+/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
import org.apache.tools.ant.filters.ReplaceTokens
import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
+import org.gradle.api.internal.PropertiesTransformer
+import org.gradle.util.ConfigureUtil
import org.gradle.plugins.ide.eclipse.model.Output
import org.gradle.plugins.ide.eclipse.model.Library
import java.security.MessageDigest
import groovy.transform.ExternalizeMethods
import groovy.util.XmlParser
import groovy.xml.XmlUtil
-
+import com.vladsch.flexmark.util.ast.Node
+import com.vladsch.flexmark.html.HtmlRenderer
+import com.vladsch.flexmark.parser.Parser
+import com.vladsch.flexmark.util.data.MutableDataSet
+import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
+import com.vladsch.flexmark.ext.tables.TablesExtension
+import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
+import com.vladsch.flexmark.ext.autolink.AutolinkExtension
+import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
+import com.vladsch.flexmark.ext.toc.TocExtension
buildscript {
repositories {
mavenLocal()
}
dependencies {
- classpath 'org.openclover:clover:4.4.1'
+ classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
}
}
id 'java'
id 'application'
id 'eclipse'
+ id "com.diffplug.gradle.spotless" version "3.28.0"
id 'com.github.johnrengelman.shadow' version '4.0.3'
- id 'com.install4j.gradle' version '8.0.4'
+ id 'com.install4j.gradle' version '9.0.6'
id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+ id 'com.palantir.git-version' version '0.13.0' apply false
}
repositories {
}
+
// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
def string(Object o) {
return o == null ? "" : o.toString()
}
-
-ext {
- jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
- jalviewDirRelativePath = jalviewDir
-
- // local build environment properties
- // can be "projectDir/local.properties"
- def localProps = "${projectDir}/local.properties"
- def propsFile = null;
- if (file(localProps).exists()) {
- propsFile = localProps
- }
- // or "../projectDir_local.properties"
- def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
- if (file(dirLocalProps).exists()) {
- propsFile = dirLocalProps
+def overrideProperties(String propsFileName, boolean output = false) {
+ if (propsFileName == null) {
+ return
}
- if (propsFile != null) {
+ def propsFile = file(propsFileName)
+ if (propsFile != null && propsFile.exists()) {
+ println("Using properties from file '${propsFileName}'")
try {
def p = new Properties()
def localPropsFIS = new FileInputStream(propsFile)
localPropsFIS.close()
p.each {
key, val ->
- def oldval = findProperty(key)
- setProperty(key, val)
- if (oldval != null) {
- println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ def oldval
+ if (project.hasProperty(key)) {
+ oldval = project.findProperty(key)
+ project.setProperty(key, val)
+ if (output) {
+ println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ }
} else {
- println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ ext.setProperty(key, val)
+ if (output) {
+ println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ }
}
}
} catch (Exception e) {
- System.out.println("Exception reading local.properties")
+ println("Exception reading local.properties")
+ e.printStackTrace()
}
}
+}
+ext {
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+ getdownChannelName = CHANNEL.toLowerCase()
+ // default to "default". Currently only has different cosmetics for "develop", "release", "default"
+ propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+ // Import channel_properties
+ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+ channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
+ overrideProperties(channelGradleProperties, false)
+ // local build environment properties
+ // can be "projectDir/local.properties"
+ overrideProperties("${projectDir}/local.properties", true)
+ // or "../projectDir_local.properties"
+ overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
+
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+ // Expect jalview.version and target release branch in jalview.release
+ releaseProps = new Properties();
+ def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+ def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+ try {
+ (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
+ releaseProps.load(it)
+ }
+ } catch (Exception fileLoadError) {
+ throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+ }
+ ////
+ // Set JALVIEW_VERSION if it is not already set
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+
// this property set when running Eclipse headlessly
j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
// this property set by Eclipse
J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
if (J2S_ENABLED) {
println("J2S ENABLED")
- }
-
+ }
/* *-/
System.properties.sort { it.key }.each {
key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
}
*/
+ // datestamp
+ buildDate = new Date().format("yyyyMMdd")
+
// essentials
bareSourceDir = string(source_dir)
sourceDir = string("${jalviewDir}/${bareSourceDir}")
resourceDir = string("${jalviewDir}/${resource_dir}")
bareTestSourceDir = string(test_source_dir)
- testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+ testDir = string("${jalviewDir}/${bareTestSourceDir}")
- // clover
- cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
- cloverDb = string("${buildDir}/clover/clover.db")
classesDir = string("${jalviewDir}/${classes_dir}")
- if (clover.equals("true")) {
- use_clover = true
- classesDir = string("${buildDir}/${cloverClassesDir}")
- } else {
- use_clover = false
- classesDir = string("${jalviewDir}/${classes_dir}")
- }
- classes = classesDir
+ // clover
+ useClover = clover.equals("true")
+ cloverBuildDir = "${buildDir}/clover"
+ cloverInstrDir = file("${cloverBuildDir}/clover-instr")
+ cloverClassesDir = file("${cloverBuildDir}/clover-classes")
+ cloverReportDir = file("${buildDir}/reports/clover")
+ cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
+ cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
+ //cloverTestClassesDir = cloverClassesDir
+ cloverDb = string("${cloverBuildDir}/clover.db")
+
+ testSourceDir = useClover ? cloverTestInstrDir : testDir
+ testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
buildDist = true
+ buildProperties = null
// the following values might be overridden by the CHANNEL switch
- getdownChannelName = CHANNEL.toLowerCase()
getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
getdownAppDistDir = getdown_app_dir_alt
- buildProperties = string("${resourceDir}/${build_properties_file}")
+ getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
+ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
reportRsyncCommand = false
jvlChannelName = CHANNEL.toLowerCase()
+ install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
+ install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+ install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
+ install4jInstallerName = "${jalview_name} Non-Release Installer"
+ install4jExecutableName = install4j_executable_name
+ install4jExtraScheme = "jalviewx"
+ install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
+ install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
+ install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
+ install4jBackground = string("${install4j_images_dir}/${install4j_background}")
switch (CHANNEL) {
case "BUILD":
getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
jvlChannelName += "_${getdownChannelName}"
// automatically add the test group Not-bamboo for exclusion
- if ("".equals(testngExcludedGroups)) {
- testngExcludedGroups = "Not-bamboo"
+ if ("".equals(testng_excluded_groups)) {
+ testng_excluded_groups = "Not-bamboo"
}
+ install4jExtraScheme = "jalviewb"
break
- case "RELEASE":
+ case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
getdownAppDistDir = getdown_app_dir_release
reportRsyncCommand = true
- // Don't ignore transpile errors for release build
- if (jalviewjs_ignore_transpile_errors.equals("true")) {
- jalviewjs_ignore_transpile_errors = "false"
- println("Setting jalviewjs_ignore_transpile_errors to 'false'")
- }
+ install4jSuffix = ""
+ install4jInstallerName = "${jalview_name} Installer"
break
case "ARCHIVE":
getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
- if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = string("${ARCHIVEDIR}/${packageDir}")
- buildProperties = string("${buildDir}/archive/${build_properties_file}")
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
+ install4jExtraScheme = "jalviewa"
break
case "ARCHIVELOCAL":
getdownChannelName = string("archive/${JALVIEW_VERSION}")
getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
getdownAppBase = file(getdownWebsiteDir).toURI().toString()
- if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = string("${ARCHIVEDIR}/${packageDir}")
- buildProperties = string("${buildDir}/archive/${build_properties_file}")
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jSuffix = "Archive"
+ install4jExtraScheme = "jalviewa"
break
case "DEVELOP":
reportRsyncCommand = true
+ getdownSetAppBaseProperty = true
+ // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+ JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
+
+ install4jSuffix = "Develop"
+ install4jExtraScheme = "jalviewd"
+ install4jInstallerName = "${jalview_name} Develop Installer"
break
case "TEST-RELEASE":
jalviewjs_ignore_transpile_errors = "false"
println("Setting jalviewjs_ignore_transpile_errors to 'false'")
}
+ JALVIEW_VERSION = JALVIEW_VERSION+"-test"
+ install4jSuffix = "Test"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
break
case ~/^SCRATCH(|-[-\w]*)$/:
getdownChannelName = CHANNEL
+ JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
+
getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
reportRsyncCommand = true
+ install4jSuffix = "Scratch"
break
case "TEST-LOCAL":
getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
}
+ JALVIEW_VERSION = "TEST"
+ install4jSuffix = "Test-Local"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
break
- case "LOCAL":
+ case [ "LOCAL", "JALVIEWJS" ]:
+ JALVIEW_VERSION = "TEST"
getdownAppBase = file(getdownWebsiteDir).toURI().toString()
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jExtraScheme = "jalviewl"
break
default: // something wrong specified
}
// override getdownAppBase if requested
if (findProperty("getdown_appbase_override") != null) {
- getdownAppBase = string(getProperty("getdown_appbase_override"))
+ // revert to LOCAL if empty string
+ if (string(getdown_appbase_override) == "") {
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ } else if (string(getdown_appbase_override).startsWith("file://")) {
+ getdownAppBase = string(getdown_appbase_override)
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ } else {
+ getdownAppBase = string(getdown_appbase_override)
+ }
println("Overriding getdown appbase with '${getdownAppBase}'")
}
// sanitise file name for jalview launcher file for this channel
- jvlChannelName = jvlChannelName.replaceAll(/[^\w\-]/,"_")
-
+ jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
+ // install4j application and folder names
+ if (install4jSuffix == "") {
+ install4jApplicationName = "${jalview_name}"
+ install4jBundleId = "${install4j_bundle_id}"
+ install4jWinApplicationId = install4j_release_win_application_id
+ } else {
+ install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+ install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
+ // add int hash of install4jSuffix to the last part of the application_id
+ def id = install4j_release_win_application_id
+ def idsplitreverse = id.split("-").reverse()
+ idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
+ install4jWinApplicationId = idsplitreverse.reverse().join("-")
+ }
+ // sanitise folder and id names
+ // install4jApplicationFolder = e.g. "Jalview Build"
+ install4jApplicationFolder = install4jApplicationName
+ .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
+ .replaceAll("_+", "_") // collapse __
+ install4jInternalId = install4jApplicationName
+ .replaceAll(" ","_")
+ .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+ .replaceAll("_+", "") // collapse __
+ //.replaceAll("_*-_*", "-") // collapse _-_
+ install4jUnixApplicationFolder = install4jApplicationName
+ .replaceAll(" ","_")
+ .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+ .replaceAll("_+", "_") // collapse __
+ .replaceAll("_*-_*", "-") // collapse _-_
+ .toLowerCase()
+
+ getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
//getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
*/
- gitHash = string("")
- gitBranch = string("")
+
+ gitHash = "SOURCE"
+ gitBranch = "Source"
+ try {
+ apply plugin: "com.palantir.git-version"
+ def details = versionDetails()
+ gitHash = details.gitHash
+ gitBranch = details.branchName
+ } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
+ println("Not in a git repository. Using git values from RELEASE properties file.")
+ gitHash = releaseProps.getProperty("git.hash")
+ gitBranch = releaseProps.getProperty("git.branch")
+ } catch(java.lang.RuntimeException e1) {
+ throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
+ }
println("Using a ${CHANNEL} profile.")
