---- a/build.gradle 2021-09-21 09:52:04.653972716 +0100
-+++ b/build.gradle 2021-09-21 09:52:18.117985307 +0100
-@@ -2,56 +2,12 @@
+diff --git a/build.gradle b/build.gradle
+index ca599a85a..ce7f13634 100644
+--- a/build.gradle
++++ b/build.gradle
+@@ -2,66 +2,12 @@
* For properties set within build.gradle, use camelCaseNoSpace.
*/
import org.apache.tools.ant.filters.ReplaceTokens
-import org.gradle.plugins.ide.eclipse.model.Output
-import org.gradle.plugins.ide.eclipse.model.Library
-import java.security.MessageDigest
+-import java.util.regex.Matcher
-import groovy.transform.ExternalizeMethods
-import groovy.util.XmlParser
-import groovy.xml.XmlUtil
+-import groovy.json.JsonBuilder
-import com.vladsch.flexmark.util.ast.Node
-import com.vladsch.flexmark.html.HtmlRenderer
-import com.vladsch.flexmark.parser.Parser
-import com.vladsch.flexmark.ext.autolink.AutolinkExtension
-import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
-import com.vladsch.flexmark.ext.toc.TocExtension
+-import com.google.common.hash.HashCode
+-import com.google.common.hash.Hashing
+-import com.google.common.io.Files
+-import org.jsoup.Jsoup
+-import org.jsoup.nodes.Element
-
-buildscript {
- repositories {
- }
- dependencies {
- classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
+- classpath "org.jsoup:jsoup:1.14.3"
+- classpath "com.eowise:gradle-imagemagick:0.5.1"
- }
-}
-
- id 'eclipse'
- id "com.diffplug.gradle.spotless" version "3.28.0"
- id 'com.github.johnrengelman.shadow' version '4.0.3'
-- id 'com.install4j.gradle' version '8.0.10'
-- 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'
+- id 'com.install4j.gradle' version '10.0.3'
+- id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+- id 'com.palantir.git-version' version '0.13.0' apply false
-}
-
-repositories {
}
-
+-
// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
def string(Object o) {
return o == null ? "" : o.toString()
-@@ -92,23 +48,15 @@
+@@ -102,34 +48,20 @@ def overrideProperties(String propsFileName, boolean output = false) {
}
}
+project.ext {
jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
jalviewDirRelativePath = jalviewDir
+- date = new Date()
- getdownChannelName = CHANNEL.toLowerCase()
- // default to "default". Currently only has different cosmetics for "develop", "release", "default"
- propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+- channelDirName = propertiesChannelName
- // Import channel_properties
+- if (getdownChannelName.startsWith("develop-")) {
+- channelDirName = "develop-SUFFIX"
+- }
+- channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
+ propertiesChannelName = "release"
- channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
++ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+- channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
overrideProperties(channelGradleProperties, false)
- // local build environment properties
- // can be "projectDir/local.properties"
////
// Import releaseProps from the RELEASE file
// or a file specified via JALVIEW_RELEASE_FILE if defined
-@@ -128,41 +76,6 @@
+ // Expect jalview.version and target release branch in jalview.release
+- releaseProps = new Properties();
++ def releaseProps = new Properties();
+ def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+ def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+ try {
+@@ -144,42 +76,6 @@ ext {
if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
JALVIEW_VERSION = releaseProps.get("jalview.version")
}
+- println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
-
- // this property set when running Eclipse headlessly
- j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
// essentials
bareSourceDir = string(source_dir)
-@@ -173,218 +86,18 @@
+@@ -190,273 +86,18 @@ ext {
classesDir = string("${jalviewDir}/${classes_dir}")
- cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
- //cloverTestClassesDir = cloverClassesDir
- cloverDb = string("${cloverBuildDir}/clover.db")
--
++ useClover = false
+
- testSourceDir = useClover ? cloverTestInstrDir : testDir
- testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
--
-- getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
++ resourceClassesDir = classesDir
+
+- channelSuffix = ""
+- backgroundImageText = BACKGROUNDIMAGETEXT
+- getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
+- getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
+- getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
+- getdownFullArchiveDir = null
+- getdownTextLines = []
+- getdownLaunchJvl = null
+- getdownVersionLaunchJvl = null
- buildDist = true
- buildProperties = null
--
++ testSourceDir = testDir
++ testClassesDir = "${jalviewDir}/${test_output_dir}"
+
- // the following values might be overridden by the CHANNEL switch
- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- getdownArchiveAppBase = getdown_archive_base
- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
- getdownAppDistDir = getdown_app_dir_alt
- getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
-- getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
+- getdownImagesBuildDir = string("${buildDir}/imagemagick/getdown")
++ buildProperties = string("${classesDir}/${build_properties_file}")
+ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
- reportRsyncCommand = false
- jvlChannelName = CHANNEL.toLowerCase()
- install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
- install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
-- install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
+- install4jDMGBackgroundImageDir = "${install4j_images_dir}"
+- install4jDMGBackgroundImageBuildDir = "build/imagemagick/install4j"
+- install4jDMGBackgroundImageFile = "${install4j_dmg_background}"
- install4jInstallerName = "${jalview_name} Non-Release Installer"
- install4jExecutableName = install4j_executable_name
- install4jExtraScheme = "jalviewx"
- install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
- install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
- install4jBackground = string("${install4j_images_dir}/${install4j_background}")
+- install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
+- install4jCheckSums = true
+-
+- applicationName = "${jalview_name}"
- switch (CHANNEL) {
-
- case "BUILD":
- testng_excluded_groups = "Not-bamboo"
- }
- install4jExtraScheme = "jalviewb"
+- backgroundImageText = true
- break
-+ useClover = false
-
+-
- case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
- getdownAppDistDir = getdown_app_dir_release
+- getdownSetAppBaseProperty = true
- reportRsyncCommand = true
- install4jSuffix = ""
- install4jInstallerName = "${jalview_name} Installer"
- case "ARCHIVELOCAL":
- getdownChannelName = string("archive/${JALVIEW_VERSION}")
- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
-- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownAppBase = file(getdownAppBaseDir).toURI().toString()
- if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
-- throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
+- throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution [did not find '${ARCHIVEDIR}/${package_dir}']")
- } else {
- package_dir = string("${ARCHIVEDIR}/${package_dir}")
- buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
- install4jExtraScheme = "jalviewa"
- break
-
+- case ~/^DEVELOP-([\.\-\w]*)$/:
+- def suffix = Matcher.lastMatcher[0][1]
+- reportRsyncCommand = true
+- getdownSetAppBaseProperty = true
+- JALVIEW_VERSION=JALVIEW_VERSION+"-d${suffix}-${buildDate}"
+- install4jSuffix = "Develop ${suffix}"
+- install4jExtraScheme = "jalviewd"
+- install4jInstallerName = "${jalview_name} Develop ${suffix} Installer"
+- getdownChannelName = string("develop-${suffix}")
