X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.gradle;h=cbd65f2f92e73ead0e39a234210adbfcecfed25c;hp=5abde5047a92f300901676eac37fdb817552fca8;hb=e6dea4b93a53786199b36a4c428afd3ca1faf6bf;hpb=870cce42ccbadc4208e17cbe04d6a5ea739d31b0 diff --git a/build.gradle b/build.gradle index 5abde50..cbd65f2 100644 --- a/build.gradle +++ b/build.gradle @@ -2,14 +2,37 @@ * For properties set within build.gradle, use camelCaseNoSpace. */ import org.apache.tools.ant.filters.ReplaceTokens - - +import org.gradle.internal.os.OperatingSystem +import org.gradle.plugins.ide.eclipse.model.Output +import org.gradle.plugins.ide.eclipse.model.Library +import java.security.MessageDigest +import groovy.transform.ExternalizeMethods +import groovy.util.XmlParser +import groovy.xml.XmlUtil + + +buildscript { + repositories { + mavenCentral() + mavenLocal() + } +} plugins { id 'java' + id 'application' + id 'eclipse' + id 'com.github.johnrengelman.shadow' version '4.0.3' + id 'com.install4j.gradle' version '8.0.4' + id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree } +repositories { + jcenter() + mavenCentral() + mavenLocal() +} // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use @@ -444,6 +467,25 @@ sourceSets { runtimeClasspath = compileClasspath } + clover { + java { + srcDirs cloverInstrDir + outputDir = cloverClassesDir + } + + resources { + srcDirs = sourceSets.main.resources.srcDirs + } + + compileClasspath = files( sourceSets.clover.java.outputDir ) + //compileClasspath += files( testClassesDir ) + compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) + + runtimeClasspath = compileClasspath + } + test { java { srcDirs testSourceDir @@ -451,11 +493,11 @@ sourceSets { } resources { - srcDirs = sourceSets.main.resources.srcDirs + srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs } compileClasspath = files( sourceSets.test.java.outputDir ) - compileClasspath += sourceSets.main.compileClasspath + compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath @@ -464,6 +506,358 @@ sourceSets { } +// eclipse project and settings files creation, also used by buildship +eclipse { + project { + name = eclipse_project_name + + natures 'org.eclipse.jdt.core.javanature', + 'org.eclipse.jdt.groovy.core.groovyNature', + 'org.eclipse.buildship.core.gradleprojectnature' + + buildCommand 'org.eclipse.jdt.core.javabuilder' + buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder' + } + + classpath { + //defaultOutputDir = sourceSets.main.java.outputDir + def removeThese = [] + configurations.each{ + if (it.isCanBeResolved()) { + removeThese += it + } + } + + minusConfigurations += removeThese + plusConfigurations = [ ] + file { + + whenMerged { cp -> + def removeTheseToo = [] + HashMap alreadyAddedSrcPath = new HashMap<>(); + cp.entries.each { entry -> + // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test". + // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover + // we add the resources and help/help dirs in as libs afterwards (see below) + if (entry.kind == 'src') { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) { + removeTheseToo += entry + } else { + alreadyAddedSrcPath.putAt(entry.path, true) + } + } + + } + cp.entries.removeAll(removeTheseToo) + + //cp.entries += new Output("${eclipse_bin_dir}/main") + if (file(helpParentDir).isDirectory()) { + cp.entries += new Library(fileReference(helpParentDir)) + } + if (file(resourceDir).isDirectory()) { + cp.entries += new Library(fileReference(resourceDir)) + } + + HashMap alreadyAddedLibPath = new HashMap<>(); + + sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any { + //don't want to add outputDir as eclipse is using its own output dir in bin/main + if (it.isDirectory() || ! it.exists()) { + // don't add dirs to classpath, especially if they don't exist + return false // groovy "continue" in .any closure + } + def itPath = it.toString() + if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { + // make relative path + itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) + } + if (alreadyAddedLibPath.get(itPath)) { + //println("Not adding duplicate entry "+itPath) + } else { + //println("Adding entry "+itPath) + cp.entries += new Library(fileReference(itPath)) + alreadyAddedLibPath.put(itPath, true) + } + } + + sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { + //no longer want to add outputDir as eclipse is using its own output dir in bin/main + if (it.isDirectory() || ! it.exists()) { + // don't add dirs to classpath + return false // groovy "continue" in .any closure + } + + def itPath = it.toString() + if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { + itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) + } + if (alreadyAddedLibPath.get(itPath)) { + // don't duplicate + } else { + def lib = new Library(fileReference(itPath)) + lib.entryAttributes["test"] = "true" + cp.entries += lib + alreadyAddedLibPath.put(itPath, true) + } + } + + } // whenMerged + + } // file + + containers 'org.eclipse.buildship.core.gradleclasspathcontainer' + + } // classpath + + jdt { + // for the IDE, use java 11 compatibility + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + javaRuntimeName = eclipseJavaRuntimeName + + // add in jalview project specific properties/preferences into eclipse core preferences + file { + withProperties { props -> + def jalview_prefs = new Properties() + def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}") + jalview_prefs.load(ins) + ins.close() + jalview_prefs.forEach { t, v -> + if (props.getAt(t) == null) { + props.putAt(t, v) + } + } + } + } + + } // jdt + + if (IN_ECLIPSE) { + // Don't want these to be activated if in headless build + synchronizationTasks "eclipseSynchronizationTask" + autoBuildTasks "eclipseAutoBuildTask" + + } +} + + +// clover bits + + +task cleanClover { + doFirst { + delete cloverBuildDir + delete cloverReportDir + } +} + + +task cloverInstrJava(type: JavaExec) { + group = "Verification" + description = "Create clover instrumented source java files" + + dependsOn cleanClover + + inputs.files(sourceSets.main.allJava) + outputs.dir(cloverInstrDir) + + //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) + classpath = sourceSets.clover.compileClasspath + main = "com.atlassian.clover.CloverInstr" + + def argsList = [ + "--encoding", + "UTF-8", + "--initstring", + cloverDb, + "--destdir", + cloverInstrDir.getPath(), + ] + def srcFiles = sourceSets.main.allJava.files + argsList.addAll( + srcFiles.collect( + { file -> file.absolutePath } + ) + ) + args argsList.toArray() + + doFirst { + delete cloverInstrDir + println("Clover: About to instrument "+srcFiles.size() +" files") + } +} + + +task cloverInstrTests(type: JavaExec) { + group = "Verification" + description = "Create clover instrumented source test files" + + dependsOn cleanClover + + inputs.files(testDir) + outputs.dir(cloverTestInstrDir) + + classpath = sourceSets.clover.compileClasspath + main = "com.atlassian.clover.CloverInstr" + + def argsList = [ + "--encoding", + "UTF-8", + "--initstring", + cloverDb, + "--srcdir", + testDir, + "--destdir", + cloverTestInstrDir.getPath(), + ] + args argsList.toArray() + + doFirst { + delete cloverTestInstrDir + println("Clover: About to instrument test files") + } +} + + +task cloverInstr { + group = "Verification" + description = "Create clover instrumented all source files" + + dependsOn cloverInstrJava + dependsOn cloverInstrTests +} + + +cloverClasses.dependsOn cloverInstr + + +task cloverConsoleReport(type: JavaExec) { + group = "Verification" + description = "Creates clover console report" + + onlyIf { + file(cloverDb).exists() + } + + inputs.dir cloverClassesDir + + classpath = sourceSets.clover.runtimeClasspath + main = "com.atlassian.clover.reporters.console.ConsoleReporter" + + if (cloverreport_mem.length() > 0) { + maxHeapSize = cloverreport_mem + } + if (cloverreport_jvmargs.length() > 0) { + jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) + } + + def argsList = [ + "--alwaysreport", + "--initstring", + cloverDb, + "--unittests" + ] + + args