JAL-3456 re-use of existing jar files
[jalview.git] / build.gradle
index 9aef0ff..2615932 100644 (file)
-import org.apache.tools.ant.filters.ReplaceTokens
 import org.gradle.internal.os.OperatingSystem
-import org.gradle.plugins.ide.eclipse.model.*
-import groovy.transform.ExternalizeMethods
-//import org.eclipse.osgi.*
+import org.gradle.plugins.ide.eclipse.model.Output
+import org.gradle.plugins.ide.eclipse.model.Library
+
 import com.diffplug.gradle.GoomphCacheLocations
 
-/*
 buildscript {
-  repositories {
-    repos
-    mavenCentral()
-    jcenter()
-  }
-  dependencies {
-    //eclipseDeps.each { compile "p2:${it}:+" }
-    //classpath 'org.eclipse.platform:org.eclipse.osgi:3.15.0'
-    //compile group: 'org.eclipse.platform', name: 'org.eclipse.osgi', version: '3.15.0'
-    //classpath 'biz.aQute.bnd:biz.aQute.bnd.gradle:4.4.0'
-  }
 }
-*/
 
 plugins {
   id 'java'
   id 'application'
   id 'eclipse'
+
   id 'com.diffplug.gradle.oomph.ide' version '3.18.1'
   id 'com.diffplug.gradle.equinoxlaunch' version '3.18.1'
+  id 'com.diffplug.gradle.eclipse.mavencentral' version '3.18.1'
+  id 'com.diffplug.gradle.p2.asmaven' version '3.18.1'
+}
 
-  //id 'com.diffplug.gradle.p2.asmaven' version '3.18.1'
+def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+def useIde = useGoomph.equals("true")
 
-  //id 'org.eclipse.osgi' version '3.15.0'
-  //id 'osgi'
+repositories {
+  jcenter()
+  mavenCentral()
+  flatDir {
+    dirs gradlePluginsDir
+  }
+  if (true || useIde) {
+    flatDir {
+      dirs jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir
+    }
+  }
 }
 
+configurations {
+  jalviewjsIde
+}
 
-/*
-def eclipseDeps = [
-    // The dependencies we actually use
-    'org.eclipse.jdt.core',
-    'org.eclipse.text',
-
-    // Their transitives
-    'org.eclipse.core.contenttype',
-    'org.eclipse.core.jobs',
-    'org.eclipse.core.runtime',
-    'org.eclipse.core.resources',
-    'org.eclipse.equinox.common',
-    'org.eclipse.equinox.preferences',
-    //'org.eclipse.osgi'
-]
-*/
 
-/*
-p2AsMaven {
-  group 'p2', {
-    repoEclipse goomph_eclipse_version
-    eclipseDeps.each { p2.addIU(it) }
-    eclipseDeps.each { p2.addIU(it + '.source') }
+if (useIde) {
+
+  p2AsMaven {
+    group 'eclipseDeps', {
+      repoEclipse goomph_eclipse_repo_version
+      //slicingOption 'latestVersionOnly', 'true'
+      iu 'org.eclipse.update.configurator'
+
+
+      iu 'org.eclipse.jdt.apt.core'
+      iu 'org.eclipse.jdt.core'
+      iu 'org.eclipse.jdt.annotation'
+
+    }
+    group 'ecjDeps', {
+      repo 'https://download.eclipse.org/eclipse/updates/4.13/R-4.13-201909161045/'
+      iu 'org.eclipse.debug.core'
+      iu 'org.eclipse.jdt.apt.pluggable.core'
+      iu 'org.eclipse.jdt.apt.ui'
+      iu 'org.eclipse.jdt.compiler.apt'
+      iu 'org.eclipse.jdt.compiler.tool'
+      iu 'org.eclipse.jdt.core.manipulation'
+      iu 'org.eclipse.jdt.debug'
+      iu 'org.eclipse.jdt.debug.ui'
+      iu 'org.eclipse.jdt.doc.user'
+      iu 'org.eclipse.jdt.junit'
+      iu 'org.eclipse.jdt.junit.core'
+      iu 'org.eclipse.jdt.junit4.runtime'
+      iu 'org.eclipse.jdt.junit4.runtime'
+      iu 'org.eclipse.jdt.junit5.runtime'
+      iu 'org.eclipse.jdt.launching'
+      iu 'org.eclipse.jdt.ui'
+
+      iu 'org.eclipse.jdt.launching.macosx'
+      iu 'org.eclipse.jdt.launching.ui.macosx'
+    }
+    group 'eclipseOrbit', {
+      repo goomph_orbit_repo
+      slicingOption 'latestVersionOnly', 'true'
+      iu 'javax.el'
+      iu 'javax.servlet'
+      iu 'javax.servlet.jsp'
+      iu 'org.apache.ant'
+      iu 'org.apache.batik.constants'
+      iu 'org.apache.batik.css'
+      iu 'org.apache.batik.i18n'
+      iu 'org.apache.batik.util'
+      iu 'org.apache.commons.beanutils'
+      iu 'org.apache.commons.collections'
+      iu 'org.apache.commons.jxpath'
+      iu 'org.apache.commons.io'
+      iu 'org.apache.commons.logging'
+      iu 'org.apache.xmlgraphics'
+      iu 'org.jdom'
+      iu 'org.w3c.dom.events'
+      iu 'org.w3c.dom.smil'
+      iu 'org.w3c.dom.svg'
+    }
   }
-}
-*/
 
