Integrated Pipeline: renamed FileTreeScanTask to FileTree to better reflect the actual usage

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/Main.scala

@@ -27,7 +27,7 @@ import eu.nomad_lab.TreeType.TreeType
 import eu.nomad_lab.integrated_pipeline.Main.PipelineSettings
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
 import eu.nomad_lab.integrated_pipeline.io_integrations._
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResultSignal, FileParsingTaskSignal, FileTreeParsingResult, FileTreeScanTask }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResultSignal, FileParsingTaskSignal, FileTreeParsingResult, FileTree }
 import eu.nomad_lab.integrated_pipeline.stream_components._
 import eu.nomad_lab.meta.{ KnownMetaInfoEnvs, MetaInfoEnv }
 import eu.nomad_lab.parsers.AllParsers
@@ -58,7 +58,7 @@ object Main extends StrictLogging {
   }
 
   case class PipelineSettings(
-    task: Option[FileTreeScanTask],
+    task: Option[FileTree],
     mode: OutputType,
     numWorkers: Int,
     treeType: TreeType,
@@ -94,7 +94,7 @@ object Main extends StrictLogging {
         case numWorkersRe(count) => settings.copy(numWorkers = count.toInt)
         case "--noConfigDump" => settings //already consumed by the calling function
         case x if args.isEmpty && operation == OperationMode.Console =>
-          settings.copy(task = Some(FileTreeScanTask(Paths.get(x).toAbsolutePath, treeType)))
+          settings.copy(task = Some(FileTree(Paths.get(x).toAbsolutePath, treeType)))
         case _ => ??? //TODO: show usage instructions
       }
     }
@@ -124,11 +124,11 @@ class Main {
       GraphDSL.create(sinkSummaries) { implicit builder => (sink) =>
         import GraphDSL.Implicits._
 
-        val treeParser = Flow.fromGraph(new MessageProcessorFlow[FileTreeScanTask, FileParsingTaskSignal] {
+        val treeParser = Flow.fromGraph(new MessageProcessorFlow[FileTree, FileParsingTaskSignal] {
           override val stageName = "TreeParser"
           override val processor = new TreeScanner {
             override val eventListener = eventProcessor
-            override def createProcessor(task: FileTreeScanTask) = params.treeType match {
+            override def createProcessor(task: FileTree) = params.treeType match {
               case TreeType.Zip => new ZipTreeParsingTaskGenerator(task, Main.parsers)
               case TreeType.Directory => new DirectoryTreeParsingTaskGenerator(task, Main.parsers)
             }

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/ParsingResultsProcessingManager.scala

@@ -80,7 +80,7 @@ trait ParsingResultsProcessingManager extends MessageProcessor[FileParsingResult
     }
   }
 
-  private def startFileTree(task: FileTreeScanTask): Unit = {
+  private def startFileTree(task: FileTree): Unit = {
     processedCounts(task.treeBasePath) = 0
     failedCounts(task.treeBasePath) = 0
     eventListener.processEvent(myId, ResultWriterEventStart(task))

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/ParsingResultsProcessor.scala

@@ -3,7 +3,7 @@ package eu.nomad_lab.integrated_pipeline
 import java.nio.file.Path
 
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTreeScanTask }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTree }
 
 trait ParsingResultsProcessor {
 
@@ -16,10 +16,10 @@ trait ParsingResultsProcessor {
    * @param fileTree the processed file tree
    * @return the folder where the generated results are located
    */
-  def outputLocation(fileTree: FileTreeScanTask): Path
+  def outputLocation(fileTree: FileTree): Path
 
-  def startProcessingTreeResults(treeTask: FileTreeScanTask): Unit
+  def startProcessingTreeResults(treeTask: FileTree): Unit
 
-  def finishProcessingTreeResults(treeTask: FileTreeScanTask): Unit
+  def finishProcessingTreeResults(treeTask: FileTree): Unit
 
