X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=fcacba37e3d1dfb4a75c9c92ff7914c3e29c13df;hb=18f5de004a86e5b768a8b50a9a59c2705e766d15;hp=48033f141d04646abcedb029df0dc32669fcfe4a;hpb=3f8dcb45270ca39e8fcb29db9a42c1a82a7ca8cf;p=jalview.git diff --git a/build.gradle b/build.gradle index 48033f1..fcacba3 100644 --- a/build.gradle +++ b/build.gradle @@ -2,6 +2,7 @@ import org.apache.tools.ant.filters.ReplaceTokens import org.gradle.internal.os.OperatingSystem import org.gradle.plugins.ide.eclipse.model.Output import org.gradle.plugins.ide.eclipse.model.Library +import java.security.MessageDigest import groovy.transform.ExternalizeMethods @@ -17,6 +18,7 @@ plugins { id 'eclipse' id 'com.github.johnrengelman.shadow' version '4.0.3' id 'com.install4j.gradle' version '7.0.9' + id 'com.dorongold.task-tree' version '1.4' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree } repositories { @@ -32,118 +34,192 @@ dependencies { compile 'org.apache.commons:commons-compress:1.18' } -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.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}/${JAVA_VERSION}" - getdownDir = "" + jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() + jalviewDirRelativePath = jalviewDir + + // local build environment properties + def localProps = "${jalviewDirAbsolutePath}/local.properties" + if (file(localProps).exists()) { + try { + def p = new Properties() + def localPropsFIS = new FileInputStream(localProps) + p.load(localPropsFIS) + localPropsFIS.close() + p.each { + key, val -> + def over = getProperty(key) != null + setProperty(key, val) + if (over) { + println("Overriding property '${key}' with local.properties value '${val}'") + } + } + } catch (Exception e) { + System.out.println("Exception reading local.properties") + } + } + + // 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) + testSourceDir = string("${jalviewDir}/${bareTestSourceDir}") + + // clover + cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") + classesDir = string("${jalviewDir}/${classes_dir}") + if (clover.equals("true")) { + use_clover = true + classesDir = string("${buildDir}/${cloverClassesDir}") + } else { + use_clover = false + classesDir = string("${jalviewDir}/${classes_dir}") + } + + classes = classesDir + + getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") + getdownDir = string("") reportRsyncCmd = false buildDist = true - buildProperties = buildPropertiesFile - getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}" + buildProperties = string("${resourceDir}/${build_properties_file}") + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}") switch (CHANNEL) { case "BUILD": // TODO: get bamboo build artifact URL for getdown artifacts getdown_channel_base = bamboo_channelbase - getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}" - getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}" + getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}") + getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" + buildProperties = string("${resourceDir}/${build_properties_file}") break case "RELEASE": getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") + getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_release - buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" + buildProperties = string("${resourceDir}/${build_properties_file}") reportRsyncCommand = true + // Don't ignore transpile errors for release build + if (jalviewjs_ignore_transpile_errors.equals("true")) { + jalviewjs_ignore_transpile_errors = "false" + println("Setting jalviewjs_ignore_transpile_errors to 'false'") + } break case "ARCHIVE": getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") + getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_alt if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { print "Must provide an ARCHIVEDIR value to produce an archive distribution" exit } else { - packageDir = "${ARCHIVEDIR}/${packageDir}" - buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}" + packageDir = string("${ARCHIVEDIR}/${packageDir}") + buildProperties = string("${ARCHIVEDIR}/${resource_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true break case "ARCHIVELOCAL": - getdown_channel_name = "archive/${JALVIEW_VERSION}" - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_channel_name = string("archive/${JALVIEW_VERSION}") + getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") getdown_app_base = file(getdownWebsiteDir).toURI().toString() getdown_app_dir = getdown_app_dir_alt if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { print "Must provide an ARCHIVEDIR value to produce an archive distribution" exit } else { - packageDir = "${ARCHIVEDIR}/${packageDir}" - buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}" + packageDir = string("${ARCHIVEDIR}/${packageDir}") + buildProperties = string("${ARCHIVEDIR}/${resource_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true - getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}" + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") break case "DEVELOP": getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") + getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" + buildProperties = string("${resourceDir}/${build_properties_file}") reportRsyncCommand = true break case "TEST-RELEASE": getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") + getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" + buildProperties = string("${resourceDir}/${build_properties_file}") reportRsyncCommand = true + // Don't ignore transpile errors for release build + if (jalviewjs_ignore_transpile_errors.equals("true")) { + jalviewjs_ignore_transpile_errors = "false" + println("Setting jalviewjs_ignore_transpile_errors to 'false'") + } break case ~/^SCRATCH(|-[-\w]*)$/: getdown_channel_name = CHANNEL - getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" - getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") + getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_alt - buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" + buildProperties = string("${resourceDir}/${build_properties_file}") reportRsyncCommand = true 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}" + buildProperties = string("${resourceDir}/${build_properties_file}") + getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") break default: // something wrong specified @@ -153,88 +229,135 @@ ext { } - println("Using a ${CHANNEL} profile. appbase=${getdown_app_base}") - getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}" + getdownAppDir = string("${getdownWebsiteDir}/${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}/${getdown_install_dir}" + getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}") + getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}") + getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/") + getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}") /* compile without modules -- using classpath libraries modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) modules_runtimeClasspath = modules_compileClasspath */ - gitHash = "" - gitBranch = "" - -} - -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") + gitHash = string("") + gitBranch = string("") + + println("Using a ${CHANNEL} profile.") + + additional_compiler_args = [] + // configure classpath/args for j8/j11 compilation + if (JAVA_VERSION.equals("1.8")) { + JAVA_INTEGER_VERSION = string("8") + //libDir = j8libDir + libDir = j11libDir + libDistDir = j8libDir + compile_source_compatibility = 1.8 + compile_target_compatibility = 1.8 + // these are getdown.txt properties defined dependent on the JAVA_VERSION + getdown_alt_java_min_version = getdown_alt_java8_min_version + getdown_alt_java_max_version = getdown_alt_java8_max_version + // this property is assigned below and expanded to multiple lines in the getdown task + getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location + // this property is for the Java library used in eclipse + eclipse_java_runtime_name = string("JavaSE-1.8") + } else if (JAVA_VERSION.equals("11")) { + JAVA_INTEGER_VERSION = string("11") + libDir = j11libDir + libDistDir = j11libDir + compile_source_compatibility = 11 + compile_target_compatibility = 11 + getdown_alt_java_min_version = getdown_alt_java11_min_version + getdown_alt_java_max_version = getdown_alt_java11_max_version + getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location + eclipse_java_runtime_name = string("JavaSE-11") + /* compile without modules -- using classpath libraries + additional_compiler_args += [ + '--module-path', modules_compileClasspath.asPath, + '--add-modules', j11modules + ] + */ + } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) { + JAVA_INTEGER_VERSION = JAVA_VERSION + libDir = j11libDir + libDistDir = j11libDir + compile_source_compatibility = JAVA_VERSION + compile_target_compatibility = JAVA_VERSION + getdown_alt_java_min_version = getdown_alt_java11_min_version + getdown_alt_java_max_version = getdown_alt_java11_max_version + getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location + eclipse_java_runtime_name = string("JavaSE-11") + /* 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 + macosJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre") + macosJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz") + windowsJavaVMDir = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre") + windowsJavaVMTgz = string("${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz") + install4jDir = string("${jalviewDir}/${install4jResourceDir}") + install4jConfFileName = string("jalview-installers-java${JAVA_VERSION}.install4j") + install4jConfFile = string("${install4jDir}/${install4jConfFileName}") + + + buildingHTML = string("${jalviewDir}/${docDir}/building.html") + helpFile = string("${classesDir}/${help_dir}/help.jhm") + helpParentDir = string("${jalviewDir}/${help_parent_dir}") + helpDir = string("${help_dir}") + helpSourceDir = string("${helpParentDir}/${helpDir}") + + + 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}/${jalviewjs_j2s_settings}") + jalviewjsJ2sProps = null + + eclipseJavaVersion = "55" + jalviewjsJ2sPlugin = jalviewjs_j2s_plugin + if (IN_ECLIPSE) { + //def eclipseJavaVersion = System.property["java.class.version"] + if (Float.parseFloat(eclipseJavaVersion) >= 55 && file(jalviewjs_j2s_plugin_j11).exists()) { // 55 is Java 11 + jalviewjsJ2sPlugin = jalviewjs_j2s_plugin_j11 + } + } + eclipseWorkspace = null + eclipseBinary = string("") + eclipseVersion = string("") + eclipseDebug = false + eclipseJavaVersion = string("") + // ENDEXT } -sourceSets { +sourceSets { main { java { - srcDirs "${jalviewDir}/${sourceDir}" - outputDir = file("${classes}") + srcDirs sourceDir + outputDir = file(classesDir) } resources { - srcDirs "${jalviewDir}/${resourceDir}" + srcDirs resourceDir } jar.destinationDir = file("${jalviewDir}/${packageDir}") @@ -265,7 +388,7 @@ sourceSets { test { java { - srcDirs "${jalviewDir}/${testSourceDir}" + srcDirs testSourceDir outputDir = file("${jalviewDir}/${testOutputDir}") } @@ -289,6 +412,7 @@ sourceSets { } } + // clover bits dependencies { if (use_clover) { @@ -297,6 +421,7 @@ dependencies { } } + configurations { cloverRuntime cloverRuntime.extendsFrom cloverCompile @@ -331,21 +456,23 @@ eclipse { def removeTheseToo = [] HashMap alreadyAddedSrcPath = new HashMap<>(); cp.entries.each { entry -> + // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test". + // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover + // we add the resources and help/help dirs in as libs afterwards (see below) if (entry.kind == 'src') { - if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) { removeTheseToo += entry } else { alreadyAddedSrcPath.putAt(entry.path, true) } } + } cp.entries.removeAll(removeTheseToo) - if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) { - cp.entries += new Output("${eclipse_bin_dir}/main") - } - if (file(helpParentDir).isDirectory()) { - cp.entries += new Library(fileReference(helpParentDir)) + cp.entries += new Output("${eclipse_bin_dir}/main") + if (file(helpSourceDir).isDirectory()) { + cp.entries += new Library(fileReference(helpSourceDir)) } if (file(resourceDir).isDirectory()) { cp.entries += new Library(fileReference(resourceDir)) @@ -356,8 +483,8 @@ eclipse { sourceSets.main.compileClasspath.findAll { it.name.endsWith(".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 + // don't add dirs to classpath, especially if they don't exist + return false // groovy "continue" in .any closure } def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { @@ -374,12 +501,13 @@ eclipse { } //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each { - sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each { + sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { //no longer want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath - return false // groovy "break" in .each closure + return false // groovy "continue" in .any closure } + def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) @@ -409,6 +537,7 @@ eclipse { javaRuntimeName = eclipse_java_runtime_name // add in jalview project specific properties/preferences into eclipse core preferences + // and also the codestyle XML file file { withProperties { props -> def jalview_prefs = new Properties() @@ -420,16 +549,39 @@ eclipse { props.putAt(t, v) } } + // codestyle file -- overrides previous formatter prefs + def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}") + if (csFile.exists()) { + XmlParser parser = new XmlParser() + def profiles = parser.parse(csFile) + def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") } + if (profile != null) { + profile.'setting'.each { s -> + def id = s.'@id' + def value = s.'@value' + if (id != null && value != null) { + props.putAt(id, value) + } + } + } + } } } } // jdt + if (IN_ECLIPSE) { + // Don't want these to be activated if in headless build + synchronizationTasks "eclipseSynchronizationTask" + //autoBuildTasks "eclipseAutoBuildTask" + + } } + task cloverInstr() { // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) + inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"])) outputs.dir cloverInstrDir doFirst { @@ -466,7 +618,6 @@ task cloverReport { com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) } } - // end clover bits @@ -481,6 +632,7 @@ compileJava { } + compileTestJava { if (use_clover) { dependsOn compileCloverJava @@ -508,12 +660,14 @@ compileCloverJava { classpath += configurations.cloverRuntime } + clean { doFirst { delete sourceSets.main.java.outputDir } } + cleanTest { doFirst { delete sourceSets.test.java.outputDir @@ -521,12 +675,14 @@ cleanTest { } } + // format is a string like date.format("dd MMMM yyyy") def getDate(format) { def date = new Date() return date.format(format) } + task setGitVals { def hashStdOut = new ByteArrayOutputStream() exec { @@ -542,34 +698,45 @@ task setGitVals { ignoreExitValue true } - project.ext.gitHash = hashStdOut.toString().trim() - project.ext.gitBranch = branchStdOut.toString().trim() + gitHash = hashStdOut.toString().trim() + gitBranch = branchStdOut.toString().trim() outputs.upToDateWhen { false } } + task createBuildProperties(type: WriteProperties) { + group = "build" + description = "Create the ${buildProperties} file" dependsOn setGitVals - inputs.dir("${jalviewDir}/${sourceDir}") - inputs.dir("${classes}") - inputs.dir("${jalviewDir}/${resourceDir}") + inputs.dir(sourceDir) + inputs.dir(resourceDir) + file(buildProperties).getParentFile().mkdirs() outputFile (buildProperties) // taking time specific comment out to allow better incremental builds 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+"]" + property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" outputs.file(outputFile) } -def buildingHTML = "${jalviewDir}/${docDir}/building.html" + +clean { + doFirst { + delete buildProperties + } +} + + task cleanBuildingHTML(type: Delete) { doFirst { delete buildingHTML } } + task convertBuildingMD(type: Exec) { dependsOn cleanBuildingHTML def buildingMD = "${jalviewDir}/${docDir}/building.md" @@ -593,7 +760,7 @@ task convertBuildingMD(type: Exec) { commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD } else { println("Cannot find pandoc. Skipping convert building.md to HTML") - throw new StopExecutionException() + throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML") } } @@ -604,35 +771,43 @@ task convertBuildingMD(type: Exec) { outputs.file(buildingHTML) } + clean { doFirst { delete buildingHTML } } + task syncDocs(type: Sync) { dependsOn convertBuildingMD - def syncDir = "${classes}/${docDir}" + def syncDir = "${classesDir}/${docDir}" from fileTree("${jalviewDir}/${docDir}") into syncDir } -def helpFile = "${classes}/${helpDir}/help.jhm" task copyHelp(type: Copy) { - def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}" - def outputDir = "${classes}/${helpDir}" + def inputDir = helpSourceDir + def outputDir = "${classesDir}/${helpDir}" from(inputDir) { exclude '**/*.gif' - exclude '**/*.jpg' - exclude '**/*.png' - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) + 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' + include '**/*.jpg' + include '**/*.png' } into outputDir @@ -641,22 +816,25 @@ task copyHelp(type: Copy) { outputs.dir(outputDir) } + task syncLib(type: Sync) { - def syncDir = "${classes}/${libDistDir}" + def syncDir = "${classesDir}/${libDistDir}" from fileTree("${jalviewDir}/${libDistDir}") into syncDir } + task syncResources(type: Sync) { - from "${jalviewDir}/${resourceDir}" + dependsOn createBuildProperties + from resourceDir include "**/*.