+} // if (useIde) {}
 
-/*
 dependencies {
-  //eclipseDeps.each { compile "p2:${it}:+" }
-  //implementation 'org.eclipse.platform:org.eclipse.osgi:3.15.0'
-  //compile 'org.eclipse.platform:org.eclipse.osgi:3.15.0'
-  //classpath 'biz.aQute.bnd:biz.aQute.bnd.gradle:4.4.0'
-}
+/*
+    source.addMaven('org.eclipse.platform:org.eclipse.osgi:3.14.0')
+    // ...
+    compile 'eclipseOrbit:org.apache.ant:1.10.5.v20190526-1402'
+    // ...
+    compile 'org.osgi:org.osgi.service.component:1.4.0'
+    // ...
 */
 
+  jalviewjsIde name: 'net.sf.j2s.core-3.2.4'
+  jalviewjsIde name: 'com.seeq.eclipse.importprojects-1.4.0'
 
+}
 
-repositories {
-  jcenter()
-  mavenCentral()
-  flatDir {
-    dirs gradlePluginsDir
+
+
+
+
+
+if (useIde) {
+
+  eclipseMavenCentral {
+    // TODO: How do I add these to the jalviewjsIde configuration and not the compile configuration?
+    release goomph_eclipse_repo_version, {
+
+      //def platformCode="cocoa.macosx.x86_64"
+      //compile 'org.eclipse.swt.'+platformCode
+      useNativesForRunningPlatform()
+      compile 'org.eclipse.swt'
+
+      compile 'org.eclipse.ant.core'
+      compile 'org.eclipse.compare.core'
+      compile 'org.eclipse.core.commands'
+      compile 'org.eclipse.core.contenttype'
+      compile 'org.eclipse.core.jobs'
+      compile 'org.eclipse.core.expressions'
+      compile 'org.eclipse.core.filesystem'
+      compile 'org.eclipse.core.resources'
+      compile 'org.eclipse.core.runtime'
+      compile 'org.eclipse.core.variables'
+      compile 'org.eclipse.equinox.common'
+      compile 'org.eclipse.equinox.ds'
+      compile 'org.eclipse.equinox.app'
+      compile 'org.eclipse.equinox.registry'
+      compile 'org.eclipse.equinox.preferences'
+      compile 'org.eclipse.jface'
+      compile 'org.eclipse.osgi'
+      compile 'org.eclipse.osgi.services'
+      compile 'org.eclipse.ui'
+      compile 'org.eclipse.ui.workbench'
+      compile 'org.eclipse.team.core'
+      compile 'org.eclipse.text'
+
+      compile 'org.eclipse.e4.core.commands'
+      compile 'org.eclipse.e4.core.contexts'
+      compile 'org.eclipse.e4.core.di'
+      compile 'org.eclipse.e4.core.di.annotations'
+      compile 'org.eclipse.e4.core.di.extensions.supplier'
+      compile 'org.eclipse.e4.core.services'
+      compile 'org.eclipse.e4.ui.bindings'
+      compile 'org.eclipse.e4.ui.model.workbench'
+      compile 'org.eclipse.e4.ui.workbench'
+      compile 'org.eclipse.e4.ui.workbench.swt'
+      compile 'org.eclipse.e4.ui.css.core'
+      compile 'org.eclipse.e4.ui.css.swt'
+      compile 'org.eclipse.e4.ui.css.swt.theme'
+      compile 'org.eclipse.e4.ui.services'
+      compile 'org.eclipse.e4.ui.di'
+
+      //compile 'org.eclipse.e4.core.di.internal.extensions'
+
+      // org.eclipse.update.configurator deliberately kept at 3.3.400 see https://github.com/diffplug/goomph/issues/69
+      // this module downloaded in equinoxLaunch configuration (to specify version)
+      //compile 'org.eclipse.update.configurator'
+
+
+    }
   }
-}
+
+} // if (useIde) {}
+
+
+
+
+
+
+
+
+
+
 
