/* Convention for properties.  Read from gradle.properties, use lower_case_underlines for property names.
 * For properties set within build.gradle, use camelCaseNoSpace.
 */
import org.apache.tools.ant.filters.ReplaceTokens
import org.gradle.internal.os.OperatingSystem
import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
import org.gradle.api.internal.PropertiesTransformer
import org.gradle.util.ConfigureUtil
import java.security.MessageDigest
import java.text.SimpleDateFormat
import java.util.regex.Matcher
import java.util.concurrent.Executors
import java.util.concurrent.Future
import java.util.concurrent.ScheduledExecutorService
import java.util.concurrent.TimeUnit
import groovy.transform.ExternalizeMethods
import groovy.util.XmlParser
import groovy.xml.XmlUtil
import groovy.json.JsonBuilder

buildscript {
  repositories {
    mavenCentral()
    mavenLocal()
  }
}


plugins {
  id 'java'
  id 'application'
}

repositories {
  mavenCentral()
  mavenLocal()
}



// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
def string(Object o) {
  return o == null ? "" : o.toString()
}

def overrideProperties(String propsFileName, boolean output = false) {
  if (propsFileName == null) {
    return
  }
  def propsFile = file(propsFileName)
  if (propsFile != null && propsFile.exists()) {
    println("Using properties from file '${propsFileName}'")
    try {
      def p = new Properties()
      def localPropsFIS = new FileInputStream(propsFile)
      p.load(localPropsFIS)
      localPropsFIS.close()
      p.each {
        key, val -> 
          def oldval
          if (project.hasProperty(key)) {
            oldval = project.findProperty(key)
            project.setProperty(key, val)
            if (output) {
              println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
            }
          } else {
            ext.setProperty(key, val)
            if (output) {
              println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
            }
          }
      }
    } catch (Exception e) {
      println("Exception reading local.properties")
      e.printStackTrace()
    }
  }
}

ext {
  jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
  jalviewDirRelativePath = jalviewDir

  // Verbose and maybe not efficient hack to put the changelog date into the
  // "date" variable, which will be used to insert e.g. years in doc files.
  // This is to make the build reproducible.
  def outBAdate = new ByteArrayOutputStream()
  exec {
    commandLine 'dpkg-parsechangelog', '-Stimestamp'
    standardOutput = outBAdate
  }
  dateWithEOL = outBAdate.toString()
  dateWithoutEOL = dateWithEOL.substring(0, dateWithEOL.length() - 1)

  def outBA = new ByteArrayOutputStream()
  exec {
    commandLine 'date', '--utc', "--date=@${dateWithoutEOL}", '+"%d/%m/%Y-%H:%M:%S"'
    standardOutput = outBA
  }
  toParseWithEOLAndQuotes = outBA.toString()
  toParseWithoutEOLAndQuotes = toParseWithEOLAndQuotes.substring(1, toParseWithEOLAndQuotes.length() - 2)
  date = new SimpleDateFormat("dd/MM/yyyy-HH:mm:ss").parse(toParseWithoutEOLAndQuotes)

  // default to "default". Currently only has different cosmetics for "develop", "release", "default"
  propertiesChannelName = "default"
  channelDirName = propertiesChannelName
  channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}")
  channelGradleProperties = string("${channelDir}/channel_gradle.properties")
  channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
  overrideProperties(channelGradleProperties, false)
  // local build environment properties
  // can be "projectDir/local.properties"
  overrideProperties("${projectDir}/local.properties", true)
  // or "../projectDir_local.properties"
  overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)

  ////  
  // Import releaseProps from the RELEASE file
  // or a file specified via JALVIEW_RELEASE_FILE if defined
  // Expect jalview.version and target release branch in jalview.release        
  releaseProps = new Properties();
  def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
  def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
  try {
    (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream { 
     releaseProps.load(it)
    }
  } catch (Exception fileLoadError) {
    throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
  }
  ////
  // Set JALVIEW_VERSION if it is not already set
  if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
    JALVIEW_VERSION = releaseProps.get("jalview.version")
  }
  println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
  
  J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
  if (J2S_ENABLED) {
    println("J2S ENABLED")
  } 
  /* *-/
  System.properties.sort { it.key }.each {
    key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
  }
  /-* *-/
  if (false && IN_ECLIPSE) {
    jalviewDir = jalviewDirAbsolutePath
  }
  */

  // datestamp
  buildDate = new Date().format("yyyyMMdd")

  // essentials
  bareSourceDir = string(source_dir)
  sourceDir = string("${jalviewDir}/${bareSourceDir}")
  resourceDir = string("${jalviewDir}/${resource_dir}")
  bareTestSourceDir = string(test_source_dir)
  testDir = string("${jalviewDir}/${bareTestSourceDir}")

  classesDir = string("${jalviewDir}/${classes_dir}")

  testSourceDir = testDir
  testClassesDir = "${jalviewDir}/${test_output_dir}"

  channelSuffix = ""
  backgroundImageText = BACKGROUNDIMAGETEXT
  buildDist = true
  buildProperties = null

  reportRsyncCommand = false
  jvlChannelName = CHANNEL.toLowerCase()

  applicationName = "${jalview_name}"
  JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
  hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
  hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")

  /* compile without modules -- using classpath libraries
  modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
  modules_runtimeClasspath = modules_compileClasspath
  */

  additional_compiler_args = []
  // configure classpath/args for j8/j11 compilation
  if (JAVA_VERSION.equals("1.8")) {
    JAVA_INTEGER_VERSION = string("8")
    //libDir = j8libDir
    libDir = "${jalviewDir}/cpJars"
    libDistDir = "${jalviewDir}/cpJars"
    compile_source_compatibility = 1.8
    compile_target_compatibility = 1.8
  } else if (JAVA_VERSION.equals("11")) {
    JAVA_INTEGER_VERSION = string("11")
    libDir = "${jalviewDir}/cpJars"
    libDistDir = "${jalviewDir}/cpJars"
    compile_source_compatibility = 11
    compile_target_compatibility = 11
    /* compile without modules -- using classpath libraries
    additional_compiler_args += [
    '--module-path', modules_compileClasspath.asPath,
    '--add-modules', j11modules
    ]
     */
  } else if (JAVA_VERSION.equals("17")) {
    JAVA_INTEGER_VERSION = string("17")
    libDir = "${jalviewDir}/cpJars"
    libDistDir = "${jalviewDir}/cpJars"
    compile_source_compatibility = 17
    compile_target_compatibility = 17
    /* compile without modules -- using classpath libraries
    additional_compiler_args += [
    '--module-path', modules_compileClasspath.asPath,
    '--add-modules', j11modules
    ]
     */
  } else {
    throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
  }


  resourceBuildDir = string("${buildDir}/resources")
  resourcesBuildDir = string("${resourceBuildDir}/resources_build")
  helpBuildDir = string("${resourceBuildDir}/help_build")
  docBuildDir = string("${resourceBuildDir}/doc_build")