*" - exclude "install4j" - into "${classes}" + into "${classesDir}" preserve { include "**" } } + task prepare { dependsOn syncResources dependsOn syncDocs @@ -687,20 +865,21 @@ test { sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility jvmArgs += additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") + } + task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" - workingDir = "${classes}/${helpDir}" + workingDir = "${classesDir}/${helpDir}" def argDir = "html" args = [ argDir ] inputs.dir("${workingDir}/${argDir}") - outputs.dir("${classes}/doc") - outputs.dir("${classes}/help") + outputs.dir("${classesDir}/doc") + outputs.dir("${classesDir}/help") outputs.file("${workingDir}/JavaHelpSearch/DOCS") outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") @@ -709,6 +888,7 @@ task buildIndices(type: JavaExec) { outputs.file("${workingDir}/JavaHelpSearch/TMAP") } + task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utilsDir}") @@ -721,26 +901,33 @@ task compileLinkCheck(type: JavaCompile) { outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class") } -def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch") + task linkCheck(type: JavaExec) { dependsOn prepare, compileLinkCheck + + def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out") classpath = files("${jalviewDir}/${utilsDir}") main = "HelpLinksChecker" workingDir = jalviewDir - def help = "${classes}/${helpDir}" - args = [ "${classes}/${helpDir}", "-nointernet" ] + def help = "${classesDir}/${helpDir}" + args = [ "${classesDir}/${helpDir}", "-nointernet" ] - doLast { - helplinkscheckertouchfile.createNewFile() - } + 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("${classes}/${helpDir}") - outputs.file(helplinkscheckertouchfile) + inputs.dir("${classesDir}/${helpDir}") + outputs.file(helpLinksCheckerOutFile) } // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" -ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}" +ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}" ant.importBuild "${utilsDir}/publishHelp.xml" @@ -750,6 +937,7 @@ task cleanPackageDir(type: Delete) { } } + jar { dependsOn linkCheck dependsOn buildIndices @@ -771,15 +959,17 @@ jar { exclude "**/*.jar" exclude "**/*.jar.*" - inputs.dir("${classes}") + inputs.dir(classesDir) outputs.file("${jalviewDir}/${packageDir}/${archiveName}") } + task copyJars(type: Copy) { - from fileTree(dir: "${classes}", include: "**/*.jar").files + from fileTree(dir: classesDir, include: "**/*.jar").files into "${jalviewDir}/${packageDir}" } + // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well task syncJars(type: Sync) { from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files @@ -789,6 +979,7 @@ task syncJars(type: Sync) { } } + task makeDist { group = "build" description = "Put all required libraries in dist" @@ -801,6 +992,7 @@ task makeDist { outputs.dir("${jalviewDir}/${packageDir}") } + task cleanDist { dependsOn cleanPackageDir dependsOn cleanTest @@ -824,6 +1016,7 @@ shadowJar { minimize() } + task getdownWebsite() { group = "distribution" description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer" @@ -833,31 +1026,31 @@ task getdownWebsite() { def getdownWebsiteResourceFilenames = [] def getdownTextString = "" - def getdownResourceDir = project.ext.getdownResourceDir - def getdownAppDir = project.ext.getdownAppDir + def getdownResourceDir = getdownResourceDir + def getdownAppDir = getdownAppDir def getdownResourceFilenames = [] doFirst { // clean the getdown website and files dir before creating getdown folders - delete project.ext.getdownWebsiteDir - delete project.ext.getdownFilesDir + delete getdownWebsiteDir + delete getdownFilesDir copy { from buildProperties - rename(buildPropertiesFile, getdown_build_properties) - into project.ext.getdownAppDir + rename(build_properties_file, getdown_build_properties) + into getdownAppDir } getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}" // go through properties looking for getdown_txt_... def props = project.properties.sort { it.key } - if (getdown_alt_java_min_version.length() > 0) { - props.put("getdown_txt_java_min_version", getdown_alt_java_min_version) - } - if (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) + 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) props.each{ prop, val -> @@ -899,7 +1092,7 @@ task getdownWebsite() { getdownResourceFilenames.each{ filename -> copy { from filename - into project.ext.getdownResourceDir + into getdownResourceDir } } @@ -918,7 +1111,7 @@ task getdownWebsite() { getdownTextString += line copy { from f.getPath() - into project.ext.getdownAppDir + into getdownAppDir } } @@ -932,7 +1125,7 @@ task getdownWebsite() { getdownTextString += line copy { from f.getPath() - into project.ext.getdownJ11libDir + into getdownJ11libDir } } } @@ -943,16 +1136,16 @@ task getdownWebsite() { getdownTextString += "resource = ${getdown_launcher_new}\n" getdownTextString += "class = ${mainClass}\n" - def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt") + def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) - def