X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=535f3b9f4b6961c63a270958b813eb93cdc67e1c;hb=54dfce251873f378d86ae2c937c6dadd32226671;hp=fb242358612acde1bacd82c81809a07d7ce61490;hpb=ccf06ac048c367e28d5e41a569bd95d5a2a77989;p=jalview.git

diff --git a/build.gradle b/build.gradle
index fb24235..535f3b9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -246,7 +246,6 @@ if (JAVA_VERSION.equals("1.8")) {
   throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
 }
 
-
 sourceSets {
 
   main {
@@ -311,7 +310,6 @@ sourceSets {
   }
 }
 
-
 // clover bits
 dependencies {
   if (use_clover) {
@@ -320,13 +318,11 @@ dependencies {
   }
 }
 
-
 configurations {
   cloverRuntime
   cloverRuntime.extendsFrom cloverCompile
 }
 
-
 eclipse {
   project {
     name = eclipse_project_name
@@ -399,13 +395,12 @@ eclipse {
         }
 
         //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
-        sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+        sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
           //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
+            return false // groovy "break" in .each closure
           }
-
           def itPath = it.toString()
           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
@@ -456,7 +451,6 @@ eclipse {
 
 }
 
-
 task cloverInstr() {
   // only instrument source, we build test classes as normal
   inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
@@ -496,6 +490,7 @@ task cloverReport {
     com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
   }
 }
+
 // end clover bits
 
 
@@ -510,7 +505,6 @@ compileJava {
 
 }
 
-
 compileTestJava {
   if (use_clover) {
     dependsOn compileCloverJava
@@ -538,14 +532,12 @@ compileCloverJava {
   classpath += configurations.cloverRuntime
 }
 
-
 clean {
   doFirst {
     delete sourceSets.main.java.outputDir
   }
 }
 
-
 cleanTest {
   doFirst {
     delete sourceSets.test.java.outputDir
@@ -553,14 +545,12 @@ cleanTest {
   }
 }
 
-
 // format is a string like date.format("dd MMMM yyyy")
 def getDate(format) {
   def date = new Date()
   return date.format(format)
 }
 
-
 task setGitVals {
   def hashStdOut = new ByteArrayOutputStream()
   exec {
@@ -582,7 +572,6 @@ task setGitVals {
   outputs.upToDateWhen { false }
 }
 
-
 task createBuildProperties(type: WriteProperties) {
   dependsOn setGitVals
   inputs.dir("${jalviewDir}/${sourceDir}")
@@ -598,7 +587,6 @@ task createBuildProperties(type: WriteProperties) {
   outputs.file(outputFile)
 }
 
-
 def buildingHTML = "${jalviewDir}/${docDir}/building.html"
 task cleanBuildingHTML(type: Delete) {
   doFirst {
@@ -606,7 +594,6 @@ task cleanBuildingHTML(type: Delete) {
   }
 }
 
-
 task convertBuildingMD(type: Exec) {
   dependsOn cleanBuildingHTML
   def buildingMD = "${jalviewDir}/${docDir}/building.md"
@@ -641,14 +628,12 @@ task convertBuildingMD(type: Exec) {
   outputs.file(buildingHTML)
 }
 
-
 clean {
   doFirst {
     delete buildingHTML
   }
 }
 
-
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
   def syncDir = "${classes}/${docDir}"
@@ -657,8 +642,8 @@ task syncDocs(type: Sync) {
 
 }
 
-
 def helpFile = "${classes}/${helpDir}/help.jhm"
+
 task copyHelp(type: Copy) {
   def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
   def outputDir = "${classes}/${helpDir}"
@@ -680,14 +665,12 @@ task copyHelp(type: Copy) {
   outputs.dir(outputDir)
 }
 
-
 task syncLib(type: Sync) {
   def syncDir = "${classes}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
 
-
 task syncResources(type: Sync) {
   from "${jalviewDir}/${resourceDir}"
   include "**/*.*"
@@ -697,7 +680,6 @@ task syncResources(type: Sync) {
   }
 }
 
-
 task prepare {
   dependsOn syncResources
   dependsOn syncDocs
@@ -731,7 +713,6 @@ test {
 
 }
 
-
 task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
@@ -751,7 +732,6 @@ task buildIndices(type: JavaExec) {
   outputs.file("${workingDir}/JavaHelpSearch/TMAP")
 }
 
-
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
   classpath = files("${jalviewDir}/${utilsDir}")
@@ -764,7 +744,6 @@ task compileLinkCheck(type: JavaCompile) {
   outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
 }
 
