JAL-3210 Almost working goomph build
[jalview.git] / build.gradle
index 62fa472..f355258 100644 (file)
@@ -2,29 +2,127 @@ 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 com.diffplug.gradle.GoomphCacheLocations
 
+buildscript {
+  repositories {
+    /*
+    mavenCentral()
+    jcenter()
+    */
+  }
+}
 
 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'
+}
+
+
+dependencies {
+    //compile group: 'org.osgi', name: 'org.osgi.service.component', version: '1.4.0'
+/*
+    source.addMaven('org.eclipse.platform:org.eclipse.osgi:3.14.0')
+    source.addMaven('org.eclipse.platform:org.eclipse.equinox.common:3.10.400')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.jobs:3.10.400')
+    source.addMaven('org.eclipse.platform:org.eclipse.update.configurator:3.4.300')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.runtime:3.16.0')
+    source.addMaven('org.eclipse.platform:org.eclipse.equinox.ds:1.6.0')
+    source.addMaven('javax.inject:com.springsource.javax.inject:1.0.0')
+*/
+  //compile 'com.ibm.icu:com.ibm.icu:4.4.2'
 }
 
+def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+
 repositories {
   jcenter()
   mavenCentral()
+  maven { url "http://maven.icm.edu.pl/artifactory/repo/" }
+  maven { url "http://maven.geomajas.org/" }
+  maven { url "https://repo.spring.io/plugins-release/" }
+  maven { url "${jalviewDirAbsolutePath}/${m2RepoDir}" }
   mavenLocal()
   flatDir {
     dirs gradlePluginsDir
   }
 }
 
+
+
+
+
+
+
+/*
+p2AsMaven {
+  def requiredBundles = [
+               'org.eclipse.core.commands',
+               'org.eclipse.core.resources',
+               'org.eclipse.core.runtime',
+               'org.eclipse.ui',
+               'org.eclipse.ui.ide',
+               'org.eclipse.jface',
+               'org.eclipse.swt',
+               //"org.eclipse.swt.${com.diffplug.common.swt.os.SwtPlatform.getNative()}",
+               'org.eclipse.equinox.registry',
+               'org.eclipse.equinox.common',
+               'org.eclipse.osgi',
+               'org.eclipse.core.jobs',
+               'org.eclipse.ui.workbench',
+               'org.eclipse.jdt.core',
+               'org.eclipse.jdt.ui',
+               'org.eclipse.text'
+  ]
+
+  group 'eclipse-deps', {
+    repoEclipse '4.12.0'
+    // reduce the number of plugins downloaded
+    slicingOption 'latestVersionOnly', 'true'
+    requiredBundles.each {
+      iu "${it}"
+    }
+    append true
+  }
+}
+*/
+
+/*
+eclipseMavenCentral {
+  release '4.13.0', {
+    compile 'org.eclipse.osgi'
+    compile 'org.eclipse.equinox.common'
+    compile 'org.eclipse.update.configurator'
+    compile 'org.eclipse.core.runtime'
+    compile 'org.eclipse.core.jobs'
+    compile 'org.eclipse.equinox.ds'
+    compile 'org.eclipse.osgi.services'
+    useNativesForRunningPlatform()
+  }
+}
+*/
+
+
+
+
+
+
+
+
+
+
+
+
 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
@@ -81,6 +179,7 @@ if (JAVA_VERSION.equals("1.8")) {
   throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
 }
 
+
 sourceSets {
 
   main {
@@ -138,9 +237,15 @@ eclipse {
         }
         cp.entries.removeAll(removeTheseToo)
 
-        cp.entries += new Output(eclipse_bin_dir+"/main")
-        cp.entries += new Library(fileReference(helpParentDir))
-        cp.entries += new Library(fileReference(resourceDir))
+       if (file(eclipse_bin_dir+"/main").isDirectory()) {
+               cp.entries += new Output(eclipse_bin_dir+"/main")
+       }
+       if (file(helpParentDir).isDirectory()) {
+               cp.entries += new Library(fileReference(helpParentDir))
+       }
+       if (file(resourceDir).isDirectory()) {
+               cp.entries += new Library(fileReference(resourceDir))
+       }
 
