + val = "${getdown_resource_dir}/" + r.getName() getdownWebsiteResourceFilenames += val getdownResourceFilenames += r.getPath() } } if (! prop.startsWith("getdown_txt_resource")) { - def line = prop.substring(12) + " = " + val + "\n" + def line = prop.substring(12) + " = ${val}\n" getdownTextString += line } } @@ -906,17 +1507,17 @@ task getdownWebsite() { } getdownWebsiteResourceFilenames.each{ filename -> - getdownTextString += "resource = "+filename+"\n" + getdownTextString += "resource = ${filename}\n" } getdownResourceFilenames.each{ filename -> copy { from filename - into project.ext.getdownResourceDir + into getdownResourceDir } } 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 @@ -925,24 +1526,26 @@ task getdownWebsite() { } } codeFiles.sort().each{f -> - def line = "code = " + getdown_app_dir + '/' + f.getName() + "\n" + def name = f.getName() + def line = "code = ${getdownAppDistDir}/${name}\n" getdownTextString += line copy { from f.getPath() - into project.ext.getdownAppDir + into getdownAppDir } } // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist /* if (JAVA_VERSION.equals("11")) { - def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles() + def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles() j11libFiles.sort().each{f -> - def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n" + def name = f.getName() + def line = "code = ${getdown_j11lib_dir}/${name}\n" getdownTextString += line copy { from f.getPath() - into project.ext.getdownJ11libDir + into getdownJ11libDir } } } @@ -950,19 +1553,20 @@ 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 += "resource = ${getdown_launcher_new}\n" + getdownTextString += "class = ${main_class}\n" - def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt") + def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) - def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl) - launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) + def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl" + def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}") + launchJvl.write("appbase=${getdownAppBase}") copy { from getdownLauncher rename(file(getdownLauncher).getName(), getdown_launcher_new) - into project.ext.getdownWebsiteDir + into getdownWebsiteDir } copy { @@ -970,14 +1574,14 @@ task getdownWebsite() { if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } - into project.ext.getdownWebsiteDir + into getdownWebsiteDir } if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { copy { from getdown_txt from getdownLauncher - from getdownWebsiteDir+"/"+getdown_build_properties + from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } @@ -992,9 +1596,9 @@ task getdownWebsite() { copy { from getdown_txt - from launch_jvl + from launchJvl from getdownLauncher - from getdownWebsiteDir+"/"+getdown_build_properties + from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } @@ -1002,39 +1606,59 @@ task getdownWebsite() { } copy { - from getdownResourceDir - into project.ext.getdownFilesDir + '/' + getdown_resource_dir + from getdownResourceDir + into "${getdownFilesDir}/${getdown_resource_dir}" } } 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 } - outputs.dir(project.ext.getdownWebsiteDir) - outputs.dir(project.ext.getdownFilesDir) + 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 project.ext.getdownWebsiteDir - inputs.dir(project.ext.getdownWebsiteDir) - outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt") + args getdownWebsiteDir + inputs.dir(getdownWebsiteDir) + outputs.file("${getdownWebsiteDir}/digest2.txt") } + task getdown() { group = "distribution" description = "Create the minimal and full getdown app folder for installers and website and create digest file" dependsOn getdownDigest doLast { if (reportRsyncCommand) { - def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/") - def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/") + def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/') + def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/') println "LIKELY RSYNC COMMAND:" println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'" if (RUNRSYNC == "true") { @@ -1049,189 +1673,306 @@ task getdown() { } } -clean { - delete project.ext.getdownWebsiteDir - delete project.ext.getdownFilesDir -} -install4j { - def install4jHomeDir = "/opt/install4j" - def hostname = "hostname".execute().text.trim() - if (hostname.equals("jv-bamboo")) { - 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 - } +tasks.withType(JavaCompile) { + options.encoding = 'UTF-8' } -def install4jConf -def macosJavaVMDir -def macosJavaVMTgz -def windowsJavaVMDir -def windowsJavaVMTgz -def install4jDir = "$jalviewDir/$install4jResourceDir" -def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j" -install4jConf = "$install4jDir/$install4jConfFile" - -task copyInstall4jTemplate(type: Copy) { - macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre" - macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz" - windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre" - windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz" - from (install4jDir) { - include install4jTemplate - rename (install4jTemplate, install4jConfFile) - filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION]) - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', - tokens: [ - 'JAVA_VERSION': JAVA_VERSION, - 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, - 'VERSION': JALVIEW_VERSION, - 'MACOS_JAVA_VM_DIR': macosJavaVMDir, - 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, - 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, - 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, - 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations, - 'COPYRIGHT_MESSAGE': install4jCopyrightMessage, - 'MACOS_BUNDLE_ID': install4jMacOSBundleId, - 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, - 'GETDOWN_DIST_DIR': getdown_app_dir, - 'GETDOWN_ALT_DIR': getdown_app_dir_alt, - 'GETDOWN_INSTALL_DIR': getdown_install_dir - ] - ) - if (OSX_KEYPASS=="") { - filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"']) - filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor']) - } - } - into install4jDir - outputs.files(install4jConf) - doLast { - // include file associations in installer - def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerFileAssociationsXml, - file: install4jConf - ) - /* - // include uninstaller applescript app files in dmg - def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerDMGUninstallerXml, - file: install4jConf - ) - */ +clean { + doFirst { + delete getdownWebsiteDir + delete getdownFilesDir } } -task installers(type: com.install4j.gradle.Install4jTask) { - group = "distribution" - description = "Create the install4j installers" - dependsOn getdown - dependsOn copyInstall4jTemplate - projectFile = file(install4jConf) - println("Using projectFile "+projectFile) - variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH] - destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION" - buildSelected = true - - if (OSX_KEYPASS) { - macKeystorePassword=OSX_KEYPASS +install4j { + if (file(install4jHomeDir).exists()) { + // good to go! + } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) { + install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" + } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) { + install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app" } + installDir(file(install4jHomeDir)) - inputs.dir(project.ext.getdownWebsiteDir) - inputs.file(install4jConf) - inputs.dir(macosJavaVMDir) - inputs.dir(windowsJavaVMDir) - outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION") - + mediaTypes = Arrays.asList(install4j_media_types.split(",")) } -clean { - delete install4jConf -} -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 +task copyInstall4jTemplate { + def install4jTemplateFile = file("${install4jDir}/${install4j_template}") + def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}") + inputs.file(install4jTemplateFile) + inputs.file(install4jFileAssociationsFile) + inputs.property("CHANNEL", { CHANNEL }) + outputs.file(install4jConfFile) + + doLast { + def install4jConfigXml = new XmlParser().parse(install4jTemplateFile) + + // turn off code signing if no OSX_KEYPASS + if (OSX_KEYPASS == "") { + install4jConfigXml.'**'.codeSigning.each { codeSigning -> + codeSigning.'@macEnabled' = "false" + } + install4jConfigXml.'**'.windows.each { windows -> + windows.'@runPostProcessor' = "false" + } + } + + // turn off checksum creation for LOCAL channel + def e = install4jConfigXml.application[0] + if (CHANNEL == "LOCAL") { + e.'@createChecksums' = "false" + } else { + e.'@createChecksums' = "true" + } + + // put file association actions where placeholder action is + def install4jFileAssociationsText = install4jFileAssociationsFile.text + def fileAssociationActions = new XmlParser().parseText("${install4jFileAssociationsText}") + install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true + if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') { + def parent = a.parent() + parent.remove(a) + fileAssociationActions.each { faa -> + parent.append(faa) + } + // don't need to continue in .any loop once replacements have been made + return true + } + } + + // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else + // NB we're deleting the /other/ one! + // Also remove the examples subdir from non-release versions + def customizedIdToDelete = "PROGRAM_GROUP_RELEASE" + // 2.11.1.0 NOT releasing with the Examples folder in the Program Group + if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel + customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE" + } else { + // remove the examples subdir from Full File Set + def files = install4jConfigXml.files[0] + def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" } + def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' } + def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' } + def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" } + dirEntry.parent().remove(dirEntry) + } + install4jConfigXml.'