launch_jvl = file("${project.ext.getdownWebsiteDir}/${getdown_launch_jvl}") + def launch_jvl = file("${getdownWebsiteDir}/${getdown_launch_jvl}") launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) copy { from getdownLauncher rename(file(getdownLauncher).getName(), getdown_launcher_new) - into project.ext.getdownWebsiteDir + into getdownWebsiteDir } copy { @@ -960,7 +1153,7 @@ task getdownWebsite() { if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } - into project.ext.getdownWebsiteDir + into getdownWebsiteDir } if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { @@ -992,18 +1185,19 @@ task getdownWebsite() { } copy { - from getdownResourceDir - into "${project.ext.getdownFilesDir}/${getdown_resource_dir}" + from getdownResourceDir + into "${getdownFilesDir}/${getdown_resource_dir}" } } if (buildDist) { inputs.dir("${jalviewDir}/${packageDir}") } - outputs.dir(project.ext.getdownWebsiteDir) - outputs.dir(project.ext.getdownFilesDir) + outputs.dir(getdownWebsiteDir) + outputs.dir(getdownFilesDir) } + task getdownDigest(type: JavaExec) { group = "distribution" description = "Digest the getdown website folder" @@ -1012,11 +1206,12 @@ task getdownDigest(type: JavaExec) { classpath = files("${getdownWebsiteDir}/${getdown_launcher}") } main = "com.threerings.getdown.tools.Digester" - args project.ext.getdownWebsiteDir - inputs.dir(project.ext.getdownWebsiteDir) - outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt") + args getdownWebsiteDir + inputs.dir(getdownWebsiteDir) + outputs.file("${getdownWebsiteDir}/digest2.txt") } + task getdown() { group = "distribution" description = "Create the minimal and full getdown app folder for installers and website and create digest file" @@ -1039,13 +1234,15 @@ task getdown() { } } + clean { doFirst { - delete project.ext.getdownWebsiteDir - delete project.ext.getdownFilesDir + delete getdownWebsiteDir + delete getdownFilesDir } } + install4j { def install4jHomeDir = "/opt/install4j" def hostname = "hostname".execute().text.trim() @@ -1066,49 +1263,57 @@ install4j { } } -def install4jConf -def macosJavaVMDir -def macosJavaVMTgz -def windowsJavaVMDir -def windowsJavaVMTgz -def install4jDir = "${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 - ] + rename (install4jTemplate, install4jConfFileName) + filter(ReplaceTokens, + beginToken: '', + endToken: '', + tokens: [ + '9999999999': JAVA_VERSION + ] + ) + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'JAVA_VERSION': JAVA_VERSION, + 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, + 'VERSION': JALVIEW_VERSION, + 'MACOS_JAVA_VM_DIR': macosJavaVMDir, + 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, + 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, + 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, + 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations, + 'COPYRIGHT_MESSAGE': install4jCopyrightMessage, + 'MACOS_BUNDLE_ID': install4jMacOSBundleId, + 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, + 'GETDOWN_DIST_DIR': getdown_app_dir, + 'GETDOWN_ALT_DIR': getdown_app_dir_alt, + 'GETDOWN_INSTALL_DIR': getdown_install_dir + ] ) - if (OSX_KEYPASS=="") { - filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"']) - filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor']) + 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) + outputs.files(install4jConfFile) doLast { // include file associations in installer @@ -1118,7 +1323,7 @@ task copyInstall4jTemplate(type: Copy) { flags: "s", match: '', replace: installerFileAssociationsXml, - file: install4jConf + file: install4jConfFile ) /* // include uninstaller applescript app files in dmg @@ -1128,41 +1333,45 @@ task copyInstall4jTemplate(type: Copy) { flags: "s", match: '', replace: installerDMGUninstallerXml, - file: install4jConf + file: install4jConfFile ) */ } } + +clean { + doFirst { + delete install4jConfFile + } +} + + 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) + projectFile = file(install4jConfFile) variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH] destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}" buildSelected = true if (OSX_KEYPASS) { macKeystorePassword=OSX_KEYPASS + } + doFirst { + println("Using projectFile "+projectFile) } - inputs.dir(project.ext.getdownWebsiteDir) - inputs.file(install4jConf) + inputs.dir(getdownWebsiteDir) + inputs.file(install4jConfFile) inputs.dir(macosJavaVMDir) inputs.dir(windowsJavaVMDir) outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}") - } -clean { - doFirst { - delete install4jConf - } -} task sourceDist (type: Tar) { @@ -1210,224 +1419,305 @@ task sourceDist (type: Tar) { 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 ("${j11modDir}/**/*.jar") -} -// from (jalviewDir) { -// // explicit includes for stuff that seemed to not get included -// include(fileTree("test/**/*.")) -// exclude(EXCLUDE_FILES) -// exclude(PROCESS_FILES) -// } + // exluding these as not using jars as modules yet + exclude ("${j11modDir}/**/*.jar") + } + // from (jalviewDir) { + // // explicit includes for stuff that seemed to not get included + // include(fileTree("test/**/*.")) + // exclude(EXCLUDE_FILES) + // exclude(PROCESS_FILES) + // } } + task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("${classes}/${helpDir}") - outputs.dir("${helpOutputDir}") -} - -def jalviewjsBuildDir -def jalviewjsSiteDir -def jalviewjsTransferSiteDir -task jalviewjsSitePath { - def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) - jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs" - if (jalviewjs_site_dir.startsWith('/')) { - jalviewjsSiteDir = jalviewjs_site_dir - } else { - jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}" + inputs.dir("${classesDir}/${helpDir}") + outputs.dir("${buildDir}/distributions/${helpDir}") +} + + +task j2sSetHeadlessBuild { + doFirst { + IN_ECLIPSE = false } - jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site" } -def eclipseWorkspace + task jalviewjsSetEclipseWorkspace { def propKey = "jalviewjs_eclipse_workspace" - def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}" - def props = new Properties() - def eclipseWsDir def propVal = null if (project.hasProperty(propKey)) { propVal = project.getProperty(propKey) - eclipseWsDir = propVal + if (propVal.startsWith("~/")) { + propVal = System.getProperty("user.home") + propVal.substring(1) + } } - if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) { - def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}") + def propsFileName = "${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() - props.setProperty(propKey, eclipseWsDir) - def propsFile = file(propsFileName) - propsFile.parentFile.mkdirs() - propsFile.createNewFile() // doesn't affect existing file - def outs = new FileOutputStream(propsFile, false) - props.store(outs, null) - outs.close() + writeProps = true } - eclipseWorkspace = file(eclipseWsDir) - - println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) - - inputs.property(propKey, propVal) - outputs.file(propsFileName) -} - -task jalviewjsUnzipFiles { - dependsOn jalviewjsSitePath - - def zipFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_libjs_dir}", include: "*.zip") - zipFiles += "${jalviewjs_utils_dir}/${jalviewjs_swingjs_zip}" + 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}") + } - doLast { - zipFiles.each { file_zip -> - copy { - from zipTree(file_zip) - into jalviewjsSiteDir - } + 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.files zipFiles - outputs.dir jalviewjsSiteDir + //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() } } -def eclipseDropinsDir -def eclipseBinary -def eclipseVersion -def fromDropinsDir + task jalviewjsEclipsePaths { - def eclipseRoot def eclipseProduct - eclipseRoot = jalviewjs_eclipse_root - if (eclipseRoot.startsWith("~")) { + + def eclipseRoot = jalviewjs_eclipse_root + if (eclipseRoot.startsWith("~/")) { eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1) } if (OperatingSystem.current().isMacOsX()) { eclipseRoot += "/Eclipse.app" - eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins" eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse" eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" } else if (OperatingSystem.current().isWindows()) { // check these paths!! if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { - eclipseRoot += "/eclipse" + eclipseRoot += "/eclipse.exe" } - eclipseDropinsDir = "${eclipseRoot}/dropins" eclipseBinary = "${eclipseRoot}/eclipse" eclipseProduct = "${eclipseRoot}/.eclipseproduct" } else { // linux or unix if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" } - eclipseDropinsDir = "${eclipseRoot}/dropins" eclipseBinary = "${eclipseRoot}/eclipse" eclipseProduct = "${eclipseRoot}/.eclipseproduct" } - eclipseVersion = "4.12" // default + eclipseVersion = "4.13" // default + def assumedVersion = true if (file(eclipseProduct).exists()) { def fis = new FileInputStream(eclipseProduct) def props = new Properties() props.load(fis) eclipseVersion = props.getProperty("version") fis.close() - println("ECLIPSE_VERSION=${eclipseVersion}") + assumedVersion = false } - String[] v = eclipseVersion.split("\\.") - def v0 = Integer.valueOf(v[0]) - def v1 = Integer.valueOf(v[1]) - if (v0 < 4 || ( v0 == 4 && v1 < 13 )) { - fromDropinsDir = "eclipse/dropins_4.12" - } else { - fromDropinsDir = "eclipse/dropins_4.13" - } + + 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 } -task jalviewjsEclipseCopyDropins { + +// 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: "${jalviewjs_utils_dir}/${fromDropinsDir}", include: "*.jar") - def outputDir = eclipseDropinsDir - inputs.files inputFiles - inputFiles.each { file -> - outputs.file("${outputDir}/${file.name}") + 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}/${jalviewjs_libjs_dir}", include: "*.zip") + doLast { - inputFiles.each { file -> + zipFiles.each { file_zip -> copy { - from file - into outputDir + from zipTree(file_zip) + into "${jalviewDir}/${jalviewjsTransferSiteLibDir}" } } } + + inputs.files zipFiles + outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}" } -// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir -task NEWjalviewjsEclipseCopyDropins(type: Copy) { - dependsOn jalviewjsEclipsePaths - from fromDropinsDir - into eclipseDropinsDir + +task jalviewjsTransferUnzipAllLibs { + dependsOn jalviewjsTransferUnzipSwingJs + dependsOn jalviewjsTransferUnzipLib } + task jalviewjsCreateJ2sSettings(type: WriteProperties) { - dependsOn jalviewjsSitePath - outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}") - def props = project.properties.sort { it.key } + group "JalviewJS" + description "Create the .j2s file from the j2s.* properties" + + jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } def siteDirProperty = "j2s.site.directory" def setSiteDir = false - props.each { prop, val -> - if (prop.startsWith("j2s.") && val != null) { + jalviewjsJ2sProps.each { prop, val -> + if (val != null) { if (prop == siteDirProperty) { if (!