argsList.toArray() +} + + +task cloverHtmlReport(type: JavaExec) { + group = "Verification" + description = "Creates clover HTML report" + + onlyIf { + file(cloverDb).exists() + } + + def cloverHtmlDir = cloverReportDir + inputs.dir cloverClassesDir + outputs.dir cloverHtmlDir + + classpath = sourceSets.clover.runtimeClasspath + main = "com.atlassian.clover.reporters.html.HtmlReporter" + + if (cloverreport_mem.length() > 0) { + maxHeapSize = cloverreport_mem + } + if (cloverreport_jvmargs.length() > 0) { + jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) + } + + def argsList = [ + "--alwaysreport", + "--initstring", + cloverDb, + "--outputdir", + cloverHtmlDir + ] + + if (cloverreport_html_options.length() > 0) { + argsList += cloverreport_html_options.split(" ") + } + + args argsList.toArray() +} + + +task cloverXmlReport(type: JavaExec) { + group = "Verification" + description = "Creates clover XML report" + + onlyIf { + file(cloverDb).exists() + } + + def cloverXmlFile = "${cloverReportDir}/clover.xml" + inputs.dir cloverClassesDir + outputs.file cloverXmlFile + + classpath = sourceSets.clover.runtimeClasspath + main = "com.atlassian.clover.reporters.xml.XMLReporter" + + if (cloverreport_mem.length() > 0) { + maxHeapSize = cloverreport_mem + } + if (cloverreport_jvmargs.length() > 0) { + jvmArgs Arrays.asList(cloverreport_jvmargs.split(" ")) + } + + def argsList = [ + "--alwaysreport", + "--initstring", + cloverDb, + "--outfile", + cloverXmlFile + ] + + if (cloverreport_xml_options.length() > 0) { + argsList += cloverreport_xml_options.split(" ") + } + + args argsList.toArray() +} + + +task cloverReport { + group = "Verification" + description = "Creates clover reports" + + dependsOn cloverXmlReport + dependsOn cloverHtmlReport +} + + +compileCloverJava { + + doFirst { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs += additional_compiler_args + print ("Setting target compatibility to "+targetCompatibility+"\n") + } + //classpath += configurations.cloverRuntime +} +// end clover bits compileJava { @@ -496,6 +890,7 @@ clean { cleanTest { + dependsOn cleanClover doFirst { delete sourceSets.test.java.outputDir } @@ -635,6 +1030,13 @@ task copyHelp(type: Copy) { } +task syncLib(type: Sync) { + def syncDir = "${resourceClassesDir}/${libDistDir}" + from fileTree("${jalviewDir}/${libDistDir}") + into syncDir +} + + task syncResources(type: Sync) { from resourceDir include "**/*.*" @@ -657,7 +1059,11 @@ test { dependsOn prepare //dependsOn compileJava ////? DELETE - dependsOn compileJava //? + if (useClover) { + dependsOn cloverClasses + } else { //? + dependsOn compileJava //? + } useTestNG() { includeGroups testng_groups @@ -685,6 +1091,9 @@ test { jvmArgs += additional_compiler_args doFirst { + if (useClover) { + println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover") + } } } @@ -780,3 +1189,633 @@ jar { inputs.dir(classesDir) outputs.file("${jalviewDir}/${package_dir}/${archiveName}") } + + +task copyJars(type: Copy) { + from fileTree(dir: classesDir, include: "**/*.jar").files + into "${jalviewDir}/${package_dir}" +} + + +// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well +task syncJars(type: Sync) { + from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files + into "${jalviewDir}/${package_dir}" + preserve { + include jar.archiveName + } +} + + +task makeDist { + group = "build" + description = "Put all required libraries in dist" + // order of "cleanPackageDir", "copyJars", "jar" important! + jar.mustRunAfter cleanPackageDir + syncJars.mustRunAfter cleanPackageDir + dependsOn cleanPackageDir + dependsOn syncJars + dependsOn jar + outputs.dir("${jalviewDir}/${package_dir}") +} + + +task cleanDist { + dependsOn cleanPackageDir + dependsOn cleanTest + dependsOn clean +} + +shadowJar { + group = "distribution" + if (buildDist) { + dependsOn makeDist + } + from ("${jalviewDir}/${libDistDir}") { + include("*.jar") + } + manifest { + attributes 'Implementation-Version': JALVIEW_VERSION + } + mainClassName = shadow_jar_main_class + mergeServiceFiles() + classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION + minimize() +} + + +task getdownWebsite() { + group = "distribution" + description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer" + if (buildDist) { + dependsOn makeDist + } + + def getdownWebsiteResourceFilenames = [] + def getdownTextString = "" + def getdownResourceDir = getdownResourceDir + def getdownResourceFilenames = [] + + doFirst { + // clean the getdown website and files dir before creating getdown folders + delete getdownWebsiteDir + delete getdownFilesDir + + copy { + from buildProperties + rename(build_properties_file, getdown_build_properties) + into getdownAppDir + } + getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}" + + // 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) { + props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion) + } + if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) { + props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion) + } + if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) { + props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation) + } + + props.put("getdown_txt_title", jalview_name) + props.put("getdown_txt_ui.name", install4jApplicationName) + + // start with appbase + getdownTextString += "appbase = ${getdownAppBase}\n" + props.each{ prop, val -> + if (prop.startsWith("getdown_txt_") && val != null) { + if (prop.startsWith("getdown_txt_multi_")) { + def key = prop.substring(18) + val.split(",").each{ v -> + def line = "${key} = ${v}\n" + getdownTextString += line + } + } else { + // file values rationalised + if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) { + def r = null + if (val.indexOf('/') == 0) { + // absolute path + r = file(val) + } else if (val.indexOf('/') > 0) { + // relative path (relative to jalviewDir) + r = file( "${jalviewDir}/${val}" ) + } + if (r.exists()) { + val = "${getdown_resource_dir}/" + r.getName() + getdownWebsiteResourceFilenames += val + getdownResourceFilenames += r.getPath() + } + } + if (! prop.startsWith("getdown_txt_resource")) { + def line = prop.substring(12) + " = ${val}\n" + getdownTextString += line + } + } + } + } + + getdownWebsiteResourceFilenames.each{ filename -> + getdownTextString += "resource = ${filename}\n" + } + getdownResourceFilenames.each{ filename -> + copy { + from filename + into getdownResourceDir + } + } + + def codeFiles = [] + fileTree(file(package_dir)).each{ f -> + if (f.isDirectory()) { + def files = fileTree(dir: f, include: ["*"]).getFiles() + codeFiles += files + } else if (f.exists()) { + codeFiles += f + } + } + codeFiles.sort().each{f -> + def name = f.getName() + def line = "code = ${getdownAppDistDir}/${name}\n" + getdownTextString += line + copy { + from f.getPath() + into getdownAppDir + } + } + + fileTree(dir: digestonlyDir, include: ["*"]).getFiles().sort().each{f -> + def name = f.getName() + def line = "digestonly = ${getdownAppDistDir}/${name}\n" + getdownTextString += line + copy { + from f.getPath() + into getdownAppDir + } + } + + // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist + /* + if (JAVA_VERSION.equals("11")) { + def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles() + j11libFiles.sort().each{f -> + def name = f.getName() + def line = "code = ${getdown_j11lib_dir}/${name}\n" + getdownTextString += line + copy { + from f.getPath() + into getdownJ11libDir + } + } + } + */ + + // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated. + //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n" + getdownTextString += "resource = ${getdown_launcher_new}\n" + getdownTextString += "class = ${main_class}\n" + /* NOT setting these properties so that getdownappbase and getdowndistdir will default to release version + * getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n" + * getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n" + */ + + def getdown_txt = file("${getdownWebsiteDir}/getdown.txt") + getdown_txt.write(getdownTextString) + + def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl" + def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}") + launchJvl.write("appbase=${getdownAppBase}") + + copy { + from getdownLauncher + rename(file(getdownLauncher).getName(), getdown_launcher_new) + into getdownWebsiteDir + } + + copy { + from getdownLauncher + if (file(getdownLauncher).getName() != getdown_launcher) { + rename(file(getdownLauncher).getName(), getdown_launcher) + } + into getdownWebsiteDir + } + + if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) { + copy { + from getdown_txt + from getdownLauncher + from "${getdownAppDir}/${getdown_build_properties}" + if (file(getdownLauncher).getName() != getdown_launcher) { + rename(file(getdownLauncher).getName(), getdown_launcher) + } + into getdownInstallDir + } + + copy { + from getdownInstallDir + into getdownFilesInstallDir + } + } + + copy { + from getdown_txt + from launchJvl + from getdownLauncher + from "${getdownWebsiteDir}/${getdown_build_properties}" + if (file(getdownLauncher).getName() != getdown_launcher) { + rename(file(getdownLauncher).getName(), getdown_launcher) + } + into getdownFilesDir + } + + copy { + from getdownResourceDir + into "${getdownFilesDir}/${getdown_resource_dir}" + } + } + + if (buildDist) { + inputs.dir("${jalviewDir}/${package_dir}") + } + outputs.dir(getdownWebsiteDir) + outputs.dir(getdownFilesDir) +} + + +// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir +task getdownDigestDir(type: JavaExec) { + group "Help" + description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..." + + def digestDirPropertyName = "DIGESTDIR" + doFirst { + classpath = files(getdownLauncher) + def digestDir = findProperty(digestDirPropertyName) + if (digestDir == null) { + throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest") + } + args digestDir + } + main = "com.threerings.getdown.tools.Digester" +} + + +task getdownDigest(type: JavaExec) { + group = "distribution" + description = "Digest the getdown website folder" + dependsOn getdownWebsite + doFirst { + classpath = files(getdownLauncher) + } + main = "com.threerings.getdown.tools.Digester" + args getdownWebsiteDir + inputs.dir(getdownWebsiteDir) + outputs.file("${getdownWebsiteDir}/digest2.txt") +} + + +task getdown() { + group = "distribution" + description = "Create the minimal and full getdown app folder for installers and website and create digest file" + dependsOn getdownDigest + doLast { + if (reportRsyncCommand) { + def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/') + def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/') + println "LIKELY RSYNC COMMAND:" + println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'" + if (RUNRSYNC == "true") { + exec { + commandLine "mkdir", "-p", toDir + } + exec { + commandLine "rsync", "-avh", "--delete", fromDir, toDir + } + } + } + } +} + + +clean { + doFirst { + delete getdownWebsiteDir + delete getdownFilesDir + } +} + + +install4j { + if (file(install4jHomeDir).exists()) { + // good to go! + } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) { + install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" + } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) { + install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app" + } + installDir(file(install4jHomeDir)) + + mediaTypes = Arrays.asList(install4j_media_types.split(",")) +} + + +task copyInstall4jTemplate { + def install4jTemplateFile = file("${install4jDir}/${install4j_template}") + def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}") + inputs.file(install4jTemplateFile) + inputs.file(install4jFileAssociationsFile) + inputs.property("CHANNEL", { CHANNEL }) + outputs.file(install4jConfFile) + + doLast { + def install4jConfigXml = new XmlParser().parse(install4jTemplateFile) + + // turn off code signing if no OSX_KEYPASS + if (OSX_KEYPASS == "") { + install4jConfigXml.'**'.codeSigning.each { codeSigning -> + codeSigning.'@macEnabled' = "false" + } + install4jConfigXml.'