 }

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/ParsingTaskGenerator.scala

@@ -4,7 +4,7 @@ import java.io.InputStream
 import java.nio.file.Path
 import java.util.NoSuchElementException
 
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTreeScanTask, TreeParserEventScanError }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTree, TreeParserEventScanError }
 import eu.nomad_lab.parsers.{ CandidateParser, ParserCollection }
 
 /**
@@ -48,7 +48,7 @@ trait ParsingTaskGenerator extends Iterator[Either[TreeParserEventScanError, Fil
     parsers.scanFile(internalFilePath, minBuf).sorted
   }
 
-  def generateRequest(fileTreeRequest: FileTreeScanTask, relativeFilePath: Path,
+  def generateRequest(fileTreeRequest: FileTree, relativeFilePath: Path,
     candidateParsers: Seq[CandidateParser]): Option[FileParsingTask] = {
     require(!relativeFilePath.isAbsolute, "internal file paths must be relative to file tree root")
 

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/TreeScanner.scala

@@ -9,9 +9,9 @@ import scala.annotation.tailrec
  * zip-archive) for files that are potential calculations of interest for NOMAD and emits file
  * parsing requests for these candidate files.
  */
-trait TreeScanner extends MessageProcessor[FileTreeScanTask, FileParsingTaskSignal] {
+trait TreeScanner extends MessageProcessor[FileTree, FileParsingTaskSignal] {
 
-  protected[this] def createProcessor(task: FileTreeScanTask): ParsingTaskGenerator
+  protected[this] def createProcessor(task: FileTree): ParsingTaskGenerator
   protected[this] val eventListener: EventListener
   protected[this] val eventReporterName: Option[String] = None
 
@@ -19,10 +19,10 @@ trait TreeScanner extends MessageProcessor[FileTreeScanTask, FileParsingTaskSign
 
   private var generator: Option[ParsingTaskGenerator] = None
   private var readyForInbound = true
-  private var request: Option[FileTreeScanTask] = None
+  private var request: Option[FileTree] = None
   private var taskCount = 0l
 
-  final override def processSignal(in: FileTreeScanTask): Unit = {
+  final override def processSignal(in: FileTree): Unit = {
     if (readyForInbound) {
       eventListener.processEvent(myId, TreeParserEventStart(in))
       if (in.treeBasePath.toFile.exists()) {

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/io_integrations/DirectoryTreeParsingTaskGenerator.scala

@@ -5,14 +5,14 @@ import java.nio.file.Files
 
 import eu.nomad_lab.TreeType
 import eu.nomad_lab.integrated_pipeline.ParsingTaskGenerator
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTreeScanTask, TreeParserEventScanError }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTree, TreeParserEventScanError }
 import eu.nomad_lab.parsers.{ CandidateParser, ParserCollection }
 
 import scala.annotation.tailrec
 import scala.collection.JavaConverters._
 import scala.util.control.NonFatal
 
-class DirectoryTreeParsingTaskGenerator(request: FileTreeScanTask, parserCollection: ParserCollection)
+class DirectoryTreeParsingTaskGenerator(request: FileTree, parserCollection: ParserCollection)
     extends ParsingTaskGenerator {
 
   require(request.treeType == TreeType.Directory, "file tree to process must be a directory")

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/io_integrations/WriteToHDF5MergedResultsProcessor.scala

@@ -4,7 +4,7 @@ import java.nio.file.{ Files, Path, Paths }
 
 import eu.nomad_lab.{ H5Lib, TreeType }
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTreeScanTask, InMemoryResult }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTree, InMemoryResult }
 import eu.nomad_lab.integrated_pipeline.{ OutputType, ParsingResultsProcessor }
 import eu.nomad_lab.meta.MetaInfoEnv
 import eu.nomad_lab.parsers.H5Backend.H5File
@@ -22,9 +22,9 @@ class WriteToHDF5MergedResultsProcessor(
     metaInfo: MetaInfoEnv
 ) extends ParsingResultsProcessor {
 