'--add-modules', j11modules
]
*/
- } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
- JAVA_INTEGER_VERSION = JAVA_VERSION
- libDir = j11libDir
- libDistDir = j11libDir
- compile_source_compatibility = JAVA_VERSION
- compile_target_compatibility = JAVA_VERSION
+ } else if (JAVA_VERSION.equals("17")) {
+ JAVA_INTEGER_VERSION = string("17")
+ libDir = j17libDir
+ libDistDir = j17libDir
+ compile_source_compatibility = 17
+ compile_target_compatibility = 17
getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
- eclipseJavaRuntimeName = string("JavaSE-11")
+ eclipseJavaRuntimeName = string("JavaSE-17")
/* compile without modules -- using classpath libraries
additional_compiler_args += [
'--module-path', modules_compileClasspath.asPath,
jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
}
macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
- macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
- windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
- linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
+ macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz")
+ windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz")
+ linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz")
install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
install4jConfFileName = string("jalview-install4j-conf.install4j")
install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
}
+ resourceBuildDir = string("${buildDir}/resources")
+ resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+ helpBuildDir = string("${resourceBuildDir}/help_build")
+ docBuildDir = string("${resourceBuildDir}/doc_build")
-
- buildingHTML = string("${jalviewDir}/${docDir}/building.html")
- helpFile = string("${classesDir}/${help_dir}/help.jhm")
+ if (buildProperties == null) {
+ buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
+ }
+ buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
helpParentDir = string("${jalviewDir}/${help_parent_dir}")
helpSourceDir = string("${helpParentDir}/${help_dir}")
+ helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
jalviewjsCoreClasslists = []
jalviewjsJalviewTemplateName = string(jalviewjs_name)
jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+ jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
jalviewjsJ2sProps = null
jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
}
resources {
- srcDirs resourceDir
- srcDirs += helpParentDir
+ srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
}
- jar.destinationDir = file("${jalviewDir}/${packageDir}")
-
compileClasspath = files(sourceSets.main.java.outputDir)
- //compileClasspath += files(sourceSets.main.resources.srcDirs)
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.main.resources.srcDirs)
}
clover {
java {
- srcDirs = [ cloverInstrDir ]
- outputDir = file("${buildDir}/${cloverClassesDir}")
+ srcDirs cloverInstrDir
+ outputDir = cloverClassesDir
}
resources {
srcDirs = sourceSets.main.resources.srcDirs
}
- compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
- compileClasspath += files(sourceSets.main.java.outputDir)
- compileClasspath += sourceSets.main.compileClasspath
- compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
+
+ compileClasspath = files( sourceSets.clover.java.outputDir )
+ //compileClasspath += files( testClassesDir )
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
}
test {
java {
srcDirs testSourceDir
- outputDir = file("${jalviewDir}/${testOutputDir}")
+ outputDir = file(testClassesDir)
}
resources {
- srcDirs = sourceSets.main.resources.srcDirs
+ srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
}
compileClasspath = files( sourceSets.test.java.outputDir )
-
- if (use_clover) {
- compileClasspath = sourceSets.clover.compileClasspath
- } else {
- compileClasspath += files(sourceSets.main.java.outputDir)
- }
-
- compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
- compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
- compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
+ compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.test.resources.srcDirs)
}
-}
-
-// clover bits
-dependencies {
- if (use_clover) {
- cloverCompile 'org.openclover:clover:4.4.1'
- testCompile 'org.openclover:clover:4.4.1'
- }
-}
-
-
-configurations {
- cloverRuntime
- cloverRuntime.extendsFrom cloverCompile
}
classpath {
//defaultOutputDir = sourceSets.main.java.outputDir
- def removeThese = []
- configurations.each{
- if (it.isCanBeResolved()) {
- removeThese += it
+ configurations.each{ c->
+ if (c.isCanBeResolved()) {
+ minusConfigurations += [c]
}
}
- minusConfigurations += removeThese
plusConfigurations = [ ]
file {
javaRuntimeName = eclipseJavaRuntimeName
// add in jalview project specific properties/preferences into eclipse core preferences
- // and also the codestyle XML file
file {
withProperties { props ->
def jalview_prefs = new Properties()
}
-task cloverInstr {
- // only instrument source, we build test classes as normal
- inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
- outputs.dir cloverInstrDir
+/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
+// Class to allow updating arbitrary properties files
+class PropertiesFile extends PropertiesPersistableConfigurationObject {
+ public PropertiesFile(PropertiesTransformer t) { super(t); }
+ @Override protected void load(Properties properties) { }
+ @Override protected void store(Properties properties) { }
+ @Override protected String getDefaultResourceName() { return ""; }
+ // This is necessary, because PropertiesPersistableConfigurationObject fails
+ // if no default properties file exists.
+ @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
+}
+
+// Task to update arbitrary properties files (set outputFile)
+class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
+ private final PropertiesFileContentMerger file;
+ public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
+ protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
+ protected void configure(PropertiesFile props) {
+ file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
+ }
+ public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
+}
+
+task eclipseUIPreferences(type: PropertiesFileTask) {
+ description = "Generate Eclipse additional settings"
+ def filename = "org.eclipse.jdt.ui.prefs"
+ outputFile = "$projectDir/.settings/${filename}" as File
+ file {
+ withProperties {
+ it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
+ }
+ }
+}
+
+task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
+ description = "Generate Eclipse additional settings"
+ def filename = "org.eclipse.jdt.groovy.core.prefs"
+ outputFile = "$projectDir/.settings/${filename}" as File
+ file {
+ withProperties {
+ it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
+ }
+ }
+}
+
+task eclipseAllPreferences {
+ dependsOn eclipseJdt
+ dependsOn eclipseUIPreferences
+ dependsOn eclipseGroovyCorePreferences
+}
+
+eclipseUIPreferences.mustRunAfter eclipseJdt
+eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
+
+/* end of eclipse preferences hack */
+
+// clover bits
+
+
+task cleanClover {
doFirst {
