Integrated Pipeline: adjusted paths inside single-calculations HDF5 to match standard

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

@@ -12,11 +12,11 @@ import eu.nomad_lab.parsers.{ H5Backend, ReindexBackend }
 class WriteToHDF5ResultsProcessor(outputLocation: Path, metaInfo: MetaInfoEnv) extends ParsingResultsProcessor {
   override def processFileParsingResult(result: FileParsingResult): Unit = {
     val id = result.task.calculationGid
+    val archiveGid = result.task.treeTask.archiveId
     val fileName = Paths.get(id + ".h5")
     val targetPath = outputLocation(result.treeTask).resolve(fileName)
     Files.createDirectories(outputLocation(result.treeTask))
-    //VERIFY: Is this path the appropriate one for single calculation HDFs? (Is there a standard?)
-    val h5file = H5File.create(targetPath, Paths.get("/", id, id))
+    val h5file = H5File.create(targetPath, Paths.get("/", archiveGid, id))
     val h5Backend = H5Backend(metaEnv = metaInfo, h5File = h5file, closeFileOnFinishedParsing = false)
     val backend = new ReindexBackend(h5Backend)
     try {

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

@@ -94,6 +94,7 @@ package object integrated_pipeline_end_to_end_tests extends TestDataBuilders {
     sample.candidateCalculationsWithParsers.foreach { entry =>
       val task = aFileParsingTask().withTreeTask(treeTask).withRelativePath(entry._1).build()
       val id = task.calculationGid
+      val archiveId = treeTask.archiveId
       val fileName = s"$id.h5"
       val targetFolder = tmpResultsFolder.resolve(treeTask.prefixFolder).resolve(treeTask.archiveId)
       val location = targetFolder.resolve(fileName)
@@ -101,7 +102,8 @@ package object integrated_pipeline_end_to_end_tests extends TestDataBuilders {
         location.toFile.exists(),
         s"HDF5 file '$location' with parsing results does not exist"
       )
-      validateHDF5(targetFolder, id, metaInfo, checkSingleCalculationHDFContent(sample))
+      validateHDF5(targetFolder, archiveId, metaInfo, checkSingleCalculationHDFContent(sample),
+        Some(fileName))
     }
     succeed
   }

integrated-pipeline/src/test/scala/eu/nomad_lab/integrated_pipeline_tests/WriteToHDF5ResultsProcessorSpec.scala

@@ -30,12 +30,14 @@ class WriteToHDF5ResultsProcessorSpec extends WordSpec with TestDataBuilders wit
         val inputs = (1 to 3).map(x => FileParsingTask(sampleTree, Paths.get(s"file$x"), "dummyParser"))
         inputs.foreach(x => writer.processFileParsingResult(createSuccessfulFileParsingResult(x)))
         val targetFolder = writer.outputLocation(sampleTree)
+        val archiveId = sampleTree.archiveId
         inputs.foreach { entry =>
           val calcName = entry.calculationGid
           val filePath = targetFolder.resolve(s"$calcName.h5")
           assert(filePath.toFile.exists(), s"calculation output HDF5 '$filePath' does not exist")
           val mainFileUri = entry.treeTask.treeBasePath.resolve(entry.relativePath).toUri.toString
-          validateHDF5(targetFolder, calcName, metaData, validateHDFContent(mainFileUri))
+          validateHDF5(targetFolder, archiveId, metaData, validateHDFContent(mainFileUri),
+            Some(s"$calcName.h5"))
         }
       }
     }