X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.gradle;h=b4636bc523f0d453e0e55b241481ccdff87c2e14;hp=66b5550fa707ea688886c32b23b226d45481a065;hb=c6977851625f96831a95b45901aa1d84bd7774fe;hpb=35c1fb0488dd0b19b880c3835613f3272e6c0fc3 diff --git a/build.gradle b/build.gradle index 66b5550..b4636bc 100644 --- a/build.gradle +++ b/build.gradle @@ -3,19 +3,34 @@ */ import org.apache.tools.ant.filters.ReplaceTokens import org.gradle.internal.os.OperatingSystem +import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject +import org.gradle.api.internal.PropertiesTransformer +import org.gradle.util.ConfigureUtil import org.gradle.plugins.ide.eclipse.model.Output import org.gradle.plugins.ide.eclipse.model.Library import java.security.MessageDigest import groovy.transform.ExternalizeMethods import groovy.util.XmlParser import groovy.xml.XmlUtil - +import com.vladsch.flexmark.util.ast.Node +import com.vladsch.flexmark.html.HtmlRenderer +import com.vladsch.flexmark.parser.Parser +import com.vladsch.flexmark.util.data.MutableDataSet +import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension +import com.vladsch.flexmark.ext.tables.TablesExtension +import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension +import com.vladsch.flexmark.ext.autolink.AutolinkExtension +import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension +import com.vladsch.flexmark.ext.toc.TocExtension buildscript { repositories { mavenCentral() mavenLocal() } + dependencies { + classpath "com.vladsch.flexmark:flexmark-all:0.62.0" + } } @@ -23,9 +38,11 @@ plugins { id 'java' id 'application' id 'eclipse' + id "com.diffplug.gradle.spotless" version "3.28.0" id 'com.github.johnrengelman.shadow' version '4.0.3' - id 'com.install4j.gradle' version '8.0.4' + id 'com.install4j.gradle' version '9.0.6' id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree + id 'com.palantir.git-version' version '0.13.0' apply false } repositories { @@ -35,29 +52,19 @@ repositories { } + // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use def string(Object o) { return o == null ? "" : o.toString() } - -ext { - jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() - jalviewDirRelativePath = jalviewDir - - // local build environment properties - // can be "projectDir/local.properties" - def localProps = "${projectDir}/local.properties" - def propsFile = null; - if (file(localProps).exists()) { - propsFile = localProps - } - // or "../projectDir_local.properties" - def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties" - if (file(dirLocalProps).exists()) { - propsFile = dirLocalProps +def overrideProperties(String propsFileName, boolean output = false) { + if (propsFileName == null) { + return } - if (propsFile != null) { + def propsFile = file(propsFileName) + if (propsFile != null && propsFile.exists()) { + println("Using properties from file '${propsFileName}'") try { def p = new Properties() def localPropsFIS = new FileInputStream(propsFile) @@ -65,24 +72,50 @@ ext { 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}'") + def oldval + if (project.hasProperty(key)) { + oldval = project.findProperty(key) + project.setProperty(key, val) + if (output) { + println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") + } } else { - println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'") + ext.setProperty(key, val) + if (output) { + println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'") + } } } } catch (Exception e) { - System.out.println("Exception reading local.properties") + println("Exception reading local.properties") + e.printStackTrace() } } +} + +ext { + jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() + jalviewDirRelativePath = jalviewDir + + getdownChannelName = CHANNEL.toLowerCase() + // default to "default". Currently only has different cosmetics for "develop", "release", "default" + propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default" + // Import channel_properties + channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}") + channelGradleProperties = string("${channelDir}/channel_gradle.properties") + channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}") + overrideProperties(channelGradleProperties, false) + // local build environment properties + // can be "projectDir/local.properties" + overrideProperties("${projectDir}/local.properties", true) + // or "../projectDir_local.properties" + overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true) //// // Import releaseProps from the RELEASE file // or a file specified via JALVIEW_RELEASE_FILE if defined // Expect jalview.version and target release branch in jalview.release - def releaseProps = new Properties(); + releaseProps = new Properties(); def releasePropFile = findProperty("JALVIEW_RELEASE_FILE"); def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE"; try { @@ -94,7 +127,7 @@ ext { } //// // Set JALVIEW_VERSION if it is not already set - if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) { + if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) { JALVIEW_VERSION = releaseProps.get("jalview.version") } @@ -115,6 +148,11 @@ ext { } else { println("HEADLESS BUILD") } + + J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable") + if (J2S_ENABLED) { + println("J2S ENABLED") + } /* *-/ System.properties.sort { it.key }.each { key, val -> println("SYSTEM PROPERTY ${key}='${val}'") @@ -125,6 +163,9 @@ ext { } */ + // datestamp + buildDate = new Date().format("yyyyMMdd") + // essentials bareSourceDir = string(source_dir) sourceDir = string("${jalviewDir}/${bareSourceDir}") @@ -145,29 +186,32 @@ ext { //cloverTestClassesDir = cloverClassesDir cloverDb = string("${cloverBuildDir}/clover.db") - resourceClassesDir = useClover ? cloverClassesDir : classesDir - testSourceDir = useClover ? cloverTestInstrDir : testDir testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}" getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") buildDist = true + buildProperties = null // the following values might be overridden by the CHANNEL switch - getdownChannelName = CHANNEL.toLowerCase() getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = string("${getdown_channel_base}/${getdownDir}") getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}") getdownAppDistDir = getdown_app_dir_alt - buildProperties = string("${classesDir}/${build_properties_file}") + getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}") + getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application reportRsyncCommand = false jvlChannelName = CHANNEL.toLowerCase() install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build - install4jDSStore = "DS_Store-NON-RELEASE" - install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png" + install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}" + install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}" install4jInstallerName = "${jalview_name} Non-Release Installer" - install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase() + install4jExecutableName = install4j_executable_name install4jExtraScheme = "jalviewx" + install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}") + install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}") + install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}") + install4jBackground = string("${install4j_images_dir}/${install4j_background}") switch (CHANNEL) { case "BUILD": @@ -183,12 +227,10 @@ ext { install4jExtraScheme = "jalviewb" break - case "RELEASE": + case [ "RELEASE", "JALVIEWJS-RELEASE" ]: getdownAppDistDir = getdown_app_dir_release reportRsyncCommand = true install4jSuffix = "" - install4jDSStore = "DS_Store" - install4jDMGBackgroundImage = "jalview_dmg_background.png" install4jInstallerName = "${jalview_name} Installer" break @@ -226,32 +268,32 @@ ext { case "DEVELOP": reportRsyncCommand = true - + getdownSetAppBaseProperty = true // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version - JALVIEW_VERSION=JALVIEW_VERSION+"-develop" + JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}" install4jSuffix = "Develop" - install4jDSStore = "DS_Store-DEVELOP" - install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png" install4jExtraScheme = "jalviewd" install4jInstallerName = "${jalview_name} Develop Installer" break case "TEST-RELEASE": reportRsyncCommand = true - - // TEST-RELEASE is usually associated with a Jalview release series so set the version - JALVIEW_VERSION=JALVIEW_VERSION+"-test" - + // Don't ignore transpile errors for release build + if (jalviewjs_ignore_transpile_errors.equals("true")) { + jalviewjs_ignore_transpile_errors = "false" + println("Setting jalviewjs_ignore_transpile_errors to 'false'") + } + JALVIEW_VERSION = JALVIEW_VERSION+"-test" install4jSuffix = "Test" - install4jDSStore = "DS_Store-TEST-RELEASE" - install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" install4jExtraScheme = "jalviewt" install4jInstallerName = "${jalview_name} Test Installer" break case ~/^SCRATCH(|-[-\w]*)$/: getdownChannelName = CHANNEL + JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL + getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = string("${getdown_channel_base}/${getdownDir}") reportRsyncCommand = true @@ -267,13 +309,12 @@ ext { } JALVIEW_VERSION = "TEST" install4jSuffix = "Test-Local" - install4jDSStore = "DS_Store-TEST-RELEASE" - install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" install4jExtraScheme = "jalviewt" install4jInstallerName = "${jalview_name} Test Installer" break - case "LOCAL": + case [ "LOCAL", "JALVIEWJS" ]: + JALVIEW_VERSION = "TEST" getdownAppBase = file(getdownWebsiteDir).toURI().toString() getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") install4jExtraScheme = "jalviewl" @@ -286,7 +327,16 @@ ext { } // override getdownAppBase if requested if (findProperty("getdown_appbase_override") != null) { - getdownAppBase = string(getProperty("getdown_appbase_override")) + // revert to LOCAL if empty string + if (string(getdown_appbase_override) == "") { + getdownAppBase = file(getdownWebsiteDir).toURI().toString() + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + } else if (string(getdown_appbase_override).startsWith("file://")) { + getdownAppBase = string(getdown_appbase_override) + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") + } else { + getdownAppBase = string(getdown_appbase_override) + } println("Overriding getdown appbase with '${getdownAppBase}'") } // sanitise file name for jalview launcher file for this channel @@ -322,6 +372,7 @@ ext { .replaceAll("_*-_*", "-") // collapse _-_ .toLowerCase() + getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local" getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}") //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}") @@ -332,8 +383,21 @@ ext { modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) modules_runtimeClasspath = modules_compileClasspath */ - gitHash = string("") - gitBranch = string("") + + gitHash = "SOURCE" + gitBranch = "Source" + try { + apply plugin: "com.palantir.git-version" + def details = versionDetails() + gitHash = details.gitHash + gitBranch = details.branchName + } catch(org.gradle.api.internal.plugins.PluginApplicationException e) { + println("Not in a git repository. Using git values from RELEASE properties file.") + gitHash = releaseProps.getProperty("git.hash") + gitBranch = releaseProps.getProperty("git.branch") + } catch(java.lang.RuntimeException e1) { + throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.") + } println("Using a ${CHANNEL} profile.") @@ -369,16 +433,16 @@ ext { '--add-modules', j11modules ] */ - } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) { - JAVA_INTEGER_VERSION = JAVA_VERSION - libDir = j11libDir - libDistDir = j11libDir - compile_source_compatibility = JAVA_VERSION - compile_target_compatibility = JAVA_VERSION + } else if (JAVA_VERSION.equals("17")) { + JAVA_INTEGER_VERSION = string("17") + libDir = j17libDir + libDistDir = j17libDir + compile_source_compatibility = 17 + compile_target_compatibility = 17 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version")) getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location")) - eclipseJavaRuntimeName = string("JavaSE-11") + eclipseJavaRuntimeName = string("JavaSE-17") /* compile without modules -- using classpath libraries additional_compiler_args += [ '--module-path', modules_compileClasspath.asPath, @@ -398,11 +462,11 @@ ext { jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1) } macosJavaVMDir = string("${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-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz") + macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz") + windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz") + linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz") install4jDir = string("${jalviewDir}/${install4j_utils_dir}") install4jConfFileName = string("jalview-install4j-conf.install4j") install4jConfFile = file("${install4jDir}/${install4jConfFileName}") @@ -411,12 +475,18 @@ ext { install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1) } + resourceBuildDir = string("${buildDir}/resources") + resourcesBuildDir = string("${resourceBuildDir}/resources_build") + helpBuildDir = string("${resourceBuildDir}/help_build") + docBuildDir = string("${resourceBuildDir}/doc_build") - + if (buildProperties == null) { + buildProperties = string("${resourcesBuildDir}/${build_properties_file}") + } buildingHTML = string("${jalviewDir}/${doc_dir}/building.html") - helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm") helpParentDir = string("${jalviewDir}/${help_parent_dir}") helpSourceDir = string("${helpParentDir}/${help_dir}") + helpFile = string("${helpBuildDir}/${help_dir}/help.jhm") relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) @@ -435,7 +505,9 @@ ext { jalviewjsCoreClasslists = [] jalviewjsJalviewTemplateName = string(jalviewjs_name) jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}") + jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}") jalviewjsJ2sProps = null + jalviewjsJ2sPlugin = jalviewjs_j2s_plugin eclipseWorkspace = null eclipseBinary = string("") @@ -453,16 +525,14 @@ sourceSets { } resources { - srcDirs resourceDir - srcDirs += helpParentDir + srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ] } - jar.destinationDir = file("${jalviewDir}/${package_dir}") - compileClasspath = files(sourceSets.main.java.outputDir) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath + runtimeClasspath += files(sourceSets.main.resources.srcDirs) } clover { @@ -499,6 +569,7 @@ sourceSets { compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath + runtimeClasspath += files(sourceSets.test.resources.srcDirs) } } @@ -519,14 +590,12 @@ eclipse { classpath { //defaultOutputDir = sourceSets.main.java.outputDir - def removeThese = [] - configurations.each{ - if (it.isCanBeResolved()) { - removeThese += it + configurations.each{ c-> + if (c.isCanBeResolved()) { + minusConfigurations += [c] } } - minusConfigurations += removeThese plusConfigurations = [ ] file { @@ -625,6 +694,22 @@ eclipse { props.putAt(t, v) } } + // codestyle file -- overrides previous formatter prefs + def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}") + if (csFile.exists()) { + XmlParser parser = new XmlParser() + def profiles = parser.parse(csFile) + def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") } + if (profile != null) { + profile.'setting'.each { s -> + def id = s.'@id' + def value = s.'@value' + if (id != null && value != null) { + props.putAt(id, value) + } + } + } + } } } @@ -633,11 +718,68 @@ eclipse { if (IN_ECLIPSE) { // Don't want these to be activated if in headless build synchronizationTasks "eclipseSynchronizationTask" - autoBuildTasks "eclipseAutoBuildTask" + //autoBuildTasks "eclipseAutoBuildTask" + + } +} + + +/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */ +// Class to allow updating arbitrary properties files +class PropertiesFile extends PropertiesPersistableConfigurationObject { + public PropertiesFile(PropertiesTransformer t) { super(t); } + @Override protected void load(Properties properties) { } + @Override protected void store(Properties properties) { } + @Override protected String getDefaultResourceName() { return ""; } + // This is necessary, because PropertiesPersistableConfigurationObject fails + // if no default properties file exists. + @Override public void loadDefaults() { load(new StringBufferInputStream("")); } +} +// Task to update arbitrary properties files (set outputFile) +class PropertiesFileTask extends PropertiesGeneratorTask { + private final PropertiesFileContentMerger file; + public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); } + protected PropertiesFile create() { return new PropertiesFile(getTransformer()); } + protected void configure(PropertiesFile props) { + file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props); + } + public void file(Closure closure) { ConfigureUtil.configure(closure, file); } +} + +task eclipseUIPreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.ui.