- delete cloverInstrDir
- def argsList = [
- "--initstring",
- cloverDb,
- "-d",
- cloverInstrDir.getPath(),
- ]
- argsList.addAll(
- inputs.files.files.collect(
- { file -> file.absolutePath }
- )
+ delete cloverBuildDir
+ delete cloverReportDir
+ }
+}
+
+
+task cloverInstrJava(type: JavaExec) {
+ group = "Verification"
+ description = "Create clover instrumented source java files"
+
+ dependsOn cleanClover
+
+ inputs.files(sourceSets.main.allJava)
+ outputs.dir(cloverInstrDir)
+
+ //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+ classpath = sourceSets.clover.compileClasspath
+ main = "com.atlassian.clover.CloverInstr"
+
+ def argsList = [
+ "--encoding",
+ "UTF-8",
+ "--initstring",
+ cloverDb,
+ "--destdir",
+ cloverInstrDir.getPath(),
+ ]
+ def srcFiles = sourceSets.main.allJava.files
+ argsList.addAll(
+ srcFiles.collect(
+ { file -> file.absolutePath }
)
- String[] args = argsList.toArray()
- println("About to instrument "+args.length +" files")
- com.atlassian.clover.CloverInstr.mainImpl(args)
+ )
+ args argsList.toArray()
+
+ doFirst {
+ delete cloverInstrDir
+ println("Clover: About to instrument "+srcFiles.size() +" files")
+ }
+}
+
+
+task cloverInstrTests(type: JavaExec) {
+ group = "Verification"
+ description = "Create clover instrumented source test files"
+
+ dependsOn cleanClover
+
+ inputs.files(testDir)
+ outputs.dir(cloverTestInstrDir)
+
+ classpath = sourceSets.clover.compileClasspath
+ main = "com.atlassian.clover.CloverInstr"
+
+ def argsList = [
+ "--encoding",
+ "UTF-8",
+ "--initstring",
+ cloverDb,
+ "--srcdir",
+ testDir,
+ "--destdir",
+ cloverTestInstrDir.getPath(),
+ ]
+ args argsList.toArray()
+
+ doFirst {
+ delete cloverTestInstrDir
+ println("Clover: About to instrument test files")
}
}
+task cloverInstr {
+ group = "Verification"
+ description = "Create clover instrumented all source files"
+
+ dependsOn cloverInstrJava
+ dependsOn cloverInstrTests
+}
+
+
cloverClasses.dependsOn cloverInstr
-task cloverReport {
+task cloverConsoleReport(type: JavaExec) {
group = "Verification"
- description = "Creates the Clover report"
- inputs.dir "${buildDir}/clover"
- outputs.dir "${reportsDir}/clover"
+ description = "Creates clover console report"
+
onlyIf {
file(cloverDb).exists()
}
- doFirst {
- def argsList = [
- "--initstring",
- cloverDb,
- "-o",
- "${reportsDir}/clover"
- ]
- String[] args = argsList.toArray()
- com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
- // and generate ${reportsDir}/clover/clover.xml
- args = [
- "--initstring",
- cloverDb,
- "-o",
- "${reportsDir}/clover/clover.xml"
- ].toArray()
- com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+ inputs.dir cloverClassesDir
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.console.ConsoleReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
}
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--unittests"
+ ]
+
+ args argsList.toArray()
}
-compileCloverJava {
+task cloverHtmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover HTML report"
- doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs += additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
+ onlyIf {
+ file(cloverDb).exists()
+ }
+
+ def cloverHtmlDir = cloverReportDir
+ inputs.dir cloverClassesDir
+ outputs.dir cloverHtmlDir
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
}
- classpath += configurations.cloverRuntime
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--outputdir",
+ cloverHtmlDir
+ ]
+
+ if (cloverreport_html_options.length() > 0) {
+ argsList += cloverreport_html_options.split(" ")
+ }
+
+ args argsList.toArray()
}
-task cleanClover {
- doFirst {
- delete cloverInstrDir
- delete cloverDb
+task cloverXmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover XML report"
+
+ onlyIf {
+ file(cloverDb).exists()
}
+
+ def cloverXmlFile = "${cloverReportDir}/clover.xml"
+ inputs.dir cloverClassesDir
+ outputs.file cloverXmlFile
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.xml.XMLReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+ }
+
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--outfile",
+ cloverXmlFile
+ ]
+
+ if (cloverreport_xml_options.length() > 0) {
+ argsList += cloverreport_xml_options.split(" ")
+ }
+
+ args argsList.toArray()
}
-// end clover bits
-compileJava {
+task cloverReport {
+ group = "Verification"
+ description = "Creates clover reports"
+
+ dependsOn cloverXmlReport
+ dependsOn cloverHtmlReport
+}
+
+
+compileCloverJava {
doFirst {
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
- options.compilerArgs = additional_compiler_args
+ options.compilerArgs += additional_compiler_args
print ("Setting target compatibility to "+targetCompatibility+"\n")
}
+ //classpath += configurations.cloverRuntime
+}
+// end clover bits
+
+
+compileJava {
+ // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ options.encoding = "UTF-8"
+ doFirst {
+ print ("Setting target compatibility to "+compile_target_compatibility+"\n")
+ }
}
compileTestJava {
- if (use_clover) {
- dependsOn compileCloverJava
- classpath += configurations.cloverRuntime
- } else {
- classpath += sourceSets.main.runtimeClasspath
- }
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs = additional_compiler_args
print ("Setting target compatibility to "+targetCompatibility+"\n")
}
}
}
-task setGitVals {
- def hashStdOut = new ByteArrayOutputStream()
- exec {
- commandLine "git", "rev-parse", "--short", "HEAD"
- standardOutput = hashStdOut
- ignoreExitValue true
- }
+def convertMdToHtml (FileTree mdFiles, File cssFile) {
+ MutableDataSet options = new MutableDataSet()
- def branchStdOut = new ByteArrayOutputStream()
- exec {
- commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
- standardOutput = branchStdOut
- ignoreExitValue true
+ def extensions = new ArrayList<>()
+ extensions.add(AnchorLinkExtension.create())
+ extensions.add(AutolinkExtension.create())
+ extensions.add(StrikethroughExtension.create())
+ extensions.add(TaskListExtension.create())
+ extensions.add(TablesExtension.create())
+ extensions.add(TocExtension.create())
+
+ options.set(Parser.EXTENSIONS, extensions)
+
+ // set GFM table parsing options
+ options.set(TablesExtension.WITH_CAPTION, false)
+ options.set(TablesExtension.COLUMN_SPANS, false)
+ options.set(TablesExtension.MIN_HEADER_ROWS, 1)
+ options.set(TablesExtension.MAX_HEADER_ROWS, 1)
+ options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
+ options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
+ options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
+ // GFM anchor links
+ options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
+ options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
+ options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
+ options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
+
+ Parser parser = Parser.builder(options).build()
+ HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+
+ mdFiles.each { mdFile ->
+ // add table of contents
+ def mdText = "[TOC]\n"+mdFile.text
+
+ // grab the first top-level title
+ def title = null
+ def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
