id 'java'
id 'application'
id 'eclipse'
- id "com.diffplug.spotless" version "6.18.0" //.gradle.spotless" "3.28.0"
- id 'com.github.johnrengelman.shadow' version '8.1.1' // was 4.0.3
+ id "com.diffplug.gradle.spotless" version "3.28.0"
+ id 'com.github.johnrengelman.shadow' version '6.0.0'
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
testDir = string("${jalviewDir}/${bareTestSourceDir}")
classesDir = string("${jalviewDir}/${classes_dir}")
- destinationDirectory = file(classesDir)
// clover
useClover = clover.equals("true")
main {
java {
srcDirs sourceDir
- destinationDirectory = file(classesDir)
+ outputDir = file(classesDir)
}
resources {
srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
}
- compileClasspath = files(sourceSets.main.java.destinationDirectory)
+ compileClasspath = files(sourceSets.main.java.outputDir)
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
clover {
java {
srcDirs cloverInstrDir
- destinationDirectory = cloverClassesDir
+ outputDir = cloverClassesDir
}
resources {
srcDirs = sourceSets.main.resources.srcDirs
}
- compileClasspath = files( sourceSets.clover.java.destinationDirectory )
+ 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"])
test {
java {
srcDirs testSourceDir
- destinationDirectory = file(testClassesDir)
+ outputDir = file(testClassesDir)
}
resources {
srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
}
- compileClasspath = files( sourceSets.test.java.destinationDirectory )
+ compileClasspath = files( sourceSets.test.java.outputDir )
compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
}
classpath {
- //defaultOutputDir = sourceSets.main.java.destinationDirectory
+ //defaultOutputDir = sourceSets.main.java.outputDir
configurations.each{ c->
if (c.isCanBeResolved()) {
minusConfigurations += [c]
HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
- //don't want to add destinationDirectory as eclipse is using its own output dir in bin/main
+ //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
}
sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
- //no longer want to add destinationDirectory as eclipse is using its own output dir in bin/main
+ //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
clean {
doFirst {
- delete sourceSets.main.java.destinationDirectory
+ delete sourceSets.main.java.outputDir
}
}
cleanTest {
dependsOn cleanClover
doFirst {
- delete sourceSets.test.java.destinationDirectory
+ delete sourceSets.test.java.outputDir
}
}
task copyDocs(type: Copy) {
def inputDir = "${jalviewDir}/${doc_dir}"
- def destinationDirectory = "${docBuildDir}/${doc_dir}"
+ def outputDir = "${docBuildDir}/${doc_dir}"
from(inputDir) {
include('**/*.txt')
include('**/*.md')
exclude('**/*.html')
exclude('**/*.xml')
}
- into destinationDirectory
+ into outputDir
inputs.dir(inputDir)
- outputs.dir(destinationDirectory)
+ outputs.dir(outputDir)
}
}
if (inFrontMatter) {
def m = null
- if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
+ 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})/) {
+ } 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+)/) {
+ } else if (m = line =~ /^channel:\s*(\S+)/) {
map["channel"] = m[0][1]
- } else if (m == line =~ /^version:\s*(\S+)/) {
+ } else if (m = line =~ /^version:\s*(\S+)/) {
map["version"] = m[0][1]
- } else if (m == line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
+ } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
map[ m[0][1] ] = m[0][2]
}
if (dateOnly && map["date"] != null) {
def inSection = false
changes.eachLine { line ->
def m = null
- if (m == line =~ /^##([^#].*)$/) {
+ if (m = line =~ /^##([^#].*)$/) {
if (inSection) {
changesHugo += "</div>\n\n"
}
section = section.replaceAll(/[^a-z0-9_\-]/, "")
