X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=d32a6b2460b907f19a2ad7611df9ea6e27dc50dd;hb=2f0f4a60825f566eb793cba837144e2de767a9a6;hp=5c6a36ca60e350525f46824e023a5e69e661d802;hpb=db39fb5c711f97b82998fdd77ca36aec43064d02;p=jalview.git diff --git a/build.gradle b/build.gradle index 5c6a36c..d32a6b2 100644 --- a/build.gradle +++ b/build.gradle @@ -1,45 +1,47 @@ import org.apache.tools.ant.filters.ReplaceTokens -//import org.apache.tools.ant.filters.ReplaceRegexp import org.gradle.internal.os.OperatingSystem -import org.gradle.plugins.ide.eclipse.model.* - +import org.gradle.plugins.ide.eclipse.model.Output +import org.gradle.plugins.ide.eclipse.model.Library import groovy.transform.ExternalizeMethods buildscript { - dependencies { - classpath 'org.openclover:clover:4.3.1' - classpath 'org.apache.commons:commons-compress:1.18' - } + dependencies { + classpath 'org.openclover:clover:4.3.1' + } } plugins { - id 'java' - id 'application' - id 'eclipse' - id 'com.github.johnrengelman.shadow' version '4.0.3' - id 'com.install4j.gradle' version '7.0.9' + id 'java' + id 'application' + id 'eclipse' + id 'com.github.johnrengelman.shadow' version '4.0.3' + id 'com.install4j.gradle' version '7.0.9' } repositories { - jcenter() - mavenCentral() - mavenLocal() - flatDir { - dirs gradlePluginsDir - } + jcenter() + mavenCentral() + mavenLocal() + flatDir { + dirs gradlePluginsDir + } +} + +dependencies { + compile 'org.apache.commons:commons-compress:1.18' } mainClassName = launcherClass -def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir") -def classes = "$jalviewDir/$classesDir" +def cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") +def classes = "${jalviewDir}/${classesDir}" if (clover.equals("true")) { - use_clover = true - classes = "$buildDir/$cloverClassesDir" + use_clover = true + classes = "${buildDir}/${cloverClassesDir}" } else { - use_clover = false - classes = "$jalviewDir/$classesDir" + use_clover = false + classes = "${jalviewDir}/${classesDir}" } // configure classpath/args for j8/j11 compilation @@ -51,1026 +53,2137 @@ def compile_source_compatibility def compile_target_compatibility ext { - - getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION - getdownDir = "" - reportRsyncCmd = false - switch (CHANNEL) { - - case "BUILD": - // TODO: get bamboo build artifact URL for getdown artifacts - getdown_app_dir = getdown_app_dir_alt - break - - case "RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_release - reportRsyncCommand = true - break - - case "ARCHIVE": - getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - reportRsyncCommand = true - break - - case "DEVELOP": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - reportRsyncCommand = true - break - - case "TEST-RELEASE": - getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - reportRsyncCommand = true - break - - case ~/^SCRATCH(|-\w*)$/: - getdown_channel_name = CHANNEL - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir - getdown_app_dir = getdown_app_dir_alt - reportRsyncCommand = true - break - - case "LOCAL": - getdown_app_base = file(getdownWebsiteDir).toURI().toString() - getdown_app_dir = getdown_app_dir_alt - break - - default: // something wrong specified - print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") - exit(1) - break - - } - - println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base) - getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir - //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir - getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir - getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir - getdownLauncher = jalviewDir + '/' + getdown_launcher - getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/' - getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir - modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"]) - modules_runtimeClasspath = modules_compileClasspath - gitHash = "" - gitBranch = "" + // local build environment properties + def localProps = "${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") + } + } + + getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}" + getdownDir = "" + reportRsyncCmd = false + buildDist = true + buildProperties = build_properties_file + getdownLauncher = "${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_app_dir = getdown_app_dir_alt + buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + break + + case "RELEASE": + getdown_channel_name = CHANNEL.toLowerCase() + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdown_app_dir = getdown_app_dir_release + buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + reportRsyncCommand = true + break + + case "ARCHIVE": + getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdown_app_dir = getdown_app_dir_alt + if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { + print "Must provide an ARCHIVEDIR value to produce an archive distribution" + exit + } else { + packageDir = "${ARCHIVEDIR}/${packageDir}" + buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}" + buildDist = false + } + reportRsyncCommand = true + break + + case "ARCHIVELOCAL": + getdown_channel_name = "archive/${JALVIEW_VERSION}" + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = file(getdownWebsiteDir).toURI().toString() + getdown_app_dir = getdown_app_dir_alt + if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { + print "Must provide an ARCHIVEDIR value to produce an archive distribution" + exit + } else { + packageDir = "${ARCHIVEDIR}/${packageDir}" + buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}" + buildDist = false + } + reportRsyncCommand = true + getdownLauncher = "${jalviewDir}/${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}/${getdownDir}" + getdown_app_dir = getdown_app_dir_alt + buildProperties = "${jalviewDir}/${classesDir}/${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}" + getdown_app_dir = getdown_app_dir_alt + buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + reportRsyncCommand = true + break + + case ~/^SCRATCH(|-[-\w]*)$/: + getdown_channel_name = CHANNEL + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" + getdown_app_dir = getdown_app_dir_alt + buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + reportRsyncCommand = true + break + + case "LOCAL": + getdown_app_base = file(getdownWebsiteDir).toURI().toString() + getdown_app_dir = getdown_app_dir_alt + buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}" + getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}" + break + + default: // something wrong specified + print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]") + exit + break + + } + + getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}" + //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" + getdownResourceDir = "${getdownWebsiteDir}/${getdown_resource_dir}" + getdownInstallDir = "${getdownWebsiteDir}/${getdown_install_dir}" + getdownFilesDir = "${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/" + getdownFilesInstallDir = "${getdownFilesDir}/${getdown_install_dir}" + /* compile without modules -- using classpath libraries + modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) + modules_runtimeClasspath = modules_compileClasspath + */ + gitHash = "" + gitBranch = "" + + println("Using a ${CHANNEL} profile.") } 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_multi_java_location = getdown_alt_java8_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-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_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-11" - additional_compiler_args += [ - '--module-path', ext.modules_compileClasspath.asPath, - '--add-modules', j11modules - ] + 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_multi_java_location = getdown_alt_java11_txt_multi_java_location - eclipse_java_runtime_name = "JavaSE-11" - additional_compiler_args += [ - '--module-path', ext.modules_compileClasspath.asPath, - '--add-modules', j11modules - ] + 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") + throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview") } -sourceSets { - - main { - java { - srcDirs "$jalviewDir/$sourceDir" - outputDir = file("$classes") - } - - resources { - srcDirs "$jalviewDir/$resourceDir" - } - - jar.destinationDir = file("$jalviewDir/$packageDir") - - compileClasspath = files(sourceSets.main.java.outputDir) - 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 - } - - test { - java { - srcDirs "$jalviewDir/$testSourceDir" - outputDir = file("$jalviewDir/$testOutputDir") - } - resources { - srcDirs = sourceSets.main.resources.srcDirs - } - - compileClasspath = files( sourceSets.test.java.outputDir ) - - if (use_clover) { - compileClasspath += sourceSets.clover.compileClasspath - } else { - compileClasspath += files(sourceSets.main.java.outputDir) - } - - compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]) - compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"]) +sourceSets { - runtimeClasspath = compileClasspath - } + main { + java { + srcDirs "${jalviewDir}/${sourceDir}" + outputDir = file("${classes}") + } + + resources { + srcDirs "${jalviewDir}/${resourceDir}" + } + + jar.destinationDir = file("${jalviewDir}/${packageDir}") + + compileClasspath = files(sourceSets.main.java.outputDir) + compileClasspath += fileTree(dir: "${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}/${libDir}", include: ["*.jar"]) + + runtimeClasspath = compileClasspath + } + + test { + java { + srcDirs "${jalviewDir}/${testSourceDir}" + outputDir = file("${jalviewDir}/${testOutputDir}") + } + + resources { + srcDirs = sourceSets.main.resources.srcDirs + } + + compileClasspath = files( sourceSets.test.java.outputDir ) + + if (use_clover) { + compileClasspath += sourceSets.clover.compileClasspath + } else { + compileClasspath += files(sourceSets.main.java.outputDir) + } + + compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"]) + + runtimeClasspath = compileClasspath + } } + // clover bits dependencies { - if (use_clover) { - cloverCompile 'org.openclover:clover:4.3.1' - testCompile 'org.openclover:clover:4.3.1' - } + if (use_clover) { + cloverCompile 'org.openclover:clover:4.3.1' + testCompile 'org.openclover:clover:4.3.1' + } } + configurations { - cloverRuntime - cloverRuntime.extendsFrom cloverCompile + cloverRuntime + cloverRuntime.extendsFrom cloverCompile } + eclipse { - project { - name = "Jalview with gradle build" - - natures 'org.eclipse.jdt.core.javanature', - 'org.eclipse.jdt.groovy.core.groovyNature', - 'org.eclipse.buildship.core.gradleprojectnature' - - buildCommand 'org.eclipse.jdt.core.javabuilder' - buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder' - } - - classpath { - //defaultOutputDir = sourceSets.main.java.outputDir - def removeThese = [] - configurations.each{ if (it.isCanBeResolved()) { - removeThese += it - } - } - - minusConfigurations += removeThese - plusConfigurations = [ ] - file { - - whenMerged { cp -> - def removeTheseToo = [] - HashMap addedSrcPath = new HashMap<>(); - cp.entries.each { entry -> - if (entry.kind == 'src') { - if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) { - removeTheseToo += entry - } else { - addedSrcPath.putAt(entry.path, true) - } - } - } - cp.entries.removeAll(removeTheseToo) - - print ("CP="+cp.inspect()) - - cp.entries += new Output("bin/main") - cp.entries += new Library(fileReference(helpParentDir)) - cp.entries += new Library(fileReference(resourceDir)) - - HashMap addedLibPath = new HashMap<>(); - - // changing from sourcesets.main.classpath to specific Java version lib - //sourceSets.main.compileClasspath.each{ - fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each { - //don't want to add outputDir as eclipse is using its own output dir in bin/main - if (it.isDirectory() || ! it.exists()) { - // don't add dirs to classpath - return - } - def itPath = it.toString() - if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { - itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) - } - if (addedLibPath.get(itPath)) { - //println("Not adding duplicate entry "+itPath) - } else { - //println("Adding entry "+itPath) - cp.entries += new Library(fileReference(itPath)) - addedLibPath.put(itPath, true) - } - } - - // changing from sourcesets.main.classpath to specific Java version lib - //sourceSets.test.compileClasspath.each{ - fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each { - //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) { - //no longer want to add outputDir as eclipse is using its own output dir in bin/main - if (it.isDirectory() || ! it.exists()) { - // don't add dirs to classpath - return false // groovy "break" in .each loop - } - def itPath = it.toString() - if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { - itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) - } - if (addedLibPath.get(itPath)) { - // don't duplicate - } else { - def lib = new Library(fileReference(itPath)) - // this doesn't work... yet. Adding test=true attribute using withXml below - //def attrs = new Node(null, 'attributes', ["test":"true"]) - //lib.appendNode(attrs) // - cp.entries += lib - addedLibPath.put(itPath, true) - } - } - } - - // withXml changes ignored by buildship, these add the "test=true" attribute - withXml { - def node = it.asNode() - - def srcTestAttributes - node.children().each{ cpe -> - def attributes = cpe.attributes() - if (attributes.get("kind") == "src" && attributes.get("path") == "test") { - srcTestAttributes = cpe.find { a -> a.name() == "attributes" } - return - } - } - def addTestAttribute = true - srcTestAttributes.each{a -> - if (a.name() == "attribute" && a.attributes().getAt("name") == "test") { - addTestAttribute = false - } - } - if (addTestAttribute) { - srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"])) - } - - node.children().each{ cpe -> - def attributes = cpe.attributes() - if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) { - cpe.appendNode('attributes') - .appendNode('attribute', [name:"test", value:"true"]) - } - } - } // withXML - } // file - - containers 'org.eclipse.buildship.core.gradleclasspathcontainer' - } // classpath - - jdt { - // for the IDE, use java 11 compatibility - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - javaRuntimeName = eclipse_java_runtime_name - - 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) - } - } - } - } - } - - //synchronizationTasks eclipseClasspath - //autoBuildTasks eclipseClasspath + 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 -> + if (entry.kind == 'src') { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) { + 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)) + } + if (file(resourceDir).isDirectory()) { + cp.entries += new Library(fileReference(resourceDir)) + } + + HashMap alreadyAddedLibPath = new HashMap<>(); + + 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 + } + def itPath = it.toString() + if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { + // make relative path + itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) + } + if (alreadyAddedLibPath.get(itPath)) { + //println("Not adding duplicate entry "+itPath) + } else { + //println("Adding entry "+itPath) + cp.entries += new Library(fileReference(itPath)) + alreadyAddedLibPath.put(itPath, true) + } + } + + //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each { + sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { + //no longer want to add outputDir as eclipse is using its own output dir in bin/main + if (it.isDirectory() || ! it.exists()) { + // don't add dirs to classpath + return false // groovy "continue" in .any closure + } + + def itPath = it.toString() + if (itPath.startsWith("${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 = eclipse_java_runtime_name + + // 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 + + 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"])) - outputs.dir cloverInstrDir - doFirst { - delete cloverInstrDir - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-d", "${buildDir}/${cloverSourcesInstrDir}"] - argsList.addAll(inputs.files.files.collect({ file -> - file.absolutePath - })) - String[] args = argsList.toArray() - println("About to instrument "+args.length +" files") - com.atlassian.clover.CloverInstr.mainImpl(args) - } +task cloverInstr() { + // only instrument source, we build test classes as normal + inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) + outputs.dir cloverInstrDir + + doFirst { + delete cloverInstrDir + def argsList = ["--initstring", "${buildDir}/clover/clover.db", + "-d", "${buildDir}/${cloverSourcesInstrDir}"] + argsList.addAll(inputs.files.files.collect({ file -> + file.absolutePath + })) + String[] args = argsList.toArray() + println("About to instrument "+args.length +" files") + com.atlassian.clover.CloverInstr.mainImpl(args) + } } task cloverReport { - group = "Verification" - description = "Createst the Clover report" - inputs.dir "${buildDir}/clover" - outputs.dir "${reportsDir}/clover" - onlyIf { - file("${buildDir}/clover/clover.db").exists() - } - doFirst { - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover"] - String[] args = argsList.toArray() - com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) - - // and generate ${reportsDir}/clover/clover.xml - args = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover/clover.xml"].toArray() - com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) - } + group = "Verification" + description = "Createst the Clover report" + inputs.dir "${buildDir}/clover" + outputs.dir "${reportsDir}/clover" + onlyIf { + file("${buildDir}/clover/clover.db").exists() + } + doFirst { + def argsList = ["--initstring", "${buildDir}/clover/clover.db", + "-o", "${reportsDir}/clover"] + String[] args = argsList.toArray() + com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) + + // and generate ${reportsDir}/clover/clover.xml + args = ["--initstring", "${buildDir}/clover/clover.db", + "-o", "${reportsDir}/clover/clover.xml"].toArray() + com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) + } } - // end clover bits compileJava { - doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") - } + doFirst { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs = additional_compiler_args + print ("Setting target compatibility to "+targetCompatibility+"\n") + } } + compileTestJava { - if (use_clover) { - dependsOn compileCloverJava - classpath += configurations.cloverRuntime - } else { - classpath += sourceSets.main.runtimeClasspath - } - doFirst { - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") - } + if (use_clover) { + dependsOn compileCloverJava + classpath += configurations.cloverRuntime + } else { + classpath += sourceSets.main.runtimeClasspath + } + doFirst { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs = additional_compiler_args + print ("Setting target compatibility to "+targetCompatibility+"\n") + } } 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 + doFirst { + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + options.compilerArgs += additional_compiler_args + print ("Setting target compatibility to "+targetCompatibility+"\n") + } + classpath += configurations.cloverRuntime } + clean { - delete sourceSets.main.java.outputDir + doFirst { + delete sourceSets.main.java.outputDir + } } + cleanTest { - delete sourceSets.test.java.outputDir - delete cloverInstrDir + doFirst { + delete sourceSets.test.java.outputDir + delete cloverInstrDir + } } + // format is a string like date.format("dd MMMM yyyy") def getDate(format) { - def date = new Date() - return date.format(format) + def date = new Date() + return date.format(format) } -task setGitVals { - def hashStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--short", "HEAD" - standardOutput = hashStdOut - ignoreExitValue true - } - - def branchStdOut = new ByteArrayOutputStream() - exec { - commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" - standardOutput = branchStdOut - ignoreExitValue true - } - - project.ext.gitHash = hashStdOut.toString().trim() - project.ext.gitBranch = branchStdOut.toString().trim() - outputs.upToDateWhen { false } +task setGitVals { + def hashStdOut = new ByteArrayOutputStream() + exec { + commandLine "git", "rev-parse", "--short", "HEAD" + standardOutput = hashStdOut + ignoreExitValue true + } + + def branchStdOut = new ByteArrayOutputStream() + exec { + commandLine "git", "rev-parse", "--abbrev-ref", "HEAD" + standardOutput = branchStdOut + ignoreExitValue true + } + + project.ext.gitHash = hashStdOut.toString().trim() + project.ext.gitBranch = branchStdOut.toString().trim() + + outputs.upToDateWhen { false } } + task createBuildProperties(type: WriteProperties) { - dependsOn setGitVals - inputs.dir("$jalviewDir/$sourceDir") - inputs.dir("$classes") - inputs.dir("$jalviewDir/$resourceDir") - outputFile "$classes/$buildPropertiesFile" - // taking time specific comment out to allow better incremental builds - comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") - //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd") - property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") - property "VERSION", JALVIEW_VERSION - property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]" - outputs.file(outputFile) + dependsOn setGitVals + inputs.dir("${jalviewDir}/${sourceDir}") + inputs.dir("${jalviewDir}/${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+"]" + outputs.file(outputFile) } -def buildingHTML = "$jalviewDir/$docDir/building.html" -task deleteBuildingHTML(type: Delete) { - delete buildingHTML + +def buildingHTML = "${jalviewDir}/${docDir}/building.html" +task cleanBuildingHTML(type: Delete) { + doFirst { + delete buildingHTML + } } + task convertBuildingMD(type: Exec) { - dependsOn deleteBuildingHTML - def buildingMD = "$jalviewDir/$docDir/building.md" - def css = "$jalviewDir/$docDir/github.css" - - def pandoc = null - pandoc_exec.split(",").each { - if (file(it.trim()).exists()) { - pandoc = it.trim() - return true - } - } - - def hostname = "hostname".execute().text.trim() - if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) { - pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" - } - - if (pandoc != null && file(pandoc).exists()) { - commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD - } else { - commandLine "true" - } - - ignoreExitValue true - - inputs.file(buildingMD) - inputs.file(css) - outputs.file(buildingHTML) + dependsOn cleanBuildingHTML + def buildingMD = "${jalviewDir}/${docDir}/building.md" + def css = "${jalviewDir}/${docDir}/github.css" + + def pandoc = null + pandoc_exec.split(",").each { + if (file(it.trim()).exists()) { + pandoc = it.trim() + return true + } + } + + def hostname = "hostname".execute().text.trim() + if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) { + pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc" + } + + doFirst { + if (pandoc != null && file(pandoc).exists()) { + commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD + } else { + println("Cannot find pandoc. Skipping convert building.md to HTML") + throw new StopExecutionException() + } + } + + ignoreExitValue true + + inputs.file(buildingMD) + inputs.file(css) + outputs.file(buildingHTML) } + + clean { - delete buildingHTML + doFirst { + delete buildingHTML + } } + task syncDocs(type: Sync) { - dependsOn convertBuildingMD - def syncDir = "$classes/$docDir" - from fileTree("$jalviewDir/$docDir") - into syncDir + dependsOn convertBuildingMD + def syncDir = "${classes}/${docDir}" + from fileTree("${jalviewDir}/${docDir}") + into syncDir } -def helpFile = "$classes/$helpDir/help.jhm" +def helpFile = "${classes}/${helpDir}/help.jhm" task copyHelp(type: Copy) { - def inputDir = "$jalviewDir/$helpParentDir/$helpDir" - def outputDir = "$classes/$helpDir" - from(inputDir) { - exclude '**/*.gif' - exclude '**/*.jpg' - exclude '**/*.png' - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION]) - } - from(inputDir) { - include '**/*.gif' - include '**/*.jpg' - include '**/*.png' - } - into outputDir - - inputs.dir(inputDir) - outputs.files(helpFile) - outputs.dir(outputDir) + def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}" + def outputDir = "${classes}/${helpDir}" + from(inputDir) { + exclude '**/*.gif' + exclude '**/*.jpg' + exclude '**/*.png' + filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) + } + from(inputDir) { + include '**/*.gif' + include '**/*.jpg' + include '**/*.png' + } + into outputDir + + inputs.dir(inputDir) + outputs.files(helpFile) + outputs.dir(outputDir) } + task syncLib(type: Sync) { - def syncDir = "$classes/$libDistDir" - from fileTree("$jalviewDir/$libDistDir") - into syncDir + def syncDir = "${classes}/${libDistDir}" + from fileTree("${jalviewDir}/${libDistDir}") + into syncDir } + task syncResources(type: Sync) { - from "$jalviewDir/$resourceDir" - include "**/*.*" - exclude "install4j" - into "$classes" - preserve { - include "**" - } + from "${jalviewDir}/${resourceDir}" + include "**/*.*" + into "${classes}" + preserve { + include "**" + } } + task prepare { - dependsOn syncResources - dependsOn syncDocs - dependsOn copyHelp + dependsOn syncResources + dependsOn syncDocs + dependsOn copyHelp } //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir test { - dependsOn prepare - dependsOn compileJava - if (use_clover) { - dependsOn cloverInstr - } + dependsOn prepare + dependsOn compileJava + if (use_clover) { + dependsOn cloverInstr + } + + if (use_clover) { + print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") + } + + useTestNG() { + includeGroups testngGroups + preserveOrder true + useDefaultListeners=true + } + + workingDir = jalviewDir + //systemProperties 'clover.jar' System.properties.clover.jar + sourceCompatibility = compile_source_compatibility + targetCompatibility = compile_target_compatibility + jvmArgs += additional_compiler_args - print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") - - useTestNG() { - includeGroups testngGroups - preserveOrder true - useDefaultListeners=true - } - - workingDir = jalviewDir - //systemProperties 'clover.jar' System.properties.clover.jar - sourceCompatibility = compile_source_compatibility - targetCompatibility = compile_target_compatibility - jvmArgs += additional_compiler_args - print ("Setting target compatibility to "+targetCompatibility+"\n") } + task buildIndices(type: JavaExec) { - dependsOn copyHelp - classpath = sourceSets.main.compileClasspath - main = "com.sun.java.help.search.Indexer" - workingDir = "$classes/$helpDir" - def argDir = "html" - args = [ argDir ] - inputs.dir("$workingDir/$argDir") - - outputs.dir("$classes/doc") - outputs.dir("$classes/help") - outputs.file("$workingDir/JavaHelpSearch/DOCS") - outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB") - outputs.file("$workingDir/JavaHelpSearch/OFFSETS") - outputs.file("$workingDir/JavaHelpSearch/POSITIONS") - outputs.file("$workingDir/JavaHelpSearch/SCHEMA") - outputs.file("$workingDir/JavaHelpSearch/TMAP") + dependsOn copyHelp + classpath = sourceSets.main.compileClasspath + main = "com.sun.java.help.search.Indexer" + workingDir = "${classes}/${helpDir}" + def argDir = "html" + args = [ argDir ] + inputs.dir("${workingDir}/${argDir}") + + outputs.dir("${classes}/doc") + outputs.dir("${classes}/help") + outputs.file("${workingDir}/JavaHelpSearch/DOCS") + outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") + outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") + outputs.file("${workingDir}/JavaHelpSearch/POSITIONS") + outputs.file("${workingDir}/JavaHelpSearch/SCHEMA") + outputs.file("${workingDir}/JavaHelpSearch/TMAP") } -task compileLinkCheck(type: JavaCompile) { - options.fork = true - classpath = files("$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/$utilsDir/BufferedLineReader.class") +task compileLinkCheck(type: JavaCompile) { + options.fork = true + classpath = files("${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}/${utilsDir}/BufferedLineReader.class") } -def helplinkscheckeroutputfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.out") + task linkCheck(type: JavaExec) { - dependsOn prepare, compileLinkCheck - classpath = files("$jalviewDir/$utilsDir") - main = "HelpLinksChecker" - workingDir = jalviewDir - def help = "$classes/$helpDir" - args = [ "$classes/$helpDir", "-nointernet" ] + dependsOn prepare, compileLinkCheck + + def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out") + classpath = files("${jalviewDir}/${utilsDir}") + main = "HelpLinksChecker" + workingDir = jalviewDir + def help = "${classes}/${helpDir}" + args = [ "${classes}/${helpDir}", "-nointernet" ] + + def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append + def errFOS = outFOS + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + outFOS, + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + outFOS, + errorOutput) + + inputs.dir("${classes}/${helpDir}") + outputs.file(helpLinksCheckerOutFile) +} - doFirst { - helplinkscheckeroutputfile.createNewFile() - standardOutput new FileOutputStream(helplinkscheckeroutputfile, false) - } +// import the pubhtmlhelp target +ant.properties.basedir = "${jalviewDir}" +ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}" +ant.importBuild "${utilsDir}/publishHelp.xml" - outputs.file(helplinkscheckeroutputfile) -} task cleanPackageDir(type: Delete) { - delete fileTree("$jalviewDir/$packageDir").include("*.jar") + doFirst { + delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar") + } } jar { - dependsOn linkCheck - dependsOn buildIndices - dependsOn createBuildProperties - - manifest { - attributes "Main-Class": mainClass, - "Permissions": "all-permissions", - "Application-Name": "Jalview Desktop", - "Codebase": application_codebase - } - - destinationDir = file("$jalviewDir/$packageDir") - archiveName = rootProject.name+".jar" - - exclude "cache*/**" - exclude "*.jar" - exclude "*.jar.*" - exclude "**/*.jar" - exclude "**/*.jar.*" - - inputs.dir("$classes") - outputs.file("$jalviewDir/$packageDir/$archiveName") + dependsOn linkCheck + dependsOn buildIndices + dependsOn createBuildProperties + + manifest { + attributes "Main-Class": mainClass, + "Permissions": "all-permissions", + "Application-Name": "Jalview Desktop", + "Codebase": application_codebase + } + + destinationDir = file("${jalviewDir}/${packageDir}") + archiveName = rootProject.name+".jar" + + exclude "cache*/**" + exclude "*.jar" + exclude "*.jar.