  if (buildProperties == null) {
    buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
  }
  buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
  helpParentDir = string("${jalviewDir}/${help_parent_dir}")
  helpSourceDir = string("${helpParentDir}/${help_dir}")
  helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")

  convertBinary = null
  convertBinaryExpectedLocation = imagemagick_convert
  if (convertBinaryExpectedLocation.startsWith("~/")) {
    convertBinaryExpectedLocation = System.getProperty("user.home") + convertBinaryExpectedLocation.substring(1)
  }
  if (file(convertBinaryExpectedLocation).exists()) {
    convertBinary = convertBinaryExpectedLocation
  }

  relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
  jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
  jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
    jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
  jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
  jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
  jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
  jalviewjsJalviewCoreHtmlFile = string("")
  jalviewjsJalviewCoreName = string(jalviewjs_core_name)
  jalviewjsCoreClasslists = []
  jalviewjsJalviewTemplateName = string(jalviewjs_name)
  jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
  jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
  jalviewjsJ2sProps = null
  jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
  jalviewjsStderrLaunchFilename = "${jalviewjsSiteDir}/"+(file(jalviewjs_stderr_launch).getName())

  jalviewjsChromiumUserDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}"
  jalviewjsChromiumProfileDir = "${ext.jalviewjsChromiumUserDir}/${jalviewjs_chromium_profile_name}"

  // ENDEXT
}


sourceSets {
  main {
    java {
      srcDirs sourceDir
      outputDir = file(classesDir)
      exclude "**/appletgui/**"
      exclude "**/AppletPDBViewer.java"
      exclude "**/AppletPDBCanvas.java"
      exclude "**/javascript/J*.java"
      exclude "**/javascript/MouseOverListener.java"
      exclude "**/javascript/MouseOverStructureListener.java"
      exclude "**/JalviewLite*"
    }

    resources {
      srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
    }

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

    runtimeClasspath = compileClasspath
    runtimeClasspath += files(sourceSets.main.resources.srcDirs)
  }

  test {
    java {
      srcDirs testSourceDir
      outputDir = file(testClassesDir)
      exclude "**/CommandLineOperationsNG.java"
      exclude "**/JalviewLiteTest.java"
    }

    resources {
      srcDirs = sourceSets.main.resources.srcDirs
    }

    compileClasspath = files( sourceSets.test.java.outputDir )
    compileClasspath += sourceSets.main.compileClasspath

    runtimeClasspath = compileClasspath
    runtimeClasspath += files(sourceSets.test.resources.srcDirs)
  }

}


/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
// Class to allow updating arbitrary properties files
class PropertiesFile extends PropertiesPersistableConfigurationObject {
  public PropertiesFile(PropertiesTransformer t) { super(t); }
  @Override protected void load(Properties properties) { }
  @Override protected void store(Properties properties) { }
  @Override protected String getDefaultResourceName() { return ""; }
  // This is necessary, because PropertiesPersistableConfigurationObject fails
  // if no default properties file exists.
  @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
}

// Task to update arbitrary properties files (set outputFile)
class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
  private final PropertiesFileContentMerger file;
  public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
  protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
  protected void configure(PropertiesFile props) {
    file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
  }
  public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
}


compileJava {
  // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
  sourceCompatibility = compile_source_compatibility
  targetCompatibility = compile_target_compatibility
  options.compilerArgs += additional_compiler_args
  options.encoding = "UTF-8"
  excludes = ["**/GetdownLauncherUpdate.java"]
  doFirst {
    print ("Setting target compatibility to "+compile_target_compatibility+"\n")
  }

}


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


clean {
  doFirst {
    delete sourceSets.main.java.outputDir
  }
}


cleanTest {
  doFirst {
    delete sourceSets.test.java.outputDir
  }
}


// format is a string like date.format("dd MMMM yyyy")
def getDate(format) {
  return date.format(format)
}


task copyDocs(type: Copy) {
  def inputDir = "${jalviewDir}/${doc_dir}"
  def outputDir = "${docBuildDir}/${doc_dir}"
  from(inputDir) {
    include('**/*.txt')
    include('**/*.md')
    include('**/*.html')
    include('**/*.xml')
    filter(ReplaceTokens,
      beginToken: '$$',
      endToken: '$$',
      tokens: [
        'Version-Rel': JALVIEW_VERSION,
        'Year-Rel': getDate("yyyy")
      ]
    )
  }
  from(inputDir) {
    exclude('**/*.txt')
    exclude('**/*.md')
    exclude('**/*.html')
    exclude('**/*.xml')
  }
  into outputDir

  inputs.dir(inputDir)
  outputs.dir(outputDir)
}


task convertMdFiles {
  dependsOn copyDocs
  def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
  def cssFile = file("${jalviewDir}/${flexmark_css}")

  inputs.files(mdFiles)
  inputs.file(cssFile)

  def htmlFiles = []
  mdFiles.each { mdFile ->
    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
    htmlFiles.add(file(htmlFilePath))
  }
  outputs.files(htmlFiles)
}


def hugoTemplateSubstitutions(String input, Map extras=null) {
  def replacements = [
    DATE: getDate("yyyy-MM-dd"),
    CHANNEL: propertiesChannelName,
    APPLICATION_NAME: applicationName,
    GIT_HASH: gitHash,
    GIT_BRANCH: gitBranch,
    VERSION: JALVIEW_VERSION,
    JAVA_VERSION: JAVA_VERSION,
    VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
    DRAFT: "false",
    JVL_HEADER: ""
  ]
  def output = input
  if (extras != null) {
    extras.each{ k, v ->
      output = output.replaceAll("__${k}__", ((v == null)?"":v))
    }
  }
  replacements.each{ k, v ->
    output = output.replaceAll("__${k}__", ((v == null)?"":v))
  }
  return output
}

def mdFileComponents(File mdFile, def dateOnly=false) {
  def map = [:]
  def content = ""
  if (mdFile.exists()) {
    def inFrontMatter = false
    def firstLine = true
    mdFile.eachLine { line ->
      if (line.matches("---")) {
        def prev = inFrontMatter
        inFrontMatter = firstLine
        if (inFrontMatter != prev)
          return false
      }
      if (inFrontMatter) {
        if (dateOnly && map["date"] != null) {
          return false
        }
      } else {
        if (dateOnly)
          return false
        content += line+"\n"
      }
      firstLine = false
    }
  }
  return dateOnly ? map["date"] : [map, content]
}

def setReleaseAndWhatsNew(File whatsnewMdFile, File releaseMdFile) {
  if (CHANNEL != "") {
    // we may have a version string that has additional bits vs the actual release version
    if (CHANNEL != "RELEASE")
    {
      var nearestVersion = "${JALVIEW_VERSION_UNDERSCORES}"
      println "Stripping rc/test/etc for ${nearestVersion}"
      nearestVersion = nearestVersion.replaceAll(~/-?(d|rc|test|develop|dev).*/,"")
      var nearestMd = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${nearestVersion}.md")
      println "Looking in ${nearestMd}"
      if (nearestMd.exists()) {
        whatsnewMdFile = nearestMd
        releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${nearestVersion}.md")
      }
    }
  }
  return [whatsnewMdFile,releaseMdFile]
}