**'.action.any { a -> + if (a.'@customizedId' == customizedIdToDelete) { + def parent = a.parent() + parent.remove(a) + return true + } + } + + // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores + if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) { + def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" } + symlink.parent().remove(symlink) + } + + // write install4j file + install4jConfFile.text = XmlUtil.serialize(install4jConfigXml) + } +} + + +clean { + doFirst { + delete install4jConfFile + } +} + + +task installers(type: com.install4j.gradle.Install4jTask) { + group = "distribution" + description = "Create the install4j installers" + dependsOn getdown + dependsOn copyInstall4jTemplate + + projectFile = install4jConfFile + + // create an md5 for the input files to use as version for install4j conf file + def digest = MessageDigest.getInstance("MD5") + digest.update( + (file("${install4jDir}/${install4j_template}").text + + file("${install4jDir}/${install4j_info_plist_file_associations}").text + + file("${install4jDir}/${install4j_installer_file_associations}").text).bytes) + def filesMd5 = new BigInteger(1, digest.digest()).toString(16) + if (filesMd5.length() >= 8) { + filesMd5 = filesMd5.substring(0,8) + } + def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}" + // make install4jBuildDir relative to jalviewDir + def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}" + + variables = [ + 'JALVIEW_NAME': jalview_name, + 'JALVIEW_APPLICATION_NAME': install4jApplicationName, + 'JALVIEW_DIR': "../..", + 'OSX_KEYSTORE': OSX_KEYSTORE, + 'JSIGN_SH': JSIGN_SH, + 'JRE_DIR': getdown_app_dir_java, + 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion, + 'JALVIEW_VERSION': JALVIEW_VERSION, + 'JAVA_MIN_VERSION': JAVA_MIN_VERSION, + 'JAVA_MAX_VERSION': JAVA_MAX_VERSION, + 'JAVA_VERSION': JAVA_VERSION, + 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, + 'VERSION': JALVIEW_VERSION, + 'MACOS_JAVA_VM_DIR': macosJavaVMDir, + 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, + 'LINUX_JAVA_VM_DIR': linuxJavaVMDir, + 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, + 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, + 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, + 'COPYRIGHT_MESSAGE': install4j_copyright_message, + 'BUNDLE_ID': install4jBundleId, + 'INTERNAL_ID': install4jInternalId, + 'WINDOWS_APPLICATION_ID': install4jWinApplicationId, + 'MACOS_DS_STORE': install4jDSStore, + 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage, + 'INSTALLER_NAME': install4jInstallerName, + 'INSTALL4J_UTILS_DIR': install4j_utils_dir, + 'GETDOWN_WEBSITE_DIR': getdown_website_dir, + 'GETDOWN_FILES_DIR': getdown_files_dir, + 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, + 'GETDOWN_DIST_DIR': getdownAppDistDir, + 'GETDOWN_ALT_DIR': getdown_app_dir_alt, + 'GETDOWN_INSTALL_DIR': getdown_install_dir, + 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations, + 'BUILD_DIR': install4jBuildDir, + 'APPLICATION_CATEGORIES': install4j_application_categories, + 'APPLICATION_FOLDER': install4jApplicationFolder, + 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder, + 'EXECUTABLE_NAME': install4jExecutableName, + 'EXTRA_SCHEME': install4jExtraScheme, + ] + + //println("INSTALL4J VARIABLES:") + //variables.each{k,v->println("${k}=${v}")} + + destination = "${jalviewDir}/${install4jBuildDir}" + buildSelected = true + + if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) { + faster = true + disableSigning = true + } + + if (OSX_KEYPASS) { + macKeystorePassword = OSX_KEYPASS + } + + doFirst { + println("Using projectFile "+projectFile) + } + + inputs.dir(getdownWebsiteDir) + inputs.file(install4jConfFile) + inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") + inputs.dir(macosJavaVMDir) + inputs.dir(windowsJavaVMDir) + outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}") +} + + +spotless { + java { + eclipse().configFile(eclipse_codestyle_file) } +} + + +task sourceDist(type: Tar) { + group "distribution" + description "Create a source .tar.gz file for distribution" + + dependsOn convertMdFiles + + def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") + def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" + archiveFileName = outputFileName compression Compression.GZIP into project.name - def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*" - ,".