X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=5abde5047a92f300901676eac37fdb817552fca8;hb=870cce42ccbadc4208e17cbe04d6a5ea739d31b0;hp=e9c9da460a88a475a75caf27180d8a26619ef4f0;hpb=77745a47387bb12c3e4dea8bbec8ff38499571f2;p=jalview.git diff --git a/build.gradle b/build.gradle index e9c9da4..5abde50 100644 --- a/build.gradle +++ b/build.gradle @@ -1,38 +1,15 @@ +/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names. + * For properties set within build.gradle, use camelCaseNoSpace. + */ import org.apache.tools.ant.filters.ReplaceTokens -import org.gradle.internal.os.OperatingSystem -import org.gradle.plugins.ide.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() - } - dependencies { - classpath 'org.openclover:clover:4.4.1' - } -} + + 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 @@ -78,6 +55,26 @@ ext { } } + //// + // Import releaseProps from the RELEASE file + // or a file specified via JALVIEW_RELEASE_FILE if defined + // Expect jalview.version and target release branch in jalview.release + def releaseProps = new Properties(); + def releasePropFile = findProperty("JALVIEW_RELEASE_FILE"); + def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE"; + try { + (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { + releaseProps.load(it) + } + } catch (Exception fileLoadError) { + throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError); + } + //// + // Set JALVIEW_VERSION if it is not already set + if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) { + JALVIEW_VERSION = releaseProps.get("jalview.version") + } + // this property set when running Eclipse headlessly j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild") // this property set by Eclipse @@ -110,21 +107,25 @@ ext { sourceDir = string("${jalviewDir}/${bareSourceDir}") resourceDir = string("${jalviewDir}/${resource_dir}") bareTestSourceDir = string(test_source_dir) - testSourceDir = string("${jalviewDir}/${bareTestSourceDir}") + testDir = string("${jalviewDir}/${bareTestSourceDir}") - // clover - cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") - cloverDb = string("${buildDir}/clover/clover.db") 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 + // clover + useClover = clover.equals("true") + cloverBuildDir = "${buildDir}/clover" + cloverInstrDir = file("${cloverBuildDir}/clover-instr") + cloverClassesDir = file("${cloverBuildDir}/clover-classes") + cloverReportDir = file("${buildDir}/reports/clover") + cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr") + cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes") + //cloverTestClassesDir = cloverClassesDir + cloverDb = string("${cloverBuildDir}/clover.db") + + resourceClassesDir = useClover ? cloverClassesDir : classesDir + + testSourceDir = useClover ? cloverTestInstrDir : testDir + testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}" getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") buildDist = true @@ -153,8 +154,8 @@ ext { getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") jvlChannelName += "_${getdownChannelName}" // automatically add the test group Not-bamboo for exclusion - if ("".equals(testngExcludedGroups)) { - testngExcludedGroups = "Not-bamboo" + if ("".equals(testng_excluded_groups)) { + testng_excluded_groups = "Not-bamboo" } install4jExtraScheme = "jalviewb" break @@ -172,10 +173,10 @@ ext { getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = string("${getdown_channel_base}/${getdownDir}") - if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { + if (!file("${ARCHIVEDIR}/${package_dir}").exists()) { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { - packageDir = string("${ARCHIVEDIR}/${packageDir}") + package_dir = string("${ARCHIVEDIR}/${package_dir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } @@ -187,10 +188,10 @@ ext { getdownChannelName = string("archive/${JALVIEW_VERSION}") getdownDir = string("${getdownChannelName}/${JAVA_VERSION}") getdownAppBase = file(getdownWebsiteDir).toURI().toString() - if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { + if (!file("${ARCHIVEDIR}/${package_dir}").exists()) { throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution") } else { - packageDir = string("${ARCHIVEDIR}/${packageDir}") + package_dir = string("${ARCHIVEDIR}/${package_dir}") buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } @@ -202,15 +203,26 @@ ext { case "DEVELOP": reportRsyncCommand = true + + // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version + JALVIEW_VERSION=JALVIEW_VERSION+"-develop" + + install4jSuffix = "Develop" + install4jDSStore = "DS_Store-DEVELOP" + install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png" install4jExtraScheme = "jalviewd" + install4jInstallerName = "${jalview_name} Develop Installer" break case "TEST-RELEASE": reportRsyncCommand = true - JALVIEW_VERSION = "TEST" + + // TEST-RELEASE is usually associated with a Jalview release series so set the version + JALVIEW_VERSION=JALVIEW_VERSION+"-test" + install4jSuffix = "Test" install4jDSStore = "DS_Store-TEST-RELEASE" - install4jDMGBackgroundImage = "jalview_dmg_background.png" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" install4jExtraScheme = "jalviewt" install4jInstallerName = "${jalview_name} Test Installer" break @@ -233,7 +245,7 @@ ext { JALVIEW_VERSION = "TEST" install4jSuffix = "Test-Local" install4jDSStore = "DS_Store-TEST-RELEASE" - install4jDMGBackgroundImage = "jalview_dmg_background.png" + install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png" install4jExtraScheme = "jalviewt" install4jInstallerName = "${jalview_name} Test Installer" break @@ -260,21 +272,31 @@ ext { if (install4jSuffix == "") { install4jApplicationName = "${jalview_name}" install4jBundleId = "${install4j_bundle_id}" + install4jWinApplicationId = install4j_release_win_application_id } else { install4jApplicationName = "${jalview_name} ${install4jSuffix}" install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase() + // add int hash of install4jSuffix to the last part of the application_id + def id = install4j_release_win_application_id + def idsplitreverse = id.split("-").reverse() + idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode() + install4jWinApplicationId = idsplitreverse.reverse().join("-") } // sanitise folder and id names // install4jApplicationFolder = e.g. "Jalview Build" install4jApplicationFolder = install4jApplicationName - .replaceAll("[\"'~:/\\\\]", "_") // replace all awkward filename chars " ' ~ : / \ + .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \ .replaceAll("_+", "_") // collapse __ - install4jInternalId = install4jApplicationFolder + install4jInternalId = install4jApplicationName + .replaceAll(" ","_") + .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] + .replaceAll("_+", "") // collapse __ + //.replaceAll("_*-_*", "-") // collapse _-_ + install4jUnixApplicationFolder = install4jApplicationName .replaceAll(" ","_") .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.] .replaceAll("_+", "_") // collapse __ .replaceAll("_*-_*", "-") // collapse _-_ - install4jUnixApplicationFolder = install4jInternalId .toLowerCase() getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}") @@ -299,6 +321,7 @@ ext { //libDir = j8libDir libDir = j11libDir libDistDir = j8libDir + digestonlyDir = j8digestonlyDir compile_source_compatibility = 1.8 compile_target_compatibility = 1.8 // these are getdown.txt properties defined dependent on the JAVA_VERSION @@ -312,6 +335,7 @@ ext { JAVA_INTEGER_VERSION = string("11") libDir = j11libDir libDistDir = j11libDir + digestonlyDir = j11digestonlyDir compile_source_compatibility = 11 compile_target_compatibility = 11 getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version")) @@ -368,8 +392,8 @@ ext { - buildingHTML = string("${jalviewDir}/${docDir}/building.html") - helpFile = string("${classesDir}/${help_dir}/help.jhm") + buildingHTML = string("${jalviewDir}/${doc_dir}/building.html") + helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm") helpParentDir = string("${jalviewDir}/${help_parent_dir}") helpSourceDir = string("${helpParentDir}/${help_dir}") @@ -412,28 +436,9 @@ sourceSets { srcDirs += helpParentDir } - jar.destinationDir = file("${jalviewDir}/${packageDir}") + jar.destinationDir = file("${jalviewDir}/${package_dir}") compileClasspath = files(sourceSets.main.java.outputDir) - //compileClasspath += files(sourceSets.main.resources.srcDirs) - compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) - - runtimeClasspath = compileClasspath - } - - clover { - java { - srcDirs = [ cloverInstrDir ] - outputDir = file("${buildDir}/${cloverClassesDir}") - } - - resources { - srcDirs = sourceSets.main.resources.srcDirs - } - compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir ) - compileClasspath += files(sourceSets.main.java.outputDir) - compileClasspath += sourceSets.main.compileClasspath - compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"]) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath @@ -442,7 +447,7 @@ sourceSets { test { java { srcDirs testSourceDir - outputDir = file("${jalviewDir}/${testOutputDir}") + outputDir = file(testClassesDir) } resources { @@ -450,248 +455,15 @@ sourceSets { } compileClasspath = files( sourceSets.test.java.outputDir ) - - if (use_clover) { - compileClasspath = sourceSets.clover.compileClasspath - } else { - compileClasspath += files(sourceSets.main.java.outputDir) - } - - compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) - compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"]) - compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"]) + compileClasspath += sourceSets.main.compileClasspath + compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath } -} - - -// clover bits -dependencies { - if (use_clover) { - cloverCompile 'org.openclover:clover:4.4.1' - testCompile 'org.openclover:clover:4.4.1' - } -} - -configurations { - cloverRuntime - cloverRuntime.extendsFrom cloverCompile -} - - -// eclipse project and settings files creation, also used by buildship -eclipse { - project { - name = 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}/${eclipse_extra_jdt_prefs_file}") - jalview_prefs.load(ins) - ins.close() - jalview_prefs.forEach { t, v -> - if (props.getAt(t) == null) { - props.putAt(t, v) - } - } - } - } - - } // jdt - - if (IN_ECLIPSE) { - // Don't want these to be activated if in headless build - synchronizationTasks "eclipseSynchronizationTask" - autoBuildTasks "eclipseAutoBuildTask" - - } -} - - -task cloverInstr { - // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) - outputs.dir cloverInstrDir - - doFirst { - delete cloverInstrDir - def argsList = [ - "--initstring", - cloverDb, - "-d", - cloverInstrDir.getPath(), - ] - argsList.addAll( - inputs.files.files.collect( - { file -> file.absolutePath } - ) - ) - String[] args = argsList.toArray() - println("About to instrument "+args.length +" files") - com.atlassian.clover.CloverInstr.mainImpl(args) - } -} - - -cloverClasses.dependsOn cloverInstr - - -task cloverReport { - group = "Verification" - description = "Creates the Clover report" - inputs.dir "${buildDir}/clover" - outputs.dir "${reportsDir}/clover" - onlyIf { - file(cloverDb).exists() - } - doFirst { - def argsList = [ - "--initstring", - cloverDb, - "-o", - "${reportsDir}/clover" - ] - String[] args = argsList.toArray() - com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) - - // and generate ${reportsDir}/clover/clover.xml - args = [ - "--initstring", - cloverDb, - "-o", - "${reportsDir}/clover/clover.xml" - ].toArray() - com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) - } -} - -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 } -task cleanClover { - doFirst { - delete cloverInstrDir - delete cloverDb - } -} -// end clover bits compileJava { @@ -707,12 +479,6 @@ compileJava { compileTestJava { - if (use_clover) { - dependsOn compileCloverJava - classpath += configurations.cloverRuntime - } else { - classpath += sourceSets.main.runtimeClasspath - } doFirst { sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility @@ -730,7 +496,6 @@ clean { cleanTest { - dependsOn cleanClover doFirst { delete sourceSets.test.java.outputDir } @@ -791,8 +556,8 @@ task cleanBuildingHTML(type: Delete) { task convertBuildingMD(type: Exec) { dependsOn cleanBuildingHTML - def buildingMD = "${jalviewDir}/${docDir}/building.md" - def css = "${jalviewDir}/${docDir}/github.css" + def buildingMD = "${jalviewDir}/${doc_dir}/building.md" + def css = "${jalviewDir}/${doc_dir}/github.css" def pandoc = null pandoc_exec.split(",").each { @@ -834,8 +599,8 @@ clean { task syncDocs(type: Sync) { dependsOn convertBuildingMD - def syncDir = "${classesDir}/${docDir}" - from fileTree("${jalviewDir}/${docDir}") + def syncDir = "${resourceClassesDir}/${doc_dir}" + from fileTree("${jalviewDir}/${doc_dir}") into syncDir } @@ -843,7 +608,7 @@ task syncDocs(type: Sync) { task copyHelp(type: Copy) { def inputDir = helpSourceDir - def outputDir = "${classesDir}/${help_dir}" + def outputDir = "${resourceClassesDir}/${help_dir}" from(inputDir) { exclude '**/*.gif' exclude '**/*.jpg' @@ -870,17 +635,10 @@ task copyHelp(type: Copy) { } -task syncLib(type: Sync) { - def syncDir = "${classesDir}/${libDistDir}" - from fileTree("${jalviewDir}/${libDistDir}") - into syncDir -} - - task syncResources(type: Sync) { from resourceDir include "**/*.