*" + exclude "**/*.jar" + exclude "**/*.jar.*" + + inputs.dir("${classes}") + outputs.file("${jalviewDir}/${packageDir}/${archiveName}") } + task copyJars(type: Copy) { - from fileTree("$classes").include("**/*.jar").include("*.jar").files - into "$jalviewDir/$packageDir" + from fileTree(dir: "${classes}", 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("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files - into "$jalviewDir/$packageDir" - preserve { - include jar.archiveName - } + 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") + 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 + dependsOn cleanPackageDir + dependsOn cleanTest + dependsOn clean } shadowJar { - group = "distribution" - dependsOn makeDist - from ("$jalviewDir/$libDistDir") { - include("*.jar") - } - mainClassName = shadowJarMainClass - mergeServiceFiles() - classifier = "all-"+JAVA_VERSION - minimize() + 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" - dependsOn makeDist - def getdownWebsiteResourceFilenames = [] - def getdownTextString = "" - def getdownResourceDir = project.ext.getdownResourceDir - def getdownAppDir = project.ext.getdownAppDir - def getdownResourceFilenames = [] - - doFirst { - copy { - from "$classes/$buildPropertiesFile" - rename(buildPropertiesFile, getdown_build_properties) - into project.ext.getdownWebsiteDir - } - getdownWebsiteResourceFilenames += getdown_build_properties - - // go through properties looking for getdown_txt_... - def props = project.properties.sort { it.key } - props.put("getdown_txt_java_min_version", getdown_alt_java_min_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 -> - 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 project.ext.getdownResourceDir - } - } - - def codeFiles = [] - makeDist.outputs.files.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 line = "code = " + getdown_app_dir + '/' + f.getName() + "\n" - getdownTextString += line - copy { - from f.getPath() - into project.ext.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 line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n" - getdownTextString += line - copy { - from f.getPath() - into project.ext.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(project.ext.getdownWebsiteDir + "/getdown.txt") - getdown_txt.write(getdownTextString) - - def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl) - launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) - - copy { - from getdownLauncher - rename(file(getdownLauncher).getName(), getdown_launcher_new) - into project.ext.getdownWebsiteDir - } - - copy { - from getdownLauncher - into project.ext.getdownWebsiteDir - } - - copy { - from getdown_txt - from getdownLauncher - from getdownWebsiteDir+"/"+getdown_build_properties - into getdownInstallDir - } - - copy { - from getdown_txt - from launch_jvl - from getdownLauncher - from getdownWebsiteDir+"/"+getdown_build_properties - into getdownFilesDir - } - - copy { - from getdownInstallDir - into getdownFilesInstallDir - } - - copy { - from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image') - from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background') - from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image') - from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon') - from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon') - into project.ext.getdownFilesDir + '/' + getdown_resource_dir - } - } - - inputs.dir(jalviewDir + '/' + packageDir) - outputs.dir(project.ext.getdownWebsiteDir) - outputs.dir(project.ext.getdownFilesDir) + 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 = project.ext.getdownResourceDir + def getdownAppDir = project.ext.getdownAppDir + def getdownResourceFilenames = [] + + doFirst { + // clean the getdown website and files dir before creating getdown folders + delete project.ext.getdownWebsiteDir + delete project.ext.getdownFilesDir + + copy { + from buildProperties + rename(build_properties_file, getdown_build_properties) + into project.ext.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) + + props.put("getdown_txt_appbase", getdown_app_base) + 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 project.ext.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 = ${getdown_app_dir}/${name}\n" + getdownTextString += line + copy { + from f.getPath() + into project.ext.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 project.ext.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 = ${mainClass}\n" + + def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt") + getdown_txt.write(getdownTextString) + + def launch_jvl = file("${project.ext.getdownWebsiteDir}/${getdown_launch_jvl}") + launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) + + copy { + from getdownLauncher + rename(file(getdownLauncher).getName(), getdown_launcher_new) + into project.ext.getdownWebsiteDir + } + + copy { + from getdownLauncher + if (file(getdownLauncher).getName() != getdown_launcher) { + rename(file(getdownLauncher).getName(), getdown_launcher) + } + into project.ext.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 launch_jvl + 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 "${project.ext.getdownFilesDir}/${getdown_resource_dir}" + } + } + + if (buildDist) { + inputs.dir("${jalviewDir}/${packageDir}") + } + outputs.dir(project.ext.getdownWebsiteDir) + outputs.dir(project.ext.getdownFilesDir) } + task getdownDigest(type: JavaExec) { - group = "distribution" - description = "Digest the getdown website folder" - dependsOn getdownWebsite - classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher) - main = "com.threerings.getdown.tools.Digester" - args project.ext.getdownWebsiteDir - inputs.dir(project.ext.getdownWebsiteDir) - outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt") + group = "distribution" + description = "Digest the getdown website folder" + dependsOn getdownWebsite + doFirst { + classpath = files("${getdownWebsiteDir}/${getdown_launcher}") + } + main = "com.threerings.getdown.tools.Digester" + args project.ext.getdownWebsiteDir + inputs.dir(project.ext.getdownWebsiteDir) + outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt") } + task getdown() { - group = "distribution" - description = "Create the minimal and full getdown app folder for installers and website and create digest file" - dependsOn getdownDigest - doLast { - if (reportRsyncCommand) { - def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/") - def toDir = getdown_smb_mount + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/") - println "rsync -avh --delete '$fromDir' '$toDir'" - } - } + group = "distribution" + description = "Create the minimal and full getdown app folder for installers and website and create digest file" + dependsOn getdownDigest + doLast { + if (reportRsyncCommand) { + def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/') + def toDir = "${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 { - delete project.ext.getdownWebsiteDir - delete project.ext.getdownFilesDir + doFirst { + delete project.ext.getdownWebsiteDir + delete project.ext.getdownFilesDir + } } + install4j { - def install4jHomeDir = "/opt/install4j" - def hostname = "hostname".execute().text.trim() - if (hostname.equals("jv-bamboo")) { - install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" - } else if (OperatingSystem.current().isMacOsX()) { - install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app' - if (! file(install4jHomeDir).exists()) { - install4jHomeDir = System.getProperty("user.home")+install4jHomeDir - } - } else if (OperatingSystem.current().isLinux()) { - install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" - } - installDir = file(install4jHomeDir) - mediaTypes = Arrays.asList(install4jMediaTypes.split(",")) - if (install4jFaster.equals("true")) { - faster = true - } + def install4jHomeDir = "/opt/install4j" + def hostname = "hostname".execute().text.trim() + if (hostname.equals("jv-bamboo")) { + install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" + } else if (OperatingSystem.current().isMacOsX()) { + install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app' + if (! file(install4jHomeDir).exists()) { + install4jHomeDir = System.getProperty("user.home")+install4jHomeDir + } + } else if (OperatingSystem.current().isLinux()) { + install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j" + } + installDir = file(install4jHomeDir) + mediaTypes = Arrays.asList(install4jMediaTypes.split(",")) + if (install4jFaster.equals("true")) { + faster = true + } } + 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" +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_DIST_DIR': getdown_app_dir, - 'GETDOWN_INSTALL_DIR': getdown_install_dir - ] - ) - if (OSX_KEYPASS=="") { - filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"']) - filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor']) - } - } - into install4jDir - outputs.files(install4jConf) - - doLast { - // include file associations in installer - def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerFileAssociationsXml, - file: install4jConf - ) - /* - // include uninstaller applescript app files in dmg - def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text - ant.replaceregexp( - byline: false, - flags: "s", - match: '', - replace: installerDMGUninstallerXml, - file: install4jConf - ) - */ - } + macosJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre" + macosJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz" + windowsJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre" + windowsJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz" + from (install4jDir) { + include install4jTemplate + rename (install4jTemplate, install4jConfFile) + filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION]) + filter(ReplaceTokens, beginToken: '$$', endToken: '$$', + tokens: [ + 'JAVA_VERSION': JAVA_VERSION, + 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, + 'VERSION': JALVIEW_VERSION, + 'MACOS_JAVA_VM_DIR': macosJavaVMDir, + 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, + 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, + 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, + 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations, + 'COPYRIGHT_MESSAGE': install4jCopyrightMessage, + 'MACOS_BUNDLE_ID': install4jMacOSBundleId, + 'GETDOWN_RESOURCE_DIR': getdown_resource_dir, + 'GETDOWN_DIST_DIR': getdown_app_dir, + 'GETDOWN_ALT_DIR': getdown_app_dir_alt, + 'GETDOWN_INSTALL_DIR': getdown_install_dir + ] + ) + if (OSX_KEYPASS=="") { + filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"']) + filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor']) + } + } + into install4jDir + outputs.files(install4jConf) + + doLast { + // include file associations in installer + def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text + ant.replaceregexp( + byline: false, + flags: "s", + match: '', + replace: installerFileAssociationsXml, + file: install4jConf + ) + /* + // include uninstaller applescript app files in dmg + def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text + ant.replaceregexp( + byline: false, + flags: "s", + match: '', + replace: installerDMGUninstallerXml, + file: install4jConf + ) + */ + } } + task installers(type: com.install4j.gradle.Install4jTask) { - group = "distribution" - description = "Create the install4j installers" - dependsOn getdown - dependsOn copyInstall4jTemplate - projectFile = file(install4jConf) - println("Using projectFile "+projectFile) - variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH] - destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION" - buildSelected = true + group = "distribution" + description = "Create the install4j installers" + dependsOn getdown + dependsOn copyInstall4jTemplate + projectFile = file(install4jConf) + variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH] + destination = "${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(macosJavaVMDir) + inputs.dir(windowsJavaVMDir) + outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}") +} - if (OSX_KEYPASS) { - macKeystorePassword=OSX_KEYPASS - } +clean { + doFirst { + delete install4jConf + } +} + - inputs.dir(project.ext.getdownWebsiteDir) - inputs.file(install4jConf) - inputs.dir(macosJavaVMDir) - inputs.dir(windowsJavaVMDir) - outputs.dir("$jalviewDir/$install4jBuildDir/$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"] + 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"] + + 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 ("${j11modDir}/**/*.jar") +} +// from (jalviewDir) { +// // explicit includes for stuff that seemed to not get included +// include(fileTree("test/**/*.")) +// exclude(EXCLUDE_FILES) +// exclude(PROCESS_FILES) +// } } -clean { - delete install4jConf + +task helppages { + dependsOn copyHelp + dependsOn pubhtmlhelp + + inputs.dir("${classes}/${helpDir}") + outputs.dir("${helpOutputDir}") +} + + +def jalviewjsBuildDir +def jalviewjsSiteDir +def jalviewjsTransferSiteJsDir +def jalviewjsTransferSiteLibDir +def jalviewjsTransferSiteSwingJsDir +def jalviewjsTransferSiteCoreDir +task jalviewjsSitePath { + def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) + jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs" + jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}" + jalviewjsTransferSiteJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js" + jalviewjsTransferSiteLibDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib" + jalviewjsTransferSiteSwingJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs" + jalviewjsTransferSiteCoreDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core" +} + + +def eclipseWorkspace +task jalviewjsSetEclipseWorkspace { + def propKey = "jalviewjs_eclipse_workspace" + def propVal = null + if (project.hasProperty(propKey)) { + propVal = project.getProperty(propKey) + if (propVal.startsWith("~/")) { + propVal = System.getProperty("user.home") + propVal.substring(1) + } + } + def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}" + def propsFile = file(propsFileName) + def eclipseWsDir = propVal + def props = new Properties() + + 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) + } + } + + def writeProps = false + if (eclipseWsDir == null || !file(eclipseWsDir).exists()) { + def tempDir = File.createTempDir() + eclipseWsDir = tempDir.getAbsolutePath() + writeProps = true + } + eclipseWorkspace = file(eclipseWsDir) + + doFirst { + if (writeProps) { + props.setProperty(propKey, eclipseWsDir) + propsFile.parentFile.mkdirs() + def bytes = new ByteArrayOutputStream() + props.store(bytes, null) + def propertiesString = bytes.toString() + propsFile.text = propertiesString + } + + println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) + } + + //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date + outputs.file(propsFileName) + outputs.upToDateWhen { eclipseWorkspace.exists() } +} + + +def eclipseBinary +def eclipseVersion +def eclipseDebug = false +def eclipseVersionSuffix = "" +task jalviewjsEclipsePaths { + def eclipseProduct + + def eclipseRoot = jalviewjs_eclipse_root + if (eclipseRoot.startsWith("~/")) { + eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1) + } + if (OperatingSystem.current().isMacOsX()) { + eclipseRoot += "/Eclipse.app" + eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse" + eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" + } else if (OperatingSystem.current().isWindows()) { // check these paths!! + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { + eclipseRoot += "/eclipse.exe" + } + eclipseBinary = "${eclipseRoot}/eclipse" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" + } else { // linux or unix + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { + eclipseRoot += "/eclipse" + } + eclipseBinary = "${eclipseRoot}/eclipse" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" + } + + eclipseVersion = "4.13" // default + def assumedVersion = true + if (file(eclipseProduct).exists()) { + def fis = new FileInputStream(eclipseProduct) + def props = new Properties() + props.load(fis) + eclipseVersion = props.getProperty("version") + fis.close() + assumedVersion = false + } + + def propKey = "eclipse_debug" + eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true")) + + doFirst { + if (!assumedVersion) { + println("ECLIPSE VERSION=${eclipseVersion}") + } + } +} + + +task eclipseSetup { + dependsOn eclipseProject + dependsOn eclipseClasspath + dependsOn eclipseJdt +} + + +// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir +task jalviewjsEclipseCopyDropins(type: Copy) { + dependsOn jalviewjsEclipsePaths + + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") + inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}") + def outputDir = "${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 { + dependsOn jalviewjsSitePath + + 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 { + dependsOn jalviewjsSitePath + + def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip") + + doLast { + zipFiles.each { file_zip -> + copy { + from zipTree(file_zip) + into "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + } + } + } + + inputs.files zipFiles + outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}" +} + + +task jalviewjsTransferUnzipAllLibs { + dependsOn jalviewjsTransferUnzipSwingJs + dependsOn jalviewjsTransferUnzipLib +} + + +task jalviewjsCreateJ2sSettings(type: WriteProperties) { + group "JalviewJS" + description "Create the .j2s file from the j2s.* properties" + + dependsOn jalviewjsSitePath + + outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}") + def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } + def siteDirProperty = "j2s.site.directory" + def setSiteDir = false + j2s_props.each { prop, val -> + if (val != null) { + if (prop == siteDirProperty) { + if (!(val.startsWith('/') || val.startsWith("file://") )) { + val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}" + } + setSiteDir = true + } + property(prop,val) + } + if (!setSiteDir) { // default site location, don't override specifically set property + property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}") + } + } + inputs.properties(j2s_props) + outputs.file(outputFile) +} + + +task jalviewjsEclipseSetup { + dependsOn jalviewjsEclipseCopyDropins + dependsOn jalviewjsSetEclipseWorkspace + dependsOn jalviewjsCreateJ2sSettings +} + + +task jalviewjsSyncAllLibs (type: Sync) { + dependsOn jalviewjsSitePath + dependsOn jalviewjsTransferUnzipAllLibs + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}") + inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncResources (type: Sync) { + dependsOn jalviewjsSitePath + def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}") + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsSyncSiteResources (type: Sync) { + dependsOn jalviewjsSitePath + 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 jalviewjsSitePath + dependsOn createBuildProperties + def inputFiles = [file(buildProperties)] + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFiles +} + + +task jalviewjsProjectImport(type: Exec) { + dependsOn eclipseSetup + dependsOn jalviewjsEclipsePaths + dependsOn jalviewjsEclipseSetup + + doFirst { + // do not run a headless import when we claim to be in Eclipse + if (ECLIPSE_IDE_DEVELOPER.equals("true")) { + throw new StopExecutionException("Not running headless import whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'") + } + } + + //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" + def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview" + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath]) + if (eclipseDebug) { + args += "-debug" + } + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] + + inputs.file("${jalviewDir}/.project") + outputs.upToDateWhen { + file(projdir).exists() + } +} + + +task jalviewjsTranspile(type: Exec) { + dependsOn jalviewjsEclipseSetup + dependsOn jalviewjsProjectImport + dependsOn jalviewjsEclipsePaths + + doFirst { + // do not run a headless transpile when we claim to be in Eclipse + if (ECLIPSE_IDE_DEVELOPER.equals("true")) { + throw new StopExecutionException("Not running headless transpile whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'") + } + } + + executable(eclipseBinary) + args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ]) + if (eclipseDebug) { + args += "-debug" + } + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] + + def stdout + def stderr + doFirst { + stdout = new ByteArrayOutputStream() + stderr = new ByteArrayOutputStream() + + def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}" + def logOutFile = file(logOutFileName) + logOutFile.createNewFile() + logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} +BINARY: ${eclipseBinary} +VERSION: ${eclipseVersion} +WORKSPACE: ${eclipseWorkspace} +DEBUG: ${eclipseDebug} +---- +""" + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + // combine stdout and stderr + def logErrFOS = logOutFOS + + if (jalviewjs_j2s_to_console.equals("true")) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr), + errorOutput) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + logErrFOS, + stderr) + } + } + + doLast { + if (stdout.toString().contains("Error processing ")) { + // j2s did not complete transpile + //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + } + } + + inputs.dir("${jalviewDir}/${sourceDir}") + outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}") + outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } ) +} + + +def jalviewjsCallCore(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 = "Generating ${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_") + t.replaceAll("Class__","Clazz._") + 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 ] + + 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") +} + + +def jalviewjsJalviewTemplateName = "JalviewJS" +def jalviewjsJalviewCoreName = "_jalview" +task jalviewjsNoTranspileBuildAllCores { + dependsOn jalviewjsSitePath + dependsOn jalviewjsTransferUnzipSwingJs + + def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}" + def jsDir = "${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}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ] + + def classlists = [] + + classlistFiles.each { + hash -> + + def file = hash['file'] + if (! file.exists()) { + println("...classlist file '"+file.getPath()+"' does not exist, skipping") + return false // this is a "continue" in groovy .each closure + } + def name = hash['name'] + if (name == null) { + name = file.getName() - ".txt" + } + + def filelist = [] + file.eachLine { + line -> + filelist += line + } + def list = fileTree(dir: j2sDir, includes: filelist) + + def jsfile = "${outputDir}/core${name}.js" + def