+/* 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.apache.tools.ant.filters.ReplaceRegexp
import org.gradle.internal.os.OperatingSystem
-import org.gradle.plugins.ide.eclipse.model.*
-
-
+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 {
+ mavenCentral()
+ mavenLocal()
+ }
dependencies {
- classpath 'org.openclover:clover:4.3.1'
- classpath 'org.apache.commons:commons-compress:1.18'
+ classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
}
}
+
plugins {
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 '7.0.9'
+ id 'com.install4j.gradle' version '8.0.4'
+ id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+ id 'com.palantir.git-version' version '0.12.3'
}
repositories {
jcenter()
mavenCentral()
mavenLocal()
- flatDir {
- dirs gradlePluginsDir
- }
}
-mainClassName = launcherClass
-def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
-def classes = "$jalviewDir/$classesDir"
-if (clover.equals("true")) {
- use_clover = true
- classes = "$buildDir/$cloverClassesDir"
-} else {
- use_clover = false
- classes = "$jalviewDir/$classesDir"
+// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
+def string(Object o) {
+ return o == null ? "" : o.toString()
}
-// configure classpath/args for j8/j11 compilation
-
-def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
-def libDir
-def libDistDir
-def compile_source_compatibility
-def compile_target_compatibility
ext {
- getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
- getdownDir = ""
- reportRsyncCmd = false
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+ // local build environment properties
+ // can be "projectDir/local.properties"
+ def localProps = "${projectDir}/local.properties"
+ def propsFile = null;
+ if (file(localProps).exists()) {
+ propsFile = localProps
+ }
+ // or "../projectDir_local.properties"
+ def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
+ if (file(dirLocalProps).exists()) {
+ propsFile = dirLocalProps
+ }
+ if (propsFile != null) {
+ try {
+ def p = new Properties()
+ def localPropsFIS = new FileInputStream(propsFile)
+ p.load(localPropsFIS)
+ localPropsFIS.close()
+ p.each {
+ key, val ->
+ def oldval = findProperty(key)
+ setProperty(key, val)
+ if (oldval != null) {
+ println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ } else {
+ println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ }
+ }
+ } catch (Exception e) {
+ System.out.println("Exception reading local.properties")
+ }
+ }
+
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+ // Expect jalview.version and target release branch in jalview.release
+ def releaseProps = new Properties();
+ def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+ def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+ try {
+ (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
+ releaseProps.load(it)
+ }
+ } catch (Exception fileLoadError) {
+ throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+ }
+ ////
+ // Set JALVIEW_VERSION if it is not already set
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+
+ // this property set when running Eclipse headlessly
+ j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
+ // this property set by Eclipse
+ eclipseApplicationProperty = string("eclipse.application")
+ // CHECK IF RUNNING FROM WITHIN ECLIPSE
+ def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
+ IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
+ // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
+ if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
+ println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
+ IN_ECLIPSE = false
+ }
+ if (IN_ECLIPSE) {
+ println("WITHIN ECLIPSE IDE")
+ } else {
+ println("HEADLESS BUILD")
+ }
+
+ J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+ if (J2S_ENABLED) {
+ println("J2S ENABLED")
+ }
+ /* *-/
+ System.properties.sort { it.key }.each {
+ key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
+ }
+ /-* *-/
+ if (false && IN_ECLIPSE) {
+ jalviewDir = jalviewDirAbsolutePath
+ }
+ */
+
+ // essentials
+ bareSourceDir = string(source_dir)
+ sourceDir = string("${jalviewDir}/${bareSourceDir}")
+ resourceDir = string("${jalviewDir}/${resource_dir}")
+ bareTestSourceDir = string(test_source_dir)
+ testDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+ classesDir = string("${jalviewDir}/${classes_dir}")
+
+ // 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 = buildPropertiesFile
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher
+
+ // 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}/${getdown_launcher}")
+ getdownAppDistDir = getdown_app_dir_alt
+ reportRsyncCommand = false
+ jvlChannelName = CHANNEL.toLowerCase()
+ install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
+ install4jDSStore = "DS_Store-NON-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
+ install4jInstallerName = "${jalview_name} Non-Release Installer"
+ install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+ install4jExtraScheme = "jalviewx"
switch (CHANNEL) {
case "BUILD":
// TODO: get bamboo build artifact URL for getdown artifacts
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdown_channel_base = bamboo_channelbase
+ getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
+ getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
+ jvlChannelName += "_${getdownChannelName}"
+ // automatically add the test group Not-bamboo for exclusion
+ if ("".equals(testng_excluded_groups)) {
+ testng_excluded_groups = "Not-bamboo"
+ }
+ install4jExtraScheme = "jalviewb"
break
case "RELEASE":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
- getdown_app_dir = getdown_app_dir_release
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdownAppDistDir = getdown_app_dir_release
reportRsyncCommand = true
+ install4jSuffix = ""
+ install4jDSStore = "DS_Store"
+ install4jDMGBackgroundImage = "jalview_dmg_background.png"
+ install4jInstallerName = "${jalview_name} Installer"
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
+ getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = ARCHIVEDIR + "/" + packageDir
- buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
+ install4jExtraScheme = "jalviewa"
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
+ getdownChannelName = string("archive/${JALVIEW_VERSION}")
+ getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+ throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
} else {
- packageDir = ARCHIVEDIR + "/" + packageDir
- buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ package_dir = string("${ARCHIVEDIR}/${package_dir}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jSuffix = "Archive"
+ install4jExtraScheme = "jalviewa"
break
case "DEVELOP":
- getdown_channel_name = CHANNEL.toLowerCase()
- getdownDir = getdown_channel_name + "/" + JAVA_VERSION
- getdown_app_base = getdown_channel_base + "/" + getdownDir
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
reportRsyncCommand = true
+
+ // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+ JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
+
+ channelPropertiesFile = string("${channel_properties_dir}/develop_properties")
+ getdownImagesDir = "${getdown_images_dir}/develop"
+ getdownBgColour = "000000"
+ getdownFgColour = "FFFFFF"
+ getdownLightFgColour = "CCCCFF"
+ install4jSuffix = "Develop"
+ install4jDSStore = "DS_Store-DEVELOP"
+ install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
+ install4jExtraScheme = "jalviewd"
+ install4jInstallerName = "${jalview_name} Develop Installer"
+ install4jMacIconsFile = string("${install4j_utils_dir}/develop/${install4j_mac_icons_file}")
+ install4jWindowsIconsFile = string("${install4j_utils_dir}/develop/${install4j_windows_icons_file}")
+ install4jPngIconFile = string("${install4j_utils_dir}/develop/${install4j_png_icon_file}")
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 +"/" + buildPropertiesFile
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'")
+ }
+ JALVIEW_VERSION = JALVIEW_VERSION+"-test"
+ install4jSuffix = "Test"
+ install4jDSStore = "DS_Store-TEST-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
break
case ~/^SCRATCH(|-[-\w]*)$/:
- 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 +"/" + buildPropertiesFile
+ 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":
+ if (!file("${LOCALDIR}").exists()) {
+ throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
+ } else {
+ getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ }
+ JALVIEW_VERSION = "TEST"
+ install4jSuffix = "Test-Local"
+ install4jDSStore = "DS_Store-TEST-RELEASE"
+ install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
+ install4jExtraScheme = "jalviewt"
+ install4jInstallerName = "${jalview_name} Test Installer"
break
case "LOCAL":
- getdown_app_base = file(getdownWebsiteDir).toURI().toString()
- getdown_app_dir = getdown_app_dir_alt
- buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
- getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ JALVIEW_VERSION = "TEST"
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ install4jExtraScheme = "jalviewl"
break
default: // something wrong specified
- print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
- exit
+ throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
break
}
-
- println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base)
- getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
- //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
- getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
- getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir
- getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
- getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir
+ // override getdownAppBase if requested
+ if (findProperty("getdown_appbase_override") != null) {
+ getdownAppBase = string(getProperty("getdown_appbase_override"))
+ println("Overriding getdown appbase with '${getdownAppBase}'")
+ }
+ // sanitise file name for jalview launcher file for this channel
+ 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()
+
+ getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
+ //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
+ getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
+ getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
+ getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
+ getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
/* compile without modules -- using classpath libraries
- modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
+ modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
*/
- gitHash = ""
- gitBranch = ""
-}
-
-def JAVA_INTEGER_VERSION
-def additional_compiler_args = []
-// these are getdown.txt properties defined dependent on the JAVA_VERSION
-def getdown_alt_java_min_version
-def getdown_alt_java_max_version
-// this property is assigned below and expanded to multiple lines in the getdown task
-def getdown_alt_multi_java_location
-// this property is for the Java library used in eclipse
-def eclipse_java_runtime_name
-if (JAVA_VERSION.equals("1.8")) {
- JAVA_INTEGER_VERSION = "8"
- //libDir = j8libDir
- libDir = j11libDir
- libDistDir = j8libDir
- compile_source_compatibility = 1.8
- compile_target_compatibility = 1.8
- getdown_alt_java_min_version = getdown_alt_java8_min_version
- getdown_alt_java_max_version = getdown_alt_java8_max_version
- getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
- eclipse_java_runtime_name = "JavaSE-1.8"
-} else if (JAVA_VERSION.equals("11")) {
- JAVA_INTEGER_VERSION = "11"
- libDir = j11libDir
- libDistDir = j11libDir
- compile_source_compatibility = 11
- compile_target_compatibility = 11
- getdown_alt_java_min_version = getdown_alt_java11_min_version
- getdown_alt_java_max_version = getdown_alt_java11_max_version
- getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
- eclipse_java_runtime_name = "JavaSE-11"
- /* compile without modules -- using classpath libraries
- additional_compiler_args += [
- '--module-path', ext.modules_compileClasspath.asPath,
- '--add-modules', j11modules
- ]
- */
-} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
- JAVA_INTEGER_VERSION = JAVA_VERSION
- libDir = j11libDir
- libDistDir = j11libDir
- compile_source_compatibility = JAVA_VERSION
- compile_target_compatibility = JAVA_VERSION
- getdown_alt_java_min_version = getdown_alt_java11_min_version
- getdown_alt_java_max_version = getdown_alt_java11_max_version
- getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
- eclipse_java_runtime_name = "JavaSE-11"
- /* compile without modules -- using classpath libraries
- additional_compiler_args += [
- '--module-path', ext.modules_compileClasspath.asPath,
- '--add-modules', j11modules
- ]
- */
-} else {
- throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
+ def details = versionDetails()
+ gitHash = details.gitHash
+ gitBranch = details.branchName
+
+ println("Using a ${CHANNEL} profile.")