task hugoTemplates {
  group "website"
  description "Create partially populated md pages for hugo website build"

  def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
  def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
  def templateFiles = fileTree(dir: hugoTemplatesDir)
  def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
  def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
  def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
  def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")

  doFirst {
    // specific release template for version archive
    def changes = ""
    def whatsnew = null
    def givenDate = null
    def givenChannel = null
    def givenVersion = null
    
    if (CHANNEL!="") {
      (whatsnewMdFile, releaseMdFile) = setReleaseAndWhatsNew(whatsnewMdFile, releaseMdFile)

      def (map, content) = mdFileComponents(releaseMdFile)
      givenDate = map.date
      givenChannel = map.channel
      givenVersion = map.version
      changes = content
      if (CHANNEL=="RELEASE" && givenVersion != null && givenVersion != JALVIEW_VERSION) {
        throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
      }
      if (whatsnewMdFile.exists())
        whatsnew = whatsnewMdFile.text
    }

    def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
    def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []

    def changesHugo = null
    if (changes != null) {
      changesHugo = '<div class="release_notes">\n\n'
      def inSection = false
      changes.eachLine { line ->
        changesHugo += line+"\n"
      }
      if (inSection) {
        changesHugo += "\n</div>\n\n"
      }
      changesHugo += '</div>'
    }

    templateFiles.each{ templateFile ->
      def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
      def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
      def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )

      def outPathName = string("${hugoBuildDir}/$newRelPathName")

      copy {
        from templateFile
        rename(templateFile.getName(), newFileName)
        into outPathName
      }

      def newFile = file("${outPathName}/${newFileName}".toString())
      def content = newFile.text
      newFile.text = hugoTemplateSubstitutions(content,
        [
          WHATSNEW: whatsnew,
          CHANGES: changesHugo,
          DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
          DRAFT: givenDate == null ? "true" : "false",
          JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
          JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
        ]
      )
    }

  }

  inputs.file(oldJvlFile)
  inputs.dir(hugoTemplatesDir)
  inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
  inputs.property("CHANNEL", { CHANNEL })
}

def getMdDate(File mdFile) {
  return mdFileComponents(mdFile, true)
}

def getMdSections(String content) {
  def sections = [:]
  def sectionContent = ""
  def sectionName = null
  if (sectionContent != null) {
    sections[sectionName] = sectionContent
  }
  return sections
}


task copyHelp(type: Copy) {
  def inputDir = helpSourceDir
  def outputDir = "${helpBuildDir}/${help_dir}"
  from(inputDir) {
    include('**/*.txt')
    include('**/*.md')
    include('**/*.html')
    include('**/*.hs')
    include('**/*.xml')
    include('**/*.jhm')
    filter(ReplaceTokens,
      beginToken: '$$',
      endToken: '$$',
      tokens: [
        'Version-Rel': JALVIEW_VERSION,
        'Year-Rel': getDate("yyyy")
      ]
    )
  }
  from(inputDir) {
    exclude('**/*.txt')
    exclude('**/*.md')
    exclude('**/*.html')
    exclude('**/*.hs')
    exclude('**/*.xml')
    exclude('**/*.jhm')
  }
  into outputDir

  inputs.dir(inputDir)
  outputs.files(helpFile)
  outputs.dir(outputDir)
}


task releasesTemplates {
  group "help"
  description "Recreate whatsNew.html and releases.html from markdown files and templates in help"

  dependsOn copyHelp

  def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
  def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
  def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
  def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
  def releasesMdDir = "${jalviewDir}/${releases_dir}"
  def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"

  inputs.file(releasesTemplateFile)
  inputs.file(whatsnewTemplateFile)
  inputs.dir(releasesMdDir)
  inputs.dir(whatsnewMdDir)
  outputs.file(releasesHtmlFile)
  outputs.file(whatsnewHtmlFile)
}


task copyResources(type: Copy) {
  group = "build"
  description = "Copy (and make text substitutions in) the resources dir to the build area"

  def inputDir = resourceDir
  def outputDir = resourcesBuildDir
  from(inputDir) {
    include('**/*.txt')
    include('**/*.md')
    include('**/*.html')
    include('**/*.xml')
    filter(ReplaceTokens,
      beginToken: '$$',
      endToken: '$$',
      tokens: [
        'Version-Rel': JALVIEW_VERSION,
        'Year-Rel': getDate("yyyy")
      ]
    )
  }
  from(inputDir) {
    exclude('**/*.txt')
    exclude('**/*.md')
    exclude('**/*.html')
    exclude('**/*.xml')
  }
  into outputDir

  inputs.dir(inputDir)
  outputs.dir(outputDir)
}

task copyChannelResources(type: Copy) {
  dependsOn copyResources
  group = "build"
  description = "Copy the channel resources dir to the build resources area"

  def inputDir = "${channelDir}/${resource_dir}"
  def outputDir = resourcesBuildDir
  from(inputDir) {
    include(channel_props)
    filter(ReplaceTokens,
      beginToken: '__',
      endToken: '__',
      tokens: [
        'SUFFIX': channelSuffix
      ]
    )
  }
  from(inputDir) {
    exclude(channel_props)
  }
  into outputDir

  inputs.dir(inputDir)
  outputs.dir(outputDir)
}

//task createBuildProperties(type: WriteProperties) {
task createBuildProperties(type: Exec) {
  dependsOn copyResources
  group = "build"
  description = "Create the ${buildProperties} file"
  
  commandLine 'sh', 'debian/write_build_properties_file.sh'
}


task buildIndices(type: JavaExec) {
  dependsOn copyHelp
  classpath = sourceSets.main.compileClasspath
  main = "com.sun.java.help.search.Indexer"
  workingDir = "${helpBuildDir}/${help_dir}"
  def argDir = "html"
  args = [ argDir ]
  inputs.dir("${workingDir}/${argDir}")

  outputs.dir("${classesDir}/doc")
  outputs.dir("${classesDir}/help")
  outputs.file("${workingDir}/JavaHelpSearch/DOCS")
  outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
  outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
  outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
  outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
  outputs.file("${workingDir}/JavaHelpSearch/TMAP")
}

task buildResources {
  dependsOn copyResources
  dependsOn copyChannelResources
  dependsOn createBuildProperties
}

task prepare {
  dependsOn buildResources
  dependsOn copyDocs
  dependsOn copyHelp
  dependsOn releasesTemplates
  dependsOn convertMdFiles
  dependsOn buildIndices
}


compileJava.dependsOn prepare
run.dependsOn compileJava
compileTestJava.dependsOn compileJava