+ def matcher = mdText =~ titleRegex
+ if (matcher.size() > 0) {
+ // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
+ title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
+ }
+ // or use the filename if none found
+ if (title == null) {
+ title = mdFile.getName()
+ }
+
+ Node document = parser.parse(mdText)
+ String htmlBody = renderer.render(document)
+ def htmlText = '''<html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <meta http-equiv="Content-Style-Type" content="text/css" />
+ <meta name="generator" content="flexmark" />
+'''
+ htmlText += ((title != null) ? " <title>${title}</title>" : '' )
+ htmlText += '''
+ <style type="text/css">code{white-space: pre;}</style>
+'''
+ htmlText += ((cssFile != null) ? cssFile.text : '')
+ htmlText += '''</head>
+ <body>
+'''
+ htmlText += htmlBody
+ htmlText += '''
+ </body>
+</html>
+'''
+
+ def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+ def htmlFile = file(htmlFilePath)
+ println("Creating ${htmlFilePath}")
+ htmlFile.text = htmlText
+ }
+}
+
+
+task copyDocs(type: Copy) {
+ def inputDir = "${jalviewDir}/${doc_dir}"
+ def outputDir = "${docBuildDir}/${doc_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
}
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
+ }
+ into outputDir
- gitHash = hashStdOut.toString().trim()
- gitBranch = branchStdOut.toString().trim()
-
- outputs.upToDateWhen { false }
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
}
-task createBuildProperties(type: WriteProperties) {
- group = "build"
- description = "Create the ${buildProperties} file"
- dependsOn setGitVals
- inputs.dir(sourceDir)
- inputs.dir(resourceDir)
- file(buildProperties).getParentFile().mkdirs()
- outputFile (buildProperties)
- // taking time specific comment out to allow better incremental builds
- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
- property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
- property "VERSION", JALVIEW_VERSION
- property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
- outputs.file(outputFile)
-}
-
+task convertMdFiles {
+ dependsOn copyDocs
+ def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+ def cssFile = file("${jalviewDir}/${flexmark_css}")
-clean {
- doFirst {
- delete buildProperties
+ doLast {
+ convertMdToHtml(mdFiles, cssFile)
}
-}
+ inputs.files(mdFiles)
+ inputs.file(cssFile)
-task cleanBuildingHTML(type: Delete) {
- doFirst {
- delete buildingHTML
+ def htmlFiles = []
+ mdFiles.each { mdFile ->
+ def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+ htmlFiles.add(file(htmlFilePath))
}
+ outputs.files(htmlFiles)
}
-task convertBuildingMD(type: Exec) {
- 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 buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
- if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
- pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${helpBuildDir}/${help_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.hs')
+ include('**/*.xml')
+ include('**/*.jhm')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
}
-
- doFirst {
- if (pandoc != null && file(pandoc).exists()) {
- commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
- } else {
- println("Cannot find pandoc. Skipping convert building.md to HTML")
- throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
- }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.hs')
+ exclude('**/*.xml')
+ exclude('**/*.jhm')
}
+ into outputDir
- ignoreExitValue true
-
- inputs.file(buildingMD)
- inputs.file(css)
- outputs.file(buildingHTML)
+ inputs.dir(inputDir)
+ outputs.files(helpFile)
+ outputs.dir(outputDir)
}
-task syncDocs(type: Sync) {
- dependsOn convertBuildingMD
- def syncDir = "${classesDir}/${docDir}"
- from fileTree("${jalviewDir}/${docDir}")
- into syncDir
-
-}
-
+task copyResources(type: Copy) {
+ group = "build"
+ description = "Copy (and make text substitutions in) the resources dir to the build area"
-task copyHelp(type: Copy) {
- def inputDir = helpSourceDir
- def outputDir = "${classesDir}/${help_dir}"
+ def inputDir = resourceDir
+ def outputDir = resourcesBuildDir
from(inputDir) {
- exclude '**/*.gif'
- exclude '**/*.jpg'
- exclude '**/*.png'
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
filter(ReplaceTokens,
beginToken: '$$',
endToken: '$$',
)
}
from(inputDir) {
- include '**/*.gif'
- include '**/*.jpg'
- include '**/*.png'
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
}
into outputDir
inputs.dir(inputDir)
- outputs.files(helpFile)
outputs.dir(outputDir)
}
+task copyChannelResources(type: Copy) {
+ dependsOn copyResources
+ group = "build"
+ description = "Copy the channel resources dir to the build resources area"
-task syncLib(type: Sync) {
- def syncDir = "${classesDir}/${libDistDir}"
- from fileTree("${jalviewDir}/${libDistDir}")
- into syncDir
-}
+ def inputDir = "${channelDir}/${resource_dir}"
+ def outputDir = resourcesBuildDir
+ from inputDir
+ into outputDir
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
-task syncResources(type: Sync) {
- dependsOn createBuildProperties
- from resourceDir
- include "**/*.*"
- into "${classesDir}"
- preserve {
- include "**"
+task createBuildProperties(type: WriteProperties) {
+ dependsOn copyResources
+ group = "build"
+ description = "Create the ${buildProperties} file"
+
+ inputs.dir(sourceDir)
+ inputs.dir(resourcesBuildDir)
+ outputFile (buildProperties)
+ // taking time specific comment out to allow better incremental builds
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+ property "VERSION", JALVIEW_VERSION
+ property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+ if (getdownSetAppBaseProperty) {
+ property "GETDOWNAPPBASE", getdownAppBase
+ property "GETDOWNAPPDISTDIR", getdownAppDistDir
}
+ outputs.file(outputFile)
+}
+
+
+task buildIndices(type: JavaExec) {
+ dependsOn copyHelp
+ classpath = sourceSets.main.compileClasspath
+ main = "com.sun.java.help.search.Indexer"
+ workingDir = "${helpBuildDir}/${help_dir}"
+ def argDir = "html"
+ args = [ argDir ]
+ inputs.dir("${workingDir}/${argDir}")
+
+ outputs.dir("${classesDir}/doc")
+ outputs.dir("${classesDir}/help")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+ outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+ outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+ outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+ outputs.file("${workingDir}/JavaHelpSearch/TMAP")
}
+task buildResources {
+ dependsOn copyResources
+ dependsOn copyChannelResources
+ dependsOn createBuildProperties
+}
task prepare {
- dependsOn syncResources
- dependsOn syncDocs
+ dependsOn buildResources
+ dependsOn copyDocs
dependsOn copyHelp
+ dependsOn convertMdFiles
+ dependsOn buildIndices
}
+compileJava.dependsOn prepare
+run.dependsOn compileJava
+//run.dependsOn prepare
+
+
//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
test {
dependsOn prepare
- dependsOn compileJava
- if (use_clover) {
- dependsOn cloverInstr
- }
- if (use_clover) {
- print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+ if (useClover) {
+ dependsOn cloverClasses
+ } else { //?
+ dependsOn compileJava //?