-
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
 
@@ -825,13 +804,11 @@ jar {
   outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
 }
 
-
 task copyJars(type: Copy) {
   from fileTree(dir: "${classes}", include: "**/*.jar").files
   into "${jalviewDir}/${packageDir}"
 }
 
-
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
@@ -841,7 +818,6 @@ task syncJars(type: Sync) {
   }
 }
 
-
 task makeDist {
   group = "build"
   description = "Put all required libraries in dist"
@@ -854,7 +830,6 @@ task makeDist {
   outputs.dir("${jalviewDir}/${packageDir}")
 }
 
-
 task cleanDist {
   dependsOn cleanPackageDir
   dependsOn cleanTest
@@ -878,7 +853,6 @@ shadowJar {
   minimize()
 }
 
-
 task getdownWebsite() {
   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"
@@ -1059,7 +1033,6 @@ task getdownWebsite() {
   outputs.dir(project.ext.getdownFilesDir)
 }
 
-
 task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
@@ -1073,7 +1046,6 @@ task getdownDigest(type: JavaExec) {
   outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt")
 }
 
-
 task getdown() {
   group = "distribution"
   description = "Create the minimal and full getdown app folder for installers and website and create digest file"
@@ -1096,7 +1068,6 @@ task getdown() {
   }
 }
 
-
 clean {
   doFirst {
     delete project.ext.getdownWebsiteDir
@@ -1104,7 +1075,6 @@ clean {
   }
 }
 
-
 install4j {
   def install4jHomeDir = "/opt/install4j"
   def hostname = "hostname".execute().text.trim()
@@ -1125,7 +1095,6 @@ install4j {
   }
 }
 
-
 def install4jConf
 def macosJavaVMDir
 def macosJavaVMTgz
@@ -1194,7 +1163,6 @@ task copyInstall4jTemplate(type: Copy) {
   }
 }
 
-
 task installers(type: com.install4j.gradle.Install4jTask) {
   group = "distribution"
   description = "Create the install4j installers"
@@ -1220,14 +1188,12 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}")
 }
 
-
 clean {
   doFirst {
     delete install4jConf
   }
 }
 
-
 task sourceDist (type: Tar) {
   
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
@@ -1298,7 +1264,6 @@ task sourceDist (type: Tar) {
 //  }
 }
 
-
 task helppages  {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
@@ -1307,24 +1272,18 @@ task helppages  {
   outputs.dir("${helpOutputDir}")
 }
 
-
 def jalviewjsBuildDir
 def jalviewjsSiteDir
-def jalviewjsTransferSiteJsDir
+def jalviewjsTransferSiteJSDir
 def jalviewjsTransferSiteLibDir
-def jalviewjsTransferSiteSwingJsDir
-def jalviewjsTransferSiteCoreDir
 task jalviewjsSitePath {
   def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
   jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
   jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
-  jalviewjsTransferSiteJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js"
+  jalviewjsTransferSiteJSDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js"
   jalviewjsTransferSiteLibDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib"
-  jalviewjsTransferSiteSwingJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs"
-  jalviewjsTransferSiteCoreDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core"
 }
 
-
 def eclipseWorkspace
 task jalviewjsSetEclipseWorkspace {
   def propKey = "jalviewjs_eclipse_workspace"
@@ -1370,9 +1329,8 @@ task jalviewjsSetEclipseWorkspace {
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
   }
 
-  //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
+  inputs.property(propKey, eclipseWsDir)
   outputs.file(propsFileName)
-  outputs.upToDateWhen { eclipseWorkspace.exists() }
 }
 
 
@@ -1393,7 +1351,7 @@ task jalviewjsEclipsePaths {
     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
-      eclipseRoot += "/eclipse.exe"
+      eclipseRoot += "/eclipse"
     }
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
@@ -1405,7 +1363,7 @@ task jalviewjsEclipsePaths {
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   }
 
-  eclipseVersion = "4.13" // default
+  eclipseVersion = "4.12" // default
   def assumedVersion = true
   if (file(eclipseProduct).exists()) {
     def fis = new FileInputStream(eclipseProduct)
@@ -1415,6 +1373,17 @@ task jalviewjsEclipsePaths {
     fis.close()
     assumedVersion = false
   }
+  /*
+  String[] v = eclipseVersion.split("\\.")
+  def v0 = Integer.valueOf(v[0])
+  def v1 = Integer.valueOf(v[1])
+  if (v0 < 4 || ( v0 == 4 && v1 < 13 )) {
+    eclipseVersionSuffix = "_4.12"
+  } else {
+    eclipseVersionSuffix = "_4.13"
+  }
+  */
+
   
   def propKey = "eclipse_debug"
   eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
@@ -1426,13 +1395,35 @@ task jalviewjsEclipsePaths {
   }
 }
 
