import org.gradle.internal.os.OperatingSystem
import org.gradle.plugins.ide.eclipse.model.Output
import org.gradle.plugins.ide.eclipse.model.Library
+import java.security.MessageDigest
import groovy.transform.ExternalizeMethods
ext {
jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
// local build environment properties
def localProps = "${jalviewDirAbsolutePath}/local.properties"
}
}
-
// this property set when running Eclipse headlessly
j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
// this property set by Eclipse
} else {
println("HEADLESS BUILD")
}
- /*
+ /* *-/
System.properties.sort { it.key }.each {
key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
}
+ /-* *-/
+ if (false && IN_ECLIPSE) {
+ jalviewDir = jalviewDirAbsolutePath
+ }
*/
+ // essentials
+ bareSourceDir = string(source_dir)
+ sourceDir = string("${jalviewDir}/${bareSourceDir}")
+ resourceDir = string("${jalviewDir}/${resource_dir}")
+ bareTestSourceDir = string(test_source_dir)
+ testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+ // clover
cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
- classes = string("${jalviewDir}/${classesDir}")
+ classesDir = string("${jalviewDir}/${classes_dir}")
if (clover.equals("true")) {
use_clover = true
- classes = string("${buildDir}/${cloverClassesDir}")
+ classesDir = string("${buildDir}/${cloverClassesDir}")
} else {
use_clover = false
- classes = string("${jalviewDir}/${classesDir}")
+ classesDir = string("${jalviewDir}/${classes_dir}")
}
+ classes = classesDir
+
getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
getdownDir = string("")
reportRsyncCmd = false
getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}")
getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${classesDir}/${build_properties_file}")
break
case "RELEASE":
getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_release
- buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
break
exit
} else {
packageDir = string("${ARCHIVEDIR}/${packageDir}")
- buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
exit
} else {
packageDir = string("${ARCHIVEDIR}/${packageDir}")
- buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
buildDist = false
}
reportRsyncCommand = true
getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
break
getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
break
getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${classesDir}/${build_properties_file}")
reportRsyncCommand = true
break
case "LOCAL":
getdown_app_base = file(getdownWebsiteDir).toURI().toString()
getdown_app_dir = getdown_app_dir_alt
- buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+ buildProperties = string("${classesDir}/${build_properties_file}")
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
break
buildingHTML = string("${jalviewDir}/${docDir}/building.html")
- helpFile = string("${classes}/${helpDir}/help.jhm")
+ helpFile = string("${classesDir}/${help_dir}/help.jhm")
+ helpParentDir = string("${jalviewDir}/${help_parent_dir}")
+ helpDir = string("${help_dir}")
+ helpSourceDir = string("${helpParentDir}/${helpDir}")
relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
jalviewjsJalviewCoreName = string(jalviewjs_core_name)
jalviewjsCoreClasslists = []
jalviewjsJalviewTemplateName = string(jalviewjs_name)
+ jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+ jalviewjsJ2sProps = null
eclipseWorkspace = null
eclipseBinary = string("")
sourceSets {
main {
java {
- srcDirs "${jalviewDir}/${sourceDir}"
- outputDir = file(project.classes)
+ srcDirs sourceDir
+ outputDir = file(classesDir)
}
resources {
- srcDirs "${jalviewDir}/${resourceDir}"
+ srcDirs resourceDir
}
jar.destinationDir = file("${jalviewDir}/${packageDir}")
test {
java {
- srcDirs "${jalviewDir}/${testSourceDir}"
+ srcDirs testSourceDir
outputDir = file("${jalviewDir}/${testOutputDir}")
}
def removeTheseToo = []
HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
cp.entries.each { entry ->
+ // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+ // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+ // we add the resources and help/help dirs in as libs afterwards (see below)
if (entry.kind == 'src') {
- if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) {
+ if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
removeTheseToo += entry
} else {
alreadyAddedSrcPath.putAt(entry.path, true)
}
}
+
}
cp.entries.removeAll(removeTheseToo)
- if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
- cp.entries += new Output("${eclipse_bin_dir}/main")
- }
- if (file(helpParentDir).isDirectory()) {
- cp.entries += new Library(fileReference(helpParentDir))
+ //cp.entries += new Output("${eclipse_bin_dir}/main")
+ if (file(helpSourceDir).isDirectory()) {
+ cp.entries += new Library(fileReference(helpSourceDir))
}
