import org.gradle.plugins.ide.eclipse.model.Library
import java.security.MessageDigest
import java.util.regex.Matcher
+import java.util.concurrent.Executors
+import java.util.concurrent.Future
+import java.util.concurrent.ScheduledExecutorService
+import java.util.concurrent.TimeUnit
import groovy.transform.ExternalizeMethods
import groovy.util.XmlParser
import groovy.xml.XmlUtil
id 'application'
id 'eclipse'
id "com.diffplug.gradle.spotless" version "3.28.0"
- id 'com.github.johnrengelman.shadow' version '4.0.3'
+ 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
}
jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
+ jalviewjsTransferSiteMergeDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_merge")
jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
jalviewjsJalviewCoreHtmlFile = string("")
jalviewjsJalviewCoreName = string(jalviewjs_core_name)
eclipseBinary = string("")
eclipseVersion = string("")
eclipseDebug = false
-
+
+ jalviewjsChromiumUserDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}"
+ jalviewjsChromiumProfileDir = "${ext.jalviewjsChromiumUserDir}/${jalviewjs_chromium_profile_name}"
+
// ENDEXT
}
}
}
+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
if (buildDist) {
dependsOn makeDist
}
- from ("${jalviewDir}/${libDistDir}") {
- include("*.jar")
- }
- manifest {
- attributes "Implementation-Version": JALVIEW_VERSION,
- "Application-Name": applicationName
+
+ 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
+
+ // 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 {
+ attributes "Implementation-Version": JALVIEW_VERSION, "Application-Name": applicationName
+ from (jarFileManifests) {
+ eachEntry { details ->
+ if (!details.key.equals("Import-Package")) {
+ details.exclude()
+ }
+ }
+ }
+ }
}
duplicatesStrategy "INCLUDE"
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}/${v}"
into project.name
def EXCLUDE_FILES=[
+ "dist/*",
"build/*",
"bin/*",
"test-output/",
task jalviewjsTransferUnzipLib {
- def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+ def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip").sort()
doLast {
zipFiles.each { file_zip ->
copy {
from zipTree(file_zip)
into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+
+ // rename files in jsmol/j2s/... to swingjs/j2s/...
+ if (file_zip.getName().startsWith("Jmol-j2s-site")) {
+ eachFile { fcd ->
+ // jsmol/... -> swingjs/...
+ def relPathSegments = fcd.relativePath.getSegments()
+ if (relPathSegments[0] == "jsmol") {
+ def newRelPathSegments = relPathSegments
+ newRelPathSegments[0] = "swingjs"
+ fcd.relativePath = new RelativePath(true, newRelPathSegments)
+ }
+ }
+ }
+
+ // The following replace() is needed due to a mismatch in Jmol calls to
+ // colorPtToFFRGB$javajs_util_T3d when only colorPtToFFRGB$javajs_util_T3 is defined
+ // in the SwingJS.zip (github or the one distributed with JSmol)
+ if (file_zip.getName().startsWith("Jmol-SwingJS")) {
+ filter { line ->
+ def l = ""
+ while(!line.equals(l)) {
+ line = line.replace('colorPtToFFRGB$javajs_util_T3d', 'colorPtToFFRGB$javajs_util_T3')
+ l = line
+ }
+ return line
+ }
+ }
}
}
}
task jalviewjsTransferUnzipAllLibs {
- dependsOn jalviewjsTransferUnzipSwingJs
dependsOn jalviewjsTransferUnzipLib
+ dependsOn jalviewjsTransferUnzipSwingJs
}
task jalviewjsSyncAllLibs (type: Sync) {
dependsOn jalviewjsTransferUnzipAllLibs
- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+ def inputFiles = []
+ inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
include "**"
}
- // should this be exclude really ?
+ // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
duplicatesStrategy "INCLUDE"
outputs.files outputFiles
}
+task jalviewjsTranserSiteMergeLibDirs (type: Sync) {
+ dependsOn jalviewjsTransferUnzipAllLibs
+ dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTranspile
+
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+ // merge swingjs lib last
+ inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+
+ exclude "**/*.html"
+ exclude "**/*.htm"
+
+ // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
+ duplicatesStrategy "INCLUDE"
+
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsTranserSiteMergeSwingDir (type: Sync) {
+ dependsOn jalviewjsTransferUnzipAllLibs
+ dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTranspile
+
+ // merge jalview files very last
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+
+ // should this be exclude really ? No, jalview dir should be transferred last (and overwrite)
+ duplicatesStrategy "INCLUDE"
+
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+task jalviewjsTranserSiteMergeDirs {
+ dependsOn jalviewjsTranserSiteMergeLibDirs
+ dependsOn jalviewjsTranserSiteMergeSwingDir
+}
+
+
def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
def stdout = new ByteArrayOutputStream()
def coreTop = file(prefixFile)
def coreBottom = file(suffixFile)
+ def missingFiles = []
coreFile.getParentFile().mkdirs()
coreFile.createNewFile()
coreFile.write( coreTop.getText("UTF-8") )
msg = "...file '"+f.getPath()+"' does not exist, skipping"
println(msg)
logOutFile.append(msg+"\n")
+ missingFiles += f
}
}
coreFile.append( coreBottom.getText("UTF-8") )
classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
main = "com.google.javascript.jscomp.CommandLineRunner"
jvmArgs = [ "-Dfile.encoding=UTF-8" ]
- args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+ args = [ "--compilation_level", jalviewjs_closure_compiler_optimization_level, "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
maxHeapSize = "2g"
msg = "\nRunning '"+commandLine.join(' ')+"'\n"
}
}
msg = "--"
+ if (missingFiles.size() > 0) {
+ msg += "\n!!! These files were listed but missing:\n"
+ missingFiles.each { file -> msg += "!!! " + file.getPath() + "\n" }
+ msg = "--"
+ }
println(msg)
logOutFile.append(msg+"\n")
}
task jalviewjsBuildAllCores {
group "JalviewJS"
description "Build the core js lib closures listed in the classlists dir"
- dependsOn jalviewjsTranspile
- dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTranserSiteMergeDirs
- def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
- def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
- def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
- def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+ def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
+ def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
+ def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
+ def jsDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_js_subdir}"
def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
def prefixFile = "${jsDir}/core/coretop2.js"
def suffixFile = "${jsDir}/core/corebottom2.js"
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")
task jalviewjsPublishCoreTemplates {
dependsOn jalviewjsBuildAllCores
+
def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
def inputFile = file(inputFileName)
def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
task jalviewjsSyncCore (type: Sync) {
dependsOn jalviewjsBuildAllCores
dependsOn jalviewjsPublishCoreTemplates
+
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
// this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteMergeDir(type: Copy) {
+ dependsOn jalviewjsTranserSiteMergeDirs
+
+ from "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+}
+
+
+// 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}"
}
task jalviewjsPrepareSite {
group "JalviewJS"
description "Prepares the website folder including unzipping files and copying resources"
- dependsOn jalviewjsSyncAllLibs
+ //dependsOn jalviewjsSyncAllLibs // now using jalviewjsCopyTransferSiteMergeDir
dependsOn jalviewjsSyncResources
dependsOn jalviewjsSyncSiteResources
dependsOn jalviewjsSyncBuildProperties
task jalviewjsBuildSite {
group "JalviewJS"
description "Builds the whole website including transpiled code"
- dependsOn jalviewjsCopyTransferSiteJs
+ dependsOn jalviewjsCopyTransferSiteMergeDir
dependsOn jalviewjsPrepareSite
}
}
-task jalviewjs {
- group "JalviewJS"
- description "Build the site"
- dependsOn jalviewjsBuildSite
-}
-
-
task jalviewjsCopyStderrLaunchFile(type: Copy) {