+
+ additional_compiler_args = []
+ // configure classpath/args for j8/j11 compilation
+ if (JAVA_VERSION.equals("1.8")) {
+ JAVA_INTEGER_VERSION = string("8")
+ //libDir = j8libDir
+ libDir = j11libDir
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+ // these are getdown.txt properties defined dependent on the JAVA_VERSION
+ getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
+ getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
+ // this property is assigned below and expanded to multiple lines in the getdown task
+ getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
+ // this property is for the Java library used in eclipse
+ eclipseJavaRuntimeName = string("JavaSE-1.8")
+ } else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = string("11")
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+ 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")
+ /* compile without modules -- using classpath libraries
+ additional_compiler_args += [
+ '--module-path', modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ */
+ } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+ JAVA_INTEGER_VERSION = JAVA_VERSION
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = JAVA_VERSION
+ compile_target_compatibility = JAVA_VERSION
+ 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")
+ /* compile without modules -- using classpath libraries
+ additional_compiler_args += [
+ '--module-path', modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ */
+ } else {
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
+ }
+
+
+ // for install4j
+ JAVA_MIN_VERSION = JAVA_VERSION
+ JAVA_MAX_VERSION = JAVA_VERSION
+ def jreInstallsDir = string(jre_installs_dir)
+ if (jreInstallsDir.startsWith("~/")) {
+ 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")
+ install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
+ install4jConfFileName = string("jalview-install4j-conf.install4j")
+ install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
+ install4jHomeDir = install4j_home_dir
+ if (install4jHomeDir.startsWith("~/")) {
+ 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")
+
+ 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())
+ jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
+ jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
+ if (IN_ECLIPSE) {
+ jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
+ } else {
+ jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
+ }
+ jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
+ jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
+ jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
+ jalviewjsJalviewCoreHtmlFile = string("")
+ jalviewjsJalviewCoreName = string(jalviewjs_core_name)
+ jalviewjsCoreClasslists = []
+ jalviewjsJalviewTemplateName = string(jalviewjs_name)
+ jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+ jalviewjsJ2sProps = null
+ jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+
+ eclipseWorkspace = null
+ eclipseBinary = string("")
+ eclipseVersion = string("")
+ eclipseDebug = false
+ // ENDEXT
}
-sourceSets {
+sourceSets {
main {
java {
- srcDirs "$jalviewDir/$sourceDir"
- outputDir = file("$classes")
+ srcDirs sourceDir
+ outputDir = file(classesDir)
}
resources {
- srcDirs "$jalviewDir/$resourceDir"
+ srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
}
- jar.destinationDir = file("$jalviewDir/$packageDir")
-
compileClasspath = files(sourceSets.main.java.outputDir)
- compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ 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 += fileTree(dir: "$jalviewDir/$libDir", 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 "$jalviewDir/$testSourceDir"
- outputDir = file("$jalviewDir/$testOutputDir")
+ srcDirs testSourceDir
+ 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: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
- compileClasspath += fileTree(dir: "$jalviewDir/$libDir", 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:4.3.1'
- testCompile 'org.openclover:clover:4.3.1'
- }
}
-configurations {
- cloverRuntime
- cloverRuntime.extendsFrom cloverCompile
-}
+// eclipse project and settings files creation, also used by buildship
eclipse {
project {
- name = "Jalview with gradle build"
+ name = eclipse_project_name
natures 'org.eclipse.jdt.core.javanature',
'org.eclipse.jdt.groovy.core.groovyNature',
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 {
+ plusConfigurations = [ ]
+ file {
- whenMerged { cp ->
- def removeTheseToo = []
- HashMap<String, Boolean> 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)
+ whenMerged { cp ->
+ def removeTheseToo = []
+ HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
+ cp.entries.each { entry ->
+ // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+ // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+ // we add the resources and help/help dirs in as libs afterwards (see below)
+ if (entry.kind == 'src') {
+ if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
+ removeTheseToo += entry
+ } else {
+ alreadyAddedSrcPath.putAt(entry.path, true)
+ }
}
- }
- }
- cp.entries.removeAll(removeTheseToo)
-
- print ("CP="+cp.inspect())
-
- cp.entries += new Output("bin/main")
- cp.entries += new Library(fileReference(helpParentDir))
- cp.entries += new Library(fileReference(resourceDir))
-
- HashMap<String, Boolean> 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)
- }
- }
+ cp.entries.removeAll(removeTheseToo)
- // 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
+ //cp.entries += new Output("${eclipse_bin_dir}/main")
+ if (file(helpParentDir).isDirectory()) {
+ cp.entries += new Library(fileReference(helpParentDir))
}
- def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ if (file(resourceDir).isDirectory()) {
+ cp.entries += new Library(fileReference(resourceDir))
}
- if (addedLibPath.get(itPath)) {
- // don't duplicate
- } else {
- def lib = new Library(fileReference(itPath))
- // this doesn't work... yet. Adding test=true attribute using withXml below
- //def attrs = new Node(null, 'attributes', ["test":"true"])
- //lib.appendNode(attrs) //
- cp.entries += lib
- addedLibPath.put(itPath, true)
- }
- }
- }
- // withXml changes ignored by buildship, these add the "test=true" attribute
- withXml {
- def node = it.asNode()
+ HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
- def srcTestAttributes
- node.children().each{ cpe ->
- def attributes = cpe.attributes()
- if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
- srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
- return
+ sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+ //don't want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath, especially if they don't exist
+ return false // groovy "continue" in .any closure
}
- }
- def addTestAttribute = true
- srcTestAttributes.each{a ->
- if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
- addTestAttribute = false
+ def itPath = it.toString()
+ if (itPath.startsWith("${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)
}
- }
- 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"])
+ 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("${jalviewDirAbsolutePath}/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ // don't duplicate
+ } else {
+ def lib = new Library(fileReference(itPath))
+ lib.entryAttributes["test"] = "true"
+ cp.entries += lib
+ alreadyAddedLibPath.put(itPath, true)
}
}
- } // withXML
+
+ } // whenMerged
+
} // file
containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+
} // classpath
jdt {
// for the IDE, use java 11 compatibility
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
- javaRuntimeName = eclipse_java_runtime_name
+ javaRuntimeName = eclipseJavaRuntimeName
+ // add in jalview project specific properties/preferences into eclipse core preferences
file {
withProperties { props ->
def jalview_prefs = new Properties()
- def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
+ def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
jalview_prefs.load(ins)
ins.close()
jalview_prefs.forEach { t, v ->
props.putAt(t, v)
}
}
+ // codestyle file -- overrides previous formatter prefs
+ def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
+ if (csFile.exists()) {
+ XmlParser parser = new XmlParser()
+ def profiles = parser.parse(csFile)
+ def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
+ if (profile != null) {
+ profile.'setting'.each { s ->
+ def id = s.'@id'
+ def value = s.'@value'
+ if (id != null && value != null) {
+ props.putAt(id, value)
+ }
+ }
+ }
+ }
}
}
- }
- //synchronizationTasks eclipseClasspath
- //autoBuildTasks eclipseClasspath
-}
+ } // jdt
-task cloverInstr() {
- // only instrument source, we build test classes as normal
- inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
- outputs.dir cloverInstrDir
+ if (IN_ECLIPSE) {
+ // Don't want these to be activated if in headless build
+ synchronizationTasks "eclipseSynchronizationTask"
+ //autoBuildTasks "eclipseAutoBuildTask"
- doFirst {