 mainClassName = launcherClass
 def classes = "$jalviewDir/$classesDir"
 
 // configure classpath/args for j8/j11 compilation
 
-def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
 def libDir
 def libDistDir
 def compile_source_compatibility
@@ -144,6 +254,7 @@ if (JAVA_VERSION.equals("1.8")) {
   throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
 }
 
+
 sourceSets {
 
   main {
@@ -192,7 +303,7 @@ eclipse {
         HashMap<String, Boolean> addedSrcPath = new HashMap<>();
         cp.entries.each { entry ->
           if (entry.kind == 'src') {
-            if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+            if (addedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == "test")) {
               removeTheseToo += entry
             } else {
               addedSrcPath.putAt(entry.path, true)
@@ -304,63 +415,143 @@ clean {
 
 
 
+def eclipseWorkspace
+task jalviewjsSetEclipseWorkspace {
+  def eclipseWsDir = useIde?goomph_workspace:jalviewjs_eclipse_workspace
+  eclipseWorkspace = file(eclipseWsDir)
+  if (!eclipseWorkspace.exists()) {
+    eclipseWorkspace = file("${buildDir}/tmp/eclipse-workspace")
+    //eclipseWorkspace.deleteOnExit()
+  } else if (useIde) {
+    com.diffplug.gradle.GoomphCacheLocations.override_workspaces = file(eclipseWorkspace.getAbsolutePath())
+    eclipseWorkspace = oomphIde.workspaceRegistry.workspaceDir(project, file(oomphIde.ideDir))
+  }
+  println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+}
 
 
+if (useIde) {
 
-GoomphCacheLocations.override_workspaces = file(jalviewDirAbsolutePath+"/"+goomph_workspace)
-oomphIde {
-  repoEclipse goomph_eclipse_version
-  jdt {
-    /*
-    installedJre {
+  oomphIde {
+    repoEclipse goomph_eclipse_version
+    jdt {
+      /*
+      installedJre {
       //markDefault = true
       //executionEnvironments = [ eclipse.jdt.javaRuntimeName ]
+      }
+       */
+      //compilerComplianceLevel( JAVA_INTEGER_VERSION )
     }
-    */
-    //compilerComplianceLevel( JAVA_INTEGER_VERSION )
-  }
-  //repo 'http://download.eclipse.org/buildship/updates/e45/milestones/3.x/'
-  repo goomph_repo_buildship
-       feature goomph_feature_buildship
-}
 
-equinoxLaunch {
-  headlessAppSetup {
+    repo "https://download.eclipse.org/releases/${goomph_eclipse_version_name}/"
+    feature goomph_eclipse_jee_feature, goomph_eclipse_jee_version
+
+    thirdParty {
+      buildship {
+        repo goomph_repo_buildship
+        feature goomph_feature_buildship
+      }
 
-    launchTask 'ideJalviewjsBuild', {
-      //it.args = ["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", tempEclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ]
-      it.args = ["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ]
     }
-  }
-}
 
-task ideCopyDropins (type: Copy) {
-  dependsOn ideSetupP2
+    workspaceProp '.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.launching.prefs', {
+      it.put('org.eclipse.jdt.launching.PREF_VM_XML', goomph_PREF_VM_XML)
+    }
 
-  def inputFiles = fileTree(jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir)
-  def outputDir = oomphIde.ideDir + "/" + com.diffplug.gradle.FileMisc.macContentsEclipse() + "/dropins"
 