-
 task eclipseSetup {
   dependsOn eclipseProject
   dependsOn eclipseClasspath
   dependsOn eclipseJdt
 }
 
+/* using the Copy task below
+task OLDjalviewjsEclipseCopyDropins {
+  dependsOn jalviewjsEclipsePaths
+  dependsOn jalviewjsCleanEclipse
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+  inputFiles += file(jalviewjs_j2s_plugin)
+  def outputDir = "${buildDir}/jalviewjs
+
+  inputs.files inputFiles
+  inputFiles.each { file ->
+    outputs.file("${outputDir}/${file.name}")
+  }
+
+  doLast {
+    inputFiles.each { file ->
+      copy {
+        from file
+        into outputDir
+      }
+    }
+  }
+}
+*/
 
 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
 task jalviewjsEclipseCopyDropins(type: Copy) {
@@ -1446,7 +1437,6 @@ task jalviewjsEclipseCopyDropins(type: Copy) {
   into outputDir
 }
 
-
 // this eclipse -clean doesn't actually work
 task jalviewjsCleanEclipse(type: Exec) {
   dependsOn eclipseSetup
@@ -1466,33 +1456,16 @@ y
   def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
   standardInput = inputByteStream
 }
-
 /* not really working yet
 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
 */
 
-
-task jalviewjsTransferUnzipSwingJs {
-  dependsOn jalviewjsSitePath
-
-  def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
-
-  doLast {
-    copy {
-      from zipTree(file_zip)
-      into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
-    }
-  }
-
-  inputs.file file_zip
-  outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
-}
-
-
+def jalviewjsTransferSiteUnzipDir
 task jalviewjsTransferUnzipLib {
   dependsOn jalviewjsSitePath
 
   def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+  zipFiles += "${jalviewDir}/${jalviewjs_swingjs_zip}"
 
   doLast {
     zipFiles.each { file_zip -> 
@@ -1507,13 +1480,6 @@ task jalviewjsTransferUnzipLib {
   outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
 }
 
-
-task jalviewjsTransferUnzipAllLibs {
-  dependsOn jalviewjsTransferUnzipSwingJs
-  dependsOn jalviewjsTransferUnzipLib
-}
-
-
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   group "JalviewJS"
   description "Create the .j2s file from the j2s.* properties"
@@ -1528,33 +1494,30 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
     if (val != null) {
       if (prop == siteDirProperty) {
         if (!(val.startsWith('/') || val.startsWith("file://") )) {
-          val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
+          val = "${jalviewDir}/${jalviewjsTransferSiteJSDir}/${val}"
         }
         setSiteDir = true
       }
       property(prop,val)
     }
     if (!setSiteDir) { // default site location, don't override specifically set property
-      property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+      property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJSDir}")
     }
   }
   inputs.properties(j2s_props)
   outputs.file(outputFile)
 }
 
-
 task jalviewjsEclipseSetup {
   dependsOn jalviewjsEclipseCopyDropins
   dependsOn jalviewjsSetEclipseWorkspace
   dependsOn jalviewjsCreateJ2sSettings
 }
 
-
-task jalviewjsSyncAllLibs (type: Sync) {
+task jalviewjsSyncLib (type: Sync) {
   dependsOn jalviewjsSitePath
-  dependsOn jalviewjsTransferUnzipAllLibs
+  dependsOn jalviewjsTransferUnzipLib
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
-  inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
@@ -1571,7 +1534,6 @@ task jalviewjsSyncAllLibs (type: Sync) {
   inputs.files inputFiles
 }
 
-
 task jalviewjsSyncResources (type: Sync) {
   dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
@@ -1591,7 +1553,6 @@ task jalviewjsSyncResources (type: Sync) {
   inputs.files inputFiles
 }
 
-
 task jalviewjsSyncSiteResources (type: Sync) {
   dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
@@ -1611,7 +1572,6 @@ task jalviewjsSyncSiteResources (type: Sync) {
   inputs.files inputFiles
 }
 