         HashMap<String, Boolean> addedLibPath = new HashMap<>();
 
@@ -215,112 +320,296 @@ clean {
 }
 */
 
-task jalviewjsUnzipFiles {
-  def zipFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_libjs_dir).include("*.zip")
-  zipFiles += jalviewjs_utils_dir+"/"+jalviewjs_swingjs_zip
 
-  doLast {
-    zipFiles.each { file_zip -> 
-      copy {
-        from zipTree(file_zip)
-        into jalviewjs_site_dir
-      }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+def useIde = useGoomph.equals("true")
+
+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) {
+    GoomphCacheLocations.override_workspaces = file(eclipseWorkspace.getAbsolutePath())
+    eclipseWorkspace = oomphIde.workspaceRegistry.workspaceDir(project, file(oomphIde.ideDir))
+  }
+  println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+}
+
+oomphIde {
+  repoEclipse goomph_eclipse_version
+  jdt {
+    /*
+    installedJre {
+      //markDefault = true
+      //executionEnvironments = [ eclipse.jdt.javaRuntimeName ]
     }
+    */
+    //compilerComplianceLevel( JAVA_INTEGER_VERSION )
   }
 
-  inputs.files zipFiles
-  outputs.dir jalviewjs_site_dir
+  repo "https://download.eclipse.org/releases/${goomph_eclipse_version_name}/"
+  feature goomph_eclipse_jee_feature, goomph_eclipse_jee_version
+
+  //iu 'org.eclipse.osgi'
+
+  thirdParty {
+    buildship {
+      repo goomph_repo_buildship
+      feature goomph_feature_buildship
+    }
+
+  }
+
+
+
+  // CLI ARGS HERE!
 }
 