-  from inputFiles
-  into outputDir
-  def outputFiles = []
-  rename { filename ->
-    outputFiles += outputDir+"/"+filename
-    println("COPYING ${filename} to ${outputFiles}")
-    null
+    // CLI ARGS HERE!
   }
-  outputs.files outputFiles
-  inputs.files inputFiles
 
-}
+  equinoxLaunch {
+    ideJalviewjsBuildSetup {
+
+      source.addConfiguration(configurations.compile)
+      source.addConfiguration(configurations.jalviewjsIde)
+
+      source.addMaven('eclipseOrbit:org.apache.ant:1.10.5.v20190526-1402')
+      source.addMaven('eclipseOrbit:javax.servlet:3.1.0.v201410161800')
+      source.addMaven('eclipseOrbit:javax.servlet.jsp:2.2.0.v201112011158')
+      source.addMaven('eclipseOrbit:javax.el:2.2.0.v201303151357')
+      source.addMaven('eclipseOrbit:org.apache.batik.constants:1.11.0.v20190515-0436')
+      source.addMaven('eclipseOrbit:org.apache.batik.css:1.11.0.v20190515-0436')
+      source.addMaven('eclipseOrbit:org.apache.batik.i18n:1.11.0.v20190515-0436')
+      source.addMaven('eclipseOrbit:org.apache.batik.util:1.11.0.v20190515-0436')
+      source.addMaven('eclipseOrbit:org.apache.commons.beanutils:1.8.0.v201205091237')
+      source.addMaven('eclipseOrbit:org.apache.commons.collections:3.2.2.v201511171945')
+      source.addMaven('eclipseOrbit:org.apache.xmlgraphics:2.3.0.v20190515-0436')
+      source.addMaven('eclipseOrbit:org.apache.commons.jxpath:1.3.0.v200911051830')
+      source.addMaven('eclipseOrbit:org.apache.commons.io:2.6.0.v20190123-2029')
+      source.addMaven('eclipseOrbit:org.apache.commons.logging:1.2.0.v20180409-1502')
+      source.addMaven('eclipseOrbit:org.jdom:1.1.1.v201101151400')
+      source.addMaven('eclipseOrbit:org.w3c.dom.svg:1.1.0.v201011041433')
+      source.addMaven('eclipseOrbit:org.w3c.dom.smil:1.0.1.v200903091627')
+      source.addMaven('eclipseOrbit:org.w3c.dom.events:3.0.0.draft20060413_v201105210656')
+
+      source.addMaven('org.eclipse.birt.runtime:com.ibm.icu:56.1.0.v201601250100')
+      source.addMaven('javax.inject:com.springsource.javax.inject:1.0.0')
+      source.addMaven('org.apache.felix:org.apache.felix.scr:2.1.16')
+      source.addMaven('org.osgi:org.osgi.framework:1.9.0')
+      source.addMaven('org.osgi:org.osgi.service.component:1.4.0')
+      source.addMaven('org.osgi:org.osgi.service.event:1.4.0')
+      source.addMaven('org.osgi:org.osgi.util.promise:1.1.1')
+      source.addMaven('org.osgi:org.osgi.util.function:1.1.0')
+
+      source.addMaven('ecjDeps:org.eclipse.debug.core:3.14.0.v20190812-1404')
+      source.addMaven('ecjDeps:org.eclipse.jdt.annotation:2.2.300.v20190328-1431')
+      source.addMaven('ecjDeps:org.eclipse.jdt.apt.core:3.6.500.v20190703-0914')
+      source.addMaven('ecjDeps:org.eclipse.jdt.core:3.19.0.v20190903-0936')
+      source.addMaven('ecjDeps:org.eclipse.jdt.apt.pluggable.core:1.2.400.v20190626-1334')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.apt.ui:3.6.300.v20190727-1243')
+      source.addMaven('ecjDeps:org.eclipse.jdt.compiler.apt:1.3.700.v20190704-1731')
+      source.addMaven('ecjDeps:org.eclipse.jdt.compiler.tool:1.2.600.v20190322-0450')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.core.manipulation:1.12.100.v20190904-0645')
+      source.addMaven('ecjDeps:org.eclipse.jdt.debug:3.13.100.v20190902-1050')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.debug.ui:3.10.400.v20190815-2202')
+      source.addMaven('ecjDeps:org.eclipse.jdt.doc.user:3.15.400.v20190904-0724')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.junit:3.11.500.v20190809-1613')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.junit.core:3.10.400.v20190625-1910')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.junit4.runtime:1.1.1000.v20190510-0840')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.junit4.runtime:1.1.1000.v20190510-0840')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.junit5.runtime:1.0.600.v20190610-0439')
+      source.addMaven('ecjDeps:org.eclipse.jdt.launching:3.15.0.v20190826-1639')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.ui:3.19.0.v20190827-1733')
+
+      //source.addMaven('ecjDeps:org.eclipse.jdt.launching.macosx:3.4.300.v20190510-0639')
+      //source.addMaven('ecjDeps:org.eclipse.jdt.launching.ui.macosx:1.2.300.v20190510-0639')
+
+      // org.eclipse.update.configurator deliberately kept at 3.3.400 see https://github.com/diffplug/goomph/issues/69
+      source.addMaven('org.eclipse.platform:org.eclipse.update.configurator:3.3.400')
+
+
+      launchTask 'ideJalviewjsImport', {
+        it.args = ["-consoleLog", "-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath ]
+      }
 