test {
  group = "Verification"
  description = "Runs all testTaskN tasks)"

    dependsOn testClasses

  // not running tests in this task
  exclude "**/*"
}
/* testTask0 is the main test task */
task testTask0(type: Test) {
  group = "Verification"
  description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
  useTestNG() {
    includeGroups testng_groups.split(",")
    excludeGroups "Network"
    tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
    preserveOrder true
    useDefaultListeners=true
  }

  include '**/AtomSpecModelTest.class'
  include '**/AtomSpecTest.class'
  include '**/ClustalFileTest.class'
  include '**/ConcurrentModificationTest.class'
  include '**/ConditionTest.class'
  include '**/CustomUrlProviderTest.class'
  include '**/DesktopUrlProviderFactoryTest.class'
  include '**/EmblFlatFileTest.class'
  include '**/EmblXmlSourceTest.class'
  include '**/EnsemblRestClientTest.class'
  include '**/FeatureAttributesTest.class'
  include '**/FeatureMatcherSetTest.class'
  include '**/FeatureMatcherTest.class'
  include '**/FeatureStoreTest.class'
  include '**/FileFormatsTest.class'
  include '**/FileLoaderTest.class'
  include '**/GeneticCodesTest.class'
  include '**/HiddenColumnsCursorTest.class'
  include '**/HiddenColumnsTest.class'
  include '**/IdentifiersUrlProviderTest.class'
  include '**/JalviewColourSchemeTest.class'
  include '**/JalviewFileViewTest.class'
  include '**/JSONUtilsTest.class'
  include '**/JvCacheableInputBoxTest.class'
  include '**/MappedFeaturesTest.class'
  include '**/MatcherTest.class'
  include '**/MathUtilsTest.class'
  include '**/MatrixTest.class'
  include '**/MemorySettingTest.class'
  include '**/MessageManagerTest.class'
  include '**/OverviewDimensionsHideHiddenTest.class'
  include '**/OverviewDimensionsShowHiddenTest.class'
  include '**/PfamFullTest.class'
  include '**/PfamSeedTest.class'
  include '**/PIDModelTest.class'
  include '**/RangeElementsIteratorTest.class'
  include '**/RemoteFormatTest.class'
  include '**/RfamFullTest.class'
  include '**/RfamSeedTest.class'
  include '**/RotatableMatrixTest.class'
  include '**/ScoreMatrixFileTest.class'
  include '**/ScoreMatrixTest.class'
  include '**/ScoreModelsTest.class'
  include '**/SequenceFeaturesTest.class'
  include '**/SequenceOntologyLiteTest.class'
  include '**/SparseDoubleArrayTest.class'
  include '**/SparseMatrixTest.class'
  include '**/SpeciesTest.class'
  include '**/StartRegionIteratorTest.class'
  include '**/StructureMappingTest.class'
  include '**/UrlDownloadClientTest.class'
  include '**/UrlLinkDisplayTest.class'
  include '**/UrlLinkTableModelTest.class'
  include '**/UrlProviderTest.class'
  include '**/VCFReaderTest.class'
  include '**/ViewportRangesTest.class'
  include '**/VisibleContigsIteratorTest.class'
  include '**/VisibleRowsIteratorTest.class'
  exclude 'jalview/gui/**'
}

/* separated tests */
task testTask1(type: Test) {
  group = "Verification"
  description = "Tests that need to be isolated from the main test run"
  useTestNG() {
    includeGroups name
    excludeGroups testng_excluded_groups.split(",")
    preserveOrder true
    useDefaultListeners=true
  }
}

task testTask2(type: Test) {
  group = "Verification"
  description = "Tests that need to be isolated from the main test run"
  useTestNG() {
    includeGroups name
    excludeGroups testng_excluded_groups.split(",")
    preserveOrder true
    useDefaultListeners=true
  }
}
task testTask3(type: Test) {
  group = "Verification"
  description = "Tests that need to be isolated from the main test run"
  useTestNG() {
    includeGroups name
    excludeGroups testng_excluded_groups.split(",")
    preserveOrder true
    useDefaultListeners=true
  }
}

/* insert more testTaskNs here -- change N to next digit or other string */
/*
task testTaskN(type: Test) {
  group = "Verification"
  description = "Tests that need to be isolated from the main test run"
  useTestNG() {
    includeGroups name
    excludeGroups testng_excluded_groups.split(",")
    preserveOrder true
    useDefaultListeners=true
  }
}
*/


/*
 * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
 * to summarise test results from all Test tasks
 */
/* START of test tasks results summary */
import groovy.time.TimeCategory
import org.gradle.api.tasks.testing.logging.TestExceptionFormat
import org.gradle.api.tasks.testing.logging.TestLogEvent
rootProject.ext.testsResults = [] // Container for tests summaries

tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->

  // from original test task
    dependsOn testClasses //?

  // run main tests first
  if (!testTask.name.equals("testTask0"))
    testTask.mustRunAfter "testTask0"

  testTask.testLogging { logging ->
    events TestLogEvent.FAILED
//      TestLogEvent.SKIPPED,
//      TestLogEvent.STANDARD_OUT,
//      TestLogEvent.STANDARD_ERROR

    exceptionFormat TestExceptionFormat.FULL
    showExceptions true
    showCauses true
    showStackTraces true
    if (test_output) {
      showStandardStreams true
    }
    info.events = [ TestLogEvent.FAILED ]
  }

  if (OperatingSystem.current().isMacOsX()) {
    testTask.systemProperty "apple.awt.UIElement", "true"
    testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
  }


  ignoreFailures = true // Always try to run all tests for all modules

  afterSuite { desc, result ->
    if (desc.parent)
      return // Only summarize results for whole modules

    def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]

    rootProject.ext.testsResults.add(resultsInfo)
  }

  // from original test task
  maxHeapSize = "1024m"

  workingDir = jalviewDir
  def testLaf = project.findProperty("test_laf")
  if (testLaf != null) {
    println("Setting Test LaF to '${testLaf}'")
    systemProperty "laf", testLaf
  }
  def testHiDPIScale = project.findProperty("test_HiDPIScale")
  if (testHiDPIScale != null) {
    println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
    systemProperty "sun.java2d.uiScale", testHiDPIScale
  }
  sourceCompatibility = compile_source_compatibility
  targetCompatibility = compile_target_compatibility
  jvmArgs += additional_compiler_args

  doFirst {
    // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
    // testTasks that include the tests, and exclude all from the others.
    // get --test argument
    filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
    // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
    // commandLineIncludePatterns not matching anything.  Instead we are doing setFailOnNoMatchingTests(false) below


  }


  /* don't fail on no matching tests (so --tests will run across all testTasks) */
  testTask.filter.setFailOnNoMatchingTests(false)