-
 task jalviewjsSyncBuildProperties (type: Sync) {
   dependsOn jalviewjsSitePath
   dependsOn createBuildProperties
@@ -1632,21 +1592,12 @@ task jalviewjsSyncBuildProperties (type: Sync) {
   inputs.files inputFiles
 }
 
-
 task jalviewjsProjectImport(type: Exec) {
   dependsOn eclipseSetup
   dependsOn jalviewjsEclipsePaths
   dependsOn jalviewjsEclipseSetup
 
-  doFirst {
-    // do not run a headless import when we claim to be in Eclipse
-    if (ECLIPSE_IDE_DEVELOPER.equals("true")) {
-      throw new StopExecutionException("Not running headless import whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'")
-    }
-  }
-
-  //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
-  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
+  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
   if (eclipseDebug) {
@@ -1655,24 +1606,14 @@ task jalviewjsProjectImport(type: Exec) {
   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   inputs.file("${jalviewDir}/.project")
-  outputs.upToDateWhen { 
-    file(projdir).exists()
-  }
+  outputs.upToDateWhen { file(projdir).exists() }
 }
 
-
 task jalviewjsTranspile(type: Exec) {
   dependsOn jalviewjsEclipseSetup 
   dependsOn jalviewjsProjectImport
   dependsOn jalviewjsEclipsePaths
 
-  doFirst {
-    // do not run a headless transpile when we claim to be in Eclipse
-    if (ECLIPSE_IDE_DEVELOPER.equals("true")) {
-      throw new StopExecutionException("Not running headless transpile whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'")
-    }
-  }
-
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
   if (eclipseDebug) {
@@ -1686,7 +1627,7 @@ task jalviewjsTranspile(type: Exec) {
     stdout = new ByteArrayOutputStream()
     stderr = new ByteArrayOutputStream()
 
-    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
     def logOutFile = file(logOutFileName)
     logOutFile.createNewFile()
     logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
@@ -1728,56 +1669,25 @@ DEBUG: ${eclipseDebug}
   doLast {
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
-      //throw new TaskExecutionException("Error during transpilation:\n${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}/${jalviewjs_j2s_transpile_stdout}'")
+      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
     }
   }
 
   inputs.dir("${jalviewDir}/${sourceDir}")
-  outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
-  outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
-}
-
-
-task jalviewjsNoTranspileSyncCore (type: Sync) {
-  dependsOn jalviewjsSitePath
-  dependsOn "jalviewjsNoTranspileBuildAllCores"
-  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
-
-  from inputFiles
-  into outputDir
-  def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
-  }
-  preserve {
-    include "**"
-  }
-  outputs.files outputFiles
-  inputs.files inputFiles
-}
-
-
-task jalviewjsSyncCore (type: Sync) {
-  dependsOn jalviewjsTranspile
-  dependsOn jalviewjsNoTranspileSyncCore
-  dependsOn "jalviewjsBuildAllCores"
+  outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJSDir}")
+  outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJSDir}${jalviewjs_server_resource}").exists() } )
 }
 
-
-// this Copy version of TransferSiteJs will delete anything else in the target dir
-task jalviewjsCopyTransferSiteJs(type: Copy) {
+// this Copy version of TransferSite will delete anything else in the target dir
+task jalviewjsCopyTransferSite(type: Copy) {
   dependsOn jalviewjsTranspile
-  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+  from "${jalviewDir}/${jalviewjsTransferSiteJSDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
-
 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
-task jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) {
-  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+task jalviewjsSyncTransferSite(type: Sync) {
+  from "${jalviewDir}/${jalviewjsTransferSiteJSDir}"
   include "**/*.*"
   into "${jalviewDir}/${jalviewjsSiteDir}"
   preserve {
@@ -1785,56 +1695,39 @@ task jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) {
   }
 }
 
-jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
-jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
-jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
-
-jalviewjsSyncAllLibs.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
-jalviewjsSyncResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
-jalviewjsSyncSiteResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
-
-
-task jalviewjsNoTranspilePrepareSite {
-  dependsOn jalviewjsSyncAllLibs
-  dependsOn jalviewjsSyncResources
-  dependsOn jalviewjsSyncSiteResources
-  dependsOn jalviewjsSyncBuildProperties
-  dependsOn jalviewjsNoTranspileSyncCore
-}
+jalviewjsSyncLib.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSite
 