- delete cloverInstrDir
- def argsList = ["--initstring", "${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)
+/* 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("")); }
+}
- // and generate ${reportsDir}/clover/clover.xml
- args = ["--initstring", "${buildDir}/clover/clover.db",
- "-o", "${reportsDir}/clover/clover.xml"].toArray()
- com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+// Task to update arbitrary properties files (set outputFile)
+class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
+ private final PropertiesFileContentMerger file;
+ public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
+ protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
+ protected void configure(PropertiesFile props) {
+ file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
}
+ public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
}
-// end clover bits
-
-
-compileJava {
-
- doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs = additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
+task eclipseUIPreferences(type: PropertiesFileTask) {
+ description = "Generate Eclipse additional settings"
+ def filename = "org.eclipse.jdt.ui.prefs"
+ outputFile = "$projectDir/.settings/${filename}" as File
+ file {
+ withProperties {
+ it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
+ }
}
-
}
-compileTestJava {
- if (use_clover) {
- dependsOn compileCloverJava
- classpath += configurations.cloverRuntime
- } else {
- classpath += sourceSets.main.runtimeClasspath
- }
- doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs = additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
+task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
+ description = "Generate Eclipse additional settings"
+ def filename = "org.eclipse.jdt.groovy.core.prefs"
+ outputFile = "$projectDir/.settings/${filename}" as File
+ file {
+ withProperties {
+ it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
+ }
}
}
+task eclipseAllPreferences {
+ dependsOn eclipseJdt
+ dependsOn eclipseUIPreferences
+ dependsOn eclipseGroovyCorePreferences
+}
+
+eclipseUIPreferences.mustRunAfter eclipseJdt
+eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
+
+/* end of eclipse preferences hack */
-compileCloverJava {
+// clover bits
+
+
+task cleanClover {
doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- options.compilerArgs += additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
+ delete cloverBuildDir
+ delete cloverReportDir
}
- classpath += configurations.cloverRuntime
}
-clean {
- delete sourceSets.main.java.outputDir
-}
-cleanTest {
- delete sourceSets.test.java.outputDir
- delete cloverInstrDir
-}
+task cloverInstrJava(type: JavaExec) {
+ group = "Verification"
+ description = "Create clover instrumented source java files"
-// format is a string like date.format("dd MMMM yyyy")
-def getDate(format) {
- def date = new Date()
- return date.format(format)
-}
+ dependsOn cleanClover
-task setGitVals {
- def hashStdOut = new ByteArrayOutputStream()
- exec {
- commandLine "git", "rev-parse", "--short", "HEAD"
- standardOutput = hashStdOut
- ignoreExitValue true
- }
+ inputs.files(sourceSets.main.allJava)
+ outputs.dir(cloverInstrDir)
- def branchStdOut = new ByteArrayOutputStream()
- exec {
- commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
- standardOutput = branchStdOut
- ignoreExitValue true
- }
+ //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+ classpath = sourceSets.clover.compileClasspath
+ main = "com.atlassian.clover.CloverInstr"
- project.ext.gitHash = hashStdOut.toString().trim()
- project.ext.gitBranch = branchStdOut.toString().trim()
+ def argsList = [
+ "--encoding",
+ "UTF-8",
+ "--initstring",
+ cloverDb,
+ "--destdir",
+ cloverInstrDir.getPath(),
+ ]
+ def srcFiles = sourceSets.main.allJava.files
+ argsList.addAll(
+ srcFiles.collect(
+ { file -> file.absolutePath }
+ )
+ )
+ args argsList.toArray()
- outputs.upToDateWhen { false }
+ doFirst {
+ delete cloverInstrDir
+ println("Clover: About to instrument "+srcFiles.size() +" files")
+ }
}
-task createBuildProperties(type: WriteProperties) {
- dependsOn setGitVals
- inputs.dir("$jalviewDir/$sourceDir")
- inputs.dir("$classes")
- inputs.dir("$jalviewDir/$resourceDir")
- 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
-}
+task cloverInstrTests(type: JavaExec) {
+ group = "Verification"
+ description = "Create clover instrumented source test files"
-task convertBuildingMD(type: Exec) {
- dependsOn deleteBuildingHTML
- def buildingMD = "$jalviewDir/$docDir/building.md"
- def css = "$jalviewDir/$docDir/github.css"
+ dependsOn cleanClover
- def pandoc = null
- pandoc_exec.split(",").each {
- if (file(it.trim()).exists()) {
- pandoc = it.trim()
- return true
- }
- }
+ inputs.files(testDir)
+ outputs.dir(cloverTestInstrDir)
- 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"
- }
+ 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 {
- 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()
- }
+ delete cloverTestInstrDir
+ println("Clover: About to instrument test files")
}
+}
- ignoreExitValue true
- inputs.file(buildingMD)
- inputs.file(css)
- outputs.file(buildingHTML)
-}
-clean {
- delete buildingHTML
+task cloverInstr {
+ group = "Verification"
+ description = "Create clover instrumented all source files"
+
+ dependsOn cloverInstrJava
+ dependsOn cloverInstrTests
}
-task syncDocs(type: Sync) {
- dependsOn convertBuildingMD
- def syncDir = "$classes/$docDir"
- from fileTree("$jalviewDir/$docDir")
- into syncDir
-}
+cloverClasses.dependsOn cloverInstr
-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,'Year-Rel': getDate("yyyy")])
- }
- from(inputDir) {
- include '**/*.gif'
- include '**/*.jpg'
- include '**/*.png'
+task cloverConsoleReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover console report"
+
+ onlyIf {
+ file(cloverDb).exists()
}
- into outputDir
- inputs.dir(inputDir)
- outputs.files(helpFile)
- outputs.dir(outputDir)
-}
+ inputs.dir cloverClassesDir
-task syncLib(type: Sync) {
- def syncDir = "$classes/$libDistDir"
- from fileTree("$jalviewDir/$libDistDir")
- into syncDir
-}
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.console.ConsoleReporter"
-task syncResources(type: Sync) {
- from "$jalviewDir/$resourceDir"
- include "**/*.*"
- exclude "install4j"
- into "$classes"
- preserve {
- include "**"
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
}
-}
-task prepare {
- dependsOn syncResources
- dependsOn syncDocs
- dependsOn copyHelp
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--unittests"
+ ]
+
+ args argsList.toArray()
}
-//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
-test {
- dependsOn prepare
- dependsOn compileJava
- if (use_clover) {
- dependsOn cloverInstr
+task cloverHtmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover HTML report"
+
+ onlyIf {
+ file(cloverDb).exists()
}
- if (use_clover) {
- print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+ def cloverHtmlDir = cloverReportDir
+ inputs.dir cloverClassesDir
+ outputs.dir cloverHtmlDir
+
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+ if (cloverreport_mem.length() > 0) {
+ maxHeapSize = cloverreport_mem
+ }
+ if (cloverreport_jvmargs.length() > 0) {
+ jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
}
- useTestNG() {
- includeGroups testngGroups
- preserveOrder true
- useDefaultListeners=true
+ def argsList = [
+ "--alwaysreport",
+ "--initstring",
+ cloverDb,
+ "--outputdir",
+ cloverHtmlDir
+ ]
+
+ if (cloverreport_html_options.length() > 0) {
+ argsList += cloverreport_html_options.split(" ")
}
- workingDir = jalviewDir
- //systemProperties 'clover.jar' System.properties.clover.jar
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- jvmArgs += additional_compiler_args
- print ("Setting target compatibility to "+targetCompatibility+"\n")
+ args argsList.toArray()
}
-task buildIndices(type: JavaExec) {
- dependsOn copyHelp
- classpath = sourceSets.main.compileClasspath
- main = "com.sun.java.help.search.Indexer"
- workingDir = "$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("$workingDir/JavaHelpSearch/TMAP")
-}
+task cloverXmlReport(type: JavaExec) {
+ group = "Verification"
+ description = "Creates clover XML report"
-task compileLinkCheck(type: JavaCompile) {
- options.fork = true
- classpath = files("$jalviewDir/$utilsDir")
- destinationDir = file("$jalviewDir/$utilsDir")
- source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+ onlyIf {
+ file(cloverDb).exists()
+ }
- inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
- inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
- outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
- outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
-}
+ def cloverXmlFile = "${cloverReportDir}/clover.xml"
+ inputs.dir cloverClassesDir
+ outputs.file cloverXmlFile
-def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch")
-task linkCheck(type: JavaExec) {
- dependsOn prepare, compileLinkCheck
- classpath = files("$jalviewDir/$utilsDir")
