Integrated Pipeline: moved FileTree class to top-level package

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

-package eu.nomad_lab.integrated_pipeline.messages
+package eu.nomad_lab.integrated_pipeline
 
 import java.nio.file.{ Path, Paths }
 

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, FileTree }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResultSignal, FileParsingTaskSignal, FileTreeParsingResult }
 import eu.nomad_lab.integrated_pipeline.stream_components._
 import eu.nomad_lab.meta.{ KnownMetaInfoEnvs, MetaInfoEnv }
 import eu.nomad_lab.parsers.AllParsers

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, FileTree }
+import eu.nomad_lab.integrated_pipeline.messages.FileParsingResult
 
 trait ParsingResultsProcessor {
 

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, FileTree, TreeParserEventScanError }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, TreeParserEventScanError }
 import eu.nomad_lab.parsers.{ CandidateParser, ParserCollection }
 
 /**

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

@@ -4,8 +4,8 @@ import java.io.FileInputStream
 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, FileTree, TreeParserEventScanError }
+import eu.nomad_lab.integrated_pipeline.{ FileTree, ParsingTaskGenerator }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, TreeParserEventScanError }
 import eu.nomad_lab.parsers.{ CandidateParser, ParserCollection }
 
 import scala.annotation.tailrec

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

@@ -4,8 +4,8 @@ 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, FileTree, InMemoryResult }
-import eu.nomad_lab.integrated_pipeline.{ OutputType, ParsingResultsProcessor }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, InMemoryResult }
+import eu.nomad_lab.integrated_pipeline.{ FileTree, OutputType, ParsingResultsProcessor }
 import eu.nomad_lab.meta.MetaInfoEnv
 import eu.nomad_lab.parsers.H5Backend.H5File
 import eu.nomad_lab.parsers.{ H5Backend, ReindexBackend }

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

@@ -3,8 +3,8 @@ 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, FileTree, InMemoryResult }
-import eu.nomad_lab.integrated_pipeline.{ OutputType, ParsingResultsProcessor }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, InMemoryResult }
+import eu.nomad_lab.integrated_pipeline.{ FileTree, OutputType, ParsingResultsProcessor }
 import eu.nomad_lab.meta.MetaInfoEnv
 import eu.nomad_lab.parsers.H5Backend.H5File
 import eu.nomad_lab.parsers.{ H5Backend, ReindexBackend }

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

@@ -4,8 +4,8 @@ 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, FileTree, InMemoryResult }
-import eu.nomad_lab.integrated_pipeline.{ OutputType, ParsingResultsProcessor }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingResult, InMemoryResult }
+import eu.nomad_lab.integrated_pipeline.{ FileTree, OutputType, ParsingResultsProcessor }
 import eu.nomad_lab.meta.MetaInfoEnv
 import eu.nomad_lab.parsers.JsonWriterBackend
 

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

@@ -3,8 +3,8 @@ package eu.nomad_lab.integrated_pipeline.io_integrations
 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, FileTree, TreeParserEventScanError }
+import eu.nomad_lab.integrated_pipeline.{ FileTree, ParsingTaskGenerator }
+import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, TreeParserEventScanError }
 import eu.nomad_lab.parsers.{ CandidateParser, ParserCollection }
 import org.apache.commons.compress.archivers.zip.{ ZipArchiveEntry, ZipFile }
 

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

@@ -2,6 +2,7 @@ package eu.nomad_lab.integrated_pipeline.messages
 
 import java.nio.file.Path
 
+import eu.nomad_lab.integrated_pipeline.FileTree
 import eu.nomad_lab.parsers.ParseResult.ParseResult
 import eu.nomad_lab.parsers.{ FinishedParsingSession, ParseEvent, StartedParsingSession }
 import eu.nomad_lab.{ CompactSha, TreeType }

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

@@ -2,7 +2,7 @@ package eu.nomad_lab.integrated_pipeline.messages
 
 import java.nio.file.Path
 
-import eu.nomad_lab.integrated_pipeline.OutputType
+import eu.nomad_lab.integrated_pipeline.{ FileTree, OutputType }
 
 case class FileTreeParsingResult(
   treeScanTask: FileTree,

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

@@ -2,6 +2,7 @@ package eu.nomad_lab.integrated_pipeline.messages
 
 import java.nio.file.Path
 
+import eu.nomad_lab.integrated_pipeline.FileTree
 import eu.nomad_lab.parsers.ParseResult.ParseResult
 
 /*These events are distinct from the messages passed between the different processing stage because