  /* ensure the "test" task dependsOn all the testTasks */
  test.dependsOn testTask
}

gradle.buildFinished {
    def allResults = rootProject.ext.testsResults

    if (!allResults.isEmpty()) {
        printResults allResults
        allResults.each {r ->
          if (r[2].resultType == TestResult.ResultType.FAILURE)
            throw new GradleException("Failed tests!")
        }
    }
}

private static String colString(styler, col, colour, text) {
  return col?"${styler[colour](text)}":text
}

private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
  def colour = 'black'
  def text = rt
  def nocol = false
  if (rc == 0) {
    text = "-----"
    nocol = true
  } else {
    switch(rt) {
      case TestResult.ResultType.SUCCESS:
        colour = 'green'
        break;
      case TestResult.ResultType.FAILURE:
        colour = 'red'
        break;
      default:
        nocol = true
        break;
    }
  }
  StringBuilder sb = new StringBuilder()
  sb.append("${pn}")
  if (tn != null)
    sb.append(":${tn}")
  sb.append(" results: ")
  sb.append(colString(s, col && !nocol, colour, text))
  sb.append(" (")
  sb.append("${rc} tests, ")
  sb.append(colString(s, col && rs > 0, 'green', rs))
  sb.append(" successes, ")
  sb.append(colString(s, col && rf > 0, 'red', rf))
  sb.append(" failures, ")
  sb.append("${rsk} skipped) in ${t}")
  return sb.toString()
}

private static void printResults(allResults) {

    // styler from https://stackoverflow.com/a/56139852
    def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }

    def maxLength = 0
    def failedTests = false
    def summaryLines = []
    def totalcount = 0
    def totalsuccess = 0
    def totalfail = 0
    def totalskip = 0
    def totaltime = TimeCategory.getSeconds(0)
    // sort on project name then task name
    allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
      def projectName = it[0]
      def taskName = it[1]
      def result = it[2]
      def time = it[3]
      def report = it[4]
      def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
      def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
      def reportLine = "Report file: ${report}"
      def ls = summaryPlain.length()
      def lr = reportLine.length()
      def m = [ls, lr].max()
      if (m > maxLength)
        maxLength = m
      def info = [ls, summaryCol, reportLine]
      summaryLines.add(info)
      failedTests |= result.resultType == TestResult.ResultType.FAILURE
      totalcount += result.testCount
      totalsuccess += result.successfulTestCount
      totalfail += result.failedTestCount
      totalskip += result.skippedTestCount
      totaltime += time
    }
    def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
    def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
    def tls = totalSummaryPlain.length()
    if (tls > maxLength)
      maxLength = tls
    def info = [tls, totalSummaryCol, null]
    summaryLines.add(info)

    def allSummaries = []
    for(sInfo in summaryLines) {
      def ls = sInfo[0]
      def summary = sInfo[1]
      def report = sInfo[2]

      StringBuilder sb = new StringBuilder()
      sb.append("│" + summary + " " * (maxLength - ls) + "│")
      if (report != null) {
        sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
      }
      allSummaries += sb.toString()
    }

    println "┌${"${"─" * maxLength}"}┐"
    println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
    println "└${"${"─" * maxLength}"}┘"
}
/* END of test tasks results summary */


task compileLinkCheck(type: JavaCompile) {
  options.fork = true
  classpath = files("${jalviewDir}/${utils_dir}")
  destinationDir = file("${jalviewDir}/${utils_dir}")
  source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])

  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
  outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
  outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
}


task linkCheck(type: JavaExec) {
  dependsOn prepare
  dependsOn compileLinkCheck

  def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
  classpath = files("${jalviewDir}/${utils_dir}")
  main = "HelpLinksChecker"
  workingDir = "${helpBuildDir}"
  args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]

  def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
  standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
    outFOS,
    System.out)
  errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
    outFOS,
    System.err)

  inputs.dir(helpBuildDir)
  outputs.file(helpLinksCheckerOutFile)
}


// import the pubhtmlhelp target
ant.properties.basedir = "${jalviewDir}"
ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
ant.importBuild "${utils_dir}/publishHelp.xml"


task cleanPackageDir(type: Delete) {
  doFirst {
    delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
  }
}


jar {
  dependsOn prepare

  manifest {
    attributes "Main-Class": main_class,
    "Permissions": "all-permissions",
    "Application-Name": applicationName,
    "Codebase": application_codebase,
    "Implementation-Version": JALVIEW_VERSION
  }

  def outputDir = "${jalviewDir}/${package_dir}"
  destinationDir = file(outputDir)
  archiveName = rootProject.name+".jar"
  duplicatesStrategy "EXCLUDE"


  exclude "cache*/**"
  exclude "*.jar"
  exclude "*.jar.*"
  exclude "**/*.jar"
  exclude "**/*.jar.*"

  inputs.dir(sourceSets.main.java.outputDir)
  sourceSets.main.resources.srcDirs.each{ dir ->
    inputs.dir(dir)
  }
  outputs.file("${outputDir}/${archiveName}")
}


task copyJars(type: Copy) {
  from fileTree(dir: classesDir, include: "**/*.jar").files
  into "${jalviewDir}/${package_dir}"
}


// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
task syncJars(type: Sync) {
  dependsOn jar
  from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
  into "${jalviewDir}/${package_dir}"
  preserve {
    include jar.archiveName != null ? jar.archiveName : null
  }
}


task makeDist {
  group = "build"
  description = "Put all required libraries in dist"
  // order of "cleanPackageDir", "copyJars", "jar" important!
  jar.mustRunAfter cleanPackageDir
  syncJars.mustRunAfter cleanPackageDir
  dependsOn cleanPackageDir
  dependsOn syncJars
  dependsOn jar
  outputs.dir("${jalviewDir}/${package_dir}")
}


task cleanDist {
  dependsOn cleanPackageDir
  dependsOn cleanTest
  dependsOn clean
}


task launcherJar(type: Jar) {
  manifest {
      attributes (
        "Main-Class": shadow_jar_main_class,
        "Implementation-Version": JALVIEW_VERSION,
        "Application-Name": applicationName
      )
  }
}

tasks.withType(JavaCompile) {
	options.encoding = 'UTF-8'
}

def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
  def hash = [
    "date" : getDate("yyyy-MM-dd HH:mm:ss"),
    "git-commit" : "${gitHash} [${gitBranch}]",
    "version" : JALVIEW_VERSION
  ]
  // install4j installer files
  if (installersOutputTxt.exists()) {
    def idHash = [:]
    installersOutputTxt.readLines().each { def line ->
      if (line.startsWith("#")) {
        return;
      }
      line.replaceAll("\n","")
      def vals = line.split("\t")
      def filename = vals[3]
      def filesize = file(filename).length()
      filename = filename.replaceAll(/^.*\//, "")
      hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
      idHash."${filename}" = vals[0]
    }
    if (install4jCheckSums && installersSha256.exists()) {
      installersSha256.readLines().each { def line ->
        if (line.startsWith("#")) {
          return;
        }
        line.replaceAll("\n","")
        def vals = line.split(/\s+\*?/)
        def filename = vals[1]
        def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
      }
    }
  }