- main = "HelpLinksChecker"
- workingDir = jalviewDir
- def help = "$classes/$helpDir"
- args = [ "$classes/$helpDir", "-nointernet" ]
+ classpath = sourceSets.clover.runtimeClasspath
+ main = "com.atlassian.clover.reporters.xml.XMLReporter"
- doLast {
- helplinkscheckertouchfile.createNewFile()
+ 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(" ")
}
- inputs.dir("$classes/$helpDir")
- outputs.file(helplinkscheckertouchfile)
+ args argsList.toArray()
}
-// import the pubhtmlhelp target
-ant.properties.basedir = "$jalviewDir"
-ant.properties.helpBuildDir = jalviewDirAbsolutePath+"/$classes/$helpDir"
-ant.importBuild "$utilsDir/publishHelp.xml"
+task cloverReport {
+ group = "Verification"
+ description = "Creates clover reports"
-task cleanPackageDir(type: Delete) {
- delete fileTree("$jalviewDir/$packageDir").include("*.jar")
+ dependsOn cloverXmlReport
+ dependsOn cloverHtmlReport
}
-jar {
- dependsOn linkCheck
- dependsOn buildIndices
- dependsOn createBuildProperties
- manifest {
- attributes "Main-Class": mainClass,
+compileCloverJava {
+
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs += additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ //classpath += configurations.cloverRuntime
+}
+// end clover bits
+
+
+compileJava {
+ // 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 {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ doFirst {
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+}
+
+
+clean {
+ doFirst {
+ delete sourceSets.main.java.outputDir
+ }
+}
+
+
+cleanTest {
+ dependsOn cleanClover
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ }
+}
+
+
+// format is a string like date.format("dd MMMM yyyy")
+def getDate(format) {
+ def date = new Date()
+ return date.format(format)
+}
+
+
+def convertMdToHtml (FileTree mdFiles, File cssFile) {
+ MutableDataSet options = new MutableDataSet()
+
+ 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
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+
+task convertMdFiles {
+ dependsOn copyDocs
+ def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+ def cssFile = file("${jalviewDir}/${flexmark_css}")
+
+ doLast {
+ convertMdToHtml(mdFiles, cssFile)
+ }
+
+ inputs.files(mdFiles)
+ inputs.file(cssFile)
+
+ def htmlFiles = []
+ mdFiles.each { mdFile ->
+ def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+ htmlFiles.add(file(htmlFilePath))
+ }
+ outputs.files(htmlFiles)
+}
+
+
+task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${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")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.hs')
+ exclude('**/*.xml')
+ exclude('**/*.jhm')
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.files(helpFile)
+ outputs.dir(outputDir)
+}
+
+
+task copyResources(type: Copy) {
+ def inputDir = resourceDir
+ def outputDir = resourcesBuildDir
+ 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
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+
+task createBuildProperties(type: WriteProperties) {
+ dependsOn copyResources
+ group = "build"
+ description = "Create the ${buildProperties} file"
+
+ inputs.dir(sourceDir)
+ inputs.dir(resourcesBuildDir)
+ outputFile (buildProperties)
+ // taking time specific comment out to allow better incremental builds
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+ property "VERSION", JALVIEW_VERSION
+ property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+ outputs.file(outputFile)
+}
+
+
+task buildIndices(type: JavaExec) {
+ dependsOn copyHelp
+ classpath = sourceSets.main.compileClasspath
+ main = "com.sun.java.help.search.Indexer"
+ workingDir = "${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 prepare {
+ dependsOn copyResources
+ dependsOn copyDocs
+ dependsOn copyHelp
+ dependsOn createBuildProperties
+ dependsOn convertMdFiles
+ dependsOn buildIndices
+}
+
+
+compileJava.dependsOn prepare
+run.dependsOn compileJava
+//run.dependsOn prepare
+
+
+//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+test {
+ dependsOn prepare
+
+ if (useClover) {
+ dependsOn cloverClasses
+ } else { //?
+ dependsOn compileJava //?
+ }
+
+ useTestNG() {
+ includeGroups testng_groups
+ excludeGroups testng_excluded_groups
+ preserveOrder true
+ useDefaultListeners=true
+ }
+
+ maxHeapSize = "1024m"
+
+ workingDir = jalviewDir
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+ systemProperty "laf", testLaf
+ }
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ jvmArgs += additional_compiler_args
+
+ doFirst {
+ if (useClover) {
+ println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+ }
+ }
+}
+
+
+task compileLinkCheck(type: JavaCompile) {
+ options.fork = true
+ classpath = files("${jalviewDir}/${utils_dir}")
+ destinationDir = file("${jalviewDir}/${utils_dir}")
+ source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+ outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
+}
+
+
+task linkCheck(type: JavaExec) {
+ dependsOn prepare
+ dependsOn compileLinkCheck
+
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+ classpath = files("${jalviewDir}/${utils_dir}")
+ main = "HelpLinksChecker"
+ workingDir = jalviewDir
+ args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
+
+ def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
+ def errFOS = outFOS
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ errorOutput)
+
+ inputs.dir(helpBuildDir)
+ outputs.file(helpLinksCheckerOutFile)
+}
+
+
+// import the pubhtmlhelp target
+ant.properties.basedir = "${jalviewDir}"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
+ant.importBuild "${utils_dir}/publishHelp.xml"
+
+
+task cleanPackageDir(type: Delete) {
+ doFirst {
+ delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
+ }
+}
+
+
+jar {
+ dependsOn prepare
+ dependsOn linkCheck
+
+ manifest {
+ attributes "Main-Class": main_class,
"Permissions": "all-permissions",
- "Application-Name": "Jalview Desktop",
- "Codebase": application_codebase
+ "Application-Name": install4jApplicationName,
+ "Codebase": application_codebase,
+ "Implementation-Version": JALVIEW_VERSION
}
- destinationDir = file("$jalviewDir/$packageDir")
- archiveName = rootProject.name+".jar"
+ destinationDirectory = file("${jalviewDir}/${package_dir}")
+ archiveFileName = rootProject.name+".jar"
exclude "cache*/**"
exclude "*.jar"
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir("$classes")
- outputs.file("$jalviewDir/$packageDir/$archiveName")
+ inputs.dir(sourceSets.main.java.outputDir)
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+ outputs.file("${destinationDirectory}/${archiveFileName}")
}
+
task copyJars(type: Copy) {
- from fileTree("$classes").include("**/*.jar").include("*.jar").files
- into "$jalviewDir/$packageDir"
+ from fileTree(dir: classesDir, include: "**/*.jar").files
+ into "${jalviewDir}/${package_dir}"
}
+
// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
task syncJars(type: Sync) {
- from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files
- into "$jalviewDir/$packageDir"
+ dependsOn jar
+ from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
+ into "${jalviewDir}/${package_dir}"
preserve {
- include jar.archiveName
+ include jar.archiveFileName.getOrNull()
}
}
+
task makeDist {
group = "build"
description = "Put all required libraries in dist"
dependsOn cleanPackageDir
dependsOn syncJars
dependsOn jar
- outputs.dir("$jalviewDir/$packageDir")
+ outputs.dir("${jalviewDir}/${package_dir}")
}
+
task cleanDist {
dependsOn cleanPackageDir
dependsOn cleanTest
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
}
- from ("$jalviewDir/$libDistDir") {
+ from ("${jalviewDir}/${libDistDir}") {
include("*.jar")
}
manifest {
- attributes 'Implementation-Version': JALVIEW_VERSION
+ attributes "Implementation-Version": JALVIEW_VERSION,
+ "Application-Name": install4jApplicationName
}
- mainClassName = shadowJarMainClass
+ mainClassName = shadow_jar_main_class
mergeServiceFiles()
classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
}
+
task getdownWebsite() {
group = "distribution"
description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
dependsOn makeDist
}
- // clean the getdown website and files dir before creating getdown folders
- delete project.ext.getdownWebsiteDir
- delete project.ext.getdownFilesDir
-
def getdownWebsiteResourceFilenames = []
def getdownTextString = ""
- def getdownResourceDir = project.ext.getdownResourceDir
- def getdownAppDir = project.ext.getdownAppDir
+ def getdownResourceDir = getdownResourceDir
def getdownResourceFilenames = []
doFirst {
+ // clean the getdown website and files dir before creating getdown folders
+ delete getdownWebsiteDir
+ delete getdownFilesDir
+
copy {
from buildProperties
- rename(buildPropertiesFile, getdown_build_properties)
- into project.ext.getdownAppDir
+ rename(build_properties_file, getdown_build_properties)
+ into getdownAppDir
}
- getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties
+ getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
- // go through properties looking for getdown_txt_...