-def eclipseBinary
-def eclipseDropinsDir
-def eclipsePluginsDir
-task jalviewjsEclipsePaths {
-  def eclipseRoot = jalviewjs_eclipse_root
-  if (eclipseRoot.startsWith("~")) {
-    eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+equinoxLaunch {
+  ideJalviewjsBuildSetup {
+    source.addThisProject()
+
+    
+    //source.addMaven('com.ibm.icu:icu4j:65.1')
+    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.ant:ant:1.7.0')
+    source.addMaven('org.apache.ant:org.apache.ant:1.6.5')
+
+    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.util.promise:1.1.1')
+    source.addMaven('org.osgi:org.osgi.util.function:1.1.0')
+
+    source.addMaven('org.eclipse.jdt:org.eclipse.jdt.apt.core:3.6.500')
+    //source.addMaven('org.eclipse.jdt:org.eclipse.jdt.apt.ui:3.6.300')
+    //source.addMaven('org.eclipse.jdt:org.eclipse.jdt.compiler.apt:1.3.700')
+    source.addMaven('org.eclipse.jdt:org.eclipse.jdt.core:3.19.0')
+
+    source.addMaven('org.eclipse.platform:org.eclipse.ant.core:3.5.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.compare.core:3.6.600')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.commands:3.9.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.contenttype:3.7.400')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.jobs:3.10.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.expressions:3.6.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.filesystem:1.7.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.resources:3.13.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.runtime:3.16.0')
+    source.addMaven('org.eclipse.platform:org.eclipse.core.variables:3.4.600')
+    source.addMaven('org.eclipse.platform:org.eclipse.equinox.common:3.10.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.equinox.ds:1.6.0')
+    source.addMaven('org.eclipse.platform:org.eclipse.equinox.app:1.4.300')
+    source.addMaven('org.eclipse.platform:org.eclipse.equinox.registry:3.8.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.equinox.preferences:3.7.500')
+    source.addMaven('org.eclipse.platform:org.eclipse.osgi:3.14.0')
+    source.addMaven('org.eclipse.platform:org.eclipse.team.core:3.8.700')
+    source.addMaven('org.eclipse.platform:org.eclipse.text:3.9.0')
+    source.addMaven('org.eclipse.platform:org.eclipse.update.configurator:3.3.400')
+    /*
+    source.addMaven('org.eclipse.platform:org.eclipse.:3.')
+    source.addMaven('org.eclipse.platform:org.eclipse.:3.')
+    source.addMaven('org.eclipse.platform:org.eclipse.:3.')
+    source.addMaven('org.eclipse.platform:org.eclipse.:3.')
+    source.addMaven('org.eclipse.platform:org.eclipse.:3.')
+    */
+
+
+
+
+    launchTask 'ideJalviewjsBuild', {
+      //it.args = ["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ]
+      //it.args = ["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ]
+      it.args = ["-consoleLog", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ]
+      //it.vmArgs = ['-Dosgi.bundles=org.eclipse.core.jobs@2:start,org.eclipse.equinox.common@3:start,org.eclipse.core.runtime@2:start']
+      //it.vmArgs = ['-Dequinox.use.ds=false']
+
+    }
   }
-       if (OperatingSystem.current().isMacOsX()) {
-    eclipseRoot += "/Eclipse.app"
-               eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins"
-               eclipsePluginsDir = eclipseRoot+"/Contents/Eclipse/plugins"
-               eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse"
-       } else if (OperatingSystem.current().isWindows()) { // check these paths!!
-               eclipseDropinsDir = eclipseRoot+"/dropins"
-               eclipsePluginsDir = eclipseRoot+"/plugins"
-               eclipseBinary = eclipseRoot+"/eclipse"
-       } else { // linux or unix
-               eclipseDropinsDir = eclipseRoot+"/dropins"
-               eclipsePluginsDir = eclipseRoot+"/plugins"
-               eclipseBinary = eclipseRoot+"/eclipse"
-       }
-  println("ECLIPSE ROOT: "+eclipseRoot)
 }
 
-task jalviewjsEclipseCopyDropins (type: Copy) {
-  dependsOn jalviewjsEclipsePaths
+/*
+task ideCopyDropins (type: Copy) {
+  dependsOn ideSetupP2
+
   def inputFiles = fileTree(jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir)
-  def outputDir = eclipseDropinsDir
+  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
   }
   outputs.files outputFiles
   inputs.files inputFiles
+
 }
+*/
 
-task jalviewjsEclipseCopyPlugins (type: Copy) {
-  dependsOn jalviewjsEclipsePaths
-  def inputFiles = fileTree(jalviewjs_utils_dir+"/"+jalviewjs_eclipse_plugins_dir)
-  def outputDir = eclipsePluginsDir
+ideSetupWorkspace.dependsOn jalviewjsSetEclipseWorkspace
+ideSetupWorkspace.outputs.upToDateWhen {file(eclipseWorkspace).exists()}
 
-  from inputFiles
-  into outputDir
-  def outputFiles = []
-  rename { filename ->
-    outputFiles += outputDir+"/"+filename
-    null
+task ideSetup {
+  dependsOn ideSetupP2
+  dependsOn ideSetupWorkspace
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+def jalviewjsBuildDir
+def jalviewjsSiteDir
+task jalviewjsSitePath {
+  if (jalviewjs_site_dir.startsWith("/")) {
+    jalviewjsSiteDir = jalviewjs_site_dir
+  } else {
+    def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+    jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
+    jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir
   }
-  outputs.files outputFiles
-  inputs.files inputFiles
 }
 
-def tempEclipseWorkspace = ""
 