+- getdownChannelDir = string("${getdown_website_dir}/${getdownChannelName}")
+- getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- channelSuffix = string(suffix)
+- backgroundImageText = true
+- break
+-
- case "DEVELOP":
- reportRsyncCommand = true
- getdownSetAppBaseProperty = true
- install4jSuffix = "Develop"
- install4jExtraScheme = "jalviewd"
- install4jInstallerName = "${jalview_name} Develop Installer"
+- backgroundImageText = true
- break
-
- case "TEST-RELEASE":
- reportRsyncCommand = true
+- getdownSetAppBaseProperty = true
- // Don't ignore transpile errors for release build
- if (jalviewjs_ignore_transpile_errors.equals("true")) {
- jalviewjs_ignore_transpile_errors = "false"
- install4jSuffix = "Test"
- install4jExtraScheme = "jalviewt"
- install4jInstallerName = "${jalview_name} Test Installer"
+- backgroundImageText = true
- break
-
- case ~/^SCRATCH(|-[-\w]*)$/:
- install4jSuffix = "Test-Local"
- install4jExtraScheme = "jalviewt"
- install4jInstallerName = "${jalview_name} Test Installer"
+- backgroundImageText = true
- break
-
- case [ "LOCAL", "JALVIEWJS" ]:
- JALVIEW_VERSION = "TEST"
-- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownAppBase = file(getdownAppBaseDir).toURI().toString()
+- getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
- install4jExtraScheme = "jalviewl"
+- install4jCheckSums = false
- break
-
- default: // something wrong specified
- break
-
- }
+- JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+- hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
+- hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
- // override getdownAppBase if requested
- if (findProperty("getdown_appbase_override") != null) {
- // revert to LOCAL if empty string
- if (string(getdown_appbase_override) == "") {
-- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownAppBase = file(getdownAppBaseDir).toURI().toString()
- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
- } else if (string(getdown_appbase_override).startsWith("file://")) {
- getdownAppBase = string(getdown_appbase_override)
- jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
- // install4j application and folder names
- if (install4jSuffix == "") {
-- install4jApplicationName = "${jalview_name}"
- install4jBundleId = "${install4j_bundle_id}"
- install4jWinApplicationId = install4j_release_win_application_id
- } else {
-- install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+- applicationName = "${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
- }
- // sanitise folder and id names
- // install4jApplicationFolder = e.g. "Jalview Build"
-- install4jApplicationFolder = install4jApplicationName
+- install4jApplicationFolder = applicationName
- .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
- .replaceAll("_+", "_") // collapse __
-- install4jInternalId = install4jApplicationName
+- install4jInternalId = applicationName
- .replaceAll(" ","_")
- .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
- .replaceAll("_+", "") // collapse __
- //.replaceAll("_*-_*", "-") // collapse _-_
-- install4jUnixApplicationFolder = install4jApplicationName
+- install4jUnixApplicationFolder = applicationName
- .replaceAll(" ","_")
- .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
- .replaceAll("_+", "_") // collapse __
- .toLowerCase()
-
- getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
-- getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
-- //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
-- getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
-- getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
+- getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
+- //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
+- getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
+- getdownInstallDir = string("${getdownAppBaseDir}/${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}/${j11modDir}", include: ["*.jar"])
- modules_runtimeClasspath = modules_compileClasspath
- */
-- def details = versionDetails()
-- gitHash = details.gitHash
-- gitBranch = details.branchName
-+ resourceClassesDir = classesDir
-+
-+ testSourceDir = testDir
-+ testClassesDir = "${jalviewDir}/${test_output_dir}"
+-
+- gitHash = "SOURCE"
+- gitBranch = "Source"
+- try {
+- apply plugin: "com.palantir.git-version"
+- def details = versionDetails()
+- gitHash = details.gitHash
+- gitBranch = details.branchName
+- } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
+- println("Not in a git repository. Using git values from RELEASE properties file.")
+- gitHash = releaseProps.getProperty("git.hash")
+- gitBranch = releaseProps.getProperty("git.branch")
+- } catch(java.lang.RuntimeException e1) {
+- throw new GradleException("Error with git-version plugin. Directory '.git' exists but versionDetails() cannot be found.")
+- }
-+ buildProperties = string("${classesDir}/${build_properties_file}")
-+ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
-+
+ install4jApplicationName = "${jalview_name}"
+
println("Using a ${CHANNEL} profile.")
additional_compiler_args = []
-@@ -396,71 +109,16 @@
+@@ -468,65 +109,16 @@ ext {
libDistDir = j8libDir
compile_source_compatibility = 1.8
compile_target_compatibility = 1.8
- '--add-modules', j11modules
- ]
- */
-- } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
-- JAVA_INTEGER_VERSION = JAVA_VERSION
-- libDir = j11libDir
-- libDistDir = j11libDir
-- compile_source_compatibility = JAVA_VERSION
-- compile_target_compatibility = JAVA_VERSION
+- } else if (JAVA_VERSION.equals("17")) {
+- JAVA_INTEGER_VERSION = string("17")
+- libDir = j17libDir
+- libDistDir = j17libDir
+- compile_source_compatibility = 17
+- compile_target_compatibility = 17
- getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
- getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
- getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
-- eclipseJavaRuntimeName = string("JavaSE-11")
+- eclipseJavaRuntimeName = string("JavaSE-17")
- /* compile without modules -- using classpath libraries
- additional_compiler_args += [
- '--module-path', modules_compileClasspath.asPath,
- // for install4j
- JAVA_MIN_VERSION = JAVA_VERSION
- JAVA_MAX_VERSION = JAVA_VERSION
-- def jreInstallsDir = string(jre_installs_dir)
+- jreInstallsDir = string(jre_installs_dir)
- if (jreInstallsDir.startsWith("~/")) {
- jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
- }
-- macosJavaVMDir = string("${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}/${install4jConfFileName}")
resourceBuildDir = string("${buildDir}/resources")
resourcesBuildDir = string("${resourceBuildDir}/resources_build")
helpBuildDir = string("${resourceBuildDir}/help_build")
-@@ -474,31 +132,6 @@
+@@ -540,39 +132,6 @@ ext {
helpSourceDir = string("${helpParentDir}/${help_dir}")
helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
+- convertBinary = null
+- convertBinaryExpectedLocation = imagemagick_convert
+- if (convertBinaryExpectedLocation.startsWith("~/")) {
+- convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
+- }
+- if (file(convertBinaryExpectedLocation).exists()) {
+- convertBinary = convertBinaryExpectedLocation
+- }
-
- relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
- jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
// ENDEXT
}
-@@ -517,27 +150,12 @@
+@@ -591,27 +150,12 @@ sourceSets {
compileClasspath = files(sourceSets.main.java.outputDir)
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
}
test {
-@@ -557,453 +175,41 @@
+@@ -631,453 +175,41 @@ sourceSets {
runtimeClasspath = compileClasspath
runtimeClasspath += files(sourceSets.test.resources.srcDirs)
}
- if (cloverreport_jvmargs.length() > 0) {
- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
- }
--
+
- def argsList = [
- "--alwaysreport",