+ // set some getdown_txt_ properties then go through all 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)
+ if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
+ props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
+ }
+ if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
+ props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
+ }
+ if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
+ props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
+ }
+
+ props.put("getdown_txt_title", jalview_name)
+ props.put("getdown_txt_ui.name", install4jApplicationName)
+
+ // start with appbase
+ getdownTextString += "appbase = ${getdownAppBase}\n"
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_") && val != null) {
if (prop.startsWith("getdown_txt_multi_")) {
def key = prop.substring(18)
val.split(",").each{ v ->
- def line = key + " = " + v + "\n"
+ def line = "${key} = ${v}\n"
getdownTextString += line
}
} else {
r = file(val)
} else if (val.indexOf('/') > 0) {
// relative path (relative to jalviewDir)
- r = file( jalviewDir + '/' + val )
+ r = file( "${jalviewDir}/${val}" )
}
if (r.exists()) {
- val = getdown_resource_dir + '/' + r.getName()
+ val = "${getdown_resource_dir}/" + r.getName()
getdownWebsiteResourceFilenames += val
getdownResourceFilenames += r.getPath()
}
}
if (! prop.startsWith("getdown_txt_resource")) {
- def line = prop.substring(12) + " = " + val + "\n"
+ def line = prop.substring(12) + " = ${val}\n"
getdownTextString += line
}
}
}
getdownWebsiteResourceFilenames.each{ filename ->
- getdownTextString += "resource = "+filename+"\n"
+ getdownTextString += "resource = ${filename}\n"
}
getdownResourceFilenames.each{ filename ->
copy {
from filename
- into project.ext.getdownResourceDir
+ into getdownResourceDir
}
}
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.sort().each{f ->
- def line = "code = " + getdown_app_dir + '/' + f.getName() + "\n"
+ def name = f.getName()
+ def line = "code = ${getdownAppDistDir}/${name}\n"
getdownTextString += line
copy {
from f.getPath()
- into project.ext.getdownAppDir
+ into getdownAppDir
}
}
// NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
/*
if (JAVA_VERSION.equals("11")) {
- def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
+ def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
j11libFiles.sort().each{f ->
- def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+ def name = f.getName()
+ def line = "code = ${getdown_j11lib_dir}/${name}\n"
getdownTextString += line
copy {
from f.getPath()
- into project.ext.getdownJ11libDir
+ into getdownJ11libDir
}
}
}
// getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
//getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
- getdownTextString += "resource = " + getdown_launcher_new + "\n"
- getdownTextString += "class = " + mainClass + "\n"
+ getdownTextString += "resource = ${getdown_launcher_new}\n"
+ getdownTextString += "class = ${main_class}\n"
- def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
+ def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
getdown_txt.write(getdownTextString)
- def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl)
- launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
+ def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+ def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+ launchJvl.write("appbase=${getdownAppBase}")
copy {
from getdownLauncher
rename(file(getdownLauncher).getName(), getdown_launcher_new)
- into project.ext.getdownWebsiteDir
+ into getdownWebsiteDir
}
copy {
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
- into project.ext.getdownWebsiteDir
+ into getdownWebsiteDir
}
if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
copy {
from getdown_txt
from getdownLauncher
- from getdownWebsiteDir+"/"+getdown_build_properties
+ from "${getdownWebsiteDir}/${getdown_build_properties}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
copy {
from getdown_txt
- from launch_jvl
+ from launchJvl
from getdownLauncher
- from getdownWebsiteDir+"/"+getdown_build_properties
+ from "${getdownWebsiteDir}/${getdown_build_properties}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
}
copy {
- from getdownResourceDir
- into project.ext.getdownFilesDir + '/' + getdown_resource_dir
+ 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"
+ doFirst {
+ classpath = files(getdownLauncher)
+ def digestDir = findProperty(digestDirPropertyName)
+ if (digestDir == null) {
+ throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
+ }
+ args digestDir
}
- outputs.dir(project.ext.getdownWebsiteDir)
- outputs.dir(project.ext.getdownFilesDir)
+ main = "com.threerings.getdown.tools.Digester"
}
+
task getdownDigest(type: JavaExec) {
group = "distribution"
description = "Digest the getdown website folder"
dependsOn getdownWebsite
doFirst {
- classpath = files(getdownWebsiteDir + '/' + getdown_launcher)
+ classpath = files(getdownLauncher)
}
main = "com.threerings.getdown.tools.Digester"
- args project.ext.getdownWebsiteDir
- inputs.dir(project.ext.getdownWebsiteDir)
- outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
+ args getdownWebsiteDir
+ inputs.dir(getdownWebsiteDir)
+ outputs.file("${getdownWebsiteDir}/digest2.txt")
}
+
task getdown() {
group = "distribution"
description = "Create the minimal and full getdown app folder for installers and website and create digest file"
dependsOn getdownDigest
doLast {
if (reportRsyncCommand) {
- def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/")
- def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/")
+ def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+ def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
println "LIKELY RSYNC COMMAND:"
println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
if (RUNRSYNC == "true") {
}
}
-clean {
- 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
- }
+tasks.withType(JavaCompile) {
+ options.encoding = 'UTF-8'
}
-def install4jConf
-def macosJavaVMDir
-def macosJavaVMTgz
-def windowsJavaVMDir
-def windowsJavaVMTgz
-def install4jDir = "$jalviewDir/$install4jResourceDir"
-def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
-install4jConf = "$install4jDir/$install4jConfFile"
-
-task copyInstall4jTemplate(type: Copy) {
- macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre"
- macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
- windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre"
- windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
- from (install4jDir) {
- include install4jTemplate
- rename (install4jTemplate, install4jConfFile)
- filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
- tokens: [
- 'JAVA_VERSION': JAVA_VERSION,
- 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
- 'VERSION': JALVIEW_VERSION,
- 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
- 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
- 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
- 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
- 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
- 'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
- 'MACOS_BUNDLE_ID': install4jMacOSBundleId,
- 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
- 'GETDOWN_DIST_DIR': getdown_app_dir,
- 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
- 'GETDOWN_INSTALL_DIR': getdown_install_dir
- ]
- )
- 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: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
- replace: installerFileAssociationsXml,
- file: install4jConf
- )
- /*
- // include uninstaller applescript app files in dmg
- def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
- ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
- replace: installerDMGUninstallerXml,
- file: install4jConf
- )
- */
+clean {
+ doFirst {
+ delete getdownWebsiteDir
+ delete getdownFilesDir
}
}
-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/$JAVA_VERSION"
- buildSelected = true
-
- if (OSX_KEYPASS) {
- macKeystorePassword=OSX_KEYPASS
+install4j {
+ if (file(install4jHomeDir).exists()) {
+ // good to go!
+ } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
+ install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+ } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
+ install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
}
+ installDir(file(install4jHomeDir))
- inputs.dir(project.ext.getdownWebsiteDir)
- inputs.file(install4jConf)
- inputs.dir(macosJavaVMDir)
- inputs.dir(windowsJavaVMDir)
- outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
-
+ mediaTypes = Arrays.asList(install4j_media_types.split(","))
}
-clean {
- delete install4jConf
+
+task copyInstall4jTemplate {
+ def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+ def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+ inputs.file(install4jTemplateFile)
+ inputs.file(install4jFileAssociationsFile)
+ inputs.property("CHANNEL", { CHANNEL })
+ outputs.file(install4jConfFile)
+
+ doLast {
+ def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
+
+ // turn off code signing if no OSX_KEYPASS
+ if (OSX_KEYPASS == "") {
+ install4jConfigXml.'**'.codeSigning.each { codeSigning ->
+ codeSigning.'@macEnabled' = "false"
+ }
+ install4jConfigXml.'**'.windows.each { windows ->
+ windows.'@runPostProcessor' = "false"
+ }
+ }
+
+ // turn off checksum creation for LOCAL channel
+ def e = install4jConfigXml.application[0]
+ if (CHANNEL == "LOCAL") {
+ e.'@createChecksums' = "false"
+ } else {
+ e.'@createChecksums' = "true"
+ }
+
+ // put file association actions where placeholder action is
+ def install4jFileAssociationsText = install4jFileAssociationsFile.text
+ def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
+ install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
+ if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
+ def parent = a.parent()
+ parent.remove(a)
+ fileAssociationActions.each { faa ->
+ parent.append(faa)
+ }
+ // don't need to continue in .any loop once replacements have been made
+ return true
+ }
+ }
+
+ // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
+ // NB we're deleting the /other/ one!