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

@@ -3,6 +3,7 @@ package eu.nomad_lab.integrated_pipeline.stream_components
 import akka.stream.stage.{ GraphStage, GraphStageLogic, InHandler, OutHandler }
 import akka.stream.{ Attributes, FlowShape, Inlet, Outlet }
 import eu.nomad_lab.TreeType
+import eu.nomad_lab.integrated_pipeline.FileTree
 import eu.nomad_lab.integrated_pipeline.io_integrations.ArchiveHandler
 import eu.nomad_lab.integrated_pipeline.messages._
 

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

@@ -5,9 +5,8 @@ import java.nio.file.Path
 import eu.nomad_lab.JsonSupport.formats
 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.{ FileTree, OutputType }
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
-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

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

@@ -4,6 +4,7 @@ import java.nio.file.{ Path, Paths }
 
 import eu.nomad_lab.TreeType
 import eu.nomad_lab.TreeType.TreeType
+import eu.nomad_lab.integrated_pipeline.FileTree
 import eu.nomad_lab.integrated_pipeline.messages._
 import eu.nomad_lab.integrated_pipeline_tests.EventBuilders._
 import eu.nomad_lab.integrated_pipeline_tests.MessageBuilders._

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

@@ -6,7 +6,7 @@ import akka.stream.ClosedShape
 import akka.stream.scaladsl.{ GraphDSL, RunnableGraph }
 import akka.stream.testkit.scaladsl.{ TestSink, TestSource }
 import eu.nomad_lab.TreeType
-import eu.nomad_lab.integrated_pipeline.CalculationParsingEngine
+import eu.nomad_lab.integrated_pipeline.{ CalculationParsingEngine, FileTree }
 import eu.nomad_lab.integrated_pipeline.messages._
 import eu.nomad_lab.integrated_pipeline.stream_components._
 import eu.nomad_lab.integrated_pipeline_tests.matchers.{ FileParsingResultMatchers, StreamAssertions }

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

@@ -2,9 +2,9 @@ package eu.nomad_lab.integrated_pipeline_tests
 
 import eu.nomad_lab.TreeType
 import eu.nomad_lab.TreeType.TreeType
-import eu.nomad_lab.integrated_pipeline.ParsingTaskGenerator
+import eu.nomad_lab.integrated_pipeline.{ FileTree, ParsingTaskGenerator }
 import eu.nomad_lab.integrated_pipeline.io_integrations.{ DirectoryTreeParsingTaskGenerator, ZipTreeParsingTaskGenerator }
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTree }
+import eu.nomad_lab.integrated_pipeline.messages.FileParsingTask
 import eu.nomad_lab.parsers.AllParsers
 import org.scalatest.{ Matchers, WordSpec }
 

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

 package eu.nomad_lab.integrated_pipeline_tests
 
 import eu.nomad_lab.integrated_pipeline.messages._
-import eu.nomad_lab.integrated_pipeline.{ EventListener, ParsingTaskGenerator, TreeScanner }
+import eu.nomad_lab.integrated_pipeline.{ EventListener, FileTree, ParsingTaskGenerator, TreeScanner }
 import eu.nomad_lab.integrated_pipeline_tests.matchers._
 import org.mockito.ArgumentMatchers._
 import org.mockito.Mockito._

integrated-pipeline/src/test/scala/eu/nomad_lab/integrated_pipeline_tests/WriteToHDF5MergedResultsProcessorSpec.scala

@@ -5,7 +5,7 @@ import java.nio.file.Paths
 import eu.nomad_lab.JsonSupport.formats
 import eu.nomad_lab.h5.CalculationH5
 import eu.nomad_lab.integrated_pipeline.io_integrations.WriteToHDF5MergedResultsProcessor
-import eu.nomad_lab.integrated_pipeline.messages.{ FileParsingTask, FileTree }
+import eu.nomad_lab.integrated_pipeline.messages.FileParsingTask
 import eu.nomad_lab.meta.KnownMetaInfoEnvs
 import eu.nomad_lab.{ H5Lib, JsonUtils, TreeType }
 import org.scalatest.{ Matchers, WordSpec }

integrated-pipeline/src/test/scala/eu/nomad_lab/integrated_pipeline_tests/matchers/MessageMatchers.scala

@@ -3,6 +3,7 @@ package eu.nomad_lab.integrated_pipeline_tests.matchers
 import java.nio.file.{ Path, Paths }
 
 import eu.nomad_lab.TreeType.TreeType
+import eu.nomad_lab.integrated_pipeline.FileTree
 import eu.nomad_lab.integrated_pipeline.OutputType.OutputType
 import eu.nomad_lab.integrated_pipeline.messages._
 import eu.nomad_lab.parsers.ParseResult.ParseResult