-  private val fileMap: mutable.Map[FileTreeScanTask, H5File] = mutable.Map()
+  private val fileMap: mutable.Map[FileTree, H5File] = mutable.Map()
 
-  override def outputLocation(fileTree: FileTreeScanTask): Path = {
+  override def outputLocation(fileTree: FileTree): Path = {
     outputLocation.resolve(fileTree.prefixFolder)
   }
 
@@ -60,14 +60,14 @@ class WriteToHDF5MergedResultsProcessor(
 
   override val outputType: OutputType = OutputType.HDF5
 
-  override def startProcessingTreeResults(treeTask: FileTreeScanTask): Unit = {
+  override def startProcessingTreeResults(treeTask: FileTree): Unit = {
     Files.createDirectories(outputLocation(treeTask))
     val targetPath = outputLocation(treeTask).resolve(treeTask.fileName)
     val h5file = H5File.create(targetPath, Paths.get("/", treeTask.archiveId))
     fileMap(treeTask) = h5file
   }
 
-  override def finishProcessingTreeResults(treeTask: FileTreeScanTask): Unit = {
+  override def finishProcessingTreeResults(treeTask: FileTree): Unit = {
     val h5file = fileMap.remove(treeTask)
     //TODO: error handling
     if (h5file.nonEmpty) {

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/io_integrations/WriteToHDF5ResultsProcessor.scala

@@ -3,7 +3,7 @@ package eu.nomad_lab.integrated_pipeline.io_integrations
 import java.nio.file.{ Files, Path, Paths }
 
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTreeScanTask, InMemoryResult }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTree, InMemoryResult }
 import eu.nomad_lab.integrated_pipeline.{ OutputType, ParsingResultsProcessor }
 import eu.nomad_lab.meta.MetaInfoEnv
 import eu.nomad_lab.parsers.H5Backend.H5File
@@ -34,11 +34,11 @@ class WriteToHDF5ResultsProcessor(outputLocation: Path, metaInfo: MetaInfoEnv) e
 
   override val outputType: OutputType = OutputType.HDF5
 
-  override def startProcessingTreeResults(treeTask: FileTreeScanTask): Unit = ()
+  override def startProcessingTreeResults(treeTask: FileTree): Unit = ()
 
-  override def finishProcessingTreeResults(treeTask: FileTreeScanTask): Unit = ()
+  override def finishProcessingTreeResults(treeTask: FileTree): Unit = ()
 
-  override def outputLocation(fileTree: FileTreeScanTask): Path = {
+  override def outputLocation(fileTree: FileTree): Path = {
     outputLocation.resolve(fileTree.prefixFolder).resolve(fileTree.archiveId)
   }
 }

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/io_integrations/WriteToJsonResultsProcessor.scala

@@ -4,7 +4,7 @@ import java.io.FileWriter
 import java.nio.file.{ Files, Path, Paths }
 
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTreeScanTask, InMemoryResult }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, FileTree, InMemoryResult }
 import eu.nomad_lab.integrated_pipeline.{ OutputType, ParsingResultsProcessor }
 import eu.nomad_lab.meta.MetaInfoEnv
 import eu.nomad_lab.parsers.JsonWriterBackend
@@ -35,11 +35,11 @@ class WriteToJsonResultsProcessor(outputLocation: Path, metaInfo: MetaInfoEnv) e
 
   override val outputType: OutputType = OutputType.Json
 
-  override def startProcessingTreeResults(treeTask: FileTreeScanTask): Unit = ()
+  override def startProcessingTreeResults(treeTask: FileTree): Unit = ()
 
-  override def finishProcessingTreeResults(treeTask: FileTreeScanTask): Unit = ()
+  override def finishProcessingTreeResults(treeTask: FileTree): Unit = ()
 
-  override def outputLocation(fileTree: FileTreeScanTask): Path = {
+  override def outputLocation(fileTree: FileTree): Path = {
     outputLocation.resolve(fileTree.prefixFolder).resolve(fileTree.archiveId)
   }
 }