+ // Also remove the examples subdir from non-release versions
+ def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
+ // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
+ if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
+ customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
+ } else {
+ // remove the examples subdir from Full File Set
+ def files = install4jConfigXml.files[0]
+ def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
+ def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
+ def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
+ def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
+ dirEntry.parent().remove(dirEntry)
+ }
+ install4jConfigXml.'**'.action.any { a ->
+ if (a.'@customizedId' == customizedIdToDelete) {
+ def parent = a.parent()
+ parent.remove(a)
+ return true
+ }
+ }
+
+ // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
+ if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
+ def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
+ symlink.parent().remove(symlink)
+ }
+
+ // write install4j file
+ install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
+ }
+}
+
+
+clean {
+ doFirst {
+ delete install4jConfFile
+ }
}
-task sourceDist (type: Tar) {
+
+task installers(type: com.install4j.gradle.Install4jTask) {
+ group = "distribution"
+ description = "Create the install4j installers"
+ dependsOn getdown
+ dependsOn copyInstall4jTemplate
+
+ projectFile = install4jConfFile
+
+ // create an md5 for the input files to use as version for install4j conf file
+ def digest = MessageDigest.getInstance("MD5")
+ digest.update(
+ (file("${install4jDir}/${install4j_template}").text +
+ file("${install4jDir}/${install4j_info_plist_file_associations}").text +
+ file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
+ def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
+ if (filesMd5.length() >= 8) {
+ filesMd5 = filesMd5.substring(0,8)
+ }
+ def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
+ // make install4jBuildDir relative to jalviewDir
+ def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
+
+ variables = [
+ 'JALVIEW_NAME': jalview_name,
+ 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
+ 'JALVIEW_DIR': "../..",
+ 'OSX_KEYSTORE': OSX_KEYSTORE,
+ 'JSIGN_SH': JSIGN_SH,
+ 'JRE_DIR': getdown_app_dir_java,
+ 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
+ 'JALVIEW_VERSION': JALVIEW_VERSION,
+ 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
+ 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
+ 'JAVA_VERSION': JAVA_VERSION,
+ 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+ 'VERSION': JALVIEW_VERSION,
+ 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+ 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+ 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
+ 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+ 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+ 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
+ 'COPYRIGHT_MESSAGE': install4j_copyright_message,
+ 'BUNDLE_ID': install4jBundleId,
+ 'INTERNAL_ID': install4jInternalId,
+ 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
+ 'MACOS_DS_STORE': install4jDSStore,
+ 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+ 'INSTALLER_NAME': install4jInstallerName,
+ 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
+ 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+ 'GETDOWN_FILES_DIR': getdown_files_dir,
+ 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+ 'GETDOWN_DIST_DIR': getdownAppDistDir,
+ 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+ 'GETDOWN_INSTALL_DIR': getdown_install_dir,
+ 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
+ 'BUILD_DIR': install4jBuildDir,
+ 'APPLICATION_CATEGORIES': install4j_application_categories,
+ 'APPLICATION_FOLDER': install4jApplicationFolder,
+ 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
+ 'EXECUTABLE_NAME': install4jExecutableName,
+ 'EXTRA_SCHEME': install4jExtraScheme,
+ ]
+
+ //println("INSTALL4J VARIABLES:")
+ //variables.each{k,v->println("${k}=${v}")}
+
+ destination = "${jalviewDir}/${install4jBuildDir}"
+ buildSelected = true
+
+ if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
+ faster = true
+ disableSigning = true
+ }
+
+ if (OSX_KEYPASS) {
+ macKeystorePassword = OSX_KEYPASS
+ }
+
+ doFirst {
+ println("Using projectFile "+projectFile)
+ }
+
+ inputs.dir(getdownWebsiteDir)
+ inputs.file(install4jConfFile)
+ inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
+ inputs.dir(macosJavaVMDir)
+ inputs.dir(windowsJavaVMDir)
+ outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
+}
+
+
+spotless {
+ java {
+ eclipse().configFile(eclipse_codestyle_file)
+ }
+}
+
+
+task sourceDist(type: Tar) {
+ group "distribution"
+ description "Create a source .tar.gz file for distribution"
+ dependsOn convertMdFiles
+
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
- archiveFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
+ archiveFileName = outputFileName
compression Compression.GZIP
into project.name
- def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
- ,".*"
- ,"benchmarking/*"
- ,"**/.*"
- ,"*.class"
- ,"**/*.class","$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"]
+ def EXCLUDE_FILES=[
+ "build/*",
+ "bin/*",
+ "test-output/",
+ "test-reports",
+ "tests",
+ "clover*/*",
+ ".*",
+ "benchmarking/*",
+ "**/.*",
+ "*.class",
+ "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
+ "*locales/**",
+ "utils/InstallAnywhere",
+ "**/*.log",
+ ]
+ def PROCESS_FILES=[
+ "AUTHORS",
+ "CITATION",
+ "FEATURETODO",
+ "JAVA-11-README",
+ "FEATURETODO",
+ "LICENSE",
+ "**/README",
+ "RELEASE",
+ "THIRDPARTYLIBS",
+ "TESTNG",
+ "build.gradle",
+ "gradle.properties",
+ "**/*.java",
+ "**/*.html",
+ "**/*.xml",
+ "**/*.gradle",
+ "**/*.groovy",
+ "**/*.properties",
+ "**/*.perl",
+ "**/*.sh",
+ ]
+ def INCLUDE_FILES=[
+ ".settings/org.eclipse.jdt.core.jalview.prefs",
+ ]
from(jalviewDir) {
exclude (EXCLUDE_FILES)
include (PROCESS_FILES)
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
}
from(jalviewDir) {
exclude (EXCLUDE_FILES)
exclude (PROCESS_FILES)
- exclude ("appletlib")
- exclude ("**/*locales")
- exclude ("*locales/**")
- exclude ("utils/InstallAnywhere")
+ exclude ("appletlib")
+ exclude ("**/*locales")
+ exclude ("*locales/**")
+ exclude ("utils/InstallAnywhere")
exclude (getdown_files_dir)
- exclude (getdown_website_dir)
+ exclude (getdown_website_dir)
- // exluding these as not using jars as modules yet
- exclude ("$j11modDir/**/*.jar")
-}
+ // exluding these as not using jars as modules yet
+ exclude ("${j11modDir}/**/*.jar")
+ }
+ from(jalviewDir) {
+ include(INCLUDE_FILES)
+ }
// from (jalviewDir) {
// // explicit includes for stuff that seemed to not get included
// include(fileTree("test/**/*."))