if (file(resourceDir).isDirectory()) {
cp.entries += new Library(fileReference(resourceDir))
sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
//don't want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return
+ // don't add dirs to classpath, especially if they don't exist
+ return false // groovy "continue" in .any closure
}
def itPath = it.toString()
if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
if (IN_ECLIPSE) {
// Don't want these to be activated if in headless build
- //synchronizationTasks "eclipseConfiguration"
+ synchronizationTasks "eclipseSynchronizationTask"
autoBuildTasks "eclipseAutoBuildTask"
+
}
}
task cloverInstr() {
// only instrument source, we build test classes as normal
- inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+ inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
outputs.dir cloverInstrDir
doFirst {
task createBuildProperties(type: WriteProperties) {
dependsOn setGitVals
- inputs.dir("${jalviewDir}/${sourceDir}")
- inputs.dir("${jalviewDir}/${resourceDir}")
+ inputs.dir(sourceDir)
+ inputs.dir(resourceDir)
file(buildProperties).getParentFile().mkdirs()
outputFile (buildProperties)
// taking time specific comment out to allow better incremental builds
commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
} else {
println("Cannot find pandoc. Skipping convert building.md to HTML")
- throw new StopExecutionException()
+ throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
}
}
task syncDocs(type: Sync) {
dependsOn convertBuildingMD
- def syncDir = "${classes}/${docDir}"
+ def syncDir = "${classesDir}/${docDir}"
from fileTree("${jalviewDir}/${docDir}")
into syncDir
task copyHelp(type: Copy) {
- def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
- def outputDir = "${classes}/${helpDir}"
+ def inputDir = helpSourceDir
+ def outputDir = "${classesDir}/${helpDir}"
from(inputDir) {
exclude '**/*.gif'
exclude '**/*.jpg'
task syncLib(type: Sync) {
- def syncDir = "${classes}/${libDistDir}"
+ def syncDir = "${classesDir}/${libDistDir}"
from fileTree("${jalviewDir}/${libDistDir}")
into syncDir
}
task syncResources(type: Sync) {
- from "${jalviewDir}/${resourceDir}"
+ from resourceDir
include "**/*.*"
- into "${classes}"
+ into "${classesDir}"
preserve {
include "**"
}
dependsOn copyHelp
classpath = sourceSets.main.compileClasspath
main = "com.sun.java.help.search.Indexer"
- workingDir = "${classes}/${helpDir}"
+ workingDir = "${classesDir}/${helpDir}"
def argDir = "html"
args = [ argDir ]
inputs.dir("${workingDir}/${argDir}")
- outputs.dir("${classes}/doc")
- outputs.dir("${classes}/help")
+ outputs.dir("${classesDir}/doc")
+ outputs.dir("${classesDir}/help")
outputs.file("${workingDir}/JavaHelpSearch/DOCS")
outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
classpath = files("${jalviewDir}/${utilsDir}")
main = "HelpLinksChecker"
workingDir = jalviewDir
- def help = "${classes}/${helpDir}"
- args = [ "${classes}/${helpDir}", "-nointernet" ]
+ def help = "${classesDir}/${helpDir}"
+ args = [ "${classesDir}/${helpDir}", "-nointernet" ]
def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
def errFOS = outFOS
outFOS,
errorOutput)
- inputs.dir("${classes}/${helpDir}")
+ inputs.dir("${classesDir}/${helpDir}")
outputs.file(helpLinksCheckerOutFile)
}
// import the pubhtmlhelp target
ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}"
+ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}"
ant.importBuild "${utilsDir}/publishHelp.xml"
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir("${classes}")
+ inputs.dir(classesDir)
outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
}
task copyJars(type: Copy) {
- from fileTree(dir: "${classes}", include: "**/*.jar").files
+ from fileTree(dir: classesDir, include: "**/*.jar").files
into "${jalviewDir}/${packageDir}"
}
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("${classes}/${helpDir}")
- outputs.dir("${helpOutputDir}")
+ inputs.dir("${classesDir}/${helpDir}")
+ outputs.dir("${buildDir}/distributions/${helpDir}")
}
def eclipseWsDir = propVal
def props = new Properties()
+ def writeProps = true
if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
def ins = new FileInputStream(propsFileName)
props.load(ins)
ins.close()
if (props.getProperty(propKey, null) != null) {
eclipseWsDir = props.getProperty(propKey)
+ writeProps = false
}
}
- def writeProps = false
if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
def tempDir = File.createTempDir()
eclipseWsDir = tempDir.getAbsolutePath()
//inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
outputs.file(propsFileName)
- outputs.upToDateWhen { eclipseWorkspace.exists() }
+ outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
}
group "JalviewJS"
description "Create the .j2s file from the j2s.* properties"
- outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