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/io_integrations/ZipTreeParsingTaskGenerator.scala

@@ -4,14 +4,14 @@ import java.nio.file.Paths
 
 import eu.nomad_lab.TreeType
 import eu.nomad_lab.integrated_pipeline.ParsingTaskGenerator
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTreeScanTask, TreeParserEventScanError }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTree, TreeParserEventScanError }
 import eu.nomad_lab.parsers.{ CandidateParser, ParserCollection }
 import org.apache.commons.compress.archivers.zip.{ ZipArchiveEntry, ZipFile }
 
 import scala.annotation.tailrec
 import scala.util.control.NonFatal
 
-class ZipTreeParsingTaskGenerator(request: FileTreeScanTask, parserCollection: ParserCollection)
+class ZipTreeParsingTaskGenerator(request: FileTree, parserCollection: ParserCollection)
     extends ParsingTaskGenerator {
 
   require(request.treeType == TreeType.Zip, "file tree to process must be a Zip archive")

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/messages/FileParsingSignals.scala

@@ -7,11 +7,11 @@ import eu.nomad_lab.parsers.{ FinishedParsingSession, ParseEvent, StartedParsing
 import eu.nomad_lab.{ CompactSha, TreeType }
 
 sealed trait FileParsingTaskSignal {
-  val treeTask: FileTreeScanTask
+  val treeTask: FileTree
 }
 
 sealed trait FileParsingResultSignal {
-  val treeTask: FileTreeScanTask
+  val treeTask: FileTree
 }
 
 /**
@@ -23,7 +23,7 @@ sealed trait FileParsingResultSignal {
  *                      archive)
  */
 case class FileParsingTask(
-    treeTask: FileTreeScanTask,
+    treeTask: FileTree,
     relativePath: Path,
     parserName: String,
     extractedPath: Option[Path] = None
@@ -46,7 +46,7 @@ case class FileParsingTask(
 }
 
 case class FileParsingSignalEndTree(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   numParsingTasks: Long = 0
 ) extends FileParsingTaskSignal with FileParsingResultSignal
 
@@ -57,7 +57,7 @@ sealed trait FileParsingResult extends FileParsingResultSignal {
   val end: Option[FinishedParsingSession]
   val error: Option[String]
 
-  val treeTask: FileTreeScanTask = task.treeTask
+  val treeTask: FileTree = task.treeTask
 }
 
 case class InMemoryResult(

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/messages/FileTreeScanTask.scala → integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/messages/FileTree.scala

@@ -6,17 +6,16 @@ import eu.nomad_lab.TreeType
 
 import scala.util.matching.Regex
 
-object FileTreeScanTask {
+object FileTree {
   val rawDataArchive: Regex = "(R[A-z0-9_-]{28}).zip".r
 }
 
 /**
- * Request a scan to identify all potential calculation files found under the given file tree root
- * @param treeBasePath the root of the file-tree
+ * abstract representation of a file tree
+ * @param treeBasePath path to the root of the file-tree
  * @param treeType type of the file tree, e.g. zip or directory
  */
-
-case class FileTreeScanTask(
+case class FileTree(
     treeBasePath: Path,
     treeType: TreeType.TreeType
 ) {
@@ -29,7 +28,7 @@ case class FileTreeScanTask(
   def archiveId: String = treeType match {
     case TreeType.Directory => treeBasePath.getFileName.toString
     case TreeType.Zip => treeBasePath.getFileName.toString match {
-      case FileTreeScanTask.rawDataArchive(id) => id
+      case FileTree.rawDataArchive(id) => id
       case path => throw new UnsupportedOperationException(s"$path is not a valid rawdata archive name")
     }
   }

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/messages/FileTreeParsingResult.scala