*" - ,"benchmarking/*" - ,"**/.*" - ,"*.class" - ,"**/*.class","$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", + ] + def PROCESS_FILES=[ + "AUTHORS", + "CITATION", + "FEATURETODO", + "JAVA-11-README", + "FEATURETODO", + "LICENSE", + "**/README", + "RELEASE", + "THIRDPARTYLIBS", + "TESTNG", + "build.gradle", + "gradle.properties", + "**/*.java", + "**/*.html", + "**/*.xml", + "**/*.gradle", + "**/*.groovy", + "**/*.properties", + "**/*.perl", + "**/*.sh", + ] + def INCLUDE_FILES=[ + ".settings/org.eclipse.jdt.core.jalview.prefs", + ] from(jalviewDir) { exclude (EXCLUDE_FILES) include (PROCESS_FILES) - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) } from(jalviewDir) { exclude (EXCLUDE_FILES) exclude (PROCESS_FILES) - exclude ("appletlib") - exclude ("**/*locales") - exclude ("*locales/**") - exclude ("utils/InstallAnywhere") + exclude ("appletlib") + exclude ("**/*locales") + exclude ("*locales/**") + exclude ("utils/InstallAnywhere") exclude (getdown_files_dir) - exclude (getdown_website_dir) + exclude (getdown_website_dir) - // exluding these as not using jars as modules yet - exclude ("$j11modDir/**/*.jar") -} + // exluding these as not using jars as modules yet + exclude ("${j11modDir}/**/*.jar") + } + from(jalviewDir) { + include(INCLUDE_FILES) + } // from (jalviewDir) { // // explicit includes for stuff that seemed to not get included // include(fileTree("test/**/*.")) @@ -1240,10 +1981,1046 @@ task sourceDist (type: Tar) { // } } -task helppages { + +task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("$classes/$helpDir") - outputs.dir("$helpOutputDir") + inputs.dir("${helpBuildDir}/${help_dir}") + outputs.dir("${buildDir}/distributions/${help_dir}") +} + + +task j2sSetHeadlessBuild { + doFirst { + IN_ECLIPSE = false + } +} + + +task jalviewjsSetEclipseWorkspace { + def propKey = "jalviewjs_eclipse_workspace" + def propVal = null + if (project.hasProperty(propKey)) { + propVal = project.getProperty(propKey) + if (propVal.startsWith("~/")) { + propVal = System.getProperty("user.home") + propVal.substring(1) + } + } + def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}" + def propsFile = file(propsFileName) + def eclipseWsDir = propVal + def props = new Properties() + + def writeProps = true + if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) { + def ins = new FileInputStream(propsFileName) + props.load(ins) + ins.close() + if (props.getProperty(propKey, null) != null) { + eclipseWsDir = props.getProperty(propKey) + writeProps = false + } + } + + if (eclipseWsDir == null || !file(eclipseWsDir).exists()) { + def tempDir = File.createTempDir() + eclipseWsDir = tempDir.getAbsolutePath() + writeProps = true + } + eclipseWorkspace = file(eclipseWsDir) + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + + if (writeProps) { + props.setProperty(propKey, eclipseWsDir) + propsFile.parentFile.mkdirs() + def bytes = new ByteArrayOutputStream() + props.store(bytes, null) + def propertiesString = bytes.toString() + propsFile.text = propertiesString + print("NEW ") + } else { + print("EXISTING ") + } + + println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) + } + + //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date + outputs.file(propsFileName) + outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() } +} + + +task jalviewjsEclipsePaths { + def eclipseProduct + + def eclipseRoot = jalviewjs_eclipse_root + if (eclipseRoot.startsWith("~/")) { + eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1) + } + if (OperatingSystem.current().isMacOsX()) { + eclipseRoot += "/Eclipse.app" + eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse" + eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" + } else if (OperatingSystem.current().isWindows()) { // check these paths!! + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { + eclipseRoot += "/eclipse" + } + eclipseBinary = "${eclipseRoot}/eclipse.exe" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" + } else { // linux or unix + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { + eclipseRoot += "/eclipse" +println("eclipseDir exists") + } + eclipseBinary = "${eclipseRoot}/eclipse" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" + } + + eclipseVersion = "4.13" // default + def assumedVersion = true + if (file(eclipseProduct).exists()) { + def fis = new FileInputStream(eclipseProduct) + def props = new Properties() + props.load(fis) + eclipseVersion = props.getProperty("version") + fis.close() + assumedVersion = false + } + + def propKey = "eclipse_debug" + eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true")) + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + + if (!assumedVersion) { + println("ECLIPSE VERSION=${eclipseVersion}") + } + } +} + + +task printProperties { + group "Debug" + description "Output to console all System.properties" + doFirst { + System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") } + } +} + + +task eclipseSetup { + dependsOn eclipseProject + dependsOn eclipseClasspath + dependsOn eclipseJdt +} + + +// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir +task jalviewjsEclipseCopyDropins(type: Copy) { + dependsOn jalviewjsEclipsePaths + + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") + inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}") + def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" + + from inputFiles + into outputDir +} + + +// this eclipse -clean doesn't actually work +task jalviewjsCleanEclipse(type: Exec) { + dependsOn eclipseSetup + dependsOn jalviewjsEclipsePaths + dependsOn jalviewjsEclipseCopyDropins + + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"]) + if (eclipseDebug) { + args += "-debug" + } + args += "-l" + + def inputString = """exit +y +""" + def inputByteStream = new ByteArrayInputStream(inputString.getBytes()) + standardInput = inputByteStream +} + +/* not really working yet +jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse +*/ + + +task jalviewjsTransferUnzipSwingJs { + def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}" + + doLast { + copy { + from zipTree(file_zip) + into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" + } + } + + inputs.file file_zip + outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" +} + + +task jalviewjsTransferUnzipLib { + def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip") + + doLast { + zipFiles.each { file_zip -> + copy { + from zipTree(file_zip) + into "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + } + } + } + + inputs.files zipFiles + outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}" +} + + +task jalviewjsTransferUnzipAllLibs { + dependsOn jalviewjsTransferUnzipSwingJs + dependsOn jalviewjsTransferUnzipLib +} + + +task jalviewjsCreateJ2sSettings(type: WriteProperties) { + group "JalviewJS" + description "Create the .j2s file from the j2s.* properties" + + jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } + def siteDirProperty = "j2s.site.directory" + def setSiteDir = false + jalviewjsJ2sProps.each { prop, val -> + if (val != null) { + if (prop == siteDirProperty) { + if (!(val.startsWith('/') || val.startsWith("file://") )) { + val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}" + } + setSiteDir = true + } + property(prop,val) + } + if (!setSiteDir) { // default site location, don't override specifically set property + property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}") + } + } + outputFile = jalviewjsJ2sSettingsFileName + + if (! IN_ECLIPSE) { + inputs.properties(jalviewjsJ2sProps) + outputs.file(jalviewjsJ2sSettingsFileName) + } +} + + +task jalviewjsEclipseSetup { + dependsOn jalviewjsEclipseCopyDropins + dependsOn jalviewjsSetEclipseWorkspace + dependsOn jalviewjsCreateJ2sSettings +} + + +task jalviewjsSyncAllLibs (type: Sync) { + dependsOn jalviewjsTransferUnzipAllLibs + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}") + inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncResources (type: Sync) { + def inputFiles = fileTree(dir: resourceDir) + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncSiteResources (type: Sync) { + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncBuildProperties (type: Sync) { + dependsOn createBuildProperties + def inputFiles = [file(buildProperties)] + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsProjectImport(type: Exec) { + dependsOn eclipseSetup + dependsOn jalviewjsEclipsePaths + dependsOn jalviewjsEclipseSetup + + doFirst { + // do not run a headless import when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + } + + //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" + def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview" + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath]) + if (eclipseDebug) { + args += "-debug" + } + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] + if (!IN_ECLIPSE) { + args += [ "-D${j2sHeadlessBuildProperty}=true" ] + } + + inputs.file("${jalviewDir}/.project") + outputs.upToDateWhen { + file(projdir).exists() + } +} + + +task jalviewjsTranspile(type: Exec) { + dependsOn jalviewjsEclipseSetup + dependsOn jalviewjsProjectImport + dependsOn jalviewjsEclipsePaths + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + if (IN_ECLIPSE) { + println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'") + } else { + println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}") + } + } + + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ]) + if (eclipseDebug) { + args += "-debug" + } + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] + if (!IN_ECLIPSE) { + args += [ "-D${j2sHeadlessBuildProperty}=true" ] + } + + def stdout + def stderr + doFirst { + stdout = new ByteArrayOutputStream() + stderr = new ByteArrayOutputStream() + + def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}" + def logOutFile = file(logOutFileName) + logOutFile.createNewFile() + logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} +BINARY: ${eclipseBinary} +VERSION: ${eclipseVersion} +WORKSPACE: ${eclipseWorkspace} +DEBUG: ${eclipseDebug} +---- +""" + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + // combine stdout and stderr + def logErrFOS = logOutFOS + + if (jalviewjs_j2s_to_console.equals("true")) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr), + errorOutput) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr) + } + } + + doLast { + if (stdout.toString().contains("Error processing ")) { + // j2s did not complete transpile + //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + if (jalviewjs_ignore_transpile_errors.equals("true")) { + println("IGNORING TRANSPILE ERRORS") + println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + } else { + throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + } + } + } + + inputs.dir("${jalviewDir}/${sourceDir}") + outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}") + outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } ) +} + + +def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) { + + def stdout = new ByteArrayOutputStream() + def stderr = new ByteArrayOutputStream() + + def coreFile = file(jsfile) + def msg = "" + msg = "Creating core for ${name}...\nGenerating ${jsfile}" + println(msg) + logOutFile.createNewFile() + logOutFile.append(msg+"\n") + + def coreTop = file(prefixFile) + def coreBottom = file(suffixFile) + coreFile.getParentFile().mkdirs() + coreFile.createNewFile() + coreFile.write( coreTop.getText("UTF-8") ) + list.each { + f -> + if (f.exists()) { + def t = f.getText("UTF-8") + t.replaceAll("Clazz\\.([^_])","Clazz_${1}") + coreFile.append( t ) + } else { + msg = "...file '"+f.getPath()+"' does not exist, skipping" + println(msg) + logOutFile.append(msg+"\n") + } + } + coreFile.append( coreBottom.getText("UTF-8") ) + + msg = "Generating ${zjsfile}" + println(msg) + logOutFile.append(msg+"\n") + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + def logErrFOS = logOutFOS + + javaexec { + classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"]) + main = "com.google.javascript.jscomp.CommandLineRunner" + jvmArgs = [ "-Dfile.encoding=UTF-8" ] + args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ] + maxHeapSize = "2g" + + msg = "\nRunning '"+commandLine.join(' ')+"'\n" + println(msg) + logOutFile.append(msg+"\n") + + if (logOutConsole) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr), + errorOutput) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr) + } + } + msg = "--" + println(msg) + logOutFile.append(msg+"\n") +} + + +task jalviewjsBuildAllCores { + group "JalviewJS" + description "Build the core js lib closures listed in the classlists dir" + dependsOn jalviewjsTranspile + dependsOn jalviewjsTransferUnzipSwingJs + + def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}" + def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}" + def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}" + def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}" + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core" + def prefixFile = "${jsDir}/core/coretop2.js" + def suffixFile = "${jsDir}/core/corebottom2.js" + + inputs.file prefixFile + inputs.file suffixFile + + def classlistFiles = [] + // add the classlists found int the jalviewjs_classlists_dir + fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each { + file -> + def name = file.getName() - ".txt" + classlistFiles += [ + 'file': file, + 'name': name + ] + } + + // _jmol and _jalview cores. Add any other peculiar classlist.txt files here + //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ] + classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ] + + jalviewjsCoreClasslists = [] + + classlistFiles.each { + hash -> + + def file = hash['file'] + if (! file.exists()) { + //println("...classlist file '"+file.getPath()+"' does not exist, skipping") + return false // this is a "continue" in groovy .each closure + } + def name = hash['name'] + if (name == null) { + name = file.getName() - ".txt" + } + + def filelist = [] + file.eachLine { + line -> + filelist += line + } + def list = fileTree(dir: j2sDir, includes: filelist) + + def jsfile = "${outputDir}/core${name}.js" + def zjsfile = "${outputDir}/core${name}.z.js" + + jalviewjsCoreClasslists += [ + 'jsfile': jsfile, + 'zjsfile': zjsfile, + 'list': list, + 'name': name + ] + + inputs.file(file) + inputs.files(list) + outputs.file(jsfile) + outputs.file(zjsfile) + } + + // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) + def stevesoftClasslistName = "_stevesoft" + def stevesoftClasslist = [ + 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js", + 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js", + 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"), + 'name': stevesoftClasslistName + ] + jalviewjsCoreClasslists += stevesoftClasslist + inputs.files(stevesoftClasslist['list']) + outputs.file(stevesoftClasslist['jsfile']) + outputs.file(stevesoftClasslist['zjsfile']) + + // _all core + def allClasslistName = "_all" + def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js") + allJsFiles += fileTree( + dir: libJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js", + "**/org/jmol/export/JSExporter.js" + ] + ) + allJsFiles += fileTree( + dir: swingJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/sun/misc/Unsafe.js", + "**/swingjs/jquery/jquery-editable-select.js", + "**/swingjs/jquery/j2sComboBox.js", + "**/sun/misc/FloatingDecimal.js" + ] + ) + def allClasslist = [ + 'jsfile': "${outputDir}/core${allClasslistName}.js", + 'zjsfile': "${outputDir}/core${allClasslistName}.z.js", + 'list': allJsFiles, + 'name': allClasslistName + ] + // not including this version of "all" core at the moment + //jalviewjsCoreClasslists += allClasslist + inputs.files(allClasslist['list']) + outputs.file(allClasslist['jsfile']) + outputs.file(allClasslist['zjsfile']) + + doFirst { + def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}") + logOutFile.getParentFile().mkdirs() + logOutFile.createNewFile() + logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n") + + jalviewjsCoreClasslists.each { + jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true")) + } + } + +} + + +def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) { + copy { + from inputFile + into file(outputFile).getParentFile() + rename { filename -> + if (filename.equals(inputFile.getName())) { + return file(outputFile).getName() + } + return null + } + filter(ReplaceTokens, + beginToken: '_', + endToken: '_', + tokens: [ + 'MAIN': '"'+main_class+'"', + 'CODE': "null", + 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]", + 'COREKEY': jalviewjs_core_key, + 'CORENAME': coreName + ] + ) + } +} + + +task jalviewjsPublishCoreTemplates { + dependsOn jalviewjsBuildAllCores + def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}" + def inputFile = file(inputFileName) + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + + def outputFiles = [] + jalviewjsCoreClasslists.each { cl -> + def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html" + cl['outputfile'] = outputFile + outputFiles += outputFile + } + + doFirst { + jalviewjsCoreClasslists.each { cl -> + jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile) + } + } + inputs.file(inputFile) + outputs.files(outputFiles) +} + + +task jalviewjsSyncCore (type: Sync) { + dependsOn jalviewjsBuildAllCores + dependsOn jalviewjsPublishCoreTemplates + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +// this Copy version of TransferSiteJs will delete anything else in the target dir +task jalviewjsCopyTransferSiteJs(type: Copy) { + dependsOn jalviewjsTranspile + from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + into "${jalviewDir}/${jalviewjsSiteDir}" +} + + +// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes +task jalviewjsSyncTransferSiteJs(type: Sync) { + from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + include "**/*.*" + into "${jalviewDir}/${jalviewjsSiteDir}" + preserve { + include "**" + } +} + + +jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs +jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs +jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs + +jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs + + +task jalviewjsPrepareSite { + group "JalviewJS" + description "Prepares the website folder including unzipping files and copying resources" + dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncResources + dependsOn jalviewjsSyncSiteResources + dependsOn jalviewjsSyncBuildProperties + dependsOn jalviewjsSyncCore +} + + +task jalviewjsBuildSite { + group "JalviewJS" + description "Builds the whole website including transpiled