(val.startsWith('/') || val.startsWith("file://") )) { - val = "${jalviewjsTransferSiteDir}/${val}" + val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}" } setSiteDir = true } property(prop,val) } - if (!setSiteDir) { - property(siteDirProperty,jalviewjsTransferSiteDir) + if (!setSiteDir) { // default site location, don't override specifically set property + property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}") } } - inputs.properties(props.findAll( { k, v -> k.startsWith("j2s.") } )) - outputs.file(outputFile) + outputFile = jalviewjsJ2sSettingsFileName + + if (! IN_ECLIPSE) { + inputs.properties(jalviewjsJ2sProps) + outputs.file(jalviewjsJ2sSettingsFileName) + } } + task jalviewjsEclipseSetup { dependsOn jalviewjsEclipseCopyDropins dependsOn jalviewjsSetEclipseWorkspace dependsOn jalviewjsCreateJ2sSettings } -task jalviewjsCopyResources (type: Copy) { - dependsOn jalviewjsSitePath - def inputFiles = fileTree(dir: jalviewjs_resource_dir) - def outputDir = "${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" + +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 @@ -1436,14 +1726,17 @@ task jalviewjsCopyResources (type: Copy) { outputFiles += "${outputDir}/${filename}" null } + preserve { + include "**" + } outputs.files outputFiles inputs.files inputFiles } -task jalviewjsCopySiteResources (type: Copy) { - dependsOn jalviewjsSitePath - def inputFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_site_resource_dir}") - def outputDir = jalviewjsSiteDir + +task jalviewjsSyncResources (type: Sync) { + def inputFiles = fileTree(dir: resourceDir) + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" from inputFiles into outputDir @@ -1452,38 +1745,111 @@ task jalviewjsCopySiteResources (type: Copy) { outputFiles += "${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) { - // work out how to do this! - dependsOn eclipseProject - dependsOn eclipseClasspath - dependsOn eclipseJdt + 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 (eclipse_debug == "true") { + 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 projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" inputs.file("${jalviewDir}/.project") - outputs.dir(projdir) - outputs.upToDateWhen { file(projdir).exists() } + 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, "-${jalviewjs_eclipseBuildArg}", eclipse_project_name ]) - if (eclipse_debug == "true") { + args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${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 @@ -1491,16 +1857,20 @@ task jalviewjsTranspile(type: Exec) { stdout = new ByteArrayOutputStream() stderr = new ByteArrayOutputStream() - def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}" + def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}" def logOutFile = file(logOutFileName) logOutFile.createNewFile() - def logOutFOS = new FileOutputStream(logOutFile, false) - //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}" - //def logErrFile = file(logFileName) - //logErrFile.createNewFile() - //def logErrFOS = new FileErrputStream(logErrFile, false) + logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} +BINARY: ${eclipseBinary} +VERSION: ${eclipseVersion} +WORKSPACE: ${eclipseWorkspace} +DEBUG: ${eclipseDebug} +---- +""" + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append // combine stdout and stderr def logErrFOS = logOutFOS + if (jalviewjs_j2s_to_console.equals("true")) { standardOutput = new org.apache.tools.ant.util.TeeOutputStream( new org.apache.tools.ant.util.TeeOutputStream( @@ -1521,53 +1891,366 @@ task jalviewjsTranspile(type: Exec) { stderr) } } + doLast { if (stdout.toString().contains("Error processing ")) { // j2s did not complete transpile - throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'") + //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}/${jalviewjs_j2s_transpile_stdout}'") + } } } - inputs.dir(sourceDir) - outputs.dir("${eclipse_bin_dir}/main") - outputs.dir(jalviewjsTransferSiteDir) - outputs.upToDateWhen { file("${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } + 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 ${jsfile}" + println(msg) + logOutFile.createNewFile() + logOutFile.append(msg+"\n") + + def coreTop = file(prefixFile) + def coreBottom = file(suffixFile) + coreFile.getParentFile().mkdirs() + coreFile.createNewFile() + coreFile.write( coreTop.text ) + list.each { + f -> + if (f.exists()) { + def t = f.text + t.replaceAll("Clazz\\.([^_])","Clazz_${1}") + coreFile.append( t ) + } else { + msg = "...file '"+f.getPath()+"' does not exist, skipping" + println(msg) + logOutFile.append(msg+"\n") + } + } + coreFile.append( coreBottom.text ) + + msg = "Generating ${zjsfile}" + println(msg) + logOutFile.append(msg+"\n") + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + def logErrFOS = logOutFOS + + javaexec { + classpath = files(["${jalviewDir}/tools/closure_compiler.jar"]) + args = [ "--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 jalviewjsCopyTransferSite(type: Copy) { + +task jalviewjsBuildAllCores { + group "JalviewJS" + description "Build the core js lib closures listed in the classlists dir" dependsOn jalviewjsTranspile - from jalviewjsTransferSiteDir - into jalviewjsSiteDir + 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': '"'+mainClass+'"', + 'CODE': "null", + 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]", + 'COREKEY': jalviewjs_core_key, + 'CORENAME': coreName + ] + ) + } } -jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite -jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite -jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite + +task jalviewjsPublishCoreTemplates { + dependsOn jalviewjsBuildAllCores + def inputFileName = "${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 jalviewjsSitePath - dependsOn jalviewjsUnzipFiles - dependsOn jalviewjsCopyResources - dependsOn jalviewjsCopySiteResources + dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncResources + dependsOn jalviewjsSyncSiteResources + dependsOn jalviewjsSyncBuildProperties + dependsOn jalviewjsSyncCore } + task jalviewjsBuildSite { group "JalviewJS" description "Builds the whole website including transpiled code" - dependsOn jalviewjsCopyTransferSite + 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 jalviewjsTransferSiteDir - delete jalviewjsSiteDir + delete "${jalviewDir}/${jalviewjsSiteDir}" } } + task jalviewjsSiteTar(type: Tar) { group "JalviewJS" description "Creates a tar.gz file for the website" @@ -1581,17 +2264,18 @@ task jalviewjsSiteTar(type: Tar) { compression Compression.GZIP - from jalviewjsSiteDir + from "${jalviewDir}/${jalviewjsSiteDir}" into jalviewjs_site_dir // this is inside the tar file - inputs.dir(jalviewjsSiteDir) + inputs.dir("${jalviewDir}/${jalviewjsSiteDir}") } + task jalviewjsServer { group "JalviewJS" - description "Starts a webserver on localhost to test the website" - dependsOn jalviewjsSitePath - def htmlFile = "${jalviewDirAbsolutePath}/jalviewjsTest.html" + 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}/${filename}" doLast { SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory() @@ -1599,78 +2283,207 @@ task jalviewjsServer { def start = port def running = false def url + def jalviewjsServer while(port < start+1000 && !running) { try { def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") - def jalviewjsServer = factory.start(doc_root, port) + jalviewjsServer = factory.start(doc_root, port) running = true url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource) println("SERVER STARTED with document root ${doc_root}.") println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).") println("For debug: "+url+"?j2sdebug") - - file(htmlFile).text = """ -

Jalview JS Test. <${url}>

-

Jalview JS Test with debug. <${url}?j2sdebug<

- """ - + println("For verbose: "+url+"?j2sverbose") } catch (Exception e) { port++; } } + def htmlText = """ +

JalviewJS Test. <${url}>

+

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

+

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

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

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

+ """ + println("For core ${cl.name}: "+urlcore) + } + file(htmlFile).text = htmlText } outputs.file(htmlFile) + outputs.upToDateWhen({false}) } + task cleanJalviewjsAll { group "JalviewJS" description "Delete all configuration and build artifacts to do with JalviewJS build" dependsOn cleanJalviewjsSite + dependsOn jalviewjsEclipsePaths doFirst { - delete jalviewjsBuildDir + delete "${jalviewDir}/${jalviewjsBuildDir}" delete "${jalviewDir}/${eclipse_bin_dir}" - delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") + if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) { + delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") + } delete "${jalviewDir}/${jalviewjs_j2s_settings}" } + + outputs.upToDateWhen( { false } ) } -task jalviewjs { - group "JalviewJS" - description "Build the site" - dependsOn jalviewjsBuildSite + +task jalviewjsIDE_checkJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)" + + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.") + } + def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}" + def eclipseJ2sPluginFile = file(eclipseJ2sPlugin) + if (!eclipseJ2sPluginFile.exists()) { + def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin" + System.err.println(msg) + throw new StopExecutionException(msg) + } + + def digest = MessageDigest.getInstance("MD5") + + digest.update(j2sPluginFile.text.bytes) + def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + //digest.update(eclipseJ2sPluginFile.text.bytes) + def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0') + + if (j2sPluginMd5 != eclipseJ2sPluginMd5) { + def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'" + System.err.println(msg) + if (! copyPlugin) { + throw new StopExecutionException(msg) + } + } else { + def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)" + println(msg) + } + } } +task jalviewjsIDE_copyJ2sPlugin { + group "00 JalviewJS in Eclipse" + description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir" -task jalviewjsIDECopyTransferSite(type: Copy) { - from jalviewjsTransferSiteDir - into jalviewjsSiteDir + doFirst { + def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}") + def j2sPluginFile = file(j2sPlugin) + def eclipseHome = System.properties["eclipse.home.location"] + if (eclipseHome == null || ! IN_ECLIPSE) { + throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.") + } + def eclipseJ2sPlugin = "${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" + println(msg) + copy { + from j2sPlugin + eclipseJ2sPluginFile.getParentFile().mkdirs() + into eclipseJ2sPluginFile.getParent() + } + } } -task jalviewjsIDEj2s { - group "JalviewJS in Eclipse" + +task jalviewjsIDE_j2sFile { + group "00 JalviewJS in Eclipse" description "Creates the .j2s file" dependsOn jalviewjsCreateJ2sSettings } -task jalviewjsIDEBuildSite { - group "JalviewJS in Eclipse" - description "Copies the Eclipse transpiled site and unzips supporting zipfiles" - dependsOn jalviewjsIDECopyTransferSite + +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 +} + + +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 jalviewjsIDESiteClean { - group "JalviewJS in Eclipse" + +task jalviewjsIDE_SiteClean { + group "00 JalviewJS in Eclipse" description "Deletes the Eclipse transpiled site" dependsOn cleanJalviewjsSite } -task jalviewjsIDEServer { - group "JalviewJS in Eclipse" + +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 +}