X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=1f1bc2f6d9ba7c01880c10075b5f210955af0fad;hb=d29795758c856e03fcec7d0d313e968a7185455c;hp=4080744ee567512d27ca95def02a4836fa6b99fd;hpb=0ddf418d7540e715e6f0d112e2375fb1d7f1f294;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 4080744..1f1bc2f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -2,6 +2,7 @@ import org.apache.tools.ant.filters.ReplaceTokens
 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
 
@@ -42,6 +43,7 @@ def string(Object o) {
 
 ext {
   jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+  jalviewDirRelativePath = jalviewDir
 
   // local build environment properties
   def localProps = "${jalviewDirAbsolutePath}/local.properties"
@@ -64,7 +66,6 @@ ext {
     }
   }
 
-
   // this property set when running Eclipse headlessly
   j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
   // this property set by Eclipse
@@ -82,27 +83,47 @@ ext {
   } else {
     println("HEADLESS BUILD")
   }
-  /*
+  
+  J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+  if (J2S_ENABLED) {
+    println("J2S ENABLED")
+  }
+  
+  /* *-/
   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}/${JAVA_VERSION}")
   getdownDir = string("")
   reportRsyncCmd = false
   buildDist = true
-  buildProperties = build_properties_file
+  buildProperties = string("${resourceDir}/${build_properties_file}")
   getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
   switch (CHANNEL) {
 
@@ -112,7 +133,7 @@ ext {
     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}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     break
 
     case "RELEASE":
@@ -120,8 +141,13 @@ ext {
     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}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     reportRsyncCommand = true
+    // Don't ignore transpile errors for release build
+    if (jalviewjs_ignore_transpile_errors.equals("true")) {
+      jalviewjs_ignore_transpile_errors = "false"
+      println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+    }
     break
 
     case "ARCHIVE":
@@ -134,7 +160,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${resource_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -150,7 +176,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${resource_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -162,7 +188,7 @@ ext {
     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}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -171,8 +197,13 @@ ext {
     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}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     reportRsyncCommand = true
+    // Don't ignore transpile errors for release build
+    if (jalviewjs_ignore_transpile_errors.equals("true")) {
+      jalviewjs_ignore_transpile_errors = "false"
+      println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+    }
     break
 
     case ~/^SCRATCH(|-[-\w]*)$/:
@@ -180,14 +211,14 @@ ext {
     getdownDir = string("${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("${resourceDir}/${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}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
     break
 
@@ -277,7 +308,10 @@ ext {
 
 
   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())
@@ -295,11 +329,22 @@ ext {
   jalviewjsJalviewCoreName = string(jalviewjs_core_name)
   jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
+  jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+  jalviewjsJ2sProps = null
 
+  eclipseJavaVersion = "55"
+  jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+  if (IN_ECLIPSE) {
+    //def eclipseJavaVersion = System.property["java.class.version"]
+    if (Float.parseFloat(eclipseJavaVersion) >= 55 && file(jalviewjs_j2s_plugin_j11).exists()) { // 55 is Java 11
+      jalviewjsJ2sPlugin = jalviewjs_j2s_plugin_j11
+    }
+  }
   eclipseWorkspace = null
   eclipseBinary = string("")
   eclipseVersion = string("")
   eclipseDebug = false
+  eclipseJavaVersion = string("")
   // ENDEXT
 }
 
@@ -307,12 +352,12 @@ ext {
 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}")
@@ -343,7 +388,7 @@ sourceSets {
 
   test {
     java {
-      srcDirs "${jalviewDir}/${testSourceDir}"
+      srcDirs testSourceDir
       outputDir = file("${jalviewDir}/${testOutputDir}")
     }
 
@@ -411,21 +456,23 @@ eclipse {
         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))
@@ -436,8 +483,8 @@ eclipse {
         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}/")) {
@@ -490,6 +537,7 @@ eclipse {
     javaRuntimeName = eclipse_java_runtime_name
 
     // add in jalview project specific properties/preferences into eclipse core preferences
+    // and also the codestyle XML file
     file {
       withProperties { props ->
         def jalview_prefs = new Properties()
@@ -501,6 +549,22 @@ eclipse {
             props.putAt(t, v)
           }
         }
+        // codestyle file -- overrides previous formatter prefs
+        def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
+        if (csFile.exists()) {
+          XmlParser parser = new XmlParser()
+          def profiles = parser.parse(csFile)
+          def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
+          if (profile != null) {
+            profile.'setting'.each { s ->
+              def id = s.'@id'
+              def value = s.'@value'
+              if (id != null && value != null) {
+                props.putAt(id, value)
+              }
+            }
+          }
+        }
       }
     }
 