changesHugo += "<div class=\"${section}\">\n\n"
inSection = true
- } else if (m == line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
+ } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
def comment = m[0][2].trim()
if (comment != "") {
comment = comment.replaceAll('"', """)
def sectionName = null
content.eachLine { line ->
def m = null
- if (m == line =~ /^##([^#].*)$/) {
+ if (m = line =~ /^##([^#].*)$/) {
if (sectionName != null) {
sections[sectionName] = sectionContent
sectionName = null
task copyHelp(type: Copy) {
def inputDir = helpSourceDir
- def destinationDirectory = "${helpBuildDir}/${help_dir}"
+ def outputDir = "${helpBuildDir}/${help_dir}"
from(inputDir) {
include('**/*.txt')
include('**/*.md')
exclude('**/*.xml')
exclude('**/*.jhm')
}
- into destinationDirectory
+ into outputDir
inputs.dir(inputDir)
outputs.files(helpFile)
- outputs.dir(destinationDirectory)
+ outputs.dir(outputDir)
}
-/*
task releasesTemplates {
group "help"
description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
def lm = null
def rContentProcessed = ""
rContent.eachLine { line ->
- if (lm == line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
+ if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
- } else if (lm == line =~ /^###([^#]+.*)$/) {
+ } else if (lm = line =~ /^###([^#]+.*)$/) {
line = "_${lm[0][1].trim()}_"
}
rContentProcessed += line + "\n"
outputs.file(whatsnewHtmlFile)
}
-*/
task copyResources(type: Copy) {
group = "build"
description = "Copy (and make text substitutions in) the resources dir to the build area"
def inputDir = resourceDir
- def destinationDirectory = resourcesBuildDir
+ def outputDir = resourcesBuildDir
from(inputDir) {
include('**/*.txt')
include('**/*.md')
exclude('**/*.html')
exclude('**/*.xml')
}
- into destinationDirectory
+ into outputDir
inputs.dir(inputDir)
- outputs.dir(destinationDirectory)
+ outputs.dir(outputDir)
}
task copyChannelResources(type: Copy) {
description = "Copy the channel resources dir to the build resources area"
def inputDir = "${channelDir}/${resource_dir}"
- def destinationDirectory = resourcesBuildDir
+ def outputDir = resourcesBuildDir
from(inputDir) {
include(channel_props)
filter(ReplaceTokens,
from(inputDir) {
exclude(channel_props)
}
- into destinationDirectory
+ into outputDir
inputs.dir(inputDir)
- outputs.dir(destinationDirectory)
+ outputs.dir(outputDir)
}
task createBuildProperties(type: WriteProperties) {
dependsOn copyResources
- dependsOn copyChannelResources
group = "build"
description = "Create the ${buildProperties} file"
task buildIndices(type: JavaExec) {
dependsOn copyHelp
- //dependsOn releasesTemplates
classpath = sourceSets.main.compileClasspath
main = "com.sun.java.help.search.Indexer"
workingDir = "${helpBuildDir}/${help_dir}"
dependsOn buildResources
dependsOn copyDocs
dependsOn copyHelp
- //dependsOn releasesTemplates
+ dependsOn releasesTemplates
dependsOn convertMdFiles
dependsOn buildIndices
}
-// random block of dependencies
compileJava.dependsOn prepare
run.dependsOn compileJava
-//run.dependsOn prepare
-compileTestJava.dependsOn compileJava //
-compileTestJava.dependsOn buildIndices //
-processResources.dependsOn copyChannelResources //
-processResources.dependsOn copyResources //
-processResources.dependsOn createBuildProperties //
-processResources.dependsOn copyDocs //
-processResources.dependsOn convertMdFiles //
-processResources.dependsOn copyHelp //
-processResources.dependsOn buildIndices //
+compileTestJava.dependsOn compileJava
+
+
+
test {
group = "Verification"
description = "Runs all testTaskN tasks)"
}
}
+task testTask2(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
+ }
+}
