From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 15 Mar 2024 12:39:49 +0000 (+0000)
Subject: JAL-4320 Improve the inputs and outputs dependencies of jalviewjs build tasks
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=19aa434e7ce0085dcb4f04173df53efa506533ae;p=jalview.git

JAL-4320 Improve the inputs and outputs dependencies of jalviewjs build tasks
---

diff --git a/build.gradle b/build.gradle
index 51c6ef2..89df34d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -14,6 +14,7 @@ import java.util.concurrent.Executors
 import java.util.concurrent.Future
 import java.util.concurrent.ScheduledExecutorService
 import java.util.concurrent.TimeUnit
+import java.nio.file.Path
 import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
@@ -559,12 +560,12 @@ ext {
   if (IN_ECLIPSE) {
     jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
   } else {
-    jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
+    jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/js")
   }
-  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")
+  jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/lib")
+  jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/swingjs")
+  jalviewjsTransferSiteMergeDir = string("${jalviewjsBuildDir}/merge/${jalviewjs_site_dir}")
+  jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/core")
   jalviewjsJalviewCoreHtmlFile = string("")
   jalviewjsJalviewCoreName = string(jalviewjs_core_name)
   jalviewjsCoreClasslists = []
@@ -3438,68 +3439,46 @@ jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
 */
 
 
-task jalviewjsTransferUnzipSwingJs {
-  def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
-
-  doLast {
-    copy {
-      from zipTree(file_zip)
-      into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
-    }
-  }
-
-  inputs.file file_zip
-  outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+task jalviewjsTransferUnzipSwingJs(type: Copy) {
+  from zipTree( "${jalviewDir}/${jalviewjs_swingjs_zip}" )
+  into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
 }
 
 
-task jalviewjsTransferUnzipLib {
+task jalviewjsTransferUnzipLib(type: Copy) {
   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)
-            }
-          }
+  zipFiles.each { file_zip ->
+    from zipTree(file_zip)
+
+    // 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
-          }
+    // 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
       }
     }
   }
-
-  inputs.files zipFiles
-  outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
-}
-
-
-task jalviewjsTransferUnzipAllLibs {
-  dependsOn jalviewjsTransferUnzipLib
-  dependsOn jalviewjsTransferUnzipSwingJs
+  into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
 }
 
 
@@ -3540,47 +3519,81 @@ task jalviewjsEclipseSetup {
 }
 
 
-task jalviewjsSyncAllLibs (type: Sync) {
-  dependsOn jalviewjsTransferUnzipAllLibs
-  def inputFiles = []
-  inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
-  inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+task jalviewjsSyncLibs (type: Sync) {
+  dependsOn jalviewjsTransferUnzipLib
+  dependsOn jalviewjsTransferUnzipSwingJs
+
+  def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+  def inputFiles = fileTree(dir: inputDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
   into outputDir
   def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
+  inputFiles.each{ file ->
+    def rfile = inputDir.toPath().relativize(file.toPath())
+    def ofile = new File("${outputDir}/${rfile}")
+    outputFiles += "${ofile}"
   }
   preserve {
-    include "**"
+    include "**/*"
+  }
+
+  duplicatesStrategy "EXCLUDE"
+
+  outputs.files outputFiles
+  inputs.files inputFiles
+}
+
+task jalviewjsSyncSwingJS (type: Sync) {
+  dependsOn jalviewjsTransferUnzipSwingJs
+  mustRunAfter jalviewjsSyncLibs
+
+  def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+  def inputFiles = fileTree(dir: inputDir)
+  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+  from inputFiles
+  into outputDir
+  def outputFiles = []
+  inputFiles.each{ file ->
+    def rfile = inputDir.toPath().relativize(file.toPath())
+    def ofile = new File("${outputDir}/${rfile}")
+    outputFiles += "${ofile}"
+  }
+  preserve {
+    include "**/*"
   }
 
-  // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
   duplicatesStrategy "INCLUDE"
 
   outputs.files outputFiles
   inputs.files inputFiles
 }
 
+task jalviewjsSyncAllLibs {
+  dependsOn jalviewjsSyncLibs
+  dependsOn jalviewjsSyncSwingJS
+}
+
 
 task jalviewjsSyncResources (type: Sync) {
   dependsOn buildResources
 
-  def inputFiles = fileTree(dir: resourcesBuildDir)
+  def inputDir = file(resourcesBuildDir)
+  def inputFiles = fileTree(dir: inputDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
   into outputDir
   def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
+  inputFiles.each{ file ->
+    def rfile = inputDir.toPath().relativize(file.toPath())
+    def ofile = new File("${outputDir}/${rfile}")
+    outputFiles += "${ofile}"
   }
   preserve {
-    include "**"
+    include "**/*"
   }
   outputs.files outputFiles
   inputs.files inputFiles
@@ -3588,19 +3601,22 @@ task jalviewjsSyncResources (type: Sync) {
 