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) + } + } +} + +task eclipseGroovyCorePreferences(type: PropertiesFileTask) { + description = "Generate Eclipse additional settings" + def filename = "org.eclipse.jdt.groovy.core.prefs" + outputFile = "$projectDir/.settings/${filename}" as File + file { + withProperties { + it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String) + } } } +task eclipseAllPreferences { + dependsOn eclipseJdt + dependsOn eclipseUIPreferences + dependsOn eclipseGroovyCorePreferences +} + +eclipseUIPreferences.mustRunAfter eclipseJdt +eclipseGroovyCorePreferences.mustRunAfter eclipseJdt + +/* end of eclipse preferences hack */ + // clover bits @@ -859,22 +1001,23 @@ compileCloverJava { 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 { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") + print ("Setting target compatibility to "+compile_target_compatibility+"\n") } } compileTestJava { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs = additional_compiler_args doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args print ("Setting target compatibility to "+targetCompatibility+"\n") } } @@ -902,110 +1045,146 @@ def getDate(format) { } -task setGitVals { - def hashStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--short", "HEAD" - standardOutput = hashStdOut - ignoreExitValue true - } - - def branchStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" - standardOutput = branchStdOut - ignoreExitValue true - } - - gitHash = hashStdOut.toString().trim() - gitBranch = branchStdOut.toString().trim() - - outputs.upToDateWhen { false } -} - - -task createBuildProperties(type: WriteProperties) { - dependsOn setGitVals - inputs.dir(sourceDir) - inputs.dir(resourceDir) - file(buildProperties).getParentFile().mkdirs() - outputFile (buildProperties) - // taking time specific comment out to allow better incremental builds - comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") - //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") - property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") - property "VERSION", JALVIEW_VERSION - property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" - outputs.file(outputFile) -} +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() + } -task cleanBuildingHTML(type: Delete) { - doFirst { - delete buildingHTML + 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 ${htmlFilePath}") + htmlFile.text = htmlText } } -task convertBuildingMD(type: Exec) { - dependsOn cleanBuildingHTML - def buildingMD = "${jalviewDir}/${doc_dir}/building.md" - def css = "${jalviewDir}/${doc_dir}/github.css" - - def pandoc = null - pandoc_exec.split(",").each { - if (file(it.trim()).exists()) { - pandoc = it.trim() - return true - } - } - - def hostname = "hostname".execute().text.trim() - def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" - if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) { - pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" +task copyDocs(type: Copy) { + def inputDir = "${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") + ] + ) } - - 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("Cannot find pandoc. Skipping convert building.md to HTML") - } + from(inputDir) { + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.xml') } + into outputDir - ignoreExitValue true - - inputs.file(buildingMD) - inputs.file(css) - outputs.file(buildingHTML) + inputs.dir(inputDir) + outputs.dir(outputDir) } -clean { - doFirst { - delete buildingHTML - } -} +task convertMdFiles { + dependsOn copyDocs + def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md") + def cssFile = file("${jalviewDir}/${flexmark_css}") + doLast { + convertMdToHtml(mdFiles, cssFile) + } -task syncDocs(type: Sync) { - dependsOn convertBuildingMD - def syncDir = "${resourceClassesDir}/${doc_dir}" - from fileTree("${jalviewDir}/${doc_dir}") - into syncDir + inputs.files(mdFiles) + inputs.file(cssFile) + def htmlFiles = [] + mdFiles.each { mdFile -> + def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html") + htmlFiles.add(file(htmlFilePath)) + } + outputs.files(htmlFiles) } task copyHelp(type: Copy) { def inputDir = helpSourceDir - def outputDir = "${resourceClassesDir}/${help_dir}" + def outputDir = "${helpBuildDir}/${help_dir}" from(inputDir) { - exclude '**/*.gif' - exclude '**/*.jpg' - exclude '**/*.png' + include('**/*.txt') + include('**/*.md') + include('**/*.html') + include('**/*.hs') + include('**/*.xml') + include('**/*.jhm') filter(ReplaceTokens, beginToken: '$$', endToken: '$$', @@ -1016,9 +1195,12 @@ task copyHelp(type: Copy) { ) } from(inputDir) { - include '**/*.gif' - include '**/*.jpg' - include '**/*.png' + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.hs') + exclude('**/*.xml') + exclude('**/*.jhm') } into outputDir @@ -1028,39 +1210,121 @@ task copyHelp(type: Copy) { } -task syncLib(type: Sync) { - def syncDir = "${resourceClassesDir}/${libDistDir}" - from fileTree("${jalviewDir}/${libDistDir}") - into syncDir +task copyResources(type: Copy) { + group = "build" + description = "Copy (and make text substitutions in) the resources dir to the build area" + + def inputDir = resourceDir + def outputDir = resourcesBuildDir + from(inputDir) { + include('**/*.txt') + include('**/*.md') + include('**/*.html') + include('**/*.xml') + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) + } + from(inputDir) { + exclude('**/*.txt') + exclude('**/*.md') + exclude('**/*.html') + exclude('**/*.xml') + } + into outputDir + + inputs.dir(inputDir) + outputs.dir(outputDir) } +task copyChannelResources(type: Copy) { + dependsOn copyResources + group = "build" + description = "Copy the channel resources dir to the build resources area" -task syncResources(type: Sync) { - from resourceDir - include "**/*.