@@ -508,15 +572,16 @@ eclipse {
 
   if (IN_ECLIPSE) {
     // Don't want these to be activated if in headless build
-    //synchronizationTasks "eclipseConfiguration"
-    autoBuildTasks "eclipseAutoBuildTask"
+    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 {
@@ -641,9 +706,11 @@ task setGitVals {
 
 
 task createBuildProperties(type: WriteProperties) {
+  group = "build"
+  description = "Create the ${buildProperties} file"
   dependsOn setGitVals
-  inputs.dir("${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
@@ -656,6 +723,13 @@ task createBuildProperties(type: WriteProperties) {
 }
 
 
+clean {
+  doFirst {
+    delete buildProperties
+  }
+}
+
+
 task cleanBuildingHTML(type: Delete) {
   doFirst {
     delete buildingHTML
@@ -686,7 +760,7 @@ task convertBuildingMD(type: Exec) {
         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")
     }
   }
 
@@ -707,7 +781,7 @@ clean {
 
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
-  def syncDir = "${classes}/${docDir}"
+  def syncDir = "${classesDir}/${docDir}"
   from fileTree("${jalviewDir}/${docDir}")
   into syncDir
 
@@ -715,8 +789,8 @@ task syncDocs(type: Sync) {
 
 
 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'
@@ -744,16 +818,17 @@ task copyHelp(type: Copy) {
 
 
 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}"
+  dependsOn createBuildProperties
+  from resourceDir
   include "**/*.*"
-  into "${classes}"
+  into "${classesDir}"
   preserve {
     include "**"
   }
@@ -798,13 +873,13 @@ task buildIndices(type: JavaExec) {
   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("${workingDir}/JavaHelpSearch/OFFSETS")
@@ -834,8 +909,8 @@ task linkCheck(type: JavaExec) {
   classpath = files("${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
@@ -846,13 +921,13 @@ task linkCheck(type: JavaExec) {
     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"
 
 
@@ -862,6 +937,7 @@ task cleanPackageDir(type: Delete) {
   }
 }
 
+
 jar {
   dependsOn linkCheck
   dependsOn buildIndices
@@ -883,13 +959,13 @@ jar {
   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}"
 }
 
@@ -1379,8 +1455,8 @@ task helppages  {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
   
-  inputs.dir("${classes}/${helpDir}")
-  outputs.dir("${helpOutputDir}")
+  inputs.dir("${classesDir}/${helpDir}")
+  outputs.dir("${buildDir}/distributions/${helpDir}")
 }
 
 
@@ -1405,16 +1481,17 @@ task jalviewjsSetEclipseWorkspace {
   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()
@@ -1448,7 +1525,7 @@ task jalviewjsSetEclipseWorkspace {
 
   //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() }
 }
 
 
@@ -1507,6 +1584,15 @@ task jalviewjsEclipsePaths {
 }
 
 
+task printProperties {
+  group "Debug"
+  description "Output to console all System.properties"
+  doFirst {
+    System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
+  }
+}
+
+
 task eclipseSetup {
   dependsOn eclipseProject
   dependsOn eclipseClasspath
@@ -1519,7 +1605,7 @@ task jalviewjsEclipseCopyDropins(type: Copy) {
   dependsOn jalviewjsEclipsePaths
 
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
-  inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
+  inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
   def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
   from inputFiles
@@ -1594,11 +1680,10 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   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://") )) {
@@ -1609,11 +1694,15 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
       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)
+  }
 }
 
 
@@ -1646,7 +1735,7 @@ task jalviewjsSyncAllLibs (type: Sync) {
 
 
 task jalviewjsSyncResources (type: Sync) {
-  def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
+  def inputFiles = fileTree(dir: resourceDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
@@ -1807,7 +1896,12 @@ DEBUG: ${eclipseDebug}
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
       //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
-      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+      if (jalviewjs_ignore_transpile_errors.equals("true")) {
+        println("IGNORING TRANSPILE ERRORS")
+        println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+      } else {
+        throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+      }
     }
   }
 
@@ -1857,6 +1951,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
   javaexec {
     classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
     args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+    maxHeapSize = "2g"
 
     msg = "\nRunning '"+commandLine.join(' ')+"'\n"
     println(msg)
@@ -1917,7 +2012,7 @@ task jalviewjsBuildAllCores {
   }
 