  return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
}

task staticMakeInstallersJsonFile {
  doFirst {
    def output = findProperty("i4j_output")
    def sha256 = findProperty("i4j_sha256")
    def json = findProperty("i4j_json")
    if (output == null || sha256 == null || json == null) {
      throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
    }
    writeDataJsonFile(file(output), file(sha256), file(json))
  }
}


task createSourceReleaseProperties(type: WriteProperties) {
  group = "distribution"
  description = "Create the source RELEASE properties file"
  
  def sourceTarBuildDir = "${buildDir}/sourceTar"
  def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
  outputFile (sourceReleasePropertiesFile)

  doFirst {
    releaseProps.each{ key, val -> property key, val }
    property "git.branch", gitBranch
    property "git.hash", gitHash
  }

  outputs.file(outputFile)
}

task sourceDist(type: Tar) {
  group "distribution"
  description "Create a source .tar.gz file for distribution"

  dependsOn createBuildProperties
  dependsOn convertMdFiles
  dependsOn createSourceReleaseProperties


  def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
  archiveName = outputFileName
  
  compression Compression.GZIP
  
  into project.name

  def EXCLUDE_FILES=[
    "dist/*",
    "build/*",
    "bin/*",
    "test-output/",
    "test-reports",
    "tests",
    ".*",
    "benchmarking/*",
    "**/.*",
    "*.class",
    "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
    "*locales/**",
    "utils/InstallAnywhere",
    "**/*.log",
    "RELEASE",
  ] 
  def PROCESS_FILES=[
    "AUTHORS",
    "CITATION",
    "FEATURETODO",
    "JAVA-11-README",
    "FEATURETODO",
    "LICENSE",
    "**/README",
    "THIRDPARTYLIBS",
    "TESTNG",
    "build.gradle",
    "gradle.properties",
    "**/*.java",
    "**/*.html",
    "**/*.xml",
    "**/*.gradle",
    "**/*.groovy",
    "**/*.properties",
    "**/*.perl",
    "**/*.sh",
  ]
  def INCLUDE_FILES=[
    ".classpath",
    ".settings/org.eclipse.buildship.core.prefs",
    ".settings/org.eclipse.jdt.core.prefs"
  ]

  from(jalviewDir) {
    exclude (EXCLUDE_FILES)
    include (PROCESS_FILES)
    filter(ReplaceTokens,
      beginToken: '$$',
      endToken: '$$',
      tokens: [
        'Version-Rel': JALVIEW_VERSION,
        'Year-Rel': getDate("yyyy")
      ]
    )
  }
  from(jalviewDir) {
    exclude (EXCLUDE_FILES)
    exclude (PROCESS_FILES)
    exclude ("appletlib")
    exclude ("**/*locales")
    exclude ("*locales/**")
    exclude ("utils/InstallAnywhere")

    // exluding these as not using jars as modules yet
    exclude ("${j11modDir}/**/*.jar")
  }
  from(jalviewDir) {
    include(INCLUDE_FILES)
  }
//  from (jalviewDir) {
//    // explicit includes for stuff that seemed to not get included
//    include(fileTree("test/**/*."))
//    exclude(EXCLUDE_FILES)
//    exclude(PROCESS_FILES)
//  }

  def sourceTarBuildDir = "${buildDir}/sourceTar"
  from(sourceTarBuildDir) {
    // this includes the appended RELEASE properties file
  }
}

task helppages {
  group "help"
  description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."

  dependsOn copyHelp
  dependsOn pubhtmlhelp
  
  inputs.dir("${helpBuildDir}/${help_dir}")
  outputs.dir("${buildDir}/distributions/${help_dir}")
}


task jalviewjsEnableAltFileProperty(type: WriteProperties) {
  group "jalviewjs"
  description "Enable the alternative J2S Config file for headless build"

  outputFile = jalviewjsJ2sSettingsFileName
  def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
  def j2sProps = new Properties()
  if (j2sPropsFile.exists()) {
    try {
      def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
      j2sProps.load(j2sPropsFileFIS)
      j2sPropsFileFIS.close()

      j2sProps.each { prop, val ->
        property(prop, val)
      }
    } catch (Exception e) {
      println("Exception reading ${jalviewjsJ2sSettingsFileName}")
      e.printStackTrace()
    }
  }
  if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
    property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
  }
}


task printProperties {
  group "Debug"
  description "Output to console all System.properties"
  doFirst {
    System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
  }
}


/* not really working yet
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 jalviewjsTransferUnzipLib {
  def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")

  doLast {
    zipFiles.each { file_zip -> 
      copy {
        from zipTree(file_zip)
        into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
      }
    }
  }

  inputs.files zipFiles
  outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
}


task jalviewjsTransferUnzipAllLibs {
  dependsOn jalviewjsTransferUnzipSwingJs
  dependsOn jalviewjsTransferUnzipLib
}


task jalviewjsCreateJ2sSettings(type: WriteProperties) {
  group "JalviewJS"
  description "Create the alternative j2s file from the j2s.* properties"

  jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
  def siteDirProperty = "j2s.site.directory"
  def setSiteDir = false
  jalviewjsJ2sProps.each { prop, val ->
    if (val != null) {
      if (prop == siteDirProperty) {
        if (!(val.startsWith('/') || val.startsWith("file://") )) {
          val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
        }
        setSiteDir = true
      }
      property(prop,val)
    }
    if (!setSiteDir) { // default site location, don't override specifically set property
      property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
    }
  }
  outputFile = jalviewjsJ2sAltSettingsFileName

    inputs.properties(jalviewjsJ2sProps)
    outputs.file(jalviewjsJ2sAltSettingsFileName)
}


task jalviewjsSyncAllLibs (type: Sync) {
  dependsOn jalviewjsTransferUnzipAllLibs
  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
  inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"

  from inputFiles
  into outputDir
  def outputFiles = []
  rename { filename ->
    outputFiles += "${outputDir}/${filename}"
    null
  }
  preserve {
    include "**"
  }

  // should this be exclude really ?
  duplicatesStrategy "INCLUDE"

  outputs.files outputFiles
  inputs.files inputFiles
}


task jalviewjsSyncResources (type: Sync) {
  dependsOn buildResources

  def inputFiles = fileTree(dir: resourcesBuildDir)
  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"

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


task jalviewjsSyncSiteResources (type: Sync) {
  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"

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


task jalviewjsSyncBuildProperties (type: Sync) {
  dependsOn createBuildProperties
  def inputFiles = [file(buildProperties)]
  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"