-task jalviewjsSetTempEclipseWorkspace {
-  tempEclipseWorkspace = file(jalviewjs_eclipse_workspace)
-  if (!tempEclipseWorkspace.exists()) {
-    tempEclipseWorkspace = File.createTempDir()
-    tempEclipseWorkspace.deleteOnExit()
+task jalviewjsUnzipFiles {
+  dependsOn jalviewjsSitePath
+
+  def zipFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_libjs_dir).include("*.zip")
+  zipFiles += jalviewjs_utils_dir+"/"+jalviewjs_swingjs_zip
+
+  doLast {
+    zipFiles.each { file_zip -> 
+      copy {
+        from zipTree(file_zip)
+        into jalviewjsSiteDir
+      }
+    }
+  }
+
+  inputs.files zipFiles
+  outputs.dir jalviewjsSiteDir
+}
+
+def eclipseDropinsDir
+def eclipseBinary
+task jalviewjsEclipsePaths {
+  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"
+    }
+  }
+  //println("ECLIPSE_ROOT=${eclipseRoot}")
+  //println("ECLIPSE_BINARY=${eclipseBinary}")
+}
+
+//task jalviewjsEclipseCopyDropins (type: Copy) {
+task jalviewjsEclipseCopyDropins {
+  dependsOn jalviewjsEclipsePaths
+  def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir, include: "*.jar")
+  def outputDir = eclipseDropinsDir
+
+  inputs.files inputFiles
+  inputFiles.each { file ->
+    outputs.file(outputDir+"/"+file.name)
+  }
+
+  doLast {
+    def outputFiles = []
+    inputFiles.each { file ->
+      copy {
+        from file
+        into outputDir
+      }
+    }
   }
-  println("ECLIPSE WORKSPACE: "+tempEclipseWorkspace.getPath())
 }
 
 task jalviewjsEclipseSetup {
   dependsOn jalviewjsEclipseCopyDropins
-  dependsOn jalviewjsEclipseCopyPlugins
-  dependsOn jalviewjsSetTempEclipseWorkspace
+  dependsOn jalviewjsSetEclipseWorkspace
 }
 
 
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+  dependsOn jalviewjsSitePath
   outputFile (jalviewDir+"/"+jalviewjs_j2s_settings)
   def props = project.properties.sort { it.key }
+  def siteDirProperty = "j2s.site.directory"
+  def setSiteDir = false
   props.each { prop, val ->
     if (prop.startsWith("j2s.") && val != null) {
+      if (prop == siteDirProperty) {
+        if (!(val.startsWith("/") || val.startsWith("file://") )) {
+          val = jalviewjsSiteDir+"/"+val
+        }
+        setSiteDir = true
+      }
       property(prop,val)
     }
+    if (!setSiteDir) {
+      property(siteDirProperty,"${jalviewjsSiteDir}")
+    }
   }
   outputs.file(outputFile)
 }
 
 task jalviewjsCopyResources (type: Copy) {
+  dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: jalviewjs_resource_dir)
-  def outputDir = jalviewjs_site_dir+"/"+jalviewjs_j2s_subdir
+  def outputDir = jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir
 
   from inputFiles
   into outputDir
@@ -334,8 +623,9 @@ task jalviewjsCopyResources (type: Copy) {
 }
 
 task jalviewjsCopySiteResources (type: Copy) {
+  dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_site_resource_dir)
-  def outputDir = jalviewjs_site_dir
+  def outputDir = jalviewjsSiteDir
 
   from inputFiles
   into outputDir
@@ -349,10 +639,11 @@ task jalviewjsCopySiteResources (type: Copy) {
 }
 
 task cleanJalviewjs {
+  dependsOn jalviewjsSitePath
   /*
-  delete jalviewDir+"/"+jalviewjs_site_dir
+  delete jalviewDir+"/"+jalviewjsSiteDir
   delete jalviewDir+"/"+eclipse_bin_dir
-  delete file(tempEclipseWorkspace.getAbsolutePath()+"/.metadata")
+  delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
   delete jalviewDir+"/"+jalviewjs_j2s_settings
   */
 }
@@ -365,26 +656,72 @@ 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() }
 }
 