@@ -5,7 +5,7 @@ import java.nio.file.Path
 import eu.nomad_lab.integrated_pipeline.OutputType
 
 case class FileTreeParsingResult(
-  treeScanTask: FileTreeScanTask,
+  treeScanTask: FileTree,
   numCalculationsFound: Long,
   numParsingFailures: Long,
   outputLocation: Path,

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/messages/ProcessEvents.scala

@@ -10,49 +10,49 @@ import eu.nomad_lab.parsers.ParseResult.ParseResult
  */
 
 sealed trait TreeParserEvent {
-  def treeTask: FileTreeScanTask
+  def treeTask: FileTree
 }
 
 case class TreeParserEventStart(
-  treeTask: FileTreeScanTask
+  treeTask: FileTree
 ) extends TreeParserEvent
 
 case class TreeParserEventCandidate(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   relativePath: Path,
   parser: String
 ) extends TreeParserEvent
 
 case class TreeParserEventScanError(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   relativePath: Path,
   error: Throwable
 ) extends TreeParserEvent
 
 case class TreeParserEventTreeFailure(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   error: Throwable
 ) extends TreeParserEvent
 
 case class TreeParserEventEnd(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   numCandidates: Long
 ) extends TreeParserEvent
 
 sealed trait CalculationParserEvent {
-  def treeTask: FileTreeScanTask
+  def treeTask: FileTree
   def relativePath: Path
   def parser: String
 }
 
 case class CalculationParserEventStart(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   relativePath: Path,
   parser: String
 ) extends CalculationParserEvent
 
 case class CalculationParserEventEnd(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   relativePath: Path,
   parser: String,
   result: ParseResult,
@@ -60,15 +60,15 @@ case class CalculationParserEventEnd(
 ) extends CalculationParserEvent
 
 sealed trait ResultWriterEvent {
-  def treeTask: FileTreeScanTask
+  def treeTask: FileTree
 }
 
 case class ResultWriterEventStart(
-  treeTask: FileTreeScanTask
+  treeTask: FileTree
 ) extends ResultWriterEvent
 
 case class ResultWriterEventResult(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   relativePath: Path,
   parser: String,
   result: ParseResult,
@@ -76,7 +76,7 @@ case class ResultWriterEventResult(
 ) extends ResultWriterEvent
 
 case class ResultWriterEventEnd(
-  treeTask: FileTreeScanTask,
+  treeTask: FileTree,
   numCalculations: Long,
   numParsingFailures: Long,
   outputLocation: Path

integrated-pipeline/src/main/scala/eu/nomad_lab/integrated_pipeline/stream_components/ArchiveCleanUpFlow.scala

@@ -17,8 +17,8 @@ class ArchiveCleanUpFlow(archiveHandler: ArchiveHandler)
 
   override def createLogic(inheritedAttributes: Attributes) = new GraphStageLogic(shape) {
 
-    private val processed: mutable.Map[FileTreeScanTask, Long] = mutable.Map()
-    private val expected: mutable.Map[FileTreeScanTask, Long] = mutable.Map()
+    private val processed: mutable.Map[FileTree, Long] = mutable.Map()
+    private val expected: mutable.Map[FileTree, Long] = mutable.Map()
 
     private def fail(msg: String): Unit = {
       failStage(new IllegalArgumentException(msg))

integrated-pipeline/src/test/scala/eu/nomad_lab/integrated_pipeline_end_to_end_tests/package.scala