*" - into "${resourceClassesDir}" - preserve { - include "**" + def inputDir = "${channelDir}/${resource_dir}" + def outputDir = resourcesBuildDir + from inputDir + into outputDir + + inputs.dir(inputDir) + outputs.dir(outputDir) +} + +task createBuildProperties(type: WriteProperties) { + dependsOn copyResources + group = "build" + description = "Create the ${buildProperties} file" + + inputs.dir(sourceDir) + inputs.dir(resourcesBuildDir) + outputFile (buildProperties) + // taking time specific comment out to allow better incremental builds + comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") + //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") + property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") + property "VERSION", JALVIEW_VERSION + property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" + if (getdownSetAppBaseProperty) { + property "GETDOWNAPPBASE", getdownAppBase + property "GETDOWNAPPDISTDIR", getdownAppDistDir } + outputs.file(outputFile) +} + + +task buildIndices(type: JavaExec) { + dependsOn copyHelp + classpath = sourceSets.main.compileClasspath + main = "com.sun.java.help.search.Indexer" + workingDir = "${helpBuildDir}/${help_dir}" + def argDir = "html" + args = [ argDir ] + inputs.dir("${workingDir}/${argDir}") + + outputs.dir("${classesDir}/doc") + outputs.dir("${classesDir}/help") + outputs.file("${workingDir}/JavaHelpSearch/DOCS") + outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") + outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") + outputs.file("${workingDir}/JavaHelpSearch/POSITIONS") + outputs.file("${workingDir}/JavaHelpSearch/SCHEMA") + outputs.file("${workingDir}/JavaHelpSearch/TMAP") } +task buildResources { + dependsOn copyResources + dependsOn copyChannelResources + dependsOn createBuildProperties +} task prepare { - dependsOn syncResources - dependsOn syncDocs + dependsOn buildResources + dependsOn copyDocs dependsOn copyHelp + dependsOn convertMdFiles + dependsOn buildIndices } +compileJava.dependsOn prepare +run.dependsOn compileJava +//run.dependsOn prepare + + //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir test { dependsOn prepare - //dependsOn compileJava ////? DELETE if (useClover) { dependsOn cloverClasses } else { //? - dependsOn compileJava //? + dependsOn compileJava //? } useTestNG() { @@ -1073,7 +1337,6 @@ test { maxHeapSize = "1024m" workingDir = jalviewDir - //systemProperties 'clover.jar' System.properties.clover.jar def testLaf = project.findProperty("test_laf") if (testLaf != null) { println("Setting Test LaF to '${testLaf}'") @@ -1096,26 +1359,6 @@ test { } -task buildIndices(type: JavaExec) { - dependsOn copyHelp - classpath = sourceSets.main.compileClasspath - main = "com.sun.java.help.search.Indexer" - workingDir = "${classesDir}/${help_dir}" - def argDir = "html" - args = [ argDir ] - inputs.dir("${workingDir}/${argDir}") - - outputs.dir("${classesDir}/doc") - outputs.dir("${classesDir}/help") - outputs.file("${workingDir}/JavaHelpSearch/DOCS") - outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") - outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") - outputs.file("${workingDir}/JavaHelpSearch/POSITIONS") - outputs.file("${workingDir}/JavaHelpSearch/SCHEMA") - outputs.file("${workingDir}/JavaHelpSearch/TMAP") -} - - task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utils_dir}") @@ -1130,30 +1373,31 @@ task compileLinkCheck(type: JavaCompile) { task linkCheck(type: JavaExec) { - dependsOn prepare, compileLinkCheck + dependsOn prepare + dependsOn compileLinkCheck def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out") classpath = files("${jalviewDir}/${utils_dir}") main = "HelpLinksChecker" workingDir = jalviewDir - args = [ "${classesDir}/${help_dir}", "-nointernet" ] + args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append - def errFOS = outFOS standardOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, - standardOutput) + System.out) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( outFOS, - errorOutput) + System.err) - inputs.dir("${classesDir}/${help_dir}") + inputs.dir(helpBuildDir) outputs.file(helpLinksCheckerOutFile) } + // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" -ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}" +ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}" ant.importBuild "${utils_dir}/publishHelp.xml" @@ -1163,20 +1407,24 @@ task cleanPackageDir(type: Delete) { } } + jar { + dependsOn prepare dependsOn linkCheck - dependsOn buildIndices - dependsOn createBuildProperties manifest { attributes "Main-Class": main_class, "Permissions": "all-permissions", - "Application-Name": "Jalview Desktop", - "Codebase": application_codebase + "Application-Name": install4jApplicationName, + "Codebase": application_codebase, + "Implementation-Version": JALVIEW_VERSION } - destinationDir = file("${jalviewDir}/${package_dir}") - archiveName = rootProject.name+".jar" + def outputDir = "${jalviewDir}/${package_dir}" + destinationDirectory = file(outputDir) + archiveFileName = rootProject.name+".jar" + duplicatesStrategy "EXCLUDE" + exclude "cache*/**" exclude "*.jar" @@ -1184,8 +1432,11 @@ jar { exclude "**/*.jar" exclude "**/*.jar.*" - inputs.dir(classesDir) - outputs.file("${jalviewDir}/${package_dir}/${archiveName}") + inputs.dir(sourceSets.main.java.outputDir) + sourceSets.main.resources.srcDirs.each{ dir -> + inputs.dir(dir) + } + outputs.file("${outputDir}/${archiveFileName}") } @@ -1197,10 +1448,11 @@ task copyJars(type: Copy) { // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well task syncJars(type: Sync) { + dependsOn jar from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files into "${jalviewDir}/${package_dir}" preserve { - include jar.archiveName + include jar.archiveFileName.getOrNull() } } @@ -1224,8 +1476,10 @@ task cleanDist { dependsOn clean } + shadowJar { group = "distribution" + description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar" if (buildDist) { dependsOn makeDist } @@ -1233,8 +1487,12 @@ shadowJar { include("*.jar") } manifest { - attributes 'Implementation-Version': JALVIEW_VERSION + attributes "Implementation-Version": JALVIEW_VERSION, + "Application-Name": install4jApplicationName } + + duplicatesStrategy "INCLUDE" + mainClassName = shadow_jar_main_class mergeServiceFiles() classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION @@ -1261,11 +1519,17 @@ task getdownWebsite() { copy { from buildProperties - rename(build_properties_file, getdown_build_properties) + rename(file(buildProperties).getName(), getdown_build_properties) into