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)
showExceptions true
showCauses true
showStackTraces true
- showStandardStreams true
-
+ if (test_output) {
+ showStandardStreams true
+ }
info.events = [ TestLogEvent.FAILED ]
}
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"
into project.name
def EXCLUDE_FILES=[
+ "dist/*",
"build/*",
"bin/*",
"test-output/",
copy {
from zipTree(file_zip)
into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+ exclude "**.html"
+ exclude "**.htm"
}
}
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}"
+ exclude "**.html"
+ exclude "**.htm"
+
+ // 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().equals("Jmol-SwingJS.zip")) {
+ 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
}
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 jalviewjsTranserSiteMergeDirs (type: Sync) {
+ dependsOn jalviewjsTransferUnzipAllLibs
+ dependsOn jalviewjsTransferUnzipSwingJs
+ dependsOn jalviewjsTranspile
+
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+ // merge swingjs lib last
+ inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+ // merge jalview files very last
+ 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, swingjs dir should be transferred last (and overwrite)
+ duplicatesStrategy "INCLUDE"
+
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
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}/${jalviewjsSiteDir}"
}
task jalviewjsPrepareSite {
group "JalviewJS"
description "Prepares the website folder including unzipping files and copying resources"
- dependsOn jalviewjsSyncAllLibs
+ //dependsOn jalviewjsSyncAllLibs // now using jalviewjsCopyTransferSiteMergeDir
dependsOn jalviewjsSyncResources
dependsOn jalviewjsSyncSiteResources
dependsOn jalviewjsSyncBuildProperties
task jalviewjsBuildSite {
group "JalviewJS"
description "Builds the whole website including transpiled code"
- dependsOn jalviewjsCopyTransferSiteJs
+ dependsOn jalviewjsCopyTransferSiteMergeDir
dependsOn jalviewjsPrepareSite
}
execStdout = stdout
execStderr = stderr
}
- def execArgs = [
+ // macOS not running properly with timeout arguments
+ def execArgs = macOS ? [] : [
+ "--virtual-time-budget=${timeoutms}",
+ ]
+ execArgs += [
"--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
"--headless=new",
"--disable-gpu",
- "--timeout=${timeoutms}",
- "--virtual-time-budget=${timeoutms}",
"--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
"--profile-directory=${jalviewjs_chromium_profile_name}",
"--allow-file-access-from-files",
git://source.jalview.org / jalview.git / blobdiff