- "--initstring",
-
- args argsList.toArray()
-}
-
-+ compileClasspath = files( sourceSets.test.java.outputDir )
-+ compileClasspath += sourceSets.main.compileClasspath
-+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["** REMOVE_THIS_GAP /*.jar"])
-
+-
+-
-task cloverReport {
- group = "Verification"
- description = "Creates clover reports"
-
-
-compileCloverJava {
--
++ compileClasspath = files( sourceSets.test.java.outputDir )
++ compileClasspath += sourceSets.main.compileClasspath
++ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["** REMOVE_THIS_GAP /*.jar"])
+
- doFirst {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
- // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
- options.compilerArgs = additional_compiler_args
+- options.compilerArgs += additional_compiler_args
- options.encoding = "UTF-8"
++ options.compilerArgs = additional_compiler_args
doFirst {
print ("Setting target compatibility to "+compile_target_compatibility+"\n")
}
compileTestJava {
- sourceCompatibility = compile_source_compatibility
- targetCompatibility = compile_target_compatibility
-- options.compilerArgs = additional_compiler_args
+- options.compilerArgs += additional_compiler_args
doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
print ("Setting target compatibility to "+targetCompatibility+"\n")
}
}
-@@ -1017,7 +223,6 @@
+@@ -1091,7 +223,6 @@ clean {
cleanTest {
doFirst {
delete sourceSets.test.java.outputDir
}
-@@ -1031,85 +236,6 @@
+@@ -1100,89 +231,11 @@ cleanTest {
+
+ // format is a string like date.format("dd MMMM yyyy")
+ def getDate(format) {
++ def date = new Date()
+ return date.format(format)
}
task copyDocs(type: Copy) {
def inputDir = "${jalviewDir}/${doc_dir}"
def outputDir = "${docBuildDir}/${doc_dir}"
-@@ -1140,27 +266,6 @@
+@@ -1213,235 +266,6 @@ task copyDocs(type: Copy) {
}
-}
-
-
+-def hugoTemplateSubstitutions(String input, Map extras=null) {
+- def replacements = [
+- DATE: getDate("yyyy-MM-dd"),
+- CHANNEL: propertiesChannelName,
+- APPLICATION_NAME: applicationName,
+- GIT_HASH: gitHash,
+- GIT_BRANCH: gitBranch,
+- VERSION: JALVIEW_VERSION,
+- JAVA_VERSION: JAVA_VERSION,
+- VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
+- DRAFT: "false",
+- JVL_HEADER: ""
+- ]
+- def output = input
+- if (extras != null) {
+- extras.each{ k, v ->
+- output = output.replaceAll("__${k}__", ((v == null)?"":v))
+- }
+- }
+- replacements.each{ k, v ->
+- output = output.replaceAll("__${k}__", ((v == null)?"":v))
+- }
+- return output
+-}
+-
+-def mdFileComponents(File mdFile, def dateOnly=false) {
+- def map = [:]
+- def content = ""
+- if (mdFile.exists()) {
+- def inFrontMatter = false
+- def firstLine = true
+- mdFile.eachLine { line ->
+- if (line.matches("---")) {
+- def prev = inFrontMatter
+- inFrontMatter = firstLine
+- if (inFrontMatter != prev)
+- return false
+- }
+- if (inFrontMatter) {
+- def m = null
+- if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
+- map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
+- } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
+- map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
+- } else if (m = line =~ /^channel:\s*(\S+)/) {
+- map["channel"] = m[0][1]
+- } else if (m = line =~ /^version:\s*(\S+)/) {
+- map["version"] = m[0][1]
+- } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
+- map[ m[0][1] ] = m[0][2]
+- }
+- if (dateOnly && map["date"] != null) {
+- return false
+- }
+- } else {
+- if (dateOnly)
+- return false
+- content += line+"\n"
+- }
+- firstLine = false
+- }
+- }
+- return dateOnly ? map["date"] : [map, content]
+-}
+-
+-task hugoTemplates {
+- group "website"
+- description "Create partially populated md pages for hugo website build"
+-
+- def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
+- def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
+- def templateFiles = fileTree(dir: hugoTemplatesDir)
+- def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
+- def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
+- def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
+- def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
+-
+- doFirst {
+- // specific release template for version archive
+- def changes = ""
+- def whatsnew = null
+- def givenDate = null
+- def givenChannel = null
+- def givenVersion = null
+- if (CHANNEL == "RELEASE") {
+- def (map, content) = mdFileComponents(releaseMdFile)
+- givenDate = map.date
+- givenChannel = map.channel
+- givenVersion = map.version
+- changes = content
+- if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
+- throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
+- }
+-
+- if (whatsnewMdFile.exists())
+- whatsnew = whatsnewMdFile.text
+- }
+-
+- def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
+- def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
+-
+- def changesHugo = null
+- if (changes != null) {
+- changesHugo = '<div class="release_notes">\n\n'
+- def inSection = false
+- changes.eachLine { line ->
+- def m = null
+- if (m = line =~ /^##([^#].*)$/) {
+- if (inSection) {
+- changesHugo += "</div>\n\n"
+- }
+- def section = m[0][1].trim()
+- section = section.toLowerCase()
+- section = section.replaceAll(/ +/, "_")
+- section = section.replaceAll(/[^a-z0-9_\-]/, "")
+- changesHugo += "<div class=\"${section}\">\n\n"
+- inSection = true
+- } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
+- def comment = m[0][2].trim()
+- if (comment != "") {
+- comment = comment.replaceAll('"', """)
+- def issuekeys = []
+- comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
+- def newline = m[0][1]
+- if (comment.trim() != "")
+- newline += "{{<comment>}}${comment}{{</comment>}} "
+- newline += m[0][3].trim()
+- if (issuekeys.size() > 0)
+- newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
+- if (m[0][4] != null)
+- newline += m[0][4]
+- line = newline
+- }
+- }
+- changesHugo += line+"\n"
+- }
+- if (inSection) {
+- changesHugo += "\n</div>\n\n"
+- }
+- changesHugo += '</div>'
+- }
+-
+- templateFiles.each{ templateFile ->
+- def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
+- def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
+- def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
+-
+- def outPathName = string("${hugoBuildDir}/$newRelPathName")
+-
+- copy {
+- from templateFile
+- rename(templateFile.getName(), newFileName)
+- into outPathName
+- }
+-
+- def newFile = file("${outPathName}/${newFileName}".toString())
+- def content = newFile.text
+- newFile.text = hugoTemplateSubstitutions(content,
+- [
+- WHATSNEW: whatsnew,
+- CHANGES: changesHugo,
+- DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
+- DRAFT: givenDate == null ? "true" : "false",
+- JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
+- JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
+- ]
+- )
+- }
+-
+- }
+-
+- inputs.file(oldJvlFile)
+- inputs.dir(hugoTemplatesDir)
+- inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
+- inputs.property("CHANNEL", { CHANNEL })
+-}
+-
+-def getMdDate(File mdFile) {
+- return mdFileComponents(mdFile, true)
+-}
+-
+-def getMdSections(String content) {
+- def sections = [:]
+- def sectionContent = ""
+- def sectionName = null
+- content.eachLine { line ->
+- def m = null
+- if (m = line =~ /^##([^#].*)$/) {
+- if (sectionName != null) {
+- sections[sectionName] = sectionContent
+- sectionName = null
+- sectionContent = ""
+- }
+- sectionName = m[0][1].trim()
+- sectionName = sectionName.toLowerCase()
+- sectionName = sectionName.replaceAll(/ +/, "_")
+- sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
+- } else if (sectionName != null) {
+- sectionContent += line+"\n"
+- }
+- }
+- if (sectionContent != null) {
+- sections[sectionName] = sectionContent
+- }