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


def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {

  def stdout = new ByteArrayOutputStream()
  def stderr = new ByteArrayOutputStream()

  def coreFile = file(jsfile)
  def msg = ""
  msg = "Creating core for ${name}...\nGenerating ${jsfile}"
  println(msg)
  logOutFile.createNewFile()
  logOutFile.append(msg+"\n")

  def coreTop = file(prefixFile)
  def coreBottom = file(suffixFile)
  coreFile.getParentFile().mkdirs()
  coreFile.createNewFile()
  coreFile.write( coreTop.getText("UTF-8") )
  list.each {
    f ->
    if (f.exists()) {
      def t = f.getText("UTF-8")
      t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
      coreFile.append( t )
    } else {
      msg = "...file '"+f.getPath()+"' does not exist, skipping"
      println(msg)
      logOutFile.append(msg+"\n")
    }
  }
  coreFile.append( coreBottom.getText("UTF-8") )

  msg = "Generating ${zjsfile}"
  println(msg)
  logOutFile.append(msg+"\n")
  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
  def logErrFOS = logOutFOS

  javaexec {
    classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
    main = "com.google.javascript.jscomp.CommandLineRunner"
    jvmArgs = [ "-Dfile.encoding=UTF-8" ]
    args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
    maxHeapSize = "2g"

    msg = "\nRunning '"+commandLine.join(' ')+"'\n"
    println(msg)
    logOutFile.append(msg+"\n")

    if (logOutConsole) {
      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
        new org.apache.tools.ant.util.TeeOutputStream(
          logOutFOS,
          stdout),
        standardOutput)
        errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
          new org.apache.tools.ant.util.TeeOutputStream(
            logErrFOS,
            stderr),
          System.err)
    } else {
      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
        logOutFOS,
        stdout)
        errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
          logErrFOS,
          stderr)
    }
  }
  msg = "--"
  println(msg)
  logOutFile.append(msg+"\n")
}


task jalviewjsBuildAllCores {
  group "JalviewJS"
  description "Build the core js lib closures listed in the classlists dir"
  dependsOn jalviewjsTransferUnzipSwingJs

  def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
  def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
  def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
  def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
  def prefixFile = "${jsDir}/core/coretop2.js"
  def suffixFile = "${jsDir}/core/corebottom2.js"

  inputs.file prefixFile
  inputs.file suffixFile

  def classlistFiles = []
  // add the classlists found int the jalviewjs_classlists_dir
  fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
    file ->
    def name = file.getName() - ".txt"
    classlistFiles += [
      'file': file,
      'name': name
    ]
  }

  // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
  //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]

  jalviewjsCoreClasslists = []

  classlistFiles.each {
    hash ->

    def file = hash['file']
    if (! file.exists()) {
      //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
      return false // this is a "continue" in groovy .each closure
    }
    def name = hash['name']
    if (name == null) {
      name = file.getName() - ".txt"
    }

    def filelist = []
    file.eachLine {
      line ->
        filelist += line
    }
    def list = fileTree(dir: j2sDir, includes: filelist)

    def jsfile = "${outputDir}/core${name}.js"
    def zjsfile = "${outputDir}/core${name}.z.js"

    jalviewjsCoreClasslists += [
      'jsfile': jsfile,
      'zjsfile': zjsfile,
      'list': list,
      'name': name
    ]

    inputs.file(file)
    inputs.files(list)
    outputs.file(jsfile)
    outputs.file(zjsfile)
  }
  
  // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
  def stevesoftClasslistName = "_stevesoft"
  def stevesoftClasslist = [
    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
    'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
    'name': stevesoftClasslistName
  ]
  jalviewjsCoreClasslists += stevesoftClasslist
  inputs.files(stevesoftClasslist['list'])
  outputs.file(stevesoftClasslist['jsfile'])
  outputs.file(stevesoftClasslist['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()
    logOutFile.createNewFile()
    logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")

    jalviewjsCoreClasslists.each {
      jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
    }
  }

}


def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
  copy {
    from inputFile
    into file(outputFile).getParentFile()
    rename { filename ->
      if (filename.equals(inputFile.getName())) {
        return file(outputFile).getName()
      }
      return null
    }
    filter(ReplaceTokens,
      beginToken: '_',
      endToken: '_',
      tokens: [
        'MAIN': '"'+main_class+'"',
        'CODE': "null",
        'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
        'COREKEY': jalviewjs_core_key,
        'CORENAME': coreName
      ]
    )
  }
}


task jalviewjsPublishCoreTemplates {
  dependsOn jalviewjsBuildAllCores
  def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
  def inputFile = file(inputFileName)
  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"

  def outputFiles = []
  jalviewjsCoreClasslists.each { cl ->
    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
    cl['outputfile'] = outputFile
    outputFiles += outputFile
  }

  doFirst {
    jalviewjsCoreClasslists.each { cl ->
      jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
    }
  }
  inputs.file(inputFile)
  outputs.files(outputFiles)
}


task jalviewjsSyncCore (type: Sync) {
  dependsOn jalviewjsBuildAllCores
  dependsOn jalviewjsPublishCoreTemplates
  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"

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


// this Copy version of TransferSiteJs will delete anything else in the target dir
task jalviewjsCopyTransferSiteJs(type: Copy) {
  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
  into "${jalviewDir}/${jalviewjsSiteDir}"
}


// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
task jalviewjsSyncTransferSiteJs(type: Sync) {
  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
  include "**/*.*"
  into "${jalviewDir}/${jalviewjsSiteDir}"
  preserve {
    include "**"
  }
}


jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs

jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs


task jalviewjsPrepareSite {
  group "JalviewJS"
  description "Prepares the website folder including unzipping files and copying resources"
  dependsOn jalviewjsSyncAllLibs
  dependsOn jalviewjsSyncResources
  dependsOn jalviewjsSyncSiteResources
  dependsOn jalviewjsSyncBuildProperties
  dependsOn jalviewjsSyncCore
}


task jalviewjsBuildSite {
  group "JalviewJS"
  description "Builds the whole website including transpiled code"
  dependsOn jalviewjsCopyTransferSiteJs
  dependsOn jalviewjsPrepareSite
}


task cleanJalviewjsTransferSite {
  doFirst {
    delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
    delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
    delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
    delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
  }
}


task cleanJalviewjsSite {
  dependsOn cleanJalviewjsTransferSite
  doFirst {
    delete "${jalviewDir}/${jalviewjsSiteDir}"
  }
}