@@ -7,7 +7,7 @@ import eu.nomad_lab.TreeType.TreeType
 import eu.nomad_lab.h5.CalculationH5
 import eu.nomad_lab.integrated_pipeline.OutputType
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
-import eu.nomad_lab.integrated_pipeline.messages.FileTreeScanTask
+import eu.nomad_lab.integrated_pipeline.messages.FileTree
 import eu.nomad_lab.integrated_pipeline_tests._
 import eu.nomad_lab.meta.MetaInfoEnv
 import org.scalatest.Assertions.succeed
@@ -23,7 +23,7 @@ package object integrated_pipeline_end_to_end_tests extends TestDataBuilders {
     val outputType: OutputType
     val treeType: TreeType
     val sample: TestTreeData
-    lazy val treeTask: FileTreeScanTask = createFileTreeScanRequest(sample, treeType)
+    lazy val treeTask: FileTree = createFileTreeScanRequest(sample, treeType)
     lazy val dataRoot: String = treeTask.treeType match {
       case TreeType.Directory => s"src/test/resources/${sample.baseName.substring(0, 3)}/${sample.baseName}"
       case TreeType.Zip => s"src/test/resources/${sample.baseName.substring(0, 3)}/${sample.baseName}.zip"
@@ -73,7 +73,7 @@ package object integrated_pipeline_end_to_end_tests extends TestDataBuilders {
     override val sample: TestTreeData = TestTreeData("purely-imaginary", Map())
   }
 
-  def assertValidityOfGeneratedJsonFiles(sample: TestTreeData, treeTask: FileTreeScanTask,
+  def assertValidityOfGeneratedJsonFiles(sample: TestTreeData, treeTask: FileTree,
     tmpResultsFolder: Path, metaInfo: MetaInfoEnv): Assertion = {
     sample.candidateCalculationsWithParsers.foreach { entry =>
       val task = aFileParsingTask().withTreeTask(treeTask).withRelativePath(entry._1).build()
@@ -94,7 +94,7 @@ package object integrated_pipeline_end_to_end_tests extends TestDataBuilders {
     succeed
   }
 
-  def assertValidityOfGeneratedHDF5Files(sample: TestTreeData, treeTask: FileTreeScanTask,
+  def assertValidityOfGeneratedHDF5Files(sample: TestTreeData, treeTask: FileTree,
     tmpResultsFolder: Path, metaInfo: MetaInfoEnv): Assertion = {
     sample.candidateCalculationsWithParsers.foreach { entry =>
       val task = aFileParsingTask().withTreeTask(treeTask).withRelativePath(entry._1).build()
@@ -113,7 +113,7 @@ package object integrated_pipeline_end_to_end_tests extends TestDataBuilders {
     succeed
   }
 
-  def assertValidityOfGeneratedMergedHDF5File(sample: TestTreeData, treeTask: FileTreeScanTask,
+  def assertValidityOfGeneratedMergedHDF5File(sample: TestTreeData, treeTask: FileTree,
     tmpResultsFolder: Path, metaInfo: MetaInfoEnv): Assertion = {
     val id = treeTask.archiveId
     val fileName = treeTask.fileName

integrated-pipeline/src/test/scala/eu/nomad_lab/integrated_pipeline_tests/Builders.scala

@@ -33,7 +33,7 @@ trait TestDataBuilders {
 
   def aTreeParserEventScanError() = BuilderTreeParserEventScanError()
 
-  implicit def build(x: BuilderFileTreeScanTask): FileTreeScanTask = x.build()
+  implicit def build(x: BuilderFileTreeScanTask): FileTree = x.build()
 
   implicit def build(x: BuilderFileParsingTask): FileParsingTask = x.build()
   implicit def build(x: BuilderFileParsingSignalEndTree): FileParsingSignalEndTree = x.build()
@@ -74,20 +74,20 @@ object MessageBuilders {
     def withBasePath(path: String) = copy(treeBasePath = Paths.get(path))
     def withTreeType(newType: TreeType) = copy(treeType = newType)
 
-    def build() = FileTreeScanTask(
+    def build() = FileTree(
       treeBasePath = treeBasePath,
       treeType = treeType
     )
   }
 
   case class BuilderFileParsingTask(
-      private val treeTask: FileTreeScanTask = BuilderFileTreeScanTask().build(),
+      private val treeTask: FileTree = BuilderFileTreeScanTask().build(),
       private val relativePath: Path = defaultPath,
       private val parserName: String = defaultParser,
       private val extractedPath: Option[Path] = None
   ) {
 