-ide.dependsOn eclipseProject
-ide.dependsOn eclipseClasspath
-ide.dependsOn eclipseJdt
-ide.dependsOn ideCopyDropins
-ideJalviewjsBuild.dependsOn ideSetupWorkspace
-ideJalviewjsBuild.dependsOn ideCopyDropins
+      launchTask 'ideJalviewjsBuild', {
 
+        oomphIde.workspaceProp '.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.launching.prefs', {
+          it.put('org.eclipse.jdt.launching.PREF_VM_XML', goomph_PREF_VM_XML)
+        }
+
+        def args = ["-consoleLog", "-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace.getPath(), "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ]
+        println("ARGS="+args)
+
+        it.args = args
 
+      }
+    }
+  }
+
+  ideSetupWorkspace.dependsOn jalviewjsSetEclipseWorkspace
+  ideSetupWorkspace.outputs.upToDateWhen {file(eclipseWorkspace).exists()}
+
+  task ideSetup {
+    dependsOn ideSetupP2
+    dependsOn ideSetupWorkspace
+  }
+
+} // if (useIde) {}
 
 
 
@@ -386,15 +577,6 @@ task jalviewjsSitePath {
   }
 }
 
-def tempEclipseWorkspace
-task jalviewjsSetTempEclipseWorkspace {
-  tempEclipseWorkspace = file(jalviewjs_eclipse_workspace)
-  if (!tempEclipseWorkspace.exists()) {
-    tempEclipseWorkspace = file("${buildDir}/tmp/eclipse-workspace")
-    //tempEclipseWorkspace.deleteOnExit()
-  }
-  println("ECLIPSE WORKSPACE: "+tempEclipseWorkspace.getPath())
-}
 
 task jalviewjsUnzipFiles {
   dependsOn jalviewjsSitePath
@@ -418,42 +600,54 @@ task jalviewjsUnzipFiles {
 def eclipseDropinsDir
 def eclipseBinary
 task jalviewjsEclipsePaths {
-  def eclipseRoot = jalviewjs_eclipse_root
-  if (eclipseRoot.startsWith("~")) {
-    eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+  def eclipseRoot
+  if (useIde) {
+    eclipseRoot = oomphIde.ideDir
+    eclipseDropinsDir = eclipseRoot+"/"+com.diffplug.gradle.FileMisc.macContentsEclipse()+"/dropins"
+    eclipseBinary = eclipseRoot+"/"+com.diffplug.common.swt.os.OS.getNative().winMacLinux("", "Contents/MacOS", "")+"/eclipse"
+  } else {
+    eclipseRoot = jalviewjs_eclipse_root
+    if (eclipseRoot.startsWith("~")) {
+      eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+    }
+    if (OperatingSystem.current().isMacOsX()) {
+      eclipseRoot += "/Eclipse.app"
+      eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins"
+      eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse"
+    } else if (OperatingSystem.current().isWindows()) { // check these paths!!
+      eclipseDropinsDir = eclipseRoot+"/dropins"
+      eclipseBinary = eclipseRoot+"/eclipse"
+    } else { // linux or unix
+      eclipseDropinsDir = eclipseRoot+"/dropins"
+      eclipseBinary = eclipseRoot+"/eclipse"
+    }
   }
-       if (OperatingSystem.current().isMacOsX()) {
-    eclipseRoot += "/Eclipse.app"
-               eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins"
-               eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse"
-       } else if (OperatingSystem.current().isWindows()) { // check these paths!!
-               eclipseDropinsDir = eclipseRoot+"/dropins"
-               eclipseBinary = eclipseRoot+"/eclipse"
-       } else { // linux or unix
-               eclipseDropinsDir = eclipseRoot+"/dropins"
-               eclipseBinary = eclipseRoot+"/eclipse"
-       }
 }
 