}
useTestNG() {
- includeGroups testngGroups
- excludeGroups testngExcludedGroups
+ includeGroups testng_groups
+ excludeGroups testng_excluded_groups
preserveOrder true
useDefaultListeners=true
}
maxHeapSize = "1024m"
workingDir = jalviewDir
- //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+ systemProperty "laf", testLaf
+ }
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
jvmArgs += additional_compiler_args
-}
-
-
-task buildIndices(type: JavaExec) {
- dependsOn copyHelp
- classpath = sourceSets.main.compileClasspath
- main = "com.sun.java.help.search.Indexer"
- workingDir = "${classesDir}/${help_dir}"
- def argDir = "html"
- args = [ argDir ]
- inputs.dir("${workingDir}/${argDir}")
-
- outputs.dir("${classesDir}/doc")
- outputs.dir("${classesDir}/help")
- outputs.file("${workingDir}/JavaHelpSearch/DOCS")
- outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
- outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
- outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
- outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
- outputs.file("${workingDir}/JavaHelpSearch/TMAP")
+ doFirst {
+ if (useClover) {
+ println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+ }
+ }
}
task compileLinkCheck(type: JavaCompile) {
options.fork = true
- classpath = files("${jalviewDir}/${utilsDir}")
- destinationDir = file("${jalviewDir}/${utilsDir}")
- source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+ classpath = files("${jalviewDir}/${utils_dir}")
+ destinationDir = file("${jalviewDir}/${utils_dir}")
+ source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
- inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
- inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
- outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
- outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+ outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
}
task linkCheck(type: JavaExec) {
- dependsOn prepare, compileLinkCheck
+ dependsOn prepare
+ dependsOn compileLinkCheck
- def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
- classpath = files("${jalviewDir}/${utilsDir}")
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+ classpath = files("${jalviewDir}/${utils_dir}")
main = "HelpLinksChecker"
workingDir = jalviewDir
- args = [ "${classesDir}/${help_dir}", "-nointernet" ]
+ args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
- def errFOS = outFOS
standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
outFOS,
- standardOutput)
+ System.out)
errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
outFOS,
- errorOutput)
+ System.err)
- inputs.dir("${classesDir}/${help_dir}")
+ inputs.dir(helpBuildDir)
outputs.file(helpLinksCheckerOutFile)
}
+
// import the pubhtmlhelp target
ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
-ant.importBuild "${utilsDir}/publishHelp.xml"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
+ant.importBuild "${utils_dir}/publishHelp.xml"
task cleanPackageDir(type: Delete) {
doFirst {
- delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
+ delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
}
}
jar {
+ dependsOn prepare
dependsOn linkCheck
- dependsOn buildIndices
- dependsOn createBuildProperties
manifest {
- attributes "Main-Class": mainClass,
+ attributes "Main-Class": main_class,
"Permissions": "all-permissions",
- "Application-Name": "Jalview Desktop",
- "Codebase": application_codebase
+ "Application-Name": install4jApplicationName,
+ "Codebase": application_codebase,
+ "Implementation-Version": JALVIEW_VERSION
}
- destinationDir = file("${jalviewDir}/${packageDir}")
- archiveName = rootProject.name+".jar"
+ def outputDir = "${jalviewDir}/${package_dir}"
+ destinationDirectory = file(outputDir)
+ archiveFileName = rootProject.name+".jar"
+ duplicatesStrategy "EXCLUDE"
+
exclude "cache*/**"
exclude "*.jar"
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir(classesDir)
- outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
+ inputs.dir(sourceSets.main.java.outputDir)
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+ outputs.file("${outputDir}/${archiveFileName}")
}
task copyJars(type: Copy) {
from fileTree(dir: classesDir, include: "**/*.jar").files
- into "${jalviewDir}/${packageDir}"
+ into "${jalviewDir}/${package_dir}"
}
// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
task syncJars(type: Sync) {
+ dependsOn jar
from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
- into "${jalviewDir}/${packageDir}"
+ into "${jalviewDir}/${package_dir}"
preserve {
- include jar.archiveName
+ include jar.archiveFileName.getOrNull()
}
}
dependsOn cleanPackageDir
dependsOn syncJars
dependsOn jar
- outputs.dir("${jalviewDir}/${packageDir}")
+ outputs.dir("${jalviewDir}/${package_dir}")
}
dependsOn clean
}
+
shadowJar {
group = "distribution"
+ description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
if (buildDist) {
dependsOn makeDist
}
include("*.jar")
}
manifest {
- attributes 'Implementation-Version': JALVIEW_VERSION
+ attributes "Implementation-Version": JALVIEW_VERSION,
+ "Application-Name": install4jApplicationName
}
- mainClassName = shadowJarMainClass
+
+ duplicatesStrategy "INCLUDE"
+
+ mainClassName = shadow_jar_main_class
mergeServiceFiles()
classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
copy {
from buildProperties
- rename(build_properties_file, getdown_build_properties)
+ rename(file(buildProperties).getName(), getdown_build_properties)
into getdownAppDir
}
getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
- // go through properties looking for getdown_txt_...
+ copy {
+ from channelPropsFile
+ into getdownWebsiteDir
+ }
+ getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
+
+ // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
}
+ if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
+ props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
+ props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
+ props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
+ props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+ props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+ props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
+ }
- props.put("getdown_txt_appbase", getdownAppBase)
+ props.put("getdown_txt_title", jalview_name)
+ props.put("getdown_txt_ui.name", install4jApplicationName)
+
+ // start with appbase
+ getdownTextString += "appbase = ${getdownAppBase}\n"
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_") && val != null) {
if (prop.startsWith("getdown_txt_multi_")) {
into getdownResourceDir
}
}
+
+ def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+ getdownWrapperScripts.each{ script ->
+ def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+ if (s.exists()) {
+ copy {
+ from s
+ into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+ }
+ getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+ }
+ }
def codeFiles = []
- fileTree(file(packageDir)).each{ f ->
+ fileTree(file(package_dir)).each{ f ->
if (f.isDirectory()) {
def files = fileTree(dir: f, include: ["*"]).getFiles()
codeFiles += files
codeFiles += f
}
}
- codeFiles.sort().each{f ->
+ def jalviewJar = jar.archiveFileName.getOrNull()
+ // put jalview.jar first for CLASSPATH and .properties files reasons
+ codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
def name = f.getName()
def line = "code = ${getdownAppDistDir}/${name}\n"
getdownTextString += line
// 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"
+ getdownTextString += "class = ${main_class}\n"
+ // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
+ if (getdownSetAppBaseProperty) {
+ getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
+ getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+ }
def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
getdown_txt.write(getdownTextString)
def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
- launchJvl.write("appbase="+props.get("getdown_txt_appbase"))
+ launchJvl.write("appbase=${getdownAppBase}")
+ // files going into the getdown website dir: getdown-launcher.jar
copy {
from getdownLauncher
rename(file(getdownLauncher).getName(), getdown_launcher_new)
into getdownWebsiteDir
}
+ // files going into the getdown website dir: getdown-launcher(-local).jar
copy {
from getdownLauncher
if (file(getdownLauncher).getName() != getdown_launcher) {
into getdownWebsiteDir
}
+ // files going into the getdown website dir: ./install dir and files
if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
copy {
from getdown_txt
from getdownLauncher
- from "${getdownWebsiteDir}/${getdown_build_properties}"
+ from "${getdownAppDir}/${getdown_build_properties}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
into getdownInstallDir
}
+ // and make a copy in the getdown files dir (these are not downloaded by getdown)
copy {
from getdownInstallDir
into getdownFilesInstallDir
}
}
+ // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
copy {
from getdown_txt
from launchJvl
from getdownLauncher
from "${getdownWebsiteDir}/${getdown_build_properties}"
+ from "${getdownWebsiteDir}/${channel_props}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
into getdownFilesDir
}
+ // and ./resources (not all downloaded by getdown)
copy {
from getdownResourceDir
into "${getdownFilesDir}/${getdown_resource_dir}"
}
if (buildDist) {
- inputs.dir("${jalviewDir}/${packageDir}")
+ inputs.dir("${jalviewDir}/${package_dir}")
}
outputs.dir(getdownWebsiteDir)
outputs.dir(getdownFilesDir)
// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
task getdownDigestDir(type: JavaExec) {
+ group "Help"
+ description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
+
def digestDirPropertyName = "DIGESTDIR"
- description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown"
doFirst {
classpath = files(getdownLauncher)
def digestDir = findProperty(digestDirPropertyName)
}
+tasks.withType(JavaCompile) {
+ options.encoding = 'UTF-8'
+}
+
+
clean {
doFirst {
delete getdownWebsiteDir
def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
inputs.file(install4jTemplateFile)
inputs.file(install4jFileAssociationsFile)
+ inputs.property("CHANNEL", { CHANNEL })
outputs.file(install4jConfFile)
doLast {
}
}
+ // disable install screen for OSX dmg (for 2.11.2.0)
+ install4jConfigXml.'**'.macosArchive.each { macosArchive ->
+ macosArchive.attributes().remove('executeSetupApp')
+ macosArchive.attributes().remove('setupAppId')
+ }
+
// turn off checksum creation for LOCAL channel
def e = install4jConfigXml.application[0]
if (CHANNEL == "LOCAL") {
// put file association actions where placeholder action is
def install4jFileAssociationsText = install4jFileAssociationsFile.text
def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
- install4jConfigXml.'**'.action.any { a ->
+ install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
def parent = a.parent()
parent.remove(a)
}
}
+ // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
+ // NB we're deleting the /other/ one!