+- return sections
+-}
+-
+-
task copyHelp(type: Copy) {
def inputDir = helpSourceDir
def outputDir = "${helpBuildDir}/${help_dir}"
-@@ -1242,24 +347,15 @@
+@@ -1476,7 +300,6 @@ task copyHelp(type: Copy) {
+ outputs.dir(outputDir)
+ }
+
+-
+ task releasesTemplates {
+ group "help"
+ description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
+@@ -1491,6 +314,7 @@ task releasesTemplates {
+ def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
+
+ doFirst {
++ def JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+ def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
+ def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
+
+@@ -1505,7 +329,7 @@ task releasesTemplates {
+
+ def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
+ def releaseFilesDates = releaseFiles.collectEntries {
+- [(it): getMdDate(it)]
++ [(it): getDate("")]
+ }
+ releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
+
+@@ -1513,96 +337,13 @@ task releasesTemplates {
+ def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
+ def versionTemplate = m[0][1]
+
+- MutableDataSet options = new MutableDataSet()
+-
+- def extensions = new ArrayList<>()
+- options.set(Parser.EXTENSIONS, extensions)
+- options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
+-
+- Parser parser = Parser.builder(options).build()
+- HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+-
+- def actualVersions = releaseFiles.collect { rf ->
+- def (rfMap, rfContent) = mdFileComponents(rf)
+- return rfMap.version
+- }
+ def versionsHtml = ""
+ def linkedVersions = []
+- releaseFiles.reverse().each { rFile ->
+- def (rMap, rContent) = mdFileComponents(rFile)
+-
+- def versionLink = ""
+- def partialVersion = ""
+- def firstPart = true
+- rMap.version.split("\\.").each { part ->
+- def displayPart = ( firstPart ? "" : "." ) + part
+- partialVersion += displayPart
+- if (
+- linkedVersions.contains(partialVersion)
+- || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
+- ) {
+- versionLink += displayPart
+- } else {
+- versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
+- linkedVersions += partialVersion
+- }
+- firstPart = false
+- }
+- def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
+-
+- def lm = null
+- def rContentProcessed = ""
+- rContent.eachLine { line ->
+- if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
+- line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
+- } else if (lm = line =~ /^###([^#]+.*)$/) {
+- line = "_${lm[0][1].trim()}_"
+- }
+- rContentProcessed += line + "\n"
+- }
+-
+- def rContentSections = getMdSections(rContentProcessed)
+- def rVersion = versionTemplate
+- if (rVersion != "") {
+- def rNewFeatures = rContentSections["new_features"]
+- def rIssuesResolved = rContentSections["issues_resolved"]
+- Node newFeaturesNode = parser.parse(rNewFeatures)
+- String newFeaturesHtml = renderer.render(newFeaturesNode)
+- Node issuesResolvedNode = parser.parse(rIssuesResolved)
+- String issuesResolvedHtml = renderer.render(issuesResolvedNode)
+- rVersion = hugoTemplateSubstitutions(rVersion,
+- [
+- VERSION: rMap.version,
+- VERSION_LINK: versionLink,
+- DISPLAY_DATE: displayDate,
+- NEW_FEATURES: newFeaturesHtml,
+- ISSUES_RESOLVED: issuesResolvedHtml
+- ]
+- )
+- versionsHtml += rVersion
+- }
+- }
+
+ releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
+- releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
+ releasesHtmlFile.text = releasesTemplate
+
+- if (whatsnewMdFile.exists()) {
+- def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
+- def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
+- Node whatsnewNode = parser.parse(whatsnewMd)
+- String whatsnewHtml = renderer.render(whatsnewNode)
+- whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
+- whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
+- [
+- VERSION: JALVIEW_VERSION,
+- DISPLAY_DATE: wnDisplayDate
+- ]
+- )
+- } else if (gradle.taskGraph.hasTask(":linkCheck")) {
+- whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
+- }
+-
++ whatsnewHtmlFile.text = "Debian build " + getDate("yyyy-MM-dd HH:mm:ss")
+ }
+
+ inputs.file(releasesTemplateFile)
+@@ -1613,7 +354,6 @@ task releasesTemplates {
+ outputs.file(whatsnewHtmlFile)
+ }
+
+-
+ task copyResources(type: Copy) {
+ group = "build"
+ description = "Copy (and make text substitutions in) the resources dir to the build area"
+@@ -1653,44 +393,22 @@ task copyChannelResources(type: Copy) {
+
+ def inputDir = "${channelDir}/${resource_dir}"
+ def outputDir = resourcesBuildDir
+- from(inputDir) {
+- include(channel_props)
+- filter(ReplaceTokens,
+- beginToken: '__',
+- endToken: '__',
+- tokens: [
+- 'SUFFIX': channelSuffix
+- ]
+- )
+- }
+- from(inputDir) {
+- exclude(channel_props)
+- }
++ from inputDir
+ into outputDir
+
+ inputs.dir(inputDir)
outputs.dir(outputDir)
}
- property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
- property "VERSION", JALVIEW_VERSION
- property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+- property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
- if (getdownSetAppBaseProperty) {
- property "GETDOWNAPPBASE", getdownAppBase
- property "GETDOWNAPPDISTDIR", getdownAppDistDir
outputs.file(outputFile)
}
-@@ -1293,7 +389,6 @@
- dependsOn buildResources
+@@ -1725,123 +443,31 @@ task prepare {
dependsOn copyDocs
dependsOn copyHelp
+ dependsOn releasesTemplates
- dependsOn convertMdFiles
dependsOn buildIndices
}
-@@ -1306,12 +401,7 @@
- //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+
+ compileJava.dependsOn prepare
+ run.dependsOn compileJava
+-compileTestJava.dependsOn compileJava
+-
++//run.dependsOn prepare
+
+
++//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
test {
- dependsOn prepare
+- group = "Verification"
+- description = "Runs all testTaskN tasks)"
-
- if (useClover) {
- dependsOn cloverClasses
-- } else { //?
-- dependsOn compileJava //?
+- } else { //?
+- dependsOn testClasses
+- }
+-
+- // not running tests in this task
+- exclude "**/*"
+-}
+-/* testTask0 is the main test task */
+-task testTask0(type: Test) {
+- group = "Verification"
+- description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
+- useTestNG() {
+- includeGroups testng_groups.split(",")
+- excludeGroups testng_excluded_groups.split(",")
+- tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
+- preserveOrder true
+- useDefaultListeners=true
+- }
+-}
+-
+-/* separated tests */
+-task testTask1(type: Test) {
+- group = "Verification"
+- description = "Tests that need to be isolated from the main test run"
+- useTestNG() {
+- includeGroups name
+- excludeGroups testng_excluded_groups.split(",")
+- preserveOrder true
+- useDefaultListeners=true
- }
+-}
++ dependsOn prepare
+ dependsOn compileJava //?
+-/* insert more testTaskNs here -- change N to next digit or other string */
+-/*
+-task testTaskN(type: Test) {
+- group = "Verification"
+- description = "Tests that need to be isolated from the main test run"
useTestNG() {
- includeGroups testng_groups
-@@ -1323,6 +413,7 @@
+- includeGroups name
+- excludeGroups testng_excluded_groups.split(",")
++ includeGroups testng_groups
++ excludeGroups testng_excluded_groups
+ preserveOrder true
+ useDefaultListeners=true
+ }
+-}
+-*/
+-
+-/*
+- * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
+- * to summarise test results from all Test tasks
+- */
+-/* START of test tasks results summary */
+-import groovy.time.TimeCategory
+-import org.gradle.api.tasks.testing.logging.TestExceptionFormat
+-import org.gradle.api.tasks.testing.logging.TestLogEvent
+-rootProject.ext.testsResults = [] // Container for tests summaries
+-
+-tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
+-
+- // from original test task
+- if (useClover) {
+- dependsOn cloverClasses
+- } else { //?