 
 task jalviewjsSyncSiteResources (type: Sync) {
-  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+  def inputDir = file("${jalviewDir}/${jalviewjs_site_resource_dir}")
+  def inputFiles = fileTree(dir: inputDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
   into outputDir
   def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
+  inputFiles.each{ file ->
+    def rfile = inputDir.toPath().relativize(file.toPath())
+    def ofile = new File("${outputDir}/${rfile}")
+    outputFiles += "${ofile}"
   }
   preserve {
-    include "**"
+    include "**/*"
   }
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
@@ -3608,19 +3624,24 @@ task jalviewjsSyncSiteResources (type: Sync) {
 
 task jalviewjsSyncBuildProperties (type: Sync) {
   dependsOn createBuildProperties
-  def inputFiles = [file(buildProperties)]
+
+  def f = file(buildProperties)
+  def inputDir = f.getParentFile()
+  def inputFiles = [f]
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
   into outputDir
   def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
+  inputFiles.each{ file ->
+    def rfile = inputDir.toPath().relativize(file.toPath())
+    def ofile = new File("${outputDir}/${rfile}")
+    outputFiles += "${ofile}"
   }
   preserve {
-    include "**"
+    include "**/*"
   }
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
@@ -3642,7 +3663,8 @@ task jalviewjsProjectImport(type: Exec) {
   }
 
   //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/${eclipse_project_name}"
+
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
   if (eclipseDebug) {
@@ -3652,19 +3674,22 @@ task jalviewjsProjectImport(type: Exec) {
   if (!IN_ECLIPSE) {
     args += [ "-D${j2sHeadlessBuildProperty}=true" ]
     args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
+    inputs.file("${jalviewjsJ2sAltSettingsFileName}")
   }
 
-  inputs.file("${jalviewDir}/.project")
-  outputs.upToDateWhen { 
-    file(projdir).exists()
-  }
+  outputs.upToDateWhen({
+    if (IN_ECLIPSE) {
+      return true
+    }
+    def projDirExists = file(projdir).exists()
+    return projDirExists
+  })
 }
 
 
 task jalviewjsTranspile(type: Exec) {
-  dependsOn jalviewjsEclipseSetup 
   dependsOn jalviewjsProjectImport
-  dependsOn jalviewjsEclipsePaths
+
   if (!IN_ECLIPSE) {
     dependsOn jalviewjsEnableAltFileProperty
   }
@@ -3791,74 +3816,118 @@ ECLIPSE DEBUG: ${eclipseDebug}
     }
   }
 
+  if (IN_ECLIPSE) {
+    inputs.file(jalviewjsJ2sSettingsFileName)
+  } else {
+    inputs.file(jalviewjsJ2sAltSettingsFileName)
+  }
   inputs.dir("${jalviewDir}/${sourceDir}")
-  outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
-  outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+
+  def inputJavaDir = file("${jalviewDir}/${sourceDir}")
+  def inputJavaFiles = fileTree(dir: inputJavaDir)
+  def outputJsDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+  def outputJsFiles = []
+  inputJavaFiles.each{ file ->
+    def rfile = inputJavaDir.toPath().relativize(file.toPath())
+    def ofile = new File("${outputJsDir}/${rfile}")
+    def ofilenamejs = ofile.getPath()
+    if (ofilenamejs.endsWith(".java")) {
+      ofilenamejs = ofilenamejs.substring(0,ofilenamejs.length()-4)+"js"
+    }
+    outputJsFiles += "${ofilenamejs}"
+  }
+
+  outputs.files outputJsFiles
+  outputs.file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}")
 }
 
 
-task jalviewjsTranserSiteMergeLibDirs (type: Sync) {
-  dependsOn jalviewjsTransferUnzipAllLibs
+task jalviewjsTransferSiteMergeLibDir (type: Copy) {
+  dependsOn jalviewjsTransferUnzipLib
+
+  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
+
+  // This takes the outputs of jalviewjsTransferUnzipLib
+  from jalviewjsTransferUnzipLib
+  into outputDir
+
+  includeEmptyDirs = false
+  exclude "**/*.html"
+  exclude "**/*.htm"
+
+  // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
+  duplicatesStrategy "INCLUDE"
+}
+
+task jalviewjsTransferSiteMergeSwingJsDir (type: Copy) {
   dependsOn jalviewjsTransferUnzipSwingJs
-  dependsOn jalviewjsTranspile
 
-  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
-  // merge swingjs lib last
-  inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+  mustRunAfter jalviewjsTransferSiteMergeLibDir 
 
   def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
 
-  from inputFiles
+  // This takes the outputs of jalviewjsTransferUnzipSwingJs
+  from jalviewjsTransferUnzipSwingJs
   into outputDir
-  def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
-  }
 
+  includeEmptyDirs = false
   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
+task jalviewjsTransferSiteMergeSiteJsDir (type: Copy) {
   dependsOn jalviewjsTranspile
 
-  // merge jalview files very last
-  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+  mustRunAfter jalviewjsTransferSiteMergeLibDir 
+  mustRunAfter jalviewjsTransferSiteMergeSwingJsDir 
 