// }
}
-task helppages {
+
+task helppages {
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("$classes/$helpDir")
- outputs.dir("$helpOutputDir")
+ inputs.dir("${helpBuildDir}/${help_dir}")
+ outputs.dir("${buildDir}/distributions/${help_dir}")
+}
+
+
+task j2sSetHeadlessBuild {
+ doFirst {
+ IN_ECLIPSE = false
+ }
+}
+
+
+task jalviewjsSetEclipseWorkspace {
+ def propKey = "jalviewjs_eclipse_workspace"
+ def propVal = null
+ if (project.hasProperty(propKey)) {
+ propVal = project.getProperty(propKey)
+ if (propVal.startsWith("~/")) {
+ propVal = System.getProperty("user.home") + propVal.substring(1)
+ }
+ }
+ def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+ def propsFile = file(propsFileName)
+ def eclipseWsDir = propVal
+ def props = new Properties()
+
+ def writeProps = true
+ if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+ def ins = new FileInputStream(propsFileName)
+ props.load(ins)
+ ins.close()
+ if (props.getProperty(propKey, null) != null) {
+ eclipseWsDir = props.getProperty(propKey)
+ writeProps = false
+ }
+ }
+
+ if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
+ def tempDir = File.createTempDir()
+ eclipseWsDir = tempDir.getAbsolutePath()
+ writeProps = true
+ }
+ eclipseWorkspace = file(eclipseWsDir)
+
+ doFirst {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+
+ if (writeProps) {
+ props.setProperty(propKey, eclipseWsDir)
+ propsFile.parentFile.mkdirs()
+ def bytes = new ByteArrayOutputStream()
+ props.store(bytes, null)
+ def propertiesString = bytes.toString()
+ propsFile.text = propertiesString
+ print("NEW ")
+ } else {
+ print("EXISTING ")
+ }
+
+ println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+ }
+
+ //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
+ outputs.file(propsFileName)
+ outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
+}
+
+
+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"
+ }
+ 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"
+ }
+
+ 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 {
+ // do not run a headless transpile when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+
+ if (!assumedVersion) {
+ println("ECLIPSE VERSION=${eclipseVersion}")
+ }
+ }
+}
+
+
+task printProperties {
+ group "Debug"
+ description "Output to console all System.properties"
+ doFirst {
+ System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
+ }
+}
+
+
+task eclipseSetup {
+ dependsOn eclipseProject
+ dependsOn eclipseClasspath
+ dependsOn eclipseJdt
+}
+
+
+// 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("${jalviewDir}/${jalviewjsJ2sPlugin}")
+ def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+
+ from inputFiles
+ into outputDir
+}
+
+
+// this eclipse -clean doesn't actually work
+task jalviewjsCleanEclipse(type: Exec) {
+ dependsOn eclipseSetup
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseCopyDropins
+
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += "-l"
+
+ def inputString = """exit
+y
+"""
+ def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
+ standardInput = inputByteStream
+}
+
+/* not really working yet
+jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
+*/
+
+
+task jalviewjsTransferUnzipSwingJs {
+ def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
+
+ doLast {
+ copy {
+ from zipTree(file_zip)
+ into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ }
+ }
+
+ inputs.file file_zip
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+}
+
+
+task jalviewjsTransferUnzipLib {
+ def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+
+ doLast {
+ zipFiles.each { file_zip ->
+ copy {
+ from zipTree(file_zip)
+ into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+ }
+ }
+ }
+
+ inputs.files zipFiles
+ outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+}
+
+
+task jalviewjsTransferUnzipAllLibs {
+ dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTransferUnzipLib
+}
+
+
+task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+ group "JalviewJS"
+ description "Create the .j2s file from the j2s.* properties"
+
+ jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+ def siteDirProperty = "j2s.site.directory"
+ def setSiteDir = false
+ jalviewjsJ2sProps.each { prop, val ->
+ if (val != null) {
+ if (prop == siteDirProperty) {
+ if (!(val.startsWith('/') || val.startsWith("file://") )) {
+ val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
+ }
+ setSiteDir = true
+ }
+ property(prop,val)
+ }
+ if (!setSiteDir) { // default site location, don't override specifically set property
+ property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
+ }
+ }
+ outputFile = jalviewjsJ2sSettingsFileName
+
+ if (! IN_ECLIPSE) {
+ inputs.properties(jalviewjsJ2sProps)
+ outputs.file(jalviewjsJ2sSettingsFileName)
+ }
+}
+
+
+task jalviewjsEclipseSetup {
+ dependsOn jalviewjsEclipseCopyDropins
+ dependsOn jalviewjsSetEclipseWorkspace
+ dependsOn jalviewjsCreateJ2sSettings
+}
+
+
+task jalviewjsSyncAllLibs (type: Sync) {
+ dependsOn jalviewjsTransferUnzipAllLibs
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+ inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsSyncResources (type: Sync) {
+ def inputFiles = fileTree(dir: resourceDir)
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsSyncSiteResources (type: Sync) {
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsSyncBuildProperties (type: Sync) {
+ dependsOn createBuildProperties
+ def inputFiles = [file(buildProperties)]
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsProjectImport(type: Exec) {
+ dependsOn eclipseSetup
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseSetup
+
+ doFirst {
+ // do not run a headless import when we claim to be in Eclipse
+ if (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+ }
+
+ //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+ def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+ if (!IN_ECLIPSE) {
+ args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+ }
+
+ 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 (IN_ECLIPSE) {
+ println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+ } else {
+ println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+ }
+ }
+
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
+ if (eclipseDebug) {
+ args += "-debug"
+ }
+ args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+ if (!IN_ECLIPSE) {
+ args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+ }
+
+ def stdout
+ def stderr
+ doFirst {
+ stdout = new ByteArrayOutputStream()
+ stderr = new ByteArrayOutputStream()
+
+ def logOutFileName = "${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}/${jalviewjs_j2s_transpile_stdout}'")
+ if (jalviewjs_ignore_transpile_errors.equals("true")) {
+ println("IGNORING TRANSPILE ERRORS")
+ println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+ } else {
+ throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+ }
+ }
+ }
+
+ inputs.dir("${jalviewDir}/${sourceDir}")
+ outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+ outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+}
+
+
+def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+
+ def stdout = new ByteArrayOutputStream()
+ def stderr = new ByteArrayOutputStream()
+
+ def coreFile = file(jsfile)
+ def msg = ""
+ msg = "Creating core for ${name}...\nGenerating ${jsfile}"
+ println(msg)
+ logOutFile.createNewFile()
+ logOutFile.append(msg+"\n")
+
+ def coreTop = file(prefixFile)
+ def coreBottom = file(suffixFile)
+ coreFile.getParentFile().mkdirs()
+ coreFile.createNewFile()
+ coreFile.write( coreTop.getText("UTF-8") )
+ list.each {
+ f ->
+ if (f.exists()) {
+ def t = f.getText("UTF-8")
+ t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
+ coreFile.append( t )
+ } else {
+ msg = "...file '"+f.getPath()+"' does not exist, skipping"
+ println(msg)
+ logOutFile.append(msg+"\n")
+ }
+ }
+ coreFile.append( coreBottom.getText("UTF-8") )
+
+ msg = "Generating ${zjsfile}"
+ println(msg)
+ logOutFile.append(msg+"\n")
+ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+ def logErrFOS = logOutFOS
+
+ javaexec {
+ classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
+ main = "com.google.javascript.jscomp.CommandLineRunner"
+ jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+ args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+ maxHeapSize = "2g"
+
+ msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+ println(msg)
+ logOutFile.append(msg+"\n")
+
+ if (logOutConsole) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr),
+ errorOutput)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logOutFOS,
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ logErrFOS,
+ stderr)
+ }
+ }
+ msg = "--"
+ println(msg)
+ logOutFile.append(msg+"\n")
+}
+
+
+task jalviewjsBuildAllCores {
+ group "JalviewJS"
+ description "Build the core js lib closures listed in the classlists dir"
+ dependsOn jalviewjsTranspile
+ dependsOn jalviewjsTransferUnzipSwingJs
+
+ def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+ def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+ def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
+ def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+ def prefixFile = "${jsDir}/core/coretop2.js"
+ def suffixFile = "${jsDir}/core/corebottom2.js"
+
+ inputs.file prefixFile
+ inputs.file suffixFile
+
+ def classlistFiles = []
+ // add the classlists found int the jalviewjs_classlists_dir
+ fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
+ file ->
+ def name = file.getName() - ".txt"
+ classlistFiles += [
+ 'file': file,
+ 'name': name
+ ]
+ }
+
+ // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+ //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+ classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
+
+ jalviewjsCoreClasslists = []
+
+ classlistFiles.each {
+ hash ->
+
+ def file = hash['file']
+ if (! file.exists()) {
+ //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+ return false // this is a "continue" in groovy .each closure
+ }
