import org.gradle.internal.os.OperatingSystem
import org.gradle.plugins.ide.eclipse.model.Output
import org.gradle.plugins.ide.eclipse.model.Library

import com.diffplug.gradle.GoomphCacheLocations

buildscript {
}

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'
}

def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
def useIde = useGoomph.equals("true")

repositories {
  jcenter()
  mavenCentral()
  flatDir {
    dirs gradlePluginsDir
  }
  if (true || useIde) {
    flatDir {
      dirs jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir
    }
  }
}

configurations {
  jalviewjsIde
}


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 {
/*
    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'

}






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 libDir
def libDistDir
def compile_source_compatibility
def compile_target_compatibility

ext {
  buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile

  gitHash = ""
  gitBranch = ""

  jalviewjsServer = ""
}

def JAVA_INTEGER_VERSION
//def additional_compiler_args = []
// this property is for the Java library used in eclipse
def eclipse_java_runtime_name
if (JAVA_VERSION.equals("1.8")) {
  JAVA_INTEGER_VERSION = "8"
  //libDir = j8libDir
  libDir = j11libDir
  libDistDir = j8libDir
  compile_source_compatibility = 1.8
  compile_target_compatibility = 1.8
  eclipse_java_runtime_name = "JavaSE-1.8"
} else if (JAVA_VERSION.equals("11")) {
  JAVA_INTEGER_VERSION = "11"
  libDir = j11libDir
  libDistDir = j11libDir
  compile_source_compatibility = 11
  compile_target_compatibility = 11
  eclipse_java_runtime_name = "JavaSE-11"
  /* compile without modules -- using classpath libraries
  additional_compiler_args += [
  '--module-path', ext.modules_compileClasspath.asPath,
  '--add-modules', j11modules
  ]
  */
} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
  JAVA_INTEGER_VERSION = JAVA_VERSION
  libDir = j11libDir
  libDistDir = j11libDir
  compile_source_compatibility = JAVA_VERSION
  compile_target_compatibility = JAVA_VERSION
  eclipse_java_runtime_name = "JavaSE-11"
  /* compile without modules -- using classpath libraries
  additional_compiler_args += [
  '--module-path', ext.modules_compileClasspath.asPath,
  '--add-modules', j11modules
  ]
  */
} else {
  throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
}


sourceSets {

  main {
    java {
      srcDirs "$jalviewDir/$sourceDir"
      outputDir = file("$classes")
    }

    resources {
      srcDirs "$jalviewDir/$resourceDir"
    }

    compileClasspath = files(sourceSets.main.java.outputDir)
    compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])

    runtimeClasspath = compileClasspath
  }

}

eclipse {
  project {
    name = eclipse_project_name

    natures 'org.eclipse.jdt.core.javanature',
    'org.eclipse.buildship.core.gradleprojectnature'

    buildCommand 'org.eclipse.jdt.core.javabuilder'
    buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
  }

  classpath {
    //defaultOutputDir = sourceSets.main.java.outputDir
    def removeThese = []
    configurations.each{ if (it.isCanBeResolved()) {
        removeThese += it
      }
    }

    minusConfigurations += removeThese
    plusConfigurations = [ ]
    file {

      whenMerged { cp ->
        def removeTheseToo = []
        HashMap<String, Boolean> addedSrcPath = new HashMap<>();
        cp.entries.each { entry ->
          if (entry.kind == 'src') {
            if (addedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == "test")) {
              removeTheseToo += entry
            } else {
              addedSrcPath.putAt(entry.path, true)
            }
          }
        }
        cp.entries.removeAll(removeTheseToo)

	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<>();

        // changing from sourcesets.main.classpath to specific Java version lib
        //sourceSets.main.compileClasspath.each{
        fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
          //don't want to add outputDir as eclipse is using its own output dir in bin/main
          if (it.isDirectory() || ! it.exists()) {
            // don't add dirs to classpath
            return
          }
          def itPath = it.toString()
          if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
            itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
          }
          if (addedLibPath.get(itPath)) {
            //println("Not adding duplicate entry "+itPath)
          } else {
            //println("Adding entry "+itPath)
            cp.entries += new Library(fileReference(itPath))
            addedLibPath.put(itPath, true)
          }
        }
      } // whenMerged