   // _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 = []
@@ -1927,7 +2022,7 @@ task jalviewjsBuildAllCores {
 
     def file = hash['file']
     if (! file.exists()) {
-      println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+      //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
       return false // this is a "continue" in groovy .each closure
     }
     def name = hash['name']
@@ -1974,15 +2069,34 @@ task jalviewjsBuildAllCores {
   // _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",
     'list': allJsFiles,
     'name': allClasslistName
   ]
-  jalviewjsCoreClasslists += allClasslist
+  // not including this version of "all" core at the moment
+  //jalviewjsCoreClasslists += allClasslist
   inputs.files(allClasslist['list'])
   outputs.file(allClasslist['jsfile'])
   outputs.file(allClasslist['zjsfile'])
@@ -2119,12 +2233,19 @@ task jalviewjsBuildSite {
 }
 
 
-task cleanJalviewjsSite {
+task cleanJalviewjsTransferSite {
   doFirst {
     delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
     delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
     delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
     delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+  }
+}
+
+
+task cleanJalviewjsSite {
+  dependsOn cleanJalviewjsTransferSite
+  doFirst {
     delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
@@ -2179,7 +2300,8 @@ task jalviewjsServer {
     }
     def htmlText = """
       <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
-      <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
+      <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&gt;</a></p>
+      <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. &lt;${url}?j2sdebug&gt;</a></p>
       """
     jalviewjsCoreClasslists.each { cl ->
       def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
@@ -2216,6 +2338,67 @@ task cleanJalviewjsAll {
 }
 
 
+task jalviewjsIDE_checkJ2sPlugin {
+  group "00 JalviewJS in Eclipse"
+  description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+
+  doFirst {
+    def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+    def j2sPluginFile = file(j2sPlugin)
+    def eclipseHome = System.properties["eclipse.home.location"]
+    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 (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin"
+      System.err.println(msg)
+      throw new StopExecutionException(msg)
+    }
+
+    def digest = MessageDigest.getInstance("MD5")
+
+    digest.update(j2sPluginFile.text.bytes)
+    def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+    //digest.update(eclipseJ2sPluginFile.text.bytes)
+    def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+     
+    if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+      def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+      System.err.println(msg)
+      throw new StopExecutionException(msg)
+    } else {
+      def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+      println(msg)
+    }
+  }
+}
+
+task jalviewjsIDE_copyJ2sPlugin {
+  group "00 JalviewJS in Eclipse"
+  description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
+
+  doFirst {
+    def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+    def j2sPluginFile = file(j2sPlugin)
+    def eclipseHome = System.properties["eclipse.home.location"]
+    if (eclipseHome == null || ! IN_ECLIPSE) {
+      throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
+    }
+    def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+    def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+    def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
+    System.err.println(msg)
+    copy {
+      from j2sPlugin
+      eclipseJ2sPluginFile.getParentFile().mkdirs()
+      into eclipseJ2sPluginFile.getParent()
+    }
+  }
+}
+
 
 task jalviewjsIDE_j2sFile {
   group "00 JalviewJS in Eclipse"
@@ -2231,9 +2414,7 @@ task jalviewjsIDE_SyncCore {
 }
 
 
-task jalviewjsIDE_PrepareSite {
-  group "00 JalviewJS in Eclipse"
-  description "Sync libs and resources to site dir, but not closure cores"
+task jalviewjsIDE_SyncSiteAll {
   dependsOn jalviewjsSyncAllLibs
   dependsOn jalviewjsSyncResources
   dependsOn jalviewjsSyncSiteResources
@@ -2241,6 +2422,18 @@ task jalviewjsIDE_PrepareSite {
 }
 
 
+cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+
+
+task jalviewjsIDE_PrepareSite {
+  group "00 JalviewJS in Eclipse"
+  description "Sync libs and resources to site dir, but not closure cores"
+
+  dependsOn jalviewjsIDE_SyncSiteAll
+  dependsOn cleanJalviewjsTransferSite
+}
+
+
 task jalviewjsIDE_AssembleSite {
   group "00 JalviewJS in Eclipse"
   description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
@@ -2262,16 +2455,22 @@ task jalviewjsIDE_Server {
 }
 
 
-// buildship runs this at import
-task eclipseConfiguration {
-  dependsOn eclipseSetup
-  dependsOn jalviewjsIDE_j2sFile
+// buildship runs this at import or gradle refresh
+task eclipseSynchronizationTask {
+  //dependsOn eclipseSetup
+  dependsOn createBuildProperties
+  if (J2S_ENABLED) {
+    dependsOn jalviewjsIDE_j2sFile
+    dependsOn jalviewjsIDE_checkJ2sPlugin
+    dependsOn jalviewjsIDE_PrepareSite
+  }
 }
 
 
-// buildship runs this at build time
+// buildship runs this at build time or project refresh
 task eclipseAutoBuildTask {
-  dependsOn jalviewjsIDE_PrepareSite
+  //dependsOn jalviewjsIDE_checkJ2sPlugin
+  //dependsOn jalviewjsIDE_PrepareSite
 }