+task testTask3(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
+ }
+}
+
/* insert more testTaskNs here -- change N to next digit or other string */
/*
task testTaskN(type: Test) {
showExceptions true
showCauses true
showStackTraces true
-
+ if (test_output) {
+ showStandardStreams true
+ }
info.events = [ TestLogEvent.FAILED ]
}
+ if (OperatingSystem.current().isMacOsX()) {
+ testTask.systemProperty "apple.awt.UIElement", "true"
+ testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
+ }
ignoreFailures = true // Always try to run all tests for all modules
/* END of test tasks results summary */
-/*
task compileLinkCheck(type: JavaCompile) {
options.fork = true
classpath = files("${jalviewDir}/${utils_dir}")
inputs.dir(helpBuildDir)
outputs.file(helpLinksCheckerOutFile)
}
-*/
// import the pubhtmlhelp target
}
}
-// block of dependencies
-//compileTestJava.dependsOn compileLinkCheck //
-//copyChannelResources.dependsOn compileLinkCheck //
-//convertMdFiles.dependsOn compileLinkCheck //
jar {
dependsOn prepare
- dependsOn //linkCheck
+ dependsOn linkCheck
manifest {
attributes "Main-Class": main_class,
"Implementation-Version": JALVIEW_VERSION
}
- def destinationDirectory = "${jalviewDir}/${package_dir}"
- destinationDirectory = file(destinationDirectory)
+ def outputDir = "${jalviewDir}/${package_dir}"
+ destinationDirectory = file(outputDir)
archiveFileName = rootProject.name+".jar"
duplicatesStrategy "EXCLUDE"
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir(sourceSets.main.java.destinationDirectory)
+ inputs.dir(sourceSets.main.java.outputDir)
sourceSets.main.resources.srcDirs.each{ dir ->
inputs.dir(dir)
}
- outputs.file("${destinationDirectory}/${archiveFileName}")
+ outputs.file("${outputDir}/${archiveFileName}")
}
}
+task launcherJar(type: Jar) {
+ manifest {
+ attributes (
+ "Main-Class": shadow_jar_main_class,
+ "Implementation-Version": JALVIEW_VERSION,
+ "Application-Name": applicationName
+ )
+ }
+}
+
shadowJar {
group = "distribution"
description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
if (buildDist) {
dependsOn makeDist
}
- from ("${jalviewDir}/${libDistDir}") {
- include("*.jar")
- }
+
+ def jarFiles = fileTree(dir: "${jalviewDir}/${libDistDir}", include: "*.jar", exclude: "regex.jar").getFiles()
+ def groovyJars = jarFiles.findAll {it1 -> file(it1).getName().startsWith("groovy-swing")}
+ def otherJars = jarFiles.findAll {it2 -> !file(it2).getName().startsWith("groovy-swing")}
+ from groovyJars
+ from otherJars
+
manifest {
- attributes "Implementation-Version": JALVIEW_VERSION,
- "Application-Name": applicationName
+ // shadowJar manifest must inheritFrom another Jar task. Can't set attributes here.
+ inheritFrom(project.tasks.launcherJar.manifest)
+ }
+ // we need to include the groovy-swing Include-Package for it to run in the shadowJar
+ doFirst {
+ def jarFileManifests = []
+ groovyJars.each { jarFile ->
+ def mf = zipTree(jarFile).getFiles().find { it.getName().equals("MANIFEST.MF") }
+ if (mf != null) {
+ jarFileManifests += mf
+ }
+ }
+ manifest {
+ from (jarFileManifests) {
+ eachEntry { details ->
+ if (!details.key.equals("Import-Package")) {
+ details.exclude()
+ }
+ }
+ }
+ }
}
duplicatesStrategy "INCLUDE"
+ // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead
mainClassName = shadow_jar_main_class
mergeServiceFiles()
- archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+ classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
}
dependsOn getdownImagesProcess
}
-task getdownWebsite() {
+task getdownWebsiteBuild() {
group = "distribution"
- description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+ description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer. No digest is created."