+ // Also remove the examples subdir from non-release versions
+ def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
+ // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
+ if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
+ customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
+ } else {
+ // remove the examples subdir from Full File Set
+ def files = install4jConfigXml.files[0]
+ def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
+ def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
+ def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
+ def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
+ dirEntry.parent().remove(dirEntry)
+ }
+ install4jConfigXml.'**'.action.any { a ->
+ if (a.'@customizedId' == customizedIdToDelete) {
+ def parent = a.parent()
+ parent.remove(a)
+ return true
+ }
+ }
+
// write install4j file
install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
}
task installers(type: com.install4j.gradle.Install4jTask) {
group = "distribution"
description = "Create the install4j installers"
- dependsOn setGitVals
dependsOn getdown
dependsOn copyInstall4jTemplate
def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
variables = [
- 'JALVIEW_NAME': getdown_txt_title,
+ 'JALVIEW_NAME': jalview_name,
+ 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
'JALVIEW_DIR': "../..",
'OSX_KEYSTORE': OSX_KEYSTORE,
+ 'OSX_APPLEID': OSX_APPLEID,
+ 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
'JSIGN_SH': JSIGN_SH,
'JRE_DIR': getdown_app_dir_java,
'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
'COPYRIGHT_MESSAGE': install4j_copyright_message,
- 'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
- 'INSTALLER_NAME': install4j_installer_name,
+ 'BUNDLE_ID': install4jBundleId,
+ 'INTERNAL_ID': install4jInternalId,
+ 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
+ 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
+ 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+ 'WRAPPER_LINK': getdownWrapperLink,
+ 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+ 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+ 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
+ 'INSTALLER_NAME': install4jInstallerName,
'INSTALL4J_UTILS_DIR': install4j_utils_dir,
'GETDOWN_WEBSITE_DIR': getdown_website_dir,
'GETDOWN_FILES_DIR': getdown_files_dir,
'GETDOWN_INSTALL_DIR': getdown_install_dir,
'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
'BUILD_DIR': install4jBuildDir,
+ 'APPLICATION_CATEGORIES': install4j_application_categories,
+ 'APPLICATION_FOLDER': install4jApplicationFolder,
+ 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
+ 'EXECUTABLE_NAME': install4jExecutableName,
+ 'EXTRA_SCHEME': install4jExtraScheme,
+ 'MAC_ICONS_FILE': install4jMacIconsFile,
+ 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
+ 'PNG_ICON_FILE': install4jPngIconFile,
+ 'BACKGROUND': install4jBackground,
+
]
+ //println("INSTALL4J VARIABLES:")
+ //variables.each{k,v->println("${k}=${v}")}
+
destination = "${jalviewDir}/${install4jBuildDir}"
buildSelected = true
if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
faster = true
disableSigning = true
+ disableNotarization = true
}
if (OSX_KEYPASS) {
macKeystorePassword = OSX_KEYPASS
+ }
+
+ if (OSX_ALTOOLPASS) {
+ appleIdPassword = OSX_ALTOOLPASS
+ disableNotarization = false
+ } else {
+ disableNotarization = true
}
doFirst {
println("Using projectFile "+projectFile)
+ if (!disableNotarization) { println("Will notarize OSX App DMG") }
}
+ //verbose=true
inputs.dir(getdownWebsiteDir)
inputs.file(install4jConfFile)
}
-task sourceDist(type: Tar) {
+spotless {
+ java {
+ eclipse().configFile(eclipse_codestyle_file)
+ }
+}
+
+task createSourceReleaseProperties(type: WriteProperties) {
+ group = "distribution"
+ description = "Create the source RELEASE properties file"
+ def sourceTarBuildDir = "${buildDir}/sourceTar"
+ def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
+ outputFile (sourceReleasePropertiesFile)
+
+ doFirst {
+ releaseProps.each{ key, val -> property key, val }
+ property "git.branch", gitBranch
+ property "git.hash", gitHash
+ }
+
+ outputs.file(outputFile)
+}
+
+task sourceDist(type: Tar) {
+ group "distribution"
+ description "Create a source .tar.gz file for distribution"
+
+ dependsOn createBuildProperties
+ dependsOn convertMdFiles
+ dependsOn eclipseAllPreferences
+ dependsOn createSourceReleaseProperties
+
+
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
- // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
- try {
- archiveFileName = outputFileName
- } catch (Exception e) {
- archiveName = outputFileName
- }
+ archiveFileName = outputFileName
compression Compression.GZIP
"*locales/**",
"utils/InstallAnywhere",
"**/*.log",
+ "RELEASE",
]
def PROCESS_FILES=[
"AUTHORS",
"FEATURETODO",
"LICENSE",
"**/README",
- "RELEASE",
"THIRDPARTYLIBS",
"TESTNG",
"build.gradle",
"**/*.sh",
]
def INCLUDE_FILES=[
- ".settings/org.eclipse.jdt.core.jalview.prefs",
+ ".classpath",
+ ".settings/org.eclipse.buildship.core.prefs",
+ ".settings/org.eclipse.jdt.core.prefs"
]
from(jalviewDir) {
// exclude(EXCLUDE_FILES)
// exclude(PROCESS_FILES)
// }
+
+ from(file(buildProperties).getParent()) {
+ include(file(buildProperties).getName())
+ rename(file(buildProperties).getName(), "build_properties")
+ filter({ line ->
+ line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+ })
+ }
+
+ def sourceTarBuildDir = "${buildDir}/sourceTar"
+ from(sourceTarBuildDir) {
+ // this includes the appended RELEASE properties file
+ }
}
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("${classesDir}/${help_dir}")
+ inputs.dir("${helpBuildDir}/${help_dir}")
outputs.dir("${buildDir}/distributions/${help_dir}")
}
}
+task jalviewjsEnableAltFileProperty(type: WriteProperties) {
+ group "jalviewjs"
+ description "Enable the alternative J2S Config file for headless build"
+
+ outputFile = jalviewjsJ2sSettingsFileName
+ def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
+ def j2sProps = new Properties()
+ if (j2sPropsFile.exists()) {
+ try {
+ def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
+ j2sProps.load(j2sPropsFileFIS)
+ j2sPropsFileFIS.close()
+
+ j2sProps.each { prop, val ->
+ property(prop, val)
+ }
+ } catch (Exception e) {
+ println("Exception reading ${jalviewjsJ2sSettingsFileName}")
+ e.printStackTrace()
+ }
+ }