*" - into "${classesDir}" + into "${resourceClassesDir}" preserve { include "**" } @@ -897,18 +655,13 @@ task prepare { //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir test { dependsOn prepare - dependsOn compileJava - if (use_clover) { - dependsOn cloverInstr - } + //dependsOn compileJava ////? DELETE - if (use_clover) { - print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") - } + dependsOn compileJava //? useTestNG() { - includeGroups testngGroups - excludeGroups testngExcludedGroups + includeGroups testng_groups + excludeGroups testng_excluded_groups preserveOrder true useDefaultListeners=true } @@ -917,10 +670,22 @@ test { workingDir = jalviewDir //systemProperties 'clover.jar' System.properties.clover.jar + def testLaf = project.findProperty("test_laf") + if (testLaf != null) { + println("Setting Test LaF to '${testLaf}'") + systemProperty "laf", testLaf + } + def testHiDPIScale = project.findProperty("test_HiDPIScale") + if (testHiDPIScale != null) { + println("Setting Test HiDPI Scale to '${testHiDPIScale}'") + systemProperty "sun.java2d.uiScale", testHiDPIScale + } sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility jvmArgs += additional_compiler_args + doFirst { + } } @@ -946,22 +711,22 @@ task buildIndices(type: JavaExec) { task compileLinkCheck(type: JavaCompile) { options.fork = true - classpath = files("${jalviewDir}/${utilsDir}") - destinationDir = file("${jalviewDir}/${utilsDir}") - source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) - - inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java") - inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java") - outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class") - outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class") + classpath = files("${jalviewDir}/${utils_dir}") + destinationDir = file("${jalviewDir}/${utils_dir}") + source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) + + inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") + inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java") + outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class") + outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class") } task linkCheck(type: JavaExec) { dependsOn prepare, compileLinkCheck - def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out") - classpath = files("${jalviewDir}/${utilsDir}") + def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out") + classpath = files("${jalviewDir}/${utils_dir}") main = "HelpLinksChecker" workingDir = jalviewDir args = [ "${classesDir}/${help_dir}", "-nointernet" ] @@ -982,12 +747,12 @@ task linkCheck(type: JavaExec) { // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}" -ant.importBuild "${utilsDir}/publishHelp.xml" +ant.importBuild "${utils_dir}/publishHelp.xml" task cleanPackageDir(type: Delete) { doFirst { - delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar") + delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar") } } @@ -997,13 +762,13 @@ jar { dependsOn createBuildProperties manifest { - attributes "Main-Class": mainClass, + attributes "Main-Class": main_class, "Permissions": "all-permissions", "Application-Name": "Jalview Desktop", "Codebase": application_codebase } - destinationDir = file("${jalviewDir}/${packageDir}") + destinationDir = file("${jalviewDir}/${package_dir}") archiveName = rootProject.name+".jar" exclude "cache*/**" @@ -1013,577 +778,5 @@ jar { exclude "**/*.jar.*" inputs.dir(classesDir) - outputs.file("${jalviewDir}/${packageDir}/${archiveName}") -} - - -task copyJars(type: Copy) { - 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 - into "${jalviewDir}/${packageDir}" - 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("${jalviewDir}/${packageDir}") -} - - -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 = shadowJarMainClass - 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(packageDir)).