-task jalviewjsEclipseCopyDropins (type: Copy) {
+task jalviewjsEclipseCopyDropins {
   dependsOn jalviewjsEclipsePaths
-  def inputFiles = fileTree(jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir)
+  def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir, include: "*.jar")
   def outputDir = eclipseDropinsDir
 
-  from inputFiles
-  into outputDir
-  def outputFiles = []
-  rename { filename ->
-    outputFiles += outputDir+"/"+filename
-    null
-  }
-  outputs.files outputFiles
   inputs.files inputFiles
+  inputFiles.each { file ->
+    outputs.file(outputDir+"/"+file.name)
+  }
+
+  doLast {
+    def outputFiles = []
+    inputFiles.each { file ->
+      copy {
+        from file
+        into outputDir
+      }
+    }
+  }
 }
 
 task jalviewjsEclipseSetup {
   dependsOn jalviewjsEclipseCopyDropins
-  dependsOn jalviewjsSetTempEclipseWorkspace
+  dependsOn jalviewjsSetEclipseWorkspace
 }
 
 
@@ -514,12 +708,10 @@ task jalviewjsCopySiteResources (type: Copy) {
 
 task cleanJalviewjs {
   dependsOn jalviewjsSitePath
-  /*
   delete jalviewDir+"/"+jalviewjsSiteDir
-  delete jalviewDir+"/"+eclipse_bin_dir
-  delete file(tempEclipseWorkspace.getAbsolutePath()+"/.metadata")
-  delete jalviewDir+"/"+jalviewjs_j2s_settings
-  */
+  //delete jalviewDir+"/"+eclipse_bin_dir
+  //delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+  //delete jalviewDir+"/"+jalviewjs_j2s_settings
 }
 
 task jalviewjsProjectImport(type: Exec) {
@@ -530,9 +722,9 @@ task jalviewjsProjectImport(type: Exec) {
   dependsOn jalviewjsEclipsePaths
   dependsOn jalviewjsEclipseSetup
   executable(eclipseBinary)
-  args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", tempEclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+  args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
 
-  def projdir = tempEclipseWorkspace.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/org.eclipse.jdt.core"
   inputs.file(jalviewDir+"/.project")
   outputs.dir(projdir)
   outputs.upToDateWhen { file(projdir).exists() }
@@ -550,7 +742,7 @@ task jalviewjsTranspile(type: Exec) {
   dependsOn jalviewjsProjectImport
   dependsOn jalviewjsEclipsePaths
   executable(eclipseBinary)
-  args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", tempEclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ])
+  args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ])
 
   def stdout
   def stderr
@@ -563,15 +755,25 @@ task jalviewjsTranspile(type: Exec) {
   doLast {
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
-      throw new TaskExecutionException("Error during transpilation:\n${stderr}\n")
+      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log files '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}' and '${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}'\n")
     }
   }
 
   inputs.dir(sourceDir)
   outputs.dir(eclipse_bin_dir+"/main")
-  outputs.dir(jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir)
+  outputs.files(
+    fileTree(
+      dir: jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir,
+      includes: [ "**/*.js" ],
+      excludes: [
+        //jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir+"/intervalstore/**",
+        //jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir+"/org/json/**",
+        "intervalstore/**",
+        "org/json/**",
+      ]
+    ).files
+  )
   outputs.file(jalviewjsSiteDir+jalviewjs_server_resource)
-  outputs.upToDateWhen { file(jalviewjsSiteDir+jalviewjs_server_resource).exists() }
 
 }
 
@@ -580,19 +782,31 @@ task jalviewjsTranspile(type: Exec) {
 
 
 