+ if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
+ property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
+ }
+}
+
+
task jalviewjsSetEclipseWorkspace {
def propKey = "jalviewjs_eclipse_workspace"
def propVal = null
eclipseProduct = "${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"
+ eclipseRoot += "/eclipse"
}
- eclipseBinary = "${eclipseRoot}/eclipse"
+ eclipseBinary = "${eclipseRoot}/eclipse.exe"
eclipseProduct = "${eclipseRoot}/.eclipseproduct"
} else { // linux or unix
if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
eclipseRoot += "/eclipse"
+println("eclipseDir exists")
}
eclipseBinary = "${eclipseRoot}/eclipse"
eclipseProduct = "${eclipseRoot}/.eclipseproduct"
task jalviewjsCreateJ2sSettings(type: WriteProperties) {
group "JalviewJS"
- description "Create the .j2s file from the j2s.* properties"
+ description "Create the alternative j2s file from the j2s.* properties"
jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
def siteDirProperty = "j2s.site.directory"
property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
}
}
- outputFile = jalviewjsJ2sSettingsFileName
+ outputFile = jalviewjsJ2sAltSettingsFileName
if (! IN_ECLIPSE) {
inputs.properties(jalviewjsJ2sProps)
- outputs.file(jalviewjsJ2sSettingsFileName)
+ outputs.file(jalviewjsJ2sAltSettingsFileName)
}
}
preserve {
include "**"
}
+
+ // should this be exclude really ?
+ duplicatesStrategy "INCLUDE"
+
outputs.files outputFiles
inputs.files inputFiles
}
task jalviewjsSyncResources (type: Sync) {
- def inputFiles = fileTree(dir: resourceDir)
+ dependsOn buildResources
+
+ def inputFiles = fileTree(dir: resourcesBuildDir)
def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
if (!IN_ECLIPSE) {
args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+ args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
}
inputs.file("${jalviewDir}/.project")
dependsOn jalviewjsEclipseSetup
dependsOn jalviewjsProjectImport
dependsOn jalviewjsEclipsePaths
+ if (!IN_ECLIPSE) {
+ dependsOn jalviewjsEnableAltFileProperty
+ }
doFirst {
// do not run a headless transpile when we claim to be in Eclipse
args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
if (!IN_ECLIPSE) {
args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+ args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
}
def stdout
new org.apache.tools.ant.util.TeeOutputStream(
logOutFOS,
stdout),
- standardOutput)
+ System.out)
errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
new org.apache.tools.ant.util.TeeOutputStream(
logErrFOS,
stderr),
- errorOutput)
+ System.err)
} else {
standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
logOutFOS,
def coreBottom = file(suffixFile)
coreFile.getParentFile().mkdirs()
coreFile.createNewFile()
- coreFile.write( coreTop.text )
+ coreFile.write( coreTop.getText("UTF-8") )
list.each {
f ->
if (f.exists()) {
- def t = f.text
+ def t = f.getText("UTF-8")
t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
coreFile.append( t )
} else {
logOutFile.append(msg+"\n")
}
}
- coreFile.append( coreBottom.text )
+ coreFile.append( coreBottom.getText("UTF-8") )
msg = "Generating ${zjsfile}"
println(msg)
def logErrFOS = logOutFOS
javaexec {
- classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
- args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+ classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
+ main = "com.google.javascript.jscomp.CommandLineRunner"
+ jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+ args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
maxHeapSize = "2g"
msg = "\nRunning '"+commandLine.join(' ')+"'\n"
new org.apache.tools.ant.util.TeeOutputStream(
logErrFOS,
stderr),
- errorOutput)
+ System.err)
} else {
standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
logOutFOS,
beginToken: '_',
endToken: '_',
tokens: [
- 'MAIN': '"'+mainClass+'"',
+ 'MAIN': '"'+main_class+'"',
'CODE': "null",
'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
'COREKEY': jalviewjs_core_key,
description "Creates a tar.gz file for the website"
dependsOn jalviewjsBuildSite
def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
- try {
- archiveFileName = outputFilename
- } catch (Exception e) {
- archiveName = outputFilename
- }
+ archiveFileName = outputFilename
compression Compression.GZIP
def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
doLast {
- SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+ def factory
+ try {
+ def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+ factory = f.newInstance()
+ } catch (ClassNotFoundException e) {
+ throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+ }
def port = Integer.valueOf(jalviewjs_server_port)
def start = port
def running = false
if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
}
- delete "${jalviewDir}/${jalviewjs_j2s_settings}"
+ delete jalviewjsJ2sAltSettingsFileName
}
outputs.upToDateWhen( { false } )
if (eclipseHome == null || ! IN_ECLIPSE) {
throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
}
- def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
- def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
- if (!eclipseJ2sPluginFile.exists()) {
- def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin"
+ def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
+ def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
+ if (altPluginsDir != null && file(altPluginsDir).exists()) {
+ eclipseJ2sPluginDirs += altPluginsDir
+ }
+ def foundPlugin = false
+ def j2sPluginFileName = j2sPluginFile.getName()
+ def eclipseJ2sPlugin
+ def eclipseJ2sPluginFile
+ eclipseJ2sPluginDirs.any { dir ->
+ eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
+ eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+ if (eclipseJ2sPluginFile.exists()) {
+ foundPlugin = true
+ return true
+ }
+ }
+ if (!foundPlugin) {
+ def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
System.err.println(msg)
throw new StopExecutionException(msg)
}
System.err.println(msg)
throw new StopExecutionException(msg)
} else {
- def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+ def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
println(msg)
}
}
description "Sync libs and resources to site dir, but not closure cores"
dependsOn jalviewjsIDE_SyncSiteAll
- dependsOn cleanJalviewjsTransferSite
+ //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
}