**'.windows.each { windows -> + windows.'@runPostProcessor' = "false" + } + } + + // turn off checksum creation for LOCAL channel + def e = install4jConfigXml.application[0] + if (CHANNEL == "LOCAL") { + e.'@createChecksums' = "false" + } else { + e.'@createChecksums' = "true" + } + + // put file association actions where placeholder action is + def install4jFileAssociationsText = install4jFileAssociationsFile.text + def fileAssociationActions = new XmlParser().parseText("${install4jFileAssociationsText}") + install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true + if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') { + def parent = a.parent() + parent.remove(a) + fileAssociationActions.each { faa -> + parent.append(faa) + } + // don't need to continue in .any loop once replacements have been made + return true + } + } + + // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else + // NB we're deleting the /other/ one! + // Also remove the examples subdir from non-release versions + def customizedIdToDelete = "PROGRAM_GROUP_RELEASE" + // 2.11.1.0 NOT releasing with the Examples folder in the Program Group + if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel + customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE" + } else { + // remove the examples subdir from Full File Set + def files = install4jConfigXml.files[0] + def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" } + def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' } + def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' } + def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" } + dirEntry.parent().remove(dirEntry) + } + install4jConfigXml.'**'.action.any { a -> + if (a.'@customizedId' == customizedIdToDelete) { + def parent = a.parent() + parent.remove(a) + return true + } + } + + // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores + if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) { + def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" } + symlink.parent().remove(symlink) + } + + // write install4j file + install4jConfFile.text = XmlUtil.serialize(install4jConfigXml) + } +} + + +clean { + doFirst { + delete install4jConfFile + } +} + + +task installers(type: com.install4j.gradle.Install4jTask) { + group = "distribution" + description = "Create the install4j installers" + dependsOn setGitVals + dependsOn getdown + dependsOn copyInstall4jTemplate + + projectFile = install4jConfFile + + // create an md5 for the input files to use as version for install4j conf file + def digest = MessageDigest.getInstance("MD5") + digest.update( + (file("${install4jDir}/${install4j_template}").text + + file("${install4jDir}/${install4j_info_plist_file_associations}").text + + file("${install4jDir}/${install4j_installer_file_associations}").text).bytes) + def filesMd5 = new BigInteger(1, digest.digest()).toString(16) + if (filesMd5.length() >= 8) { + filesMd5 = filesMd5.substring(0,8) + } + def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}" + // make install4jBuildDir relative to jalviewDir + def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}" + + variables = [ + 'JALVIEW_NAME': jalview_name, + 'JALVIEW_APPLICATION_NAME': install4jApplicationName, + 'JALVIEW_DIR': "../..", + 'OSX_KEYSTORE': OSX_KEYSTORE, + 'JSIGN_SH': JSIGN_SH, + 'JRE_DIR': getdown_app_dir_java, + 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion, + 'JALVIEW_VERSION': JALVIEW_VERSION, + 'JAVA_MIN_VERSION': JAVA_MIN_VERSION, + 'JAVA_MAX_VERSION': JAVA_MAX_VERSION, + 'JAVA_VERSION': JAVA_VERSION, + 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, + 'VERSION': JALVIEW_VERSION, + 'MACOS_JAVA_VM_DIR': macosJavaVMDir, + 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, + 'LINUX_JAVA_VM_DIR': linuxJavaVMDir, + 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, + 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, + 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, + 'COPYRIGHT_MESSAGE': install4j_copyright_message, + 'BUNDLE_ID': install4jBundleId, + 