+- dependsOn testClasses //?
+- }
+-
+- // run main tests first
+- if (!testTask.name.equals("testTask0"))
+- testTask.mustRunAfter "testTask0"
+-
+- testTask.testLogging { logging ->
+- events TestLogEvent.FAILED
+-// TestLogEvent.SKIPPED,
+-// TestLogEvent.STANDARD_OUT,
+-// TestLogEvent.STANDARD_ERROR
+-
+- exceptionFormat TestExceptionFormat.FULL
+- showExceptions true
+- showCauses true
+- showStackTraces true
+-
+- info.events = [ TestLogEvent.FAILED ]
+- }
+-
+-
+-
+- ignoreFailures = true // Always try to run all tests for all modules
+-
+- afterSuite { desc, result ->
+- if (desc.parent)
+- return // Only summarize results for whole modules
+-
+- def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
+-
+- rootProject.ext.testsResults.add(resultsInfo)
+- }
+
+- // from original test task
maxHeapSize = "1024m"
workingDir = jalviewDir
def testLaf = project.findProperty("test_laf")
if (testLaf != null) {
println("Setting Test LaF to '${testLaf}'")
-@@ -1338,9 +429,6 @@
+@@ -1857,143 +483,8 @@ tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { te
jvmArgs += additional_compiler_args
doFirst {
+- // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
+- // testTasks that include the tests, and exclude all from the others.
+- // get --test argument
+- filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
+- // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
+- // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below
+-
+-
- if (useClover) {
- println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
- }
+- }
+-
+-
+- /* don't fail on no matching tests (so --tests will run across all testTasks) */
+- testTask.filter.setFailOnNoMatchingTests(false)
+-
+- /* ensure the "test" task dependsOn all the testTasks */
+- test.dependsOn testTask
+-}
+-
+-gradle.buildFinished {
+- def allResults = rootProject.ext.testsResults
+-
+- if (!allResults.isEmpty()) {
+- printResults allResults
+- allResults.each {r ->
+- if (r[2].resultType == TestResult.ResultType.FAILURE)
+- throw new GradleException("Failed tests!")
+- }
+- }
+-}
+-
+-private static String colString(styler, col, colour, text) {
+- return col?"${styler[colour](text)}":text
+-}
+-
+-private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
+- def colour = 'black'
+- def text = rt
+- def nocol = false
+- if (rc == 0) {
+- text = "-----"
+- nocol = true
+- } else {
+- switch(rt) {
+- case TestResult.ResultType.SUCCESS:
+- colour = 'green'
+- break;
+- case TestResult.ResultType.FAILURE:
+- colour = 'red'
+- break;
+- default:
+- nocol = true
+- break;
+- }
}
+- StringBuilder sb = new StringBuilder()
+- sb.append("${pn}")
+- if (tn != null)
+- sb.append(":${tn}")
+- sb.append(" results: ")
+- sb.append(colString(s, col && !nocol, colour, text))
+- sb.append(" (")
+- sb.append("${rc} tests, ")
+- sb.append(colString(s, col && rs > 0, 'green', rs))
+- sb.append(" successes, ")
+- sb.append(colString(s, col && rf > 0, 'red', rf))
+- sb.append(" failures, ")
+- sb.append("${rsk} skipped) in ${t}")
+- return sb.toString()
+-}
+-
+-private static void printResults(allResults) {
+-
+- // styler from https://stackoverflow.com/a/56139852
+- def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
+-
+- def maxLength = 0
+- def failedTests = false
+- def summaryLines = []
+- def totalcount = 0
+- def totalsuccess = 0
+- def totalfail = 0
+- def totalskip = 0
+- def totaltime = TimeCategory.getSeconds(0)
+- // sort on project name then task name
+- allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
+- def projectName = it[0]
+- def taskName = it[1]
+- def result = it[2]
+- def time = it[3]
+- def report = it[4]
+- def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
+- def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
+- def reportLine = "Report file: ${report}"
+- def ls = summaryPlain.length()
+- def lr = reportLine.length()
+- def m = [ls, lr].max()
+- if (m > maxLength)
+- maxLength = m
+- def info = [ls, summaryCol, reportLine]
+- summaryLines.add(info)
+- failedTests |= result.resultType == TestResult.ResultType.FAILURE
+- totalcount += result.testCount
+- totalsuccess += result.successfulTestCount
+- totalfail += result.failedTestCount
+- totalskip += result.skippedTestCount
+- totaltime += time
+- }
+- def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
+- def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
+- def tls = totalSummaryPlain.length()
+- if (tls > maxLength)
+- maxLength = tls
+- def info = [tls, totalSummaryCol, null]
+- summaryLines.add(info)
+-
+- def allSummaries = []
+- for(sInfo : summaryLines) {
+- def ls = sInfo[0]
+- def summary = sInfo[1]
+- def report = sInfo[2]
+-
+- StringBuilder sb = new StringBuilder()
+- sb.append("│" + summary + " " * (maxLength - ls) + "│")
+- if (report != null) {
+- sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
+- }
+- allSummaries += sb.toString()
+- }
+-
+- println "┌${"${"─" * maxLength}"}┐"
+- println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
+- println "└${"${"─" * maxLength}"}┘"
}
+-/* END of test tasks results summary */
-@@ -1420,1752 +508,7 @@
+
+ task compileLinkCheck(type: JavaCompile) {
+@@ -2052,7 +543,7 @@ jar {
+ manifest {
+ attributes "Main-Class": main_class,
+ "Permissions": "all-permissions",
+- "Application-Name": applicationName,
++ "Application-Name": install4jApplicationName,
+ "Codebase": application_codebase,
+ "Implementation-Version": JALVIEW_VERSION
+ }
+@@ -2060,8 +551,6 @@ jar {
+ def outputDir = "${jalviewDir}/${package_dir}"
+ destinationDirectory = file(outputDir)
+ archiveFileName = rootProject.name+".jar"
+- duplicatesStrategy "EXCLUDE"
+-
+
+ exclude "cache*/**"
+ exclude "*.jar"
+@@ -2073,2137 +562,7 @@ jar {
sourceSets.main.resources.srcDirs.each{ dir ->
inputs.dir(dir)
}
- }
- manifest {
- attributes "Implementation-Version": JALVIEW_VERSION,
-- "Application-Name": install4jApplicationName
+- "Application-Name": applicationName
- }
+-
+- duplicatesStrategy "INCLUDE"
+-
- mainClassName = shadow_jar_main_class
- mergeServiceFiles()
- classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
- minimize()
-}
-
+-task getdownImagesCopy() {
+- inputs.dir getdownImagesDir
+- outputs.dir getdownImagesBuildDir
+-
+- doFirst {
+- copy {
+- from(getdownImagesDir) {
+- include("*getdown*.png")
+- }
+- into getdownImagesBuildDir
+- }
+- }
+-}
+-
+-task getdownImagesProcess() {
+- dependsOn getdownImagesCopy
+-
+- doFirst {
+- if (backgroundImageText) {
+- if (convertBinary == null) {
+- throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
+- }
+- if (!project.hasProperty("getdown_background_image_text_suffix_cmd")) {
+- throw new StopExecutionException("No property 'getdown_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
+- }
+- fileTree(dir: getdownImagesBuildDir, include: "*background*.png").getFiles().each { file ->
+- exec {
+- executable convertBinary
+- args = [
+- file.getPath(),
+- '-font', getdown_background_image_text_font,
+- '-fill', getdown_background_image_text_colour,
+- '-draw', sprintf(getdown_background_image_text_suffix_cmd, channelSuffix),
+- '-draw', sprintf(getdown_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
+- '-draw', sprintf(getdown_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
+- file.getPath()
+- ]
+- }
+- }
+- }
+- }
+-}
+-
+-task getdownImages() {
+- dependsOn getdownImagesProcess
+-}
-
-task getdownWebsite() {
- group = "distribution"