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 - } - } - - // 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 = ${mainClass}\n" - - def getdown_txt = file("${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 "${getdownWebsiteDir}/${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("${jalviewDir}/${packageDir}") - } - 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) { - def digestDirPropertyName = "DIGESTDIR" - description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown" - doFirst { - classpath = files(getdownLauncher) - def digestDir = findProperty(digestDirPropertyName) - if (digestDir == null) { - throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest") - } - args digestDir - } - main = "com.threerings.getdown.tools.Digester" -} - - -task getdownDigest(type: JavaExec) { - group = "distribution" - description = "Digest the getdown website folder" - dependsOn getdownWebsite - doFirst { - classpath = files(getdownLauncher) - } - main = "com.threerings.getdown.tools.Digester" - args getdownWebsiteDir - inputs.dir(getdownWebsiteDir) - outputs.file("${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}/${install4j_installer_file_associations}") - inputs.file(install4jTemplateFile) - inputs.file(install4jFileAssociationsFile) - outputs.file(install4jConfFile) - - doLast { - def install4jConfigXml = new XmlParser().parse(install4jTemplateFile) - - // turn off code signing if no OSX_KEYPASS - if (OSX_KEYPASS == "") { - install4jConfigXml.'**'.codeSigning.each { codeSigning -> - codeSigning.'@macEnabled' = "false" - } - install4jConfigXml.'**'.windows.each { windows -> - windows.'@runPostProcessor' = "false" - } - } - - // turn off checksum creation for LOCAL channel - def e = install4jConfigXml.application[0] - if (CHANNEL == "LOCAL") { - e.'@createChecksums' = "false" - } else { - e.'@createChecksums' = "true" - } - - // put file association actions where placeholder action is - def install4jFileAssociationsText = install4jFileAssociationsFile.text - def fileAssociationActions = new XmlParser().parseText("${install4jFileAssociationsText}") - install4jConfigXml.'**'.action.any { a -> - 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 - } - } - - // 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}/${JAVA_VERSION}" - - variables = [ - 'JALVIEW_NAME': jalview_name, - 'JALVIEW_APPLICATION_NAME': install4jApplicationName, - 'JALVIEW_DIR': "../..", - 'OSX_KEYSTORE': OSX_KEYSTORE, - 'JSIGN_SH': JSIGN_SH, - 'JRE_DIR': getdown_app_dir_java, - 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion, - 'JALVIEW_VERSION': JALVIEW_VERSION, - 'JAVA_MIN_VERSION': JAVA_MIN_VERSION, - 'JAVA_MAX_VERSION': JAVA_MAX_VERSION, - 'JAVA_VERSION': JAVA_VERSION, - 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, - 'VERSION': JALVIEW_VERSION, - 'MACOS_JAVA_VM_DIR': macosJavaVMDir, - 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, - 'LINUX_JAVA_VM_DIR': linuxJavaVMDir, - 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, - 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, - 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, - 'COPYRIGHT_MESSAGE': install4j_copyright_message, - 'BUNDLE_ID': install4jBundleId, - 'INTERNAL_ID': install4jInternalId, - 'MACOS_DS_STORE': install4jDSStore, - 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage, - 'INSTALLER_NAME': install4jInstallerName, - 'INSTALL4J_UTILS_DIR': install4j_utils_dir, - 'GETDOWN_WEBSITE_DIR': getdown_website_dir, - 'GETDOWN_FILES_DIR': getdown_files_dir, - 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, - 'GETDOWN_DIST_DIR': getdownAppDistDir, - 'GETDOWN_ALT_DIR': getdown_app_dir_alt, - 'GETDOWN_INSTALL_DIR': getdown_install_dir, - 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations, - 'BUILD_DIR': install4jBuildDir, - 'UNIX_DESKTOP_ADDITIONS': install4j_unix_desktop_additions, - 'APPLICATION_FOLDER': install4jApplicationFolder, - 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder, - 'EXECUTABLE_NAME': install4jExecutableName, - 'EXTRA_SCHEME': install4jExtraScheme, - ] - - //println("INSTALL4J VARIABLES:") - //variables.each{k,v->println("${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) { - - 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 ("$j11modDir/**/*.jar") - } - from(jalviewDir) { - include(INCLUDE_FILES) - } -// from (jalviewDir) { -// // explicit includes for stuff that seemed to not get included -// include(fileTree("test/**/*.")) -// exclude(EXCLUDE_FILES) -// exclude(PROCESS_FILES) -// } + outputs.file("${jalviewDir}/${package_dir}/${archiveName}") } - - -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 {}