+jalviewjsUnzipFiles.mustRunAfter jalviewjsTranspile
+jalviewjsTranspile.mustRunAfter jalviewjsCopyResources
+jalviewjsTranspile.mustRunAfter jalviewjsCopySiteResources
 
-
-task jalviewjsBuildSite {
+task jalviewjsPrepareSite {
+  group "JalviewJS"
+  description "Prepares the website folder including unzipping files and copying resources"
   dependsOn jalviewjsSitePath
   dependsOn jalviewjsUnzipFiles
   dependsOn jalviewjsCopyResources
   dependsOn jalviewjsCopySiteResources
+}
+
+task jalviewjsBuildSite {
+  group "JalviewJS"
+  description "Builds the whole website including transpiled code"
+  dependsOn jalviewjsPrepareSite
   dependsOn jalviewjsTranspile
 }
 
 task jalviewjsSiteTar(type: Tar) {
+  group "JalviewJS"
+  description "Creates a tar.gz file for the website"
   dependsOn jalviewjsBuildSite
-  def outputFilename = "site.tar.gz"
+  def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
   try {
     archiveFileName = outputFilename
   } catch (Exception e) {
@@ -607,12 +821,10 @@ task jalviewjsSiteTar(type: Tar) {
   inputs.dir(jalviewjsSiteDir)
 }
 
-task jalviewjs {
-  dependsOn jalviewjsBuildSite
-}
-
 def jalviewjsServer = null
 task jalviewjsServerStart {
+  group "JalviewJS"
+  description "Starts a webserver on localhost to test the website"
   dependsOn jalviewjsSitePath
   doLast {
 
@@ -629,7 +841,7 @@ task jalviewjsServerStart {
           def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir)
           jalviewjsServer = factory.start(doc_root, port)
           running = true
-          println("SERVER STARTED with document root ${doc_root}.\nGo to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run  gradle jalviewjsServerStop  to stop.")
+          println("SERVER STARTED with document root ${doc_root}.\nGo to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run  gradle --stop  to stop (kills all gradle daemons).")
           //println("Ctrl-c to stop.");java.lang.Thread.sleep(Integer.valueOf(jalviewjs_server_wait)*1000);
         } catch (Exception e) {
           port++;
@@ -659,11 +871,47 @@ task jalviewjsServerStop {
 }
 */
 
-project.afterEvaluate {
-  tasks.findByName('ideJalviewjsBuild').dependsOn eclipseProject
-  tasks.findByName('ideJalviewjsBuild').dependsOn eclipseClasspath
-  tasks.findByName('ideJalviewjsBuild').dependsOn eclipseJdt
+task ideBuildSite {
+  dependsOn jalviewjsSitePath
+  dependsOn jalviewjsUnzipFiles
+  dependsOn jalviewjsCopyResources
+  dependsOn jalviewjsCopySiteResources
+  /* see project.afterEvaluate
+  dependsOn ideJalviewjsBuild
+  */
+}
+
+
+
+
+task jalviewjs {
+  if (useIde) {
+    dependsOn ideBuildSite
+  } else {
+    dependsOn jalviewjsBuildSite
+  }
 }
 
 
+project.afterEvaluate {
+
+  tasks.findByName('eclipse').dependsOn tasks.findByName('jalviewjsCreateJ2sSettings')
+
+  if (useIde) {
+    tasks.findByName('ideJalviewjsImport').dependsOn eclipseProject
+    tasks.findByName('ideJalviewjsImport').dependsOn eclipseClasspath
+    tasks.findByName('ideJalviewjsImport').dependsOn eclipseJdt
+    tasks.findByName('ideJalviewjsImport').dependsOn jalviewjsSetEclipseWorkspace
+
+    tasks.findByName('ideJalviewjsBuild').dependsOn tasks.findByName('ideJalviewjsImport')
+    tasks.findByName('ideJalviewjsBuild').dependsOn tasks.findByName('jalviewjsCreateJ2sSettings')
+
+    tasks.findByName('ide').dependsOn eclipseProject
+    tasks.findByName('ide').dependsOn eclipseClasspath
+    tasks.findByName('ide').dependsOn eclipseJdt
+
+    ideBuildSite.dependsOn tasks.findByName('ideJalviewjsBuild')
+  }
+
+}