- description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+-
+- dependsOn getdownImages
- if (buildDist) {
- dependsOn makeDist
- }
-
- def getdownWebsiteResourceFilenames = []
-- def getdownTextString = ""
- def getdownResourceDir = getdownResourceDir
- def getdownResourceFilenames = []
-
- doFirst {
- // clean the getdown website and files dir before creating getdown folders
-- delete getdownWebsiteDir
+- delete getdownAppBaseDir
- delete getdownFilesDir
-
- copy {
- }
- getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
-
-- // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
+- copy {
+- from channelPropsFile
+- filter(ReplaceTokens,
+- beginToken: '__',
+- endToken: '__',
+- tokens: [
+- 'SUFFIX': channelSuffix
+- ]
+- )
+- into getdownAppBaseDir
+- }
+- getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
+-
+- // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
- def props = project.properties.sort { it.key }
- if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
- props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
- if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
- props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
- }
-- if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
-- props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
-- props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
-- props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
-- props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+- if (getdownImagesBuildDir != null && file(getdownImagesBuildDir).exists()) {
+- props.put("getdown_txt_ui.background_image", "${getdownImagesBuildDir}/${getdown_background_image}")
+- props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
+- props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
+- props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
- props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
- props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
- }
-
- props.put("getdown_txt_title", jalview_name)
-- props.put("getdown_txt_ui.name", install4jApplicationName)
+- props.put("getdown_txt_ui.name", applicationName)
-
- // start with appbase
-- getdownTextString += "appbase = ${getdownAppBase}\n"
+- getdownTextLines += "appbase = ${getdownAppBase}"
- props.each{ prop, val ->
- if (prop.startsWith("getdown_txt_") && val != null) {
- if (prop.startsWith("getdown_txt_multi_")) {
- def key = prop.substring(18)
- val.split(",").each{ v ->
-- def line = "${key} = ${v}\n"
-- getdownTextString += line
+- def line = "${key} = ${v}"
+- getdownTextLines += line
- }
- } else {
- // file values rationalised
- }
- }
- if (! prop.startsWith("getdown_txt_resource")) {
-- def line = prop.substring(12) + " = ${val}\n"
-- getdownTextString += line
+- def line = prop.substring(12) + " = ${val}"
+- getdownTextLines += line
- }
- }
- }
- }
-
- getdownWebsiteResourceFilenames.each{ filename ->
-- getdownTextString += "resource = ${filename}\n"
+- getdownTextLines += "resource = ${filename}"
- }
- getdownResourceFilenames.each{ filename ->
- copy {
- if (s.exists()) {
- copy {
- from s
-- into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+- into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
- }
-- getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+- getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
- }
- }
-
- codeFiles += f
- }
- }
-- codeFiles.sort().each{f ->
+- def jalviewJar = jar.archiveFileName.getOrNull()
+- // put jalview.jar first for CLASSPATH and .properties files reasons
+- codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
- def name = f.getName()
-- def line = "code = ${getdownAppDistDir}/${name}\n"
-- getdownTextString += line
+- def line = "code = ${getdownAppDistDir}/${name}"
+- getdownTextLines += line
- copy {
- from f.getPath()
- into getdownAppDir
- def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
- j11libFiles.sort().each{f ->
- def name = f.getName()
-- def line = "code = ${getdown_j11lib_dir}/${name}\n"
-- getdownTextString += line
+- def line = "code = ${getdown_j11lib_dir}/${name}"
+- getdownTextLines += line
- copy {
- from f.getPath()
- into getdownJ11libDir
- */
-
- // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
-- //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
-- getdownTextString += "resource = ${getdown_launcher_new}\n"
-- getdownTextString += "class = ${main_class}\n"
+- //getdownTextLines += "class = " + file(getdownLauncher).getName()
+- getdownTextLines += "resource = ${getdown_launcher_new}"
+- getdownTextLines += "class = ${main_class}"
- // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
- if (getdownSetAppBaseProperty) {
-- getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
-- getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+- getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
+- getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
- }
-
-- def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
-- getdown_txt.write(getdownTextString)
+- def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
+- getdownTxt.write(getdownTextLines.join("\n"))
-
-- def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
-- def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+- getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+- def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
- launchJvl.write("appbase=${getdownAppBase}")
-
- // files going into the getdown website dir: getdown-launcher.jar
- copy {
- from getdownLauncher
- rename(file(getdownLauncher).getName(), getdown_launcher_new)
-- into getdownWebsiteDir
+- into getdownAppBaseDir
- }
-
- // files going into the getdown website dir: getdown-launcher(-local).jar
- if (file(getdownLauncher).getName() != getdown_launcher) {
- rename(file(getdownLauncher).getName(), getdown_launcher)
- }
-- into getdownWebsiteDir
+- into getdownAppBaseDir
- }
-
- // files going into the getdown website dir: ./install dir and files
- if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
- copy {
-- from getdown_txt
+- from getdownTxt
- from getdownLauncher
- from "${getdownAppDir}/${getdown_build_properties}"
- if (file(getdownLauncher).getName() != getdown_launcher) {
-
- // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
- copy {
-- from getdown_txt
+- from getdownTxt
- from launchJvl
- from getdownLauncher
-- from "${getdownWebsiteDir}/${getdown_build_properties}"
+- from "${getdownAppBaseDir}/${getdown_build_properties}"
+- from "${getdownAppBaseDir}/${channel_props}"
- if (file(getdownLauncher).getName() != getdown_launcher) {
- rename(file(getdownLauncher).getName(), getdown_launcher)
- }
- into getdownFilesDir
- }
-
-- // and ./resources (not all downloaded by getdown)
+- // and ./resource (not all downloaded by getdown)
- copy {
- from getdownResourceDir
- into "${getdownFilesDir}/${getdown_resource_dir}"
- if (buildDist) {
- inputs.dir("${jalviewDir}/${package_dir}")
- }
-- outputs.dir(getdownWebsiteDir)
+- outputs.dir(getdownAppBaseDir)
- outputs.dir(getdownFilesDir)
-}
-
- classpath = files(getdownLauncher)
- }
- main = "com.threerings.getdown.tools.Digester"
-- args getdownWebsiteDir
-- inputs.dir(getdownWebsiteDir)
-- outputs.file("${getdownWebsiteDir}/digest2.txt")
+- args getdownAppBaseDir
+- inputs.dir(getdownAppBaseDir)
+- outputs.file("${getdownAppBaseDir}/digest2.txt")
-}
-
-
- dependsOn getdownDigest
- doLast {
- if (reportRsyncCommand) {