zjsfile = "${outputDir}/core${name}.z.js" + + classlists += [ + 'jsfile': jsfile, + 'zjsfile': zjsfile, + 'list': list + ] + + inputs.file(file) + inputs.files(list) + outputs.file(jsfile) + outputs.file(zjsfile) + } + + // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) + def stevesoftClasslist = [ + 'jsfile': "${outputDir}/core_stevesoft.js", + 'zjsfile': "${outputDir}/core_stevesoft.z.js", + 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js") + ] + classlists += stevesoftClasslist + inputs.files(stevesoftClasslist['list']) + outputs.file(stevesoftClasslist['jsfile']) + outputs.file(stevesoftClasslist['zjsfile']) + + doFirst { + def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}") + logOutFile.getParentFile().mkdirs() + logOutFile.createNewFile() + logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsNoTranspileBuildAllCores\n----\n") + + classlists.each { + jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true")) + } + } + +} + + +jalviewjsNoTranspileBuildAllCores.mustRunAfter jalviewjsTranspile + + +task jalviewjsBuildAllCores { + group "JalviewJS" + description "Build the core js lib closures listed in the classlists dir" + dependsOn jalviewjsTranspile + dependsOn jalviewjsNoTranspileBuildAllCores +} + + +def jalviewjsJalviewCoreHtmlFile +task jalviewjsPublishCoreTemplate(type: Sync) { + dependsOn jalviewjsSitePath + dependsOn jalviewjsBuildAllCores + + def inputFile = file("${jalviewDir}/${j2s_template_html}") + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + + from inputFile + into outputDir + def outputFiles = [] + jalviewjsJalviewCoreHtmlFile = "${jalviewjsJalviewTemplateName}_${jalviewjsJalviewCoreName}.html" + rename { filename -> + outputFiles += "${outputDir}/${filename}" + if (filename.equals(inputFile.getName())) { + return jalviewjsJalviewCoreHtmlFile + } + return null + } + filter(ReplaceTokens, beginToken: '_', endToken: '_', tokens: ['MAIN': '"'+mainClass+'"', 'CODE': "null", 'NAME': jalviewjsJalviewTemplateName]) + filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['NONE': jalviewjsJalviewCoreName]) + preserve { + include "**" + } + outputs.files outputFiles + inputs.files inputFile +} + + +task jalviewjsNoTranspileSyncCore (type: Sync) { + dependsOn jalviewjsSitePath + dependsOn jalviewjsNoTranspileBuildAllCores + dependsOn jalviewjsPublishCoreTemplate + 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 +} + + +task jalviewjsSyncCore (type: Sync) { + dependsOn jalviewjsTranspile + dependsOn jalviewjsNoTranspileSyncCore + dependsOn "jalviewjsBuildAllCores" +} + + +// 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 jalviewjsNoTranspileSyncTransferSiteJs(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 jalviewjsNoTranspileSyncTransferSiteJs +jalviewjsSyncResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs +jalviewjsSyncSiteResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs + + +task jalviewjsNoTranspilePrepareSite { + dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncResources + dependsOn jalviewjsSyncSiteResources + dependsOn jalviewjsSyncBuildProperties + dependsOn jalviewjsNoTranspileSyncCore } + +task jalviewjsPrepareSite { + group "JalviewJS" + description "Prepares the website folder including unzipping files and copying resources" + dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncResources + dependsOn jalviewjsSyncSiteResources + dependsOn jalviewjsSyncBuildProperties + dependsOn jalviewjsSyncCore +} + + +task jalviewjsBuildSite { + group "JalviewJS" + description "Builds the whole website including transpiled code" + dependsOn jalviewjsCopyTransferSiteJs + dependsOn jalviewjsPrepareSite +} + + +task cleanJalviewjsSite { + doFirst { + delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + delete "${jalviewDir}/${jalviewjsSiteDir}" + } +} + + +task jalviewjsSiteTar(type: Tar) { + group "JalviewJS" + description "Creates a tar.gz file for the website" + dependsOn jalviewjsBuildSite + def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz" + try { + archiveFileName = outputFilename + } catch (Exception e) { + archiveName = outputFilename + } + + compression Compression.GZIP + + from "${jalviewDir}/${jalviewjsSiteDir}" + into jalviewjs_site_dir // this is inside the tar file + + inputs.dir("${jalviewDir}/${jalviewjsSiteDir}") +} + + +task jalviewjsServer { + group "JalviewJS" + def filename = "jalviewjsTest.html" + description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port." + dependsOn jalviewjsSitePath + def htmlFile = "${jalviewDirAbsolutePath}/${filename}" + doLast { + + SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory() + def port = Integer.valueOf(jalviewjs_server_port) + def start = port + def running = false + def url + def urlcore + while(port < start+1000 && !running) { + try { + def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") + def jalviewjsServer = factory.start(doc_root, port) + running = true + url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource) + urlcore = jalviewjsServer.getResourceUrl(jalviewjsJalviewCoreHtmlFile) + println("SERVER STARTED with document root ${doc_root}.") + println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).") + println("For debug: "+url+"?j2sdebug") + println("For core: "+urlcore) + + file(htmlFile).text = """ +

JalviewJS Test. <${url}>

+

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

+

${jalviewjsJalviewTemplateName} Core Test. <${urlcore}>

+ """ + + } catch (Exception e) { + port++; + } + } + + } + + outputs.file(htmlFile) + outputs.upToDateWhen({false}) +} + + +task cleanJalviewjsAll { + group "JalviewJS" + description "Delete all configuration and build artifacts to do with JalviewJS build" + dependsOn cleanJalviewjsSite + dependsOn jalviewjsEclipsePaths + + doFirst { + delete "${jalviewDir}/${jalviewjsBuildDir}" + delete "${jalviewDir}/${eclipse_bin_dir}" + if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) { + delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") + } + delete "${jalviewDir}/${jalviewjs_j2s_settings}" + } + + outputs.upToDateWhen( { false } ) +} + + + +task jalviewjsIDE_CopyTransferSiteJs(type: Copy) { + from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + into "${jalviewDir}/${jalviewjsSiteDir}" +} + + +task jalviewjsIDE_j2sFile { + group "00 JalviewJS in Eclipse" + description "Creates the .j2s file" + dependsOn jalviewjsCreateJ2sSettings +} + + +task jalviewjsIDE_BuildAllCores { + group "00 JalviewJS in Eclipse" + description "Build the core js lib closures listed in the classlists dir" + dependsOn jalviewjsNoTranspileBuildAllCores +} + + +task jalviewjsIDE_AssembleSite { + group "00 JalviewJS in Eclipse" + description "Assembles the Eclipse transpiled site and unzips supporting zipfiles" + dependsOn jalviewjsIDE_CopyTransferSiteJs + dependsOn jalviewjsNoTranspilePrepareSite +} + + +task jalviewjsIDE_SiteClean { + group "00 JalviewJS in Eclipse" + description "Deletes the Eclipse transpiled site" + dependsOn cleanJalviewjsSite +} + + +task jalviewjsIDE_Server { + group "00 JalviewJS in Eclipse" + description "Starts a webserver on localhost to test the website" + dependsOn jalviewjsServer +} + + +// buildship runs this at import +task eclipseSynchronizationTask { + dependsOn eclipseSetup + dependsOn jalviewjsIDE_j2sFile +} + + +// buildship runs this at build time +task eclipseAutoBuildTask { + dependsOn jalviewjsNoTranspileSyncTransferSiteJs + dependsOn jalviewjsNoTranspilePrepareSite +} + + + + + + + + +task jalviewjs { + group "JalviewJS" + description "Build the site" + dependsOn jalviewjsBuildSite +}