+ def name = hash['name']
+ if (name == null) {
+ name = file.getName() - ".txt"
+ }
+
+ def filelist = []
+ file.eachLine {
+ line ->
+ filelist += line
+ }
+ def list = fileTree(dir: j2sDir, includes: filelist)
+
+ def jsfile = "${outputDir}/core${name}.js"
+ def zjsfile = "${outputDir}/core${name}.z.js"
+
+ jalviewjsCoreClasslists += [
+ 'jsfile': jsfile,
+ 'zjsfile': zjsfile,
+ 'list': list,
+ 'name': name
+ ]
+
+ inputs.file(file)
+ inputs.files(list)
+ outputs.file(jsfile)
+ outputs.file(zjsfile)
+ }
+
+ // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+ def stevesoftClasslistName = "_stevesoft"
+ def stevesoftClasslist = [
+ 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+ 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+ 'name': stevesoftClasslistName
+ ]
+ jalviewjsCoreClasslists += stevesoftClasslist
+ inputs.files(stevesoftClasslist['list'])
+ outputs.file(stevesoftClasslist['jsfile'])
+ outputs.file(stevesoftClasslist['zjsfile'])
+
+ // _all core
+ def allClasslistName = "_all"
+ def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+ allJsFiles += fileTree(
+ dir: libJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+ "**/org/jmol/export/JSExporter.js"
+ ]
+ )
+ allJsFiles += fileTree(
+ dir: swingJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/sun/misc/Unsafe.js",
+ "**/swingjs/jquery/jquery-editable-select.js",
+ "**/swingjs/jquery/j2sComboBox.js",
+ "**/sun/misc/FloatingDecimal.js"
+ ]
+ )
+ def allClasslist = [
+ 'jsfile': "${outputDir}/core${allClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+ 'list': allJsFiles,
+ 'name': allClasslistName
+ ]
+ // not including this version of "all" core at the moment
+ //jalviewjsCoreClasslists += allClasslist
+ inputs.files(allClasslist['list'])
+ outputs.file(allClasslist['jsfile'])
+ outputs.file(allClasslist['zjsfile'])
+
+ doFirst {
+ def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+ logOutFile.getParentFile().mkdirs()
+ logOutFile.createNewFile()
+ logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+
+ jalviewjsCoreClasslists.each {
+ jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+ }
+ }
+
+}
+
+
+def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+ copy {
+ from inputFile
+ into file(outputFile).getParentFile()
+ rename { filename ->
+ if (filename.equals(inputFile.getName())) {
+ return file(outputFile).getName()
+ }
+ return null
+ }
+ filter(ReplaceTokens,
+ beginToken: '_',
+ endToken: '_',
+ tokens: [
+ 'MAIN': '"'+main_class+'"',
+ 'CODE': "null",
+ 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+ 'COREKEY': jalviewjs_core_key,
+ 'CORENAME': coreName
+ ]
+ )
+ }
+}
+
+
+task jalviewjsPublishCoreTemplates {
+ dependsOn jalviewjsBuildAllCores
+ def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+ def inputFile = file(inputFileName)
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+
+ def outputFiles = []
+ jalviewjsCoreClasslists.each { cl ->
+ def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+ cl['outputfile'] = outputFile
+ outputFiles += outputFile
+ }
+
+ doFirst {
+ jalviewjsCoreClasslists.each { cl ->
+ jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+ }
+ }
+ inputs.file(inputFile)
+ outputs.files(outputFiles)
+}
+
+
+task jalviewjsSyncCore (type: Sync) {
+ dependsOn jalviewjsBuildAllCores
+ dependsOn jalviewjsPublishCoreTemplates
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+// this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteJs(type: Copy) {
+ dependsOn jalviewjsTranspile
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+}
+
+
+// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+task jalviewjsSyncTransferSiteJs(type: Sync) {
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ include "**/*.*"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+ preserve {
+ include "**"
+ }
+}
+
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+
+
+task jalviewjsPrepareSite {
+ group "JalviewJS"
+ description "Prepares the website folder including unzipping files and copying resources"
+ dependsOn 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 cleanJalviewjsTransferSite {
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+ }
+}
+
+
+task cleanJalviewjsSite {
+ dependsOn cleanJalviewjsTransferSite
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsSiteDir}"
+ }
+}
+
+
+task jalviewjsSiteTar(type: Tar) {
+ group "JalviewJS"
+ description "Creates a tar.gz file for the website"
+ dependsOn jalviewjsBuildSite
+ def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
+ archiveFileName = outputFilename
+
+ compression Compression.GZIP
+
+ from "${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 ${filename} to access local site on most recently used port."
+ def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
+ doLast {
+
+ SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+ def port = Integer.valueOf(jalviewjs_server_port)
+ def start = port
+ def running = false
+ def url
+ def jalviewjsServer
+ while(port < start+1000 && !running) {
+ try {
+ def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
+ jalviewjsServer = factory.start(doc_root, port)
+ running = true
+ url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
+ println("SERVER STARTED with document root ${doc_root}.")
+ println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
+ println("For debug: "+url+"?j2sdebug")
+ println("For verbose: "+url+"?j2sverbose")
+ } catch (Exception e) {
+ port++;
+ }
+ }
+ def htmlText = """
+ <p><a href="${url}">JalviewJS Test. <${url}></a></p>
+ <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
+ <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
+ """
+ jalviewjsCoreClasslists.each { cl ->
+ def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+ htmlText += """
+ <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
+ """
+ println("For core ${cl.name}: "+urlcore)
+ }
+
+ file(htmlFile).text = htmlText
+ }
+
+ outputs.file(htmlFile)
+ outputs.upToDateWhen({false})
+}
+
+
+task cleanJalviewjsAll {
+ group "JalviewJS"
+ description "Delete all configuration and build artifacts to do with JalviewJS build"
+ dependsOn cleanJalviewjsSite
+ dependsOn jalviewjsEclipsePaths
+
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsBuildDir}"
+ delete "${jalviewDir}/${eclipse_bin_dir}"
+ if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
+ delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+ }
+ delete "${jalviewDir}/${jalviewjs_j2s_settings}"
+ }
+
+ outputs.upToDateWhen( { false } )
+}
+
+
+task jalviewjsIDE_checkJ2sPlugin {
+ group "00 JalviewJS in Eclipse"
+ description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+
+ doFirst {
+ def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+ def j2sPluginFile = file(j2sPlugin)
+ def eclipseHome = System.properties["eclipse.home.location"]
+ if (eclipseHome == null || ! IN_ECLIPSE) {
+ throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+ }
+ def eclipseJ2sPluginDirs = [ "${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 '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
+ System.err.println(msg)
+ throw new StopExecutionException(msg)
+ }
+
+ def digest = MessageDigest.getInstance("MD5")
+
+ digest.update(j2sPluginFile.text.bytes)
+ def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ digest.update(eclipseJ2sPluginFile.text.bytes)
+ def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+ def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+ System.err.println(msg)
+ throw new StopExecutionException(msg)
+ } else {
+ def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
+ println(msg)
+ }
+ }
+}
+
+task jalviewjsIDE_copyJ2sPlugin {
+ group "00 JalviewJS in Eclipse"
+ description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
+
+ doFirst {
+ def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+ def j2sPluginFile = file(j2sPlugin)
+ def eclipseHome = System.properties["eclipse.home.location"]
+ if (eclipseHome == null || ! IN_ECLIPSE) {
+ throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
+ }
+ def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+ def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+ def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
+ System.err.println(msg)
+ copy {
+ from j2sPlugin
+ eclipseJ2sPluginFile.getParentFile().mkdirs()
+ into eclipseJ2sPluginFile.getParent()
+ }
+ }
+}
+
+
+task jalviewjsIDE_j2sFile {
+ group "00 JalviewJS in Eclipse"
+ description "Creates the .j2s file"
+ dependsOn jalviewjsCreateJ2sSettings
+}
+
+
+task jalviewjsIDE_SyncCore {
+ group "00 JalviewJS in Eclipse"
+ description "Build the core js lib closures listed in the classlists dir and publish core html from template"
+ dependsOn jalviewjsSyncCore
+}
+
+
+task jalviewjsIDE_SyncSiteAll {
+ dependsOn jalviewjsSyncAllLibs
+ dependsOn jalviewjsSyncResources
+ dependsOn jalviewjsSyncSiteResources
+ dependsOn jalviewjsSyncBuildProperties
+}
+
+
+cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+
+
+task jalviewjsIDE_PrepareSite {
+ group "00 JalviewJS in Eclipse"
+ description "Sync libs and resources to site dir, but not closure cores"
+
+ dependsOn jalviewjsIDE_SyncSiteAll
+ //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
+}
+
+
+task jalviewjsIDE_AssembleSite {
+ group "00 JalviewJS in Eclipse"
+ description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
+ dependsOn jalviewjsPrepareSite
+}
+
+
+task 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 or gradle refresh
+task eclipseSynchronizationTask {
+ //dependsOn eclipseSetup
+ dependsOn createBuildProperties
+ if (J2S_ENABLED) {
+ dependsOn jalviewjsIDE_j2sFile
+ dependsOn jalviewjsIDE_checkJ2sPlugin
+ dependsOn jalviewjsIDE_PrepareSite
+ }
+}
+
+
+// buildship runs this at build time or project refresh
+task eclipseAutoBuildTask {
+ //dependsOn jalviewjsIDE_checkJ2sPlugin
+ //dependsOn jalviewjsIDE_PrepareSite
+}
+
+
+task jalviewjs {
+ group "JalviewJS"
+ description "Build the site"
+ dependsOn jalviewjsBuildSite
}