+  def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
   def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
-
-  from inputFiles
   into outputDir
-  def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
-  }
-  preserve {
-    include "**"
+  from {
+    def inputFiles = fileTree(dir: inputDir)
+    return inputFiles
   }
 
-  // should this be exclude really ? No, jalview dir should be transferred last (and overwrite)
+  includeEmptyDirs = false
+  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
+  // SiteJs files should take priority and write over existing files if different
+  // so we define the output files
+  outputs.upToDateWhen(
+    {
+      def transpiledFiles = jalviewjsTransferSiteMergeSiteJsDir.getOutputs().getFiles()
+      def inputFiles = fileTree(dir: inputDir)
+      if (inputFiles.size() < transpiledFiles.size()) {
+        return false
+      }
+      def retVal = ! inputFiles.any { file ->
+        def rfile = inputDir.toPath().relativize(file.toPath())
+        def ofile = new File("${outputDir}/${rfile}")
+        if (!ofile.exists() || ofile.lastModified() < file.lastModified()) {
+          return true // this is NOTted to false
+        }
+      }
+
+      return retVal
+    }
+  )
+
+  inputs.files jalviewjsTranspile
 }
 
 
-task jalviewjsTranserSiteMergeDirs {
-  dependsOn jalviewjsTranserSiteMergeLibDirs
-  dependsOn jalviewjsTranserSiteMergeSwingDir
+task jalviewjsTransferSiteMergeDirs {
+  dependsOn jalviewjsTransferSiteMergeLibDir
+  dependsOn jalviewjsTransferSiteMergeSwingJsDir
+  dependsOn jalviewjsTransferSiteMergeSiteJsDir
 }
 
 
@@ -3906,7 +3975,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
     main = "com.google.javascript.jscomp.CommandLineRunner"
     jvmArgs = [ "-Dfile.encoding=UTF-8" ]
     args = [ "--compilation_level", jalviewjs_closure_compiler_optimization_level, "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
-    maxHeapSize = "2g"
+    maxHeapSize = "4g"
 
     msg = "\nRunning '"+commandLine.join(' ')+"'\n"
     println(msg)
@@ -3946,7 +4015,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
 task jalviewjsBuildAllCores {
   group "JalviewJS"
   description "Build the core js lib closures listed in the classlists dir"
-  dependsOn jalviewjsTranserSiteMergeDirs
+  dependsOn jalviewjsTransferSiteMergeDirs
 
   def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
   def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
@@ -4012,41 +4081,6 @@ task jalviewjsBuildAllCores {
     outputs.file(zjsfile)
   }
   
-  // _all core
-  def allClasslistName = "_all"
-  def allJsFiles = fileTree(dir: j2sDir, 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
-  ]
-  // not including this version of "all" core at the moment
-  //jalviewjsCoreClasslists += allClasslist
-  inputs.files(allClasslist['list'])
-  outputs.file(allClasslist['jsfile'])
-  outputs.file(allClasslist['zjsfile'])
-
   doFirst {
     def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
     logOutFile.getParentFile().mkdirs()
@@ -4114,19 +4148,22 @@ task jalviewjsSyncCore (type: Sync) {
   dependsOn jalviewjsBuildAllCores
   dependsOn jalviewjsPublishCoreTemplates
 
-  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+  def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+  def inputFiles = fileTree(dir: inputDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
   into outputDir
   def outputFiles = []
-  rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
-    null
+  inputFiles.each{ file ->
+    def rfile = inputDir.toPath().relativize(file.toPath())
+    def ofile = new File("${outputDir}/${rfile}")
+    outputFiles += "${ofile}"
   }
   preserve {
-    include "**"
+    include "**/*"
   }
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
@@ -4134,7 +4171,7 @@ task jalviewjsSyncCore (type: Sync) {
 
 // this Copy version of TransferSiteJs will delete anything else in the target dir
 task jalviewjsCopyTransferSiteMergeDir(type: Copy) {
-  dependsOn jalviewjsTranserSiteMergeDirs
+  dependsOn jalviewjsTransferSiteMergeDirs
 
   from "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
@@ -4156,7 +4193,7 @@ task jalviewjsSyncTransferSiteJs(type: Sync) {
   include "**/*.*"
   into "${jalviewDir}/${jalviewjsSiteDir}"
   preserve {
-    include "**"
+    include "**/*"
   }
 }
 
diff --git a/gradle.properties b/gradle.properties
index fbc9dc5..cae63c8 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -221,8 +221,8 @@ jalviewjs_site_dir = site
 jalviewjs_swingjs_subdir = swingjs
 jalviewjs_j2s_subdir = swingjs/j2s
 jalviewjs_js_subdir = swingjs/js
-#jalviewjs_eclipseBuildArg = build
-jalviewjs_eclipse_build_arg = cleanBuild
+jalviewjs_eclipse_build_arg = build
+#jalviewjs_eclipse_build_arg = cleanBuild
 jalviewjs_server_port = 9001
 jalviewjs_server_wait = 30
 jalviewjs_server_resource = /jalview_bin_Jalview.html