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"
  archiveName = outputFilename

  compression Compression.GZIP

  from "${jalviewDir}/${jalviewjsSiteDir}"
  into jalviewjs_site_dir // this is inside the tar file

  inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
}


task jalviewjsServer {
  group "JalviewJS"
  def filename = "jalviewjsTest.html"
  description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
  def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
  doLast {

    def factory
    try {
      def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
      factory = f.newInstance()
    } catch (ClassNotFoundException e) {
      throw new GradleException("Unable to create SimpleHttpFileServerFactory")
    }
    def port = Integer.valueOf(jalviewjs_server_port)
    def start = port
    def running = false
    def url
    def jalviewjsServer
    while(port < start+1000 && !running) {
      try {
        def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
        jalviewjsServer = factory.start(doc_root, port)
        running = true
        url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
        println("SERVER STARTED with document root ${doc_root}.")
        println("Go to "+url+" . Run  gradle --stop  to stop (kills all gradle daemons).")
        println("For debug: "+url+"?j2sdebug")
        println("For verbose: "+url+"?j2sverbose")
      } catch (Exception e) {
        port++;
      }
    }
    def htmlText = """
      <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
      <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&gt;</a></p>
      <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. &lt;${url}?j2sdebug&gt;</a></p>
      """
    jalviewjsCoreClasslists.each { cl ->
      def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
      htmlText += """
      <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. &lt;${urlcore}&gt;</a></p>
      """
      println("For core ${cl.name}: "+urlcore)
    }

    file(htmlFile).text = htmlText
  }

  outputs.file(htmlFile)
  outputs.upToDateWhen({false})
}


task cleanJalviewjsAll {
  group "JalviewJS"
  description "Delete all configuration and build artifacts to do with JalviewJS build"
  dependsOn cleanJalviewjsSite
  
  doFirst {
    delete "${jalviewDir}/${jalviewjsBuildDir}"
    delete "${jalviewDir}/${eclipse_bin_dir}"
    if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
      delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
    }
    delete jalviewjsJ2sAltSettingsFileName
  }

  outputs.upToDateWhen( { false } )
}


task jalviewjsIDE_j2sFile {
  group "00 JalviewJS in Eclipse"
  description "Creates the .j2s file"
  dependsOn jalviewjsCreateJ2sSettings
}


task jalviewjsIDE_SyncCore {
  group "00 JalviewJS in Eclipse"
  description "Build the core js lib closures listed in the classlists dir and publish core html from template"
  dependsOn jalviewjsSyncCore
}


task jalviewjsIDE_SyncSiteAll {
  dependsOn jalviewjsSyncAllLibs
  dependsOn jalviewjsSyncResources
  dependsOn jalviewjsSyncSiteResources
  dependsOn jalviewjsSyncBuildProperties
}


cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll


task jalviewjsIDE_PrepareSite {
  group "00 JalviewJS in Eclipse"
  description "Sync libs and resources to site dir, but not closure cores"

  dependsOn jalviewjsIDE_SyncSiteAll
  //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
}


task jalviewjsIDE_AssembleSite {
  group "00 JalviewJS in Eclipse"
  description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
  dependsOn jalviewjsPrepareSite
}


task jalviewjsIDE_SiteClean {
  group "00 JalviewJS in Eclipse"
  description "Deletes the Eclipse transpiled site"
  dependsOn cleanJalviewjsSite
}


task jalviewjsIDE_Server {
  group "00 JalviewJS in Eclipse"
  description "Starts a webserver on localhost to test the website"
  dependsOn jalviewjsServer
}


// buildship runs this at build time or project refresh
task eclipseAutoBuildTask {
  //dependsOn jalviewjsIDE_PrepareSite
}


task jalviewjsCopyStderrLaunchFile(type: Copy) {
  from file(jalviewjs_stderr_launch)
  into jalviewjsSiteDir

  inputs.file jalviewjs_stderr_launch
  outputs.file jalviewjsStderrLaunchFilename
}

task cleanJalviewjsChromiumUserDir {
  doFirst {
    delete jalviewjsChromiumUserDir
  }
  outputs.dir jalviewjsChromiumUserDir
  // always run when depended on
  outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
}

task jalviewjsChromiumProfile {
  dependsOn cleanJalviewjsChromiumUserDir
  mustRunAfter cleanJalviewjsChromiumUserDir

  def firstRun = file("${jalviewjsChromiumUserDir}/First Run")

  doFirst {
    mkdir jalviewjsChromiumProfileDir
    firstRun.text = ""
  }
  outputs.file firstRun
}

task jalviewjsLaunchTest {
  group "Test"
  description "Check JalviewJS opens in a browser"
  dependsOn jalviewjsBuildSite
  dependsOn jalviewjsCopyStderrLaunchFile
  dependsOn jalviewjsChromiumProfile

  def macOS = OperatingSystem.current().isMacOsX()
  def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
  if (chromiumBinary.startsWith("~/")) {
    chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
  }
  
  def stdout
  def stderr
  doFirst {
    def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
    
    def binary = file(chromiumBinary)
    if (!binary.exists()) {
      throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
    }
    stdout = new ByteArrayOutputStream()
    stderr = new ByteArrayOutputStream()
    def execStdout
    def execStderr
    if (jalviewjs_j2s_to_console.equals("true")) {
      execStdout = new org.apache.tools.ant.util.TeeOutputStream(
        stdout,
        System.out)
      execStderr = new org.apache.tools.ant.util.TeeOutputStream(
        stderr,
        System.err)
    } else {
      execStdout = stdout
      execStderr = stderr
    }
    def execArgs = [
      "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
      "--headless=new",
      "--disable-gpu",
      "--timeout=${timeoutms}",
      "--virtual-time-budget=${timeoutms}",
      "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
      "--profile-directory=${jalviewjs_chromium_profile_name}",
      "--allow-file-access-from-files",
      "--enable-logging=stderr",
      "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
    ]
    
    if (true || macOS) {
      ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
      Future f1 = executor.submit(
        {
          exec {
            standardOutput = execStdout
            errorOutput = execStderr
            executable(chromiumBinary)
            args(execArgs)
            println "COMMAND: '"+commandLine.join(" ")+"'"
          }
          executor.shutdownNow()
        }
      )

      def noChangeBytes = 0
      def noChangeIterations = 0
      executor.scheduleAtFixedRate(
        {
          String stderrString = stderr.toString()
          // shutdown the task if we have a success string
          if (stderrString.contains(jalviewjs_desktop_init_string)) {
            f1.cancel()
            Thread.sleep(1000)
            executor.shutdownNow()
          }
          // if no change in stderr for 10s then also end
          if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
            executor.shutdownNow()
          }
          if (stderrString.length() == noChangeBytes) {
            noChangeIterations++
          } else {
            noChangeBytes = stderrString.length()
            noChangeIterations = 0
          }
        },
        1, 1, TimeUnit.SECONDS)

      executor.schedule(new Runnable(){
        public void run(){
          f1.cancel()
          executor.shutdownNow()
        }
      }, timeoutms, TimeUnit.MILLISECONDS)

      executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
      executor.shutdownNow()
    }

  }
  
  doLast {
    def found = false
    stderr.toString().eachLine { line ->
      if (line.contains(jalviewjs_desktop_init_string)) {
        println("Found line '"+line+"'")
        found = true
        return
      }
    }
    if (!found) {
      throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
    }
  }
}
  

task jalviewjs {
  group "JalviewJS"
  description "Build the JalviewJS site and run the launch test"
  dependsOn jalviewjsBuildSite
  dependsOn jalviewjsLaunchTest
}