+jalviewjsSyncLib.mustRunAfter jalviewjsSyncTransferSite
+jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSite
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSite
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSite
 
 task jalviewjsPrepareSite {
   group "JalviewJS"
   description "Prepares the website folder including unzipping files and copying resources"
-  dependsOn jalviewjsSyncAllLibs
+  dependsOn jalviewjsSyncLib
   dependsOn jalviewjsSyncResources
   dependsOn jalviewjsSyncSiteResources
   dependsOn jalviewjsSyncBuildProperties
-  dependsOn jalviewjsSyncCore
 }
 
-
 task jalviewjsBuildSite {
   group "JalviewJS"
   description "Builds the whole website including transpiled code"
-  dependsOn jalviewjsCopyTransferSiteJs
+  dependsOn jalviewjsCopyTransferSite
   dependsOn jalviewjsPrepareSite
 }
 
-
 task cleanJalviewjsSite {
   doFirst {
-    delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
-    delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
-    delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
-    delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+    delete "${jalviewDir}/${jalviewjsTransferSiteJSDir}"
     delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
 
-
 task jalviewjsSiteTar(type: Tar) {
   group "JalviewJS"
   description "Creates a tar.gz file for the website"
@@ -1854,7 +1747,6 @@ task jalviewjsSiteTar(type: Tar) {
   inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
 }
 
-
 task jalviewjsServer {
   group "JalviewJS"
   def filename = "jalviewjsTest.html"
@@ -1894,7 +1786,6 @@ task jalviewjsServer {
   outputs.upToDateWhen({false})
 }
 
-
 task cleanJalviewjsAll {
   group "JalviewJS"
   description "Delete all configuration and build artifacts to do with JalviewJS build"
@@ -1913,7 +1804,6 @@ task cleanJalviewjsAll {
   outputs.upToDateWhen( { false } )
 }
 
-
 task jalviewjs {
   group "JalviewJS"
   description "Build the site"
@@ -1921,244 +1811,44 @@ task jalviewjs {
 }
 
 
-
-task jalviewjsIDE_CopyTransferSiteJs(type: Copy) {
-  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+task jalviewjsIDE_CopyTransferSite(type: Copy) {
+  from "${jalviewDir}/${jalviewjsTransferSiteJSDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
-
-task jalviewjsIDE_j2sFile {
+task jalviewjsIDE_j2s {
   group "00 JalviewJS in Eclipse"
   description "Creates the .j2s file"
   dependsOn jalviewjsCreateJ2sSettings
 }
 
-
 task jalviewjsIDE_AssembleSite {
   group "00 JalviewJS in Eclipse"
   description "Assembles the Eclipse transpiled site and unzips supporting zipfiles"
-  dependsOn jalviewjsIDE_CopyTransferSiteJs
-  dependsOn jalviewjsNoTranspilePrepareSite
+  dependsOn jalviewjsIDE_CopyTransferSite
+  dependsOn jalviewjsPrepareSite
 }
 
-
 task jalviewjsIDE_SiteClean {
   group "00 JalviewJS in Eclipse"
   description "Deletes the Eclipse transpiled site"
   dependsOn cleanJalviewjsSite
 }
 
-
 task jalviewjsIDE_Server {
   group "00 JalviewJS in Eclipse"
   description "Starts a webserver on localhost to test the website"
   dependsOn jalviewjsServer
 }
 
-
 // buildship runs this at import
 task eclipseSynchronizationTask {
   dependsOn eclipseSetup
-  dependsOn jalviewjsIDE_j2sFile
+  dependsOn jalviewjsIDE_j2s
 }
 