- def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+ jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
def siteDirProperty = "j2s.site.directory"
def setSiteDir = false
- j2s_props.each { prop, val ->
+ jalviewjsJ2sProps.each { prop, val ->
if (val != null) {
if (prop == siteDirProperty) {
if (!(val.startsWith('/') || val.startsWith("file://") )) {
property(prop,val)
}
if (!setSiteDir) { // default site location, don't override specifically set property
- property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+ property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
}
}
- inputs.properties(j2s_props)
- outputs.file(outputFile)
+ outputFile = jalviewjsJ2sSettingsFileName
+
+ if (! IN_ECLIPSE) {
+ inputs.properties(jalviewjsJ2sProps)
+ outputs.file(jalviewjsJ2sSettingsFileName)
+ }
}
task jalviewjsSyncResources (type: Sync) {
- def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
+ def inputFiles = fileTree(dir: resourceDir)
def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
javaexec {
classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+ maxHeapSize = "2g"
msg = "\nRunning '"+commandLine.join(' ')+"'\n"
println(msg)
}
// _jmol and _jalview cores. Add any other peculiar classlist.txt files here
- classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+ //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
jalviewjsCoreClasslists = []
// _all core
def allClasslistName = "_all"
def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
- //allJsFiles += fileTree(dir: libJ2sDir, include: "**/*.js")
- //allJsFiles += fileTree(dir: swingJ2sDir, include: "**/*.js")
+ allJsFiles += fileTree(
+ dir: libJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+ "**/org/jmol/export/JSExporter.js"
+ ]
+ )
+ allJsFiles += fileTree(
+ dir: swingJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/sun/misc/Unsafe.js",
+ "**/swingjs/jquery/jquery-editable-select.js",
+ "**/swingjs/jquery/j2sComboBox.js",
+ "**/sun/misc/FloatingDecimal.js"
+ ]
+ )
def allClasslist = [
'jsfile': "${outputDir}/core${allClasslistName}.js",
'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
}
def htmlText = """
<p><a href="${url}">JalviewJS Test. <${url}></a></p>
- <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug<</a></p>
+ <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
+ <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
"""
jalviewjsCoreClasslists.each { cl ->
def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
}
+task jalviewjsIDE_checkJ2sPlugin {
+ group "00 JalviewJS in Eclipse"
+ description "Compare the swingjs/net.sf.j2s.core.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+
+ doFirst {
+ def j2sPlugin = string("${jalviewDir}/${jalviewjs_j2s_plugin}")
+ def j2sPluginFile = file(j2sPlugin)
+ def eclipseHome = System.properties["eclipse.home.location"]
+ def copyPlugin = jalviewjs_eclipseIDE_auto_copy_j2s_plugin == "true"
+ def doCopy = false
+ if (eclipseHome == null || ! IN_ECLIPSE) {
+ throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+ }
+ def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+ def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+ if (!eclipseJ2sPluginFile.exists()) {
+ def msg = "Eclipse J2S Plugin is not installed"
+ println(msg)
+ if (! copyPlugin) {
+ throw new GradleException(msg)
+ }
+ doCopy = true
+ }
+
+ def digest = MessageDigest.getInstance("MD5")
+
+ digest.update(j2sPluginFile.text.bytes)
+ def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ digest.update(eclipseJ2sPluginFile.text.bytes)
+ def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+ if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+ def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+ println(msg)
+ if (! copyPlugin) {
+ throw new StopExecutionException(msg)
+ }
+ doCopy = true
+ }
+
+ if (doCopy) {
+ def msg = "WARNING! Auto-copying this commit's j2s plugin version '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n May require an Eclipse restart"
+ println(msg)
+ copy {
+ from j2sPlugin
+ eclipseJ2sPluginFile.getParentFile().mkdirs()
+ into eclipseJ2sPluginFile.getParent()
+ }
+ } else {
+ def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}'"
+ println(msg)
+ }
+ }
+}
+
task jalviewjsIDE_j2sFile {
group "00 JalviewJS in Eclipse"
}
-// buildship runs this at import
-task eclipseConfiguration {
- dependsOn eclipseSetup
+// buildship runs this at import or gradle refresh
+task eclipseSynchronizationTask {
+ //dependsOn eclipseSetup
dependsOn jalviewjsIDE_j2sFile
+ dependsOn jalviewjsIDE_checkJ2sPlugin
}
-// buildship runs this at build time
+// buildship runs this at build time or project refresh
task eclipseAutoBuildTask {
+ //dependsOn jalviewjsIDE_checkJ2sPlugin
dependsOn jalviewjsIDE_PrepareSite
}
git://source.jalview.org / jalview.git / blobdiff