-- def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+- def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
- def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
- println "LIKELY RSYNC COMMAND:"
- println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
- }
- }
-}
+
+-
+-task getdownArchiveBuild() {
+- group = "distribution"
+- description = "Put files in the archive dir to go on the website"
+-
+- dependsOn getdownWebsite
+-
+- def v = "v${JALVIEW_VERSION_UNDERSCORES}"
+- def vDir = "${getdownArchiveDir}/${v}"
+- getdownFullArchiveDir = "${vDir}/getdown"
+- getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
+-
+- def vAltDir = "alt_${v}"
+- def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
+-
+- doFirst {
+- // cleanup old "old" dir
+- delete getdownArchiveDir
+-
+- def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
+- getdownArchiveTxt.getParentFile().mkdirs()
+- def getdownArchiveTextLines = []
+- def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
+-
+- // the libdir
+- copy {
+- from "${getdownAppBaseDir}/${getdownAppDistDir}"
+- into "${getdownFullArchiveDir}/${vAltDir}"
+- }
+-
+- getdownTextLines.each { line ->
+- line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
+- line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
+- line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
+- line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
+- line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
+- line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
+- // remove the existing resource = resource/ or bin/ lines
+- if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
+- getdownArchiveTextLines += line
+- }
+- }
+-
+- // the resource dir -- add these files as resource lines in getdown.txt
+- copy {
+- from "${archiveImagesDir}"
+- into "${getdownFullArchiveDir}/${getdown_resource_dir}"
+- eachFile { file ->
+- getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
+- }
+- }
+-
+- getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
+-
+- def vLaunchJvl = file(getdownVersionLaunchJvl)
+- vLaunchJvl.getParentFile().mkdirs()
+- vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
+- def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
+- def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
+- // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
+- //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
+- java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
+-
+- // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
+- copy {
+- from getdownLauncher
+- from "${getdownAppBaseDir}/${getdownLaunchJvl}"
+- from "${getdownAppBaseDir}/${getdown_launcher_new}"
+- from "${getdownAppBaseDir}/${channel_props}"
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownFullArchiveDir
+- }
+-
+- }
+-}
+-
+-task getdownArchiveDigest(type: JavaExec) {
+- group = "distribution"
+- description = "Digest the getdown archive folder"
+-
+- dependsOn getdownArchiveBuild
+-
+- doFirst {
+- classpath = files(getdownLauncher)
+- args getdownFullArchiveDir
+- }
+- main = "com.threerings.getdown.tools.Digester"
+- inputs.dir(getdownFullArchiveDir)
+- outputs.file("${getdownFullArchiveDir}/digest2.txt")
+-}
-
+-task getdownArchive() {
+- group = "distribution"
+- description = "Build the website archive dir with getdown digest"
+-
+- dependsOn getdownArchiveBuild
+- dependsOn getdownArchiveDigest
+-}
-
-tasks.withType(JavaCompile) {
- options.encoding = 'UTF-8'
-
-clean {
- doFirst {
-- delete getdownWebsiteDir
+- delete getdownAppBaseDir
- delete getdownFilesDir
+- delete getdownArchiveDir
- }
-}
-
- }
- }
-
+- // disable install screen for OSX dmg (for 2.11.2.0)
+- install4jConfigXml.'**'.macosArchive.each { macosArchive ->
+- macosArchive.attributes().remove('executeSetupApp')
+- macosArchive.attributes().remove('setupAppId')
+- }
+-
- // turn off checksum creation for LOCAL channel
- def e = install4jConfigXml.application[0]
-- if (CHANNEL == "LOCAL") {
-- e.'@createChecksums' = "false"
-- } else {
-- e.'@createChecksums' = "true"
-- }
+- e.'@createChecksums' = string(install4jCheckSums)
-
- // put file association actions where placeholder action is
- def install4jFileAssociationsText = install4jFileAssociationsFile.text
- }
-}
-
+-task cleanInstallersDataFiles {
+- def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
+- def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
+- def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
+- doFirst {
+- delete installersOutputTxt
+- delete installersSha256
+- delete hugoDataJsonFile
+- }
+-}
+-
+-task install4jDMGBackgroundImageCopy {
+- inputs.file "${install4jDMGBackgroundImageDir}/${install4jDMGBackgroundImageFile}"
+- outputs.dir "${install4jDMGBackgroundImageBuildDir}"
+- doFirst {
+- copy {
+- from(install4jDMGBackgroundImageDir) {
+- include(install4jDMGBackgroundImageFile)
+- }
+- into install4jDMGBackgroundImageBuildDir
+- }
+- }
+-}
+-
+-task install4jDMGBackgroundImageProcess {
+- dependsOn install4jDMGBackgroundImageCopy
+-
+- doFirst {
+- if (backgroundImageText) {
+- if (convertBinary == null) {
+- throw new StopExecutionException("No ImageMagick convert binary installed at '${convertBinaryExpectedLocation}'")
+- }
+- if (!project.hasProperty("install4j_background_image_text_suffix_cmd")) {
+- throw new StopExecutionException("No property 'install4j_background_image_text_suffix_cmd' defined. See channel_gradle.properties for channel ${CHANNEL}")
+- }
+- fileTree(dir: install4jDMGBackgroundImageBuildDir, include: "*.png").getFiles().each { file ->
+- exec {
+- executable convertBinary
+- args = [
+- file.getPath(),
+- '-font', install4j_background_image_text_font,
+- '-fill', install4j_background_image_text_colour,
+- '-draw', sprintf(install4j_background_image_text_suffix_cmd, channelSuffix),
+- '-draw', sprintf(install4j_background_image_text_commit_cmd, "git-commit: ${gitHash}"),
+- '-draw', sprintf(install4j_background_image_text_date_cmd, getDate("yyyy-MM-dd HH:mm:ss")),
+- file.getPath()
+- ]
+- }
+- }
+- }
+- }
+-}
+-
+-task install4jDMGBackgroundImage {
+- dependsOn install4jDMGBackgroundImageProcess
+-}
-
--task installers(type: com.install4j.gradle.Install4jTask) {
+-task installerFiles(type: com.install4j.gradle.Install4jTask) {
- group = "distribution"
- description = "Create the install4j installers"
- dependsOn getdown
- dependsOn copyInstall4jTemplate
+- dependsOn cleanInstallersDataFiles
+- dependsOn install4jDMGBackgroundImage
-
- projectFile = install4jConfFile
-
- filesMd5 = filesMd5.substring(0,8)
- }
- def install4jTemplateVersion = "${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_APPLICATION_NAME': applicationName,
- 'JALVIEW_DIR': "../..",
- 'OSX_KEYSTORE': OSX_KEYSTORE,
- 'OSX_APPLEID': OSX_APPLEID,
- '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_DMG_DS_STORE': install4jDMGDSStore,
-- 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+- 'MACOS_DMG_BG_IMAGE': "${install4jDMGBackgroundImageBuildDir}/${install4jDMGBackgroundImageFile}",
- 'WRAPPER_LINK': getdownWrapperLink,
- 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
- 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+- 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
- 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
- 'INSTALLER_NAME': install4jInstallerName,
- 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