getdownAppDir } getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" + copy { + from channelPropsFile + into getdownWebsiteDir + } + getdownWebsiteResourceFilenames += file(channelPropsFile).getName() + // set some getdown_txt_ properties then go through all properties looking for getdown_txt_... def props = project.properties.sort { it.key } if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) { @@ -1277,6 +1541,14 @@ task getdownWebsite() { if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) { props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) } + if (getdownImagesDir != null && file(getdownImagesDir).exists()) { + props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}") + props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}") + props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}") + props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}") + props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}") + props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}") + } props.put("getdown_txt_title", jalview_name) props.put("getdown_txt_ui.name", install4jApplicationName) @@ -1325,6 +1597,18 @@ task getdownWebsite() { into getdownResourceDir } } + + def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ] + getdownWrapperScripts.each{ script -> + def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" ) + if (s.exists()) { + copy { + from s + into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}" + } + getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n" + } + } def codeFiles = [] fileTree(file(package_dir)).each{ f -> @@ -1335,7 +1619,9 @@ task getdownWebsite() { codeFiles += f } } - codeFiles.sort().each{f -> + def jalviewJar = jar.archiveFileName.getOrNull() + // put jalview.jar first for CLASSPATH and .properties files reasons + codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f -> def name = f.getName() def line = "code = ${getdownAppDistDir}/${name}\n" getdownTextString += line @@ -1365,8 +1651,11 @@ task getdownWebsite() { //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n" getdownTextString += "resource = ${getdown_launcher_new}\n" getdownTextString += "class = ${main_class}\n" - getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n" - getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n" + // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache + if (getdownSetAppBaseProperty) { + getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n" + getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n" + } def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) @@ -1375,12 +1664,14 @@ task getdownWebsite() { def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}") launchJvl.write("appbase=${getdownAppBase}") + // files going into the getdown website dir: getdown-launcher.jar copy { from getdownLauncher rename(file(getdownLauncher).getName(), getdown_launcher_new) into getdownWebsiteDir } + // files going into the getdown website dir: getdown-launcher(-local).jar copy { from getdownLauncher if (file(getdownLauncher).getName() != getdown_launcher) { @@ -1389,6 +1680,7 @@ task getdownWebsite() { into getdownWebsiteDir } + // files going into the getdown website dir: ./install dir and files if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { copy { from getdown_txt @@ -1400,23 +1692,27 @@ task getdownWebsite() { into getdownInstallDir } + // and make a copy in the getdown files dir (these are not downloaded by getdown) copy { from getdownInstallDir into getdownFilesInstallDir } } + // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties copy { from getdown_txt from launchJvl from getdownLauncher from "${getdownWebsiteDir}/${getdown_build_properties}" + from "${getdownWebsiteDir}/${channel_props}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } into getdownFilesDir } + // and ./resources (not all downloaded by getdown) copy { from getdownResourceDir into "${getdownFilesDir}/${getdown_resource_dir}" @@ -1486,6 +1782,11 @@ task getdown() { } +tasks.withType(JavaCompile) { + options.encoding = 'UTF-8' +} + + clean { doFirst { delete getdownWebsiteDir @@ -1529,6 +1830,12 @@ task copyInstall4jTemplate { } } + // disable install screen for OSX dmg (for 2.11.2.0) + install4jConfigXml.'**'.macosArchive.each { macosArchive -> + macosArchive.attributes().remove('executeSetupApp') + macosArchive.attributes().remove('setupAppId') + } + // turn off checksum creation for LOCAL channel def e = install4jConfigXml.application[0] if (CHANNEL == "LOCAL") { @@ -1576,12 +1883,6 @@ task copyInstall4jTemplate { } } - // 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) } @@ -1598,7 +1899,6 @@ clean { task installers(type: com.install4j.gradle.Install4jTask) { group = "distribution" description = "Create the install4j installers" - dependsOn setGitVals dependsOn getdown dependsOn copyInstall4jTemplate @@ -1623,6 +1923,8 @@ task installers(type: com.install4j.gradle.Install4jTask) { 'JALVIEW_APPLICATION_NAME': install4jApplicationName, 'JALVIEW_DIR': "../..", 'OSX_KEYSTORE': OSX_KEYSTORE, + 'OSX_APPLEID': OSX_APPLEID, + 'OSX_ALTOOLPASS': OSX_ALTOOLPASS, 'JSIGN_SH': JSIGN_SH, 'JRE_DIR': getdown_app_dir_java, 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion, @@ -1642,8 +1944,12 @@ task installers(type: com.install4j.gradle.Install4jTask) { 'BUNDLE_ID': install4jBundleId, 'INTERNAL_ID': install4jInternalId, 'WINDOWS_APPLICATION_ID': install4jWinApplicationId, - 'MACOS_DS_STORE': install4jDSStore, + 'MACOS_DMG_DS_STORE': install4jDMGDSStore, 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage, + 'WRAPPER_LINK': getdownWrapperLink, + 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script, + 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script, + 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir, 'INSTALLER_NAME': install4jInstallerName, 'INSTALL4J_UTILS_DIR': install4j_utils_dir, 