-
 // buildship runs this at build time
 task eclipseAutoBuildTask {
-  dependsOn jalviewjsNoTranspileSyncTransferSiteJs
-  dependsOn jalviewjsNoTranspilePrepareSite
-}
-
-
-
-
-
-
-
-
-// closure
-
-def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
-
-  def stdout = new ByteArrayOutputStream()
-  def stderr = new ByteArrayOutputStream()
-
-  def coreFile = file(jsfile)
-  def msg = ""
-  msg = "Generating ${jsfile}"
-  println(msg)
-  logOutFile.createNewFile()
-  logOutFile.append(msg+"\n")
-
-  def coreTop = file(prefixFile)
-  def coreBottom = file(suffixFile)
-  coreFile.getParentFile().mkdirs()
-  coreFile.createNewFile()
-  coreFile.write( coreTop.text )
-  list.each {
-    f ->
-    if (f.exists()) {
-      def t = f.text
-      t.replaceAll("Clazz\\.","Clazz_")
-      t.replaceAll("Class__","Clazz._")
-      coreFile.append( t )
-    } else {
-      msg = "...file '"+f.getPath()+"' does not exist, skipping"
-      println(msg)
-      logOutFile.append(msg+"\n")
-    }
-  }
-  coreFile.append( coreBottom.text )
-
-  msg = "Generating ${zjsfile}"
-  println(msg)
-  logOutFile.append(msg+"\n")
-  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
-  def logErrFOS = logOutFOS
-
-  javaexec {
-    classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
-    args = [ "--js", jsfile, "--js_output_file", zjsfile ]
-
-    msg = "\nRunning '"+commandLine.join(' ')+"'\n"
-    println(msg)
-    logOutFile.append(msg+"\n")
-
-    if (logOutConsole) {
-      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-        new org.apache.tools.ant.util.TeeOutputStream(
-          logOutFOS,
-          stdout),
-        standardOutput)
-        errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
-          new org.apache.tools.ant.util.TeeOutputStream(
-            logErrFOS,
-            stderr),
-          errorOutput)
-    } else {
-      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-        logOutFOS,
-        stdout)
-        errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
-          logErrFOS,
-          stderr)
-    }
-  }
-  msg = "--"
-  println(msg)
-  logOutFile.append(msg+"\n")
-}
-
-
-task jalviewjsNoTranspileBuildAllCores {
-  dependsOn jalviewjsSitePath
-  dependsOn jalviewjsTransferUnzipSwingJs
-
-  def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
-  def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
-  def prefixFile = "${jsDir}/core/coretop2.js"
-  def suffixFile = "${jsDir}/core/corebottom2.js"
-
-  inputs.file prefixFile
-  inputs.file suffixFile
-
-  def classlistFiles = []
-  // add the classlists found int the jalviewjs_classlists_dir
-  fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
-    file ->
-    def name = file.getName() - ".txt"
-    classlistFiles += [
-      'file': file,
-      'name': name
-    ]
-  }
-
-  // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
-  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
-  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': "_jalview" ]
-
-  def classlists = []
-
-  classlistFiles.each {
-    hash ->
-
-    def file = hash['file']
-    if (! file.exists()) {
-      println("...classlist file '"+file.getPath()+"' does not exist, skipping")
-      return false // this is a "continue" in groovy .each closure
-    }
-    def name = hash['name']
-    if (name == null) {
-      name = file.getName() - ".txt"
-    }
-
-    def filelist = []
-    file.eachLine {
-      line ->
-        filelist += line
-    }
-    def list = fileTree(dir: j2sDir, includes: filelist)
-
-    def jsfile = "${outputDir}/core${name}.js"
-    def zjsfile = "${outputDir}/core${name}.z.js"
-
-    classlists += [
-    'jsfile': jsfile,
-    'zjsfile': zjsfile,
-    'list': list
-    ]
-
-    inputs.file(file)
-    inputs.files(list)
-    outputs.file(jsfile)
-    outputs.file(zjsfile)
-  }
-  
-  // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
-  def stevesoftClasslist = [
-    'jsfile': "${outputDir}/core_stevesoft.js",
-    'zjsfile': "${outputDir}/core_stevesoft.z.js",
-    'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js")
-  ]
-  classlists += stevesoftClasslist
-  inputs.files(stevesoftClasslist['list'])
-  outputs.file(stevesoftClasslist['jsfile'])
-  outputs.file(stevesoftClasslist['zjsfile'])
-
-  doFirst {
-    def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
-    logOutFile.getParentFile().mkdirs()
-    logOutFile.createNewFile()
-    logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsNoTranspileBuildAllCores\n----\n")
-
-    classlists.each {
-      jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
-    }
-  }
-
-}
-
-
-jalviewjsNoTranspileBuildAllCores.mustRunAfter jalviewjsTranspile
-
-
-task jalviewjsBuildAllCores {
-  group "JalviewJS"
-  description "Build the core js lib closures listed in the classlists dir"
-  dependsOn jalviewjsTranspile
-  dependsOn jalviewjsNoTranspileBuildAllCores
-}
-
-
-task jalviewjsIDE_BuildAllCores {
-  group "00 JalviewJS in Eclipse"
-  description "Build the core js lib closures listed in the classlists dir"
-  dependsOn jalviewjsNoTranspileBuildAllCores
-}
-
-
-task jalviewjsPublishCoreTemplate {
-  dependsOn jalviewjsBuildAllCores
+  dependsOn jalviewjsSyncTransferSite
+  dependsOn jalviewjsPrepareSite
 }