-- 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+- 'GETDOWN_CHANNEL_DIR': getdownChannelDir,
- 'GETDOWN_FILES_DIR': getdown_files_dir,
- 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
- 'GETDOWN_DIST_DIR': getdownAppDistDir,
- 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
- 'PNG_ICON_FILE': install4jPngIconFile,
- 'BACKGROUND': install4jBackground,
+- ]
-
+- def varNameMap = [
+- 'mac': 'MACOS',
+- 'windows': 'WINDOWS',
+- 'linux': 'LINUX'
- ]
+-
+- // these are the bundled OS/architecture VMs needed by install4j
+- def osArch = [
+- [ "mac", "x64" ],
+- [ "mac", "aarch64" ],
+- [ "windows", "x64" ],
+- [ "linux", "x64" ],
+- [ "linux", "aarch64" ]
+- ]
+- osArch.forEach { os, arch ->
+- variables[ sprintf("%s_%s_JAVA_VM_DIR", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/jre-%s-%s-%s/jre", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
+- // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
+- // otherwise running `gradle installers` generates a non-useful error:
+- // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
+- variables[ sprintf("%s_%s_JAVA_VM_TGZ", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/tgz/jre_%s_%s_%s.tar.gz", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
+- }
-
- //println("INSTALL4J VARIABLES:")
- //variables.each{k,v->println("${k}=${v}")}
- }
- //verbose=true
-
-- inputs.dir(getdownWebsiteDir)
+- inputs.dir(getdownAppBaseDir)
- inputs.file(install4jConfFile)
- inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
-- inputs.dir(macosJavaVMDir)
-- inputs.dir(windowsJavaVMDir)
- outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
-}
-
+-def getDataHash(File myFile) {
+- HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
+- return myFile.exists()
+- ? [
+- "file" : myFile.getName(),
+- "filesize" : myFile.length(),
+- "sha256" : hash.toString()
+- ]
+- : null
+-}
+-
+-def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
+- def hash = [
+- "channel" : getdownChannelName,
+- "date" : getDate("yyyy-MM-dd HH:mm:ss"),
+- "git-commit" : "${gitHash} [${gitBranch}]",
+- "version" : JALVIEW_VERSION
+- ]
+- // install4j installer files
+- if (installersOutputTxt.exists()) {
+- def idHash = [:]
+- installersOutputTxt.readLines().each { def line ->
+- if (line.startsWith("#")) {
+- return;
+- }
+- line.replaceAll("\n","")
+- def vals = line.split("\t")
+- def filename = vals[3]
+- def filesize = file(filename).length()
+- filename = filename.replaceAll(/^.*\//, "")
+- hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
+- idHash."${filename}" = vals[0]
+- }
+- if (install4jCheckSums && installersSha256.exists()) {
+- installersSha256.readLines().each { def line ->
+- if (line.startsWith("#")) {
+- return;
+- }
+- line.replaceAll("\n","")
+- def vals = line.split(/\s+\*?/)
+- def filename = vals[1]
+- def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
+- }
+- }
+- }
+-
+- [
+- "JAR": shadowJar.archiveFile, // executable JAR
+- "JVL": getdownVersionLaunchJvl, // version JVL
+- "SOURCE": sourceDist.archiveFile // source TGZ
+- ].each { key, value ->
+- def file = file(value)
+- if (file.exists()) {
+- def fileHash = getDataHash(file)
+- if (fileHash != null) {
+- hash."${key}" = fileHash;
+- }
+- }
+- }
+- return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
+-}
+-
+-task staticMakeInstallersJsonFile {
+- doFirst {
+- def output = findProperty("i4j_output")
+- def sha256 = findProperty("i4j_sha256")
+- def json = findProperty("i4j_json")
+- if (output == null || sha256 == null || json == null) {
+- throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
+- }
+- writeDataJsonFile(file(output), file(sha256), file(json))
+- }
+-}
+-
+-task installers {
+- dependsOn installerFiles
+-}
+-
-
-spotless {
- java {
- }
-}
-
+-task createSourceReleaseProperties(type: WriteProperties) {
+- group = "distribution"
+- description = "Create the source RELEASE properties file"
+-
+- def sourceTarBuildDir = "${buildDir}/sourceTar"
+- def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
+- outputFile (sourceReleasePropertiesFile)
+-
+- doFirst {
+- releaseProps.each{ key, val -> property key, val }
+- property "git.branch", gitBranch
+- property "git.hash", gitHash
+- }
+-
+- outputs.file(outputFile)
+-}
-
-task sourceDist(type: Tar) {
- group "distribution"
-
- dependsOn createBuildProperties
- dependsOn convertMdFiles
+- dependsOn eclipseAllPreferences
+- dependsOn createSourceReleaseProperties
+-
-
-- def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
-- def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
+- def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
- archiveFileName = outputFileName
-
- compression Compression.GZIP
- "*locales/**",
- "utils/InstallAnywhere",
- "**/*.log",
+- "RELEASE",
- ]
- def PROCESS_FILES=[
- "AUTHORS",
- "FEATURETODO",
- "LICENSE",
- "**/README",
-- "RELEASE",
- "THIRDPARTYLIBS",
- "TESTNG",
- "build.gradle",
- "**/*.sh",
- ]
- def INCLUDE_FILES=[
-- ".settings/org.eclipse.jdt.core.jalview.prefs",
+- ".classpath",
+- ".settings/org.eclipse.buildship.core.prefs",
+- ".settings/org.eclipse.jdt.core.prefs"
- ]
-
- from(jalviewDir) {
- exclude ("utils/InstallAnywhere")
-
- exclude (getdown_files_dir)
-- exclude (getdown_website_dir)
+- // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
+- //exclude (getdown_website_dir)
+- //exclude (getdown_archive_dir)
-
- // exluding these as not using jars as modules yet
- exclude ("${j11modDir}/**/*.jar")
- })
- }
-
+- def sourceTarBuildDir = "${buildDir}/sourceTar"
+- from(sourceTarBuildDir) {
+- // this includes the appended RELEASE properties file
+- }
-}
-
+-task dataInstallersJson {
+- group "website"
+- description "Create the installers-VERSION.json data file for installer files created"
+-
+- mustRunAfter installers
+- mustRunAfter shadowJar
+- mustRunAfter sourceDist
+- mustRunAfter getdownArchive
+-
+- def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
+- def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
+-
+- if (installersOutputTxt.exists()) {
+- inputs.file(installersOutputTxt)
+- }
+- if (install4jCheckSums && installersSha256.exists()) {
+- inputs.file(installersSha256)
+- }
+- [
+- shadowJar.archiveFile, // executable JAR
+- getdownVersionLaunchJvl, // version JVL
+- sourceDist.archiveFile // source TGZ
+- ].each { fileName ->
+- if (file(fileName).exists()) {
+- inputs.file(fileName)
+- }
+- }
+-
+- outputs.file(hugoDataJsonFile)
+-
+- doFirst {
+- writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
+- }
+-}
-
-task helppages {
+- group "help"
+- description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
+-
- dependsOn copyHelp
- dependsOn pubhtmlhelp
-
- preserve {
- include "**"
- }
+-
+- // should this be exclude really ?
+- duplicatesStrategy "INCLUDE"
+-
- outputs.files outputFiles
- inputs.files inputFiles
-}
- 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)
- new org.apache.tools.ant.util.TeeOutputStream(
- logErrFOS,
- stderr),
-- errorOutput)
+- System.err)
- } else {
- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
- logOutFOS,
-task eclipseAutoBuildTask {
- //dependsOn jalviewjsIDE_checkJ2sPlugin
- //dependsOn jalviewjsIDE_PrepareSite
-+ outputs.file("${outputDir}/${archiveFileName}")
- }
-
+-}
+-
-
-task jalviewjs {
- group "JalviewJS"
- description "Build the site"
- dependsOn jalviewjsBuildSite
--}
++ outputs.file("${outputDir}/${archiveFileName}")
+ }
+
git://source.jalview.org / jalview.git / commitdiff