-    def withTreeTask(task: FileTreeScanTask) = copy(treeTask = task)
+    def withTreeTask(task: FileTree) = copy(treeTask = task)
     def withRelativePath(path: Path) = copy(relativePath = path)
     def withRelativePath(path: String) = copy(relativePath = Paths.get(path))
     def withParserName(name: String) = copy(parserName = name)
@@ -102,11 +102,11 @@ object MessageBuilders {
   }
 
   case class BuilderFileParsingSignalEndTree(
-      private val treeTask: FileTreeScanTask = BuilderFileTreeScanTask().build(),
+      private val treeTask: FileTree = BuilderFileTreeScanTask().build(),
       private val numTasks: Long = -1
   ) {
 
-    def withTreeTask(task: FileTreeScanTask) = copy(treeTask = task)
+    def withTreeTask(task: FileTree) = copy(treeTask = task)
     def withBasePath(path: Path) = copy(treeTask = treeTask.copy(treeBasePath = path))
     def withBasePath(path: String): BuilderFileParsingSignalEndTree = withBasePath(Paths.get(path))
     def withTreeType(newType: TreeType) = copy(treeTask = treeTask.copy(treeType = newType))
@@ -132,7 +132,7 @@ object MessageBuilders {
     def withStartEvent(event: Option[StartedParsingSession]) = copy(start = event)
     def withEvents(newEvents: Seq[ParseEvent]) = copy(events = newEvents)
     def withFinishEvent(event: Option[FinishedParsingSession]) = copy(end = event)
-    def withTreeTask(newTask: FileTreeScanTask) = copy(task = task.copy(treeTask = newTask))
+    def withTreeTask(newTask: FileTree) = copy(task = task.copy(treeTask = newTask))
     def withRelativePath(newPath: Path) = copy(task = task.copy(relativePath = newPath))
     def withRelativePath(newPath: String) = copy(task = task.copy(relativePath = Paths.get(newPath)))
     def withErrorMessage(message: Option[String]) = copy(error = message)
@@ -153,10 +153,10 @@ object EventBuilders {
   import Defaults._
 
   case class BuilderTreeParserEventStart(
-      private val treeTask: FileTreeScanTask = BuilderFileTreeScanTask().build()
+      private val treeTask: FileTree = BuilderFileTreeScanTask().build()
   ) {
 
-    def withTreeTask(task: FileTreeScanTask) = copy(treeTask = task)
+    def withTreeTask(task: FileTree) = copy(treeTask = task)
     def withBasePath(path: Path) = copy(treeTask = treeTask.copy(treeBasePath = path))
     def withBasePath(path: String): BuilderTreeParserEventStart = withBasePath(Paths.get(path))
     def withTreeType(newType: TreeType) = copy(treeTask = treeTask.copy(treeType = newType))
@@ -167,12 +167,12 @@ object EventBuilders {
   }
 
   case class BuilderTreeParserEventCandidate(
-      private val treeTask: FileTreeScanTask = BuilderFileTreeScanTask().build(),
+      private val treeTask: FileTree = BuilderFileTreeScanTask().build(),
       private val relativePath: Path = defaultPath,
       private val parser: String = defaultParser
   ) {
 
-    def withTreeTask(task: FileTreeScanTask) = copy(treeTask = task)
+    def withTreeTask(task: FileTree) = copy(treeTask = task)
     def withBasePath(path: Path) = copy(treeTask = treeTask.copy(treeBasePath = path))
     def withBasePath(path: String): BuilderTreeParserEventCandidate = withBasePath(Paths.get(path))
     def withTreeType(newType: TreeType) = copy(treeTask = treeTask.copy(treeType = newType))
@@ -188,12 +188,12 @@ object EventBuilders {
   }
 
   case class BuilderTreeParserEventScanError(
-      private val treeTask: FileTreeScanTask = BuilderFileTreeScanTask().build(),
+      private val treeTask: FileTree = BuilderFileTreeScanTask().build(),
       private val relativePath: Path = defaultPath,