'INTERNAL_ID': install4jInternalId, + 'WINDOWS_APPLICATION_ID': install4jWinApplicationId, + 'MACOS_DS_STORE': install4jDSStore, + 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage, + 'INSTALLER_NAME': install4jInstallerName, + 'INSTALL4J_UTILS_DIR': install4j_utils_dir, + 'GETDOWN_WEBSITE_DIR': getdown_website_dir, + 'GETDOWN_FILES_DIR': getdown_files_dir, + 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, + 'GETDOWN_DIST_DIR': getdownAppDistDir, + 'GETDOWN_ALT_DIR': getdown_app_dir_alt, + 'GETDOWN_INSTALL_DIR': getdown_install_dir, + 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations, + 'BUILD_DIR': install4jBuildDir, + 'APPLICATION_CATEGORIES': install4j_application_categories, + 'APPLICATION_FOLDER': install4jApplicationFolder, + 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder, + 'EXECUTABLE_NAME': install4jExecutableName, + 'EXTRA_SCHEME': install4jExtraScheme, + ] + + //println("INSTALL4J VARIABLES:") + //variables.each{k,v->println("${k}=${v}")} + + destination = "${jalviewDir}/${install4jBuildDir}" + buildSelected = true + + if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) { + faster = true + disableSigning = true + } + + if (OSX_KEYPASS) { + macKeystorePassword = OSX_KEYPASS + } + + doFirst { + println("Using projectFile "+projectFile) + } + + inputs.dir(getdownWebsiteDir) + inputs.file(install4jConfFile) + inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") + inputs.dir(macosJavaVMDir) + inputs.dir(windowsJavaVMDir) + outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}") +} + + +task sourceDist(type: Tar) { + dependsOn createBuildProperties + + def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") + def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" + // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09] + try { + archiveFileName = outputFileName + } catch (Exception e) { + archiveName = outputFileName + } + + compression Compression.GZIP + + into project.name + + def EXCLUDE_FILES=[ + "build/*", + "bin/*", + "test-output/", + "test-reports", + "tests", + "clover*/*", + ".*", + "benchmarking/*", + "**/.*", + "*.class", + "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales", + "*locales/**", + "utils/InstallAnywhere", + "**/*.log", + ] + def PROCESS_FILES=[ + "AUTHORS", + "CITATION", + "FEATURETODO", + "JAVA-11-README", + "FEATURETODO", + "LICENSE", + "**/README", + "RELEASE", + "THIRDPARTYLIBS", + "TESTNG", + "build.gradle", + "gradle.properties", + "**/*.java", + "**/*.html", + "**/*.xml", + "**/*.gradle", + "**/*.groovy", + "**/*.properties", + "**/*.perl", + "**/*.sh", + ] + def INCLUDE_FILES=[ + ".settings/org.eclipse.jdt.core.jalview.prefs", + ] + + from(jalviewDir) { + exclude (EXCLUDE_FILES) + include (PROCESS_FILES) + filter(ReplaceTokens, + beginToken: '$$', + endToken: '$$', + tokens: [ + 'Version-Rel': JALVIEW_VERSION, + 'Year-Rel': getDate("yyyy") + ] + ) + } + from(jalviewDir) { + exclude (EXCLUDE_FILES) + exclude (PROCESS_FILES) + exclude ("appletlib") + exclude ("**/*locales") + exclude ("*locales/**") + exclude ("utils/InstallAnywhere") + + exclude (getdown_files_dir) + exclude (getdown_website_dir) + + // exluding these as not using jars as modules yet + exclude ("$j11modDir/**/*.jar") + } + from(jalviewDir) { + include(INCLUDE_FILES) + } +// from (jalviewDir) { +// // explicit includes for stuff that seemed to not get included +// include(fileTree("test/**/*.")) +// exclude(EXCLUDE_FILES) +// exclude(PROCESS_FILES) +// } + + from(file(buildProperties).getParent()) { + include(file(buildProperties).getName()) + rename(file(buildProperties).getName(), "build_properties") + filter({ line -> + line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]") + }) + } + +} + + +task helppages { + dependsOn copyHelp + dependsOn pubhtmlhelp + + inputs.dir("${classesDir}/${help_dir}") + outputs.dir("${buildDir}/distributions/${help_dir}") +} + +// LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE +task eclipseAutoBuildTask {} +task eclipseSynchronizationTask {}