dependsOn getdownImages
if (buildDist) {
from s
into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
}
- getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
+ getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${script}"
}
}
task getdownDigest(type: JavaExec) {
group = "distribution"
description = "Digest the getdown website folder"
- dependsOn getdownWebsite
+
+ dependsOn getdownWebsiteBuild
+
doFirst {
classpath = files(getdownLauncher)
}
}
}
+task getdownWebsite {
+ group = "distribution"
+ description = "A task to create the whole getdown channel website dir including digest file"
+
+ dependsOn getdownWebsiteBuild
+ dependsOn getdownDigest
+}
task getdownArchiveBuild() {
group = "distribution"
description = "Put files in the archive dir to go on the website"
- dependsOn getdownWebsite
+ dependsOn getdownWebsiteBuild
def v = "v${JALVIEW_VERSION_UNDERSCORES}"
def vDir = "${getdownArchiveDir}/${v}"
into project.name
def EXCLUDE_FILES=[
+ "dist/*",
"build/*",
"bin/*",
"test-output/",
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
- def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+ def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
from inputFiles
- into destinationDirectory
+ into outputDir
}
dependsOn jalviewjsTransferUnzipAllLibs
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
- def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
- into destinationDirectory
+ into outputDir
def outputFiles = []
rename { filename ->
- outputFiles += "${destinationDirectory}/${filename}"
+ outputFiles += "${outputDir}/${filename}"
null
}
preserve {
dependsOn buildResources
def inputFiles = fileTree(dir: resourcesBuildDir)
- def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
- into destinationDirectory
+ into outputDir
def outputFiles = []
rename { filename ->
- outputFiles += "${destinationDirectory}/${filename}"
+ outputFiles += "${outputDir}/${filename}"
null
}
preserve {
task jalviewjsSyncSiteResources (type: Sync) {
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
- def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
- into destinationDirectory
+ into outputDir
def outputFiles = []
rename { filename ->
- outputFiles += "${destinationDirectory}/${filename}"
+ outputFiles += "${outputDir}/${filename}"
null
}
preserve {
task jalviewjsSyncBuildProperties (type: Sync) {
dependsOn createBuildProperties
def inputFiles = [file(buildProperties)]
- def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
- into destinationDirectory
+ into outputDir
def outputFiles = []
rename { filename ->
- outputFiles += "${destinationDirectory}/${filename}"
+ outputFiles += "${outputDir}/${filename}"
null
}
preserve {
def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
- def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
def prefixFile = "${jsDir}/core/coretop2.js"
def suffixFile = "${jsDir}/core/corebottom2.js"
}
def list = fileTree(dir: j2sDir, includes: filelist)
- def jsfile = "${destinationDirectory}/core${name}.js"
- def zjsfile = "${destinationDirectory}/core${name}.z.js"
+ def jsfile = "${outputDir}/core${name}.js"
+ def zjsfile = "${outputDir}/core${name}.z.js"
jalviewjsCoreClasslists += [
'jsfile': jsfile,
// _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
def stevesoftClasslistName = "_stevesoft"
def stevesoftClasslist = [
- 'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js",
- 'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js",
+ 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
'name': stevesoftClasslistName
]
]
)
def allClasslist = [
- 'jsfile': "${destinationDirectory}/core${allClasslistName}.js",
- 'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js",
+ 'jsfile': "${outputDir}/core${allClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
'list': allJsFiles,
'name': allClasslistName
]
dependsOn jalviewjsBuildAllCores
def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
def inputFile = file(inputFileName)
- def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
def outputFiles = []
jalviewjsCoreClasslists.each { cl ->
- def outputFile = "${destinationDirectory}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+ def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
cl['outputfile'] = outputFile
outputFiles += outputFile
}
dependsOn jalviewjsBuildAllCores
dependsOn jalviewjsPublishCoreTemplates
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
- def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
- into destinationDirectory
+ into outputDir
def outputFiles = []
rename { filename ->
- outputFiles += "${destinationDirectory}/${filename}"
+ outputFiles += "${outputDir}/${filename}"
null
}
preserve {
git://source.jalview.org / jalview.git / commitdiff