    } // file

    containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
  } // classpath

  jdt {
    // for the IDE, use java 11 compatibility
    sourceCompatibility = compile_source_compatibility
    targetCompatibility = compile_target_compatibility
    javaRuntimeName = eclipse_java_runtime_name

    /*
    file {
    withProperties { props ->
    def jalview_prefs = new Properties()
    def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
    jalview_prefs.load(ins)
    ins.close()
    jalview_prefs.forEach { t, v ->
    if (props.getAt(t) == null) {
    props.putAt(t, v)
    }
    }
    }
    }
     */
  } // jdt

  //synchronizationTasks eclipseClasspath
  //autoBuildTasks eclipseClasspath
} // eclipse

/*
compileJava {

  doFirst {
    sourceCompatibility = compile_source_compatibility
    targetCompatibility = compile_target_compatibility
    //options.compilerArgs = additional_compiler_args
    print ("Setting target compatibility to "+targetCompatibility+"\n")
  }

}

clean {
  delete sourceSets.main.java.outputDir
}
*/





















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) {

  oomphIde {
    repoEclipse goomph_eclipse_version
    jdt {
      /*
      installedJre {
      //markDefault = true
      //executionEnvironments = [ eclipse.jdt.javaRuntimeName ]
      }
       */
      //compilerComplianceLevel( JAVA_INTEGER_VERSION )
    }

    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
      }

    }

    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)
    }


    // CLI ARGS HERE!
  }

  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 ]
      }

      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) {}













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
  }
}


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"
    }
  }
}

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
      }
    }
  }
}

task jalviewjsEclipseSetup {
  dependsOn jalviewjsEclipseCopyDropins
  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 = jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir

  from inputFiles
  into outputDir
  def outputFiles = []
  rename { filename ->
    outputFiles += outputDir+"/"+filename
    null
  }
  outputs.files outputFiles
  inputs.files inputFiles
}

task jalviewjsCopySiteResources (type: Copy) {
  dependsOn jalviewjsSitePath
  def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_site_resource_dir)
  def outputDir = jalviewjsSiteDir

  from inputFiles
  into outputDir
  def outputFiles = []
  rename { filename ->
    outputFiles += outputDir+"/"+filename
    null
  }
  outputs.files outputFiles
  inputs.files inputFiles
}

task cleanJalviewjs {
  dependsOn jalviewjsSitePath
  delete jalviewDir+"/"+jalviewjsSiteDir
  //delete jalviewDir+"/"+eclipse_bin_dir
  //delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
  //delete jalviewDir+"/"+jalviewjs_j2s_settings
}

task jalviewjsProjectImport(type: Exec) {
  // work out how to do this!
  dependsOn eclipseProject
  dependsOn eclipseClasspath
  dependsOn eclipseJdt
  dependsOn jalviewjsEclipsePaths
  dependsOn jalviewjsEclipseSetup
  executable(eclipseBinary)
  args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])

  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", 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.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 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 = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
  try {
    archiveFileName = outputFilename
  } catch (Exception e) {
    archiveName = outputFilename
  }

  compression Compression.GZIP

  from jalviewjsSiteDir
  into jalviewjs_site_dir // this is inside the tar file

  inputs.dir(jalviewjsSiteDir)
}

def jalviewjsServer = null
task jalviewjsServerStart {
  group "JalviewJS"
  description "Starts a webserver on localhost to test the website"
  dependsOn jalviewjsSitePath
  doLast {

    if (jalviewjsServer != null) {
      println("SERVER ALREADY RUNNING. Go to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run  gradle jalviewjsServerStop  to stop.")
    } else {

      SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
      def port = Integer.valueOf(jalviewjs_server_port)
      def start = port
      def running = false
      while(port < start+1000 && !running) {
        try {
          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 --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++;
        }
      }

    }

  }

}

/* server persists in gradle daemon but reference is not accessible across builds
task jalviewjsServerStop {
  doLast {

    if (jalviewjsServer != null) {

      println("SERVER ON PORT "+jalviewjsServer.getPort()+" STOPPING. Run  gradle jalviewjsServerStart  to start again.")
      jalviewjsServer.stop()

    } else {
      println("SERVER NOT RUNNING. Run  gradle jalviewjsServerStart  to start.")
    }

  }
}
*/

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')
  }

}