+
+
+
+
+
+
+
 task jalviewjsTranspile(type: Exec) {
   dependsOn jalviewjsCreateJ2sSettings 
   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
+  doFirst {
+    stdout = new ByteArrayOutputStream()
+    stderr = new ByteArrayOutputStream()
+    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"), stdout);
+    errorOutput = new org.apache.tools.ant.util.TeeOutputStream(new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"), stderr);
+  }
+  doLast {
+    if (stdout.toString().contains("Error processing ")) {
+      // j2s did not complete transpile
+      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.file(eclipse_bin_dir+"/main/jalview/bin/Jalview.class")
-  outputs.dir(jalviewjs_site_dir+"/"+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)
+
 }
 
+
+
+
+
+
+jalviewjsUnzipFiles.mustRunAfter jalviewjsTranspile
+jalviewjsTranspile.mustRunAfter jalviewjsCopyResources
+jalviewjsTranspile.mustRunAfter jalviewjsCopySiteResources
+
 task jalviewjsBuildSite {
+  dependsOn jalviewjsSitePath
   dependsOn jalviewjsUnzipFiles
   dependsOn jalviewjsCopyResources
   dependsOn jalviewjsCopySiteResources
@@ -393,7 +730,7 @@ task jalviewjsBuildSite {
 
 task jalviewjsSiteTar(type: Tar) {
   dependsOn jalviewjsBuildSite
-  def outputFilename = "site.tar.gz"
+  def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
   try {
     archiveFileName = outputFilename
   } catch (Exception e) {
@@ -402,18 +739,15 @@ task jalviewjsSiteTar(type: Tar) {
 
   compression Compression.GZIP
 
-  from jalviewjs_site_dir
+  from jalviewjsSiteDir
   into jalviewjs_site_dir // this is inside the tar file
 
-  inputs.dir(jalviewjs_site_dir)
-}
-
-task jalviewjs {
-  dependsOn jalviewjsBuildSite
+  inputs.dir(jalviewjsSiteDir)
 }
 
 def jalviewjsServer = null
 task jalviewjsServerStart {
+  dependsOn jalviewjsSitePath
   doLast {
 
     if (jalviewjsServer != null) {
@@ -426,9 +760,10 @@ task jalviewjsServerStart {
       def running = false
       while(port < start+1000 && !running) {
         try {
-          jalviewjsServer = factory.start(new File(jalviewDirAbsolutePath+"/"+jalviewjs_site_dir), port)
+          def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir)
+          jalviewjsServer = factory.start(doc_root, port)
           running = true
-          println("SERVER STARTED. Go 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++;
@@ -457,3 +792,34 @@ task jalviewjsServerStop {
   }
 }
 */
+
+task ideBuildSite {
+  dependsOn jalviewjsSitePath
+  dependsOn jalviewjsUnzipFiles
+  dependsOn jalviewjsCopyResources
+  dependsOn jalviewjsCopySiteResources
+  dependsOn ideSetup
+  dependsOn ide
+}
+
+
+
+
+task jalviewjs {
+  dependsOn jalviewjsBuildSite
+}
+
+
+project.afterEvaluate {
+  tasks.findByName('ideJalviewjsBuild').dependsOn eclipseProject
+  tasks.findByName('ideJalviewjsBuild').dependsOn eclipseClasspath
+  tasks.findByName('ideJalviewjsBuild').dependsOn eclipseJdt
+  //tasks.findByName('ideJalviewjsBuild').dependsOn ideSetup
+
+  tasks.findByName('ide').dependsOn eclipseProject
+  tasks.findByName('ide').dependsOn eclipseClasspath
+  tasks.findByName('ide').dependsOn eclipseJdt
+}
+
+
+