from file(jalviewjs_stderr_launch)
into jalviewjsSiteDir
outputs.file jalviewjsStderrLaunchFilename
}
+task cleanJalviewjsChromiumUserDir {
+ doFirst {
+ delete jalviewjsChromiumUserDir
+ }
+ outputs.dir jalviewjsChromiumUserDir
+ // always run when depended on
+ outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
+}
+
task jalviewjsChromiumProfile {
- def profileDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}/${jalviewjs_chromium_profile_name}"
- def firstRun = file("${profileDir}/First Run")
+ dependsOn cleanJalviewjsChromiumUserDir
+ mustRunAfter cleanJalviewjsChromiumUserDir
+
+ def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
doFirst {
- mkdir profileDir
+ mkdir jalviewjsChromiumProfileDir
firstRun.text = ""
}
-
outputs.file firstRun
}
-task jalviewjsLaunchTest(type: Exec) {
+task jalviewjsLaunchTest {
group "Test"
description "Check JalviewJS opens in a browser"
dependsOn jalviewjsBuildSite
dependsOn jalviewjsCopyStderrLaunchFile
dependsOn jalviewjsChromiumProfile
- def chromiumBinary = jalviewjs_chromium_binary
+ def macOS = OperatingSystem.current().isMacOsX()
+ def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
if (chromiumBinary.startsWith("~/")) {
chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
}
def stdout
def stderr
doFirst {
- def exec = file(chromiumBinary)
- if (!exec.exists()) {
- throw new GradleException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
- }
+ def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
+ def binary = file(chromiumBinary)
+ if (!binary.exists()) {
+ throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
+ }
stdout = new ByteArrayOutputStream()
stderr = new ByteArrayOutputStream()
+ def execStdout
+ def execStderr
if (jalviewjs_j2s_to_console.equals("true")) {
- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ execStdout = new org.apache.tools.ant.util.TeeOutputStream(
stdout,
System.out)
- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ execStderr = new org.apache.tools.ant.util.TeeOutputStream(
stderr,
System.err)
} else {
- standardOutput = stdout
- errorOutput = stderr
+ execStdout = stdout
+ execStderr = stderr
+ }
+ // macOS not running properly with timeout arguments
+ def execArgs = macOS ? [] : [
+ "--virtual-time-budget=${timeoutms}",
+ ]
+ execArgs += [
+ "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
+ "--headless=new",
+ "--disable-gpu",
+ "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
+ "--profile-directory=${jalviewjs_chromium_profile_name}",
+ "--allow-file-access-from-files",
+ "--enable-logging=stderr",
+ "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
+ ]
+
+ if (true || macOS) {
+ ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
+ Future f1 = executor.submit(
+ () -> {
+ exec {
+ standardOutput = execStdout
+ errorOutput = execStderr
+ executable(chromiumBinary)
+ args(execArgs)
+ println "COMMAND: '"+commandLine.join(" ")+"'"
+ }
+ executor.shutdownNow()
+ }
+ )
+
+ def noChangeBytes = 0
+ def noChangeIterations = 0
+ executor.scheduleAtFixedRate(
+ () -> {
+ String stderrString = stderr.toString()
+ // shutdown the task if we have a success string
+ if (stderrString.contains(jalviewjs_desktop_init_string)) {
+ f1.cancel()
+ Thread.sleep(1000)
+ executor.shutdownNow()
+ }
+ // if no change in stderr for 10s then also end
+ if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
+ executor.shutdownNow()
+ }
+ if (stderrString.length() == noChangeBytes) {
+ noChangeIterations++
+ } else {
+ noChangeBytes = stderrString.length()
+ noChangeIterations = 0
+ }
+ },
+ 1, 1, TimeUnit.SECONDS)
+
+ executor.schedule(new Runnable(){
+ public void run(){
+ f1.cancel()
+ executor.shutdownNow()
+ }
+ }, timeoutms, TimeUnit.MILLISECONDS)
+
+ executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
+ executor.shutdownNow()
}
- }
- executable(chromiumBinary)
- args([
- "--no-sandbox",
- "--disable-gpu",
- "--headless=new",
- "--timeout=60000",
- "--virtual-time-budget=60000",
- "--user-data-dir=${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
- "--profile-directory=${jalviewjs_chromium_profile_name}",
- "--allow-file-access-from-files",
- "--enable-logging=stderr",
- jalviewjsStderrLaunchFilename
- ])
+ }
doLast {
def found = false
if (!found) {
throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
}
- }
+ }
+}
+
+
+task jalviewjs {
+ group "JalviewJS"
+ description "Build the JalviewJS site and run the launch test"
+ dependsOn jalviewjsBuildSite
+ dependsOn jalviewjsLaunchTest
}
git://source.jalview.org / jalview.git / blobdiff