'GETDOWN_WEBSITE_DIR': getdown_website_dir, @@ -1659,6 +1965,11 @@ task installers(type: com.install4j.gradle.Install4jTask) { 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder, 'EXECUTABLE_NAME': install4jExecutableName, 'EXTRA_SCHEME': install4jExtraScheme, + 'MAC_ICONS_FILE': install4jMacIconsFile, + 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile, + 'PNG_ICON_FILE': install4jPngIconFile, + 'BACKGROUND': install4jBackground, + ] //println("INSTALL4J VARIABLES:") @@ -1670,15 +1981,25 @@ task installers(type: com.install4j.gradle.Install4jTask) { if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) { faster = true disableSigning = true + disableNotarization = true } if (OSX_KEYPASS) { macKeystorePassword = OSX_KEYPASS + } + + if (OSX_ALTOOLPASS) { + appleIdPassword = OSX_ALTOOLPASS + disableNotarization = false + } else { + disableNotarization = true } doFirst { println("Using projectFile "+projectFile) + if (!disableNotarization) { println("Will notarize OSX App DMG") } } + //verbose=true inputs.dir(getdownWebsiteDir) inputs.file(install4jConfFile) @@ -1689,20 +2010,46 @@ task installers(type: com.install4j.gradle.Install4jTask) { } -task sourceDist(type: Tar) { - - def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") - def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" - // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09] - try { - archiveFileName = outputFileName - } catch (Exception e) { - archiveName = outputFileName +spotless { + java { + eclipse().configFile(eclipse_codestyle_file) } +} + +task createSourceReleaseProperties(type: WriteProperties) { + group = "distribution" + description = "Create the source RELEASE properties file" - compression Compression.GZIP - - into project.name + def sourceTarBuildDir = "${buildDir}/sourceTar" + def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE" + outputFile (sourceReleasePropertiesFile) + + doFirst { + releaseProps.each{ key, val -> property key, val } + property "git.branch", gitBranch + property "git.hash", gitHash + } + + outputs.file(outputFile) +} + +task sourceDist(type: Tar) { + group "distribution" + description "Create a source .tar.gz file for distribution" + + dependsOn createBuildProperties + dependsOn convertMdFiles + dependsOn eclipseAllPreferences + dependsOn createSourceReleaseProperties + + + def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") + def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" + archiveFileName = outputFileName + + compression Compression.GZIP + + into project.name def EXCLUDE_FILES=[ "build/*", @@ -1719,6 +2066,7 @@ task sourceDist(type: Tar) { "*locales/**", "utils/InstallAnywhere", "**/*.log", + "RELEASE", ] def PROCESS_FILES=[ "AUTHORS", @@ -1728,7 +2076,6 @@ task sourceDist(type: Tar) { "FEATURETODO", "LICENSE", "**/README", - "RELEASE", "THIRDPARTYLIBS", "TESTNG", "build.gradle", @@ -1743,7 +2090,9 @@ task sourceDist(type: Tar) { "**/*.sh", ] def INCLUDE_FILES=[ - ".settings/org.eclipse.jdt.core.jalview.prefs", + ".classpath", + ".settings/org.eclipse.buildship.core.prefs", + ".settings/org.eclipse.jdt.core.prefs" ] from(jalviewDir) { @@ -1770,7 +2119,7 @@ task sourceDist(type: Tar) { exclude (getdown_website_dir) // exluding these as not using jars as modules yet - exclude ("$j11modDir/**/*.jar") + exclude ("${j11modDir}/**/*.jar") } from(jalviewDir) { include(INCLUDE_FILES) @@ -1781,6 +2130,19 @@ task sourceDist(type: Tar) { // exclude(EXCLUDE_FILES) // exclude(PROCESS_FILES) // } + + from(file(buildProperties).getParent()) { + include(file(buildProperties).getName()) + rename(file(buildProperties).getName(), "build_properties") + filter({ line -> + line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]") + }) + } + + def sourceTarBuildDir = "${buildDir}/sourceTar" + from(sourceTarBuildDir) { + // this includes the appended RELEASE properties file + } } @@ -1788,10 +2150,1085 @@ task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("${classesDir}/${help_dir}") + inputs.dir("${helpBuildDir}/${help_dir}") outputs.dir("${buildDir}/distributions/${help_dir}") } -// LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE -task eclipseAutoBuildTask {} -task eclipseSynchronizationTask {} + +task j2sSetHeadlessBuild { + doFirst { + IN_ECLIPSE = false + } +} + + +task jalviewjsEnableAltFileProperty(type: WriteProperties) { + group "jalviewjs" + description "Enable the alternative J2S Config file for headless build" + + outputFile = jalviewjsJ2sSettingsFileName + def j2sPropsFile = file(jalviewjsJ2sSettingsFileName) + def j2sProps = new Properties() + if (j2sPropsFile.exists()) { + try { + def j2sPropsFileFIS = new FileInputStream(j2sPropsFile) + j2sProps.load(j2sPropsFileFIS) + j2sPropsFileFIS.close() + + j2sProps.each { prop, val -> + property(prop, val) + } + } catch (Exception e) { + println("Exception reading ${jalviewjsJ2sSettingsFileName}") + e.printStackTrace() + } + } + if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) { + property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property) + } +} + + +task jalviewjsSetEclipseWorkspace { + def propKey = "jalviewjs_eclipse_workspace" + def propVal = null + if (project.hasProperty(propKey)) { + propVal = project.getProperty(propKey) + if (propVal.startsWith("~/")) { + propVal = System.getProperty("user.home") + propVal.substring(1) + } + } + def propsFileName = "${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}/${jalviewjsTransferSiteLibDir}" +} + + +task jalviewjsTransferUnzipAllLibs { + dependsOn jalviewjsTransferUnzipSwingJs + dependsOn jalviewjsTransferUnzipLib +} + + +task jalviewjsCreateJ2sSettings(type: WriteProperties) { + group "JalviewJS" + description "Create the alternative j2s file from the j2s.* properties" + + jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } + def siteDirProperty = "j2s.site.directory" + def setSiteDir = false + jalviewjsJ2sProps.each { prop, val -> + if (val != null) { + if (prop == siteDirProperty) { + if (!