code" + dependsOn jalviewjsCopyTransferSiteJs + dependsOn jalviewjsPrepareSite +} + + +task cleanJalviewjsTransferSite { + doFirst { + delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + } +} + + +task cleanJalviewjsSite { + dependsOn cleanJalviewjsTransferSite + doFirst { + delete "${jalviewDir}/${jalviewjsSiteDir}" + } +} + + +task jalviewjsSiteTar(type: Tar) { + group "JalviewJS" + description "Creates a tar.gz file for the website" + dependsOn jalviewjsBuildSite + def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz" + archiveFileName = outputFilename + + compression Compression.GZIP + + from "${jalviewDir}/${jalviewjsSiteDir}" + into jalviewjs_site_dir // this is inside the tar file + + inputs.dir("${jalviewDir}/${jalviewjsSiteDir}") +} + + +task jalviewjsServer { + group "JalviewJS" + def filename = "jalviewjsTest.html" + description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port." + def htmlFile = "${jalviewDirAbsolutePath}/${filename}" + doLast { + + SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory() + def port = Integer.valueOf(jalviewjs_server_port) + def start = port + def running = false + def url + def jalviewjsServer + while(port < start+1000 && !running) { + try { + def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") + jalviewjsServer = factory.start(doc_root, port) + running = true + url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource) + println("SERVER STARTED with document root ${doc_root}.") + println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).") + println("For debug: "+url+"?j2sdebug") + println("For verbose: "+url+"?j2sverbose") + } catch (Exception e) { + port++; + } + } + def htmlText = """ +

JalviewJS Test. <${url}>

+

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

+

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

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

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

+ """ + println("For core ${cl.name}: "+urlcore) + } + + file(htmlFile).text = htmlText + } + + outputs.file(htmlFile) + outputs.upToDateWhen({false}) +} + + +task cleanJalviewjsAll { + group "JalviewJS" + description "Delete all configuration and build artifacts to do with JalviewJS build" + dependsOn cleanJalviewjsSite + dependsOn jalviewjsEclipsePaths + + doFirst { + delete "${jalviewDir}/${jalviewjsBuildDir}" + delete "${jalviewDir}/${eclipse_bin_dir}" + if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) { + delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") + } + delete "${jalviewDir}/${jalviewjs_j2s_settings}" + } + + outputs.upToDateWhen( { false } ) +} + + +task jalviewjsIDE_checkJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)" + + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.") + } + def eclipseJ2sPluginDirs = [ "${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" + description "Creates the .j2s file" + dependsOn jalviewjsCreateJ2sSettings +} + + +task jalviewjsIDE_SyncCore { + group "00 JalviewJS in Eclipse" + description "Build the core js lib closures listed in the classlists dir and publish core html from template" + dependsOn jalviewjsSyncCore +} + + +task jalviewjsIDE_SyncSiteAll { + dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncResources + dependsOn jalviewjsSyncSiteResources + dependsOn jalviewjsSyncBuildProperties +} + + +cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll + + +task jalviewjsIDE_PrepareSite { + group "00 JalviewJS in Eclipse" + description "Sync libs and resources to site dir, but not closure cores" + + dependsOn jalviewjsIDE_SyncSiteAll + //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task +} + + +task jalviewjsIDE_AssembleSite { + group "00 JalviewJS in Eclipse" + description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site" + dependsOn jalviewjsPrepareSite +} + + +task jalviewjsIDE_SiteClean { + group "00 JalviewJS in Eclipse" + description "Deletes the Eclipse transpiled site" + dependsOn cleanJalviewjsSite +} + + +task jalviewjsIDE_Server { + group "00 JalviewJS in Eclipse" + description "Starts a webserver on localhost to test the website" + dependsOn jalviewjsServer +} + + +// buildship runs this at import or gradle refresh +task eclipseSynchronizationTask { + //dependsOn eclipseSetup + dependsOn createBuildProperties + if (J2S_ENABLED) { + dependsOn jalviewjsIDE_j2sFile + dependsOn jalviewjsIDE_checkJ2sPlugin + dependsOn jalviewjsIDE_PrepareSite + } +} + + +// buildship runs this at build time or project refresh +task eclipseAutoBuildTask { + //dependsOn jalviewjsIDE_checkJ2sPlugin + //dependsOn jalviewjsIDE_PrepareSite +} + + +task jalviewjs { + group "JalviewJS" + description "Build the site" + dependsOn jalviewjsBuildSite }