(val.startsWith('/') || val.startsWith("file://") )) { + val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}" + } + setSiteDir = true + } + property(prop,val) + } + if (!setSiteDir) { // default site location, don't override specifically set property + property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}") + } + } + outputFile = jalviewjsJ2sAltSettingsFileName + + if (! IN_ECLIPSE) { + inputs.properties(jalviewjsJ2sProps) + outputs.file(jalviewjsJ2sAltSettingsFileName) + } +} + + +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 "**" + } + + // should this be exclude really ? + duplicatesStrategy "INCLUDE" + + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncResources (type: Sync) { + dependsOn buildResources + + def inputFiles = fileTree(dir: resourcesBuildDir) + 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" ] + args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ] + } + + inputs.file("${jalviewDir}/.project") + outputs.upToDateWhen { + file(projdir).exists() + } +} + + +task jalviewjsTranspile(type: Exec) { + dependsOn jalviewjsEclipseSetup + dependsOn jalviewjsProjectImport + dependsOn jalviewjsEclipsePaths + if (!IN_ECLIPSE) { + dependsOn jalviewjsEnableAltFileProperty + } + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + 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${j2sHeadlessBuildProperty}=true" ] + args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ] + } + + def stdout + def stderr + doFirst { + stdout = new ByteArrayOutputStream() + stderr = new ByteArrayOutputStream() + + def logOutFileName = "${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: ${eclipseDebug} +---- +""" + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + // combine stdout and stderr + def logErrFOS = logOutFOS + + if (jalviewjs_j2s_to_console.equals("true")) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + System.out) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr), + System.err) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr) + } + } + + doLast { + if (stdout.toString().contains("Error processing ")) { + // j2s did not complete transpile + //throw new TaskExecutionException("Error during transpilation:\n${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}/${jalviewjs_closure_compiler}"]) + main = "com.google.javascript.jscomp.CommandLineRunner" + jvmArgs = [ "-Dfile.encoding=UTF-8" ] + args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ] + maxHeapSize = "2g" + + msg = "\nRunning '"+commandLine.join(' ')+"'\n" + println(msg) + logOutFile.append(msg+"\n") + + if (logOutConsole) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr), + System.err) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr) + } + } + msg = "--" + println(msg) + logOutFile.append(msg+"\n") +} + + +task jalviewjsBuildAllCores { + group "JalviewJS" + description "Build the core js lib closures listed in the classlists dir" + dependsOn jalviewjsTranspile + dependsOn jalviewjsTransferUnzipSwingJs + + def j2sDir = "${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}/${filename}" + doLast { + + def factory + try { + def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory") + factory = f.newInstance() + } catch (ClassNotFoundException e) { + throw new GradleException("Unable to create SimpleHttpFileServerFactory") + } + def port = Integer.valueOf(jalviewjs_server_port) + def start = port + def running = false + def url + def jalviewjsServer + while(port < start+1000 && !running) { + try { + def doc_root = new File("${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}/${eclipse_bin_dir}" + if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) { + delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") + } + delete jalviewjsJ2sAltSettingsFileName + } + + outputs.upToDateWhen( { false } ) +} + + +task jalviewjsIDE_checkJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)" + + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.") + } + def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ] + def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"] + if (altPluginsDir != null && file(altPluginsDir).exists()) { + eclipseJ2sPluginDirs += altPluginsDir + } + def foundPlugin = false + def j2sPluginFileName = j2sPluginFile.getName() + def eclipseJ2sPlugin + def eclipseJ2sPluginFile + eclipseJ2sPluginDirs.any { dir -> + eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}" + eclipseJ2sPluginFile = file(eclipseJ2sPlugin) + if (eclipseJ2sPluginFile.exists()) { + foundPlugin = true + return true + } + } + if (!foundPlugin) { + def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin" + System.err.println(msg) + throw new StopExecutionException(msg) + } + + def digest = MessageDigest.getInstance("MD5") + + digest.update(j2sPluginFile.text.bytes) + def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + digest.update(eclipseJ2sPluginFile.text.bytes) + def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + if (j2sPluginMd5 != eclipseJ2sPluginMd5) { + def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'" + System.err.println(msg) + throw new StopExecutionException(msg) + } else { + def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)" + println(msg) + } + } +} + +task jalviewjsIDE_copyJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir" + + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.") + } + def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}" + def eclipseJ2sPluginFile = file(eclipseJ2sPlugin) + def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart" + System.err.println(msg) + copy { + from j2sPlugin + eclipseJ2sPluginFile.getParentFile().mkdirs() + into eclipseJ2sPluginFile.getParent() + } + } +} + + +task jalviewjsIDE_j2sFile { + group "00 JalviewJS in Eclipse" + 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 +}