How to use

getFileId

method

in

org.opencb.opencga.core.models.File$RelatedFile

for (File.RelatedFile relatedFile : file.getRelatedFiles()) {
  if (File.RelatedFile.Relation.PRODUCED_FROM.equals(relatedFile.getRelation())) {
    Query query = new Query(FileDBAdaptor.QueryParams.UID.key(), relatedFile.getFileId());
    file = get(studyStr, query, null, sessionId).first();
    break;

private File getOriginalFromTransformed(String study, File file, String sessionId)
    throws URISyntaxException, CatalogException {
  // Look for the vcf file
  String vcfId = null;
  // Matchup variant files, if missing
  if (file.getRelatedFiles() == null || file.getRelatedFiles().isEmpty()) {
    catalogManager.getFileManager().matchUpVariantFiles(null, Collections.singletonList(file), sessionId);
  }
  for (File.RelatedFile relatedFile : file.getRelatedFiles()) {
    if (File.RelatedFile.Relation.PRODUCED_FROM.equals(relatedFile.getRelation())) {
      long fileUid = relatedFile.getFileId();
      // FIXME!!!
      vcfId = catalogManager.getFileManager().get(study,
          new Query(UID.key(), fileUid),
          new QueryOptions(QueryOptions.INCLUDE, ID.key()), sessionId).first().getId();
      break;
    }
  }
  if (vcfId == null) {
    logger.error("This code should never be executed. Every transformed avro file should come from a registered vcf file");
    throw new CatalogException("Internal error. No vcf file could be found for file " + file.getPath());
  }
  QueryResult<File> vcfQueryResult = fileManager.get(study, vcfId, FILE_GET_QUERY_OPTIONS, sessionId);
  if (vcfQueryResult.getNumResults() != 1) {
    logger.error("This code should never be executed. No vcf file could be found for vcf id " + vcfId);
    throw new CatalogException("Internal error. No vcf file could be found under id " + vcfId);
  }
  file = vcfQueryResult.first();
  return file;
}

    .collect(Collectors.toList());
assertEquals(1, relatedFiles.size());
assertEquals(inputFile.getUid(), relatedFiles.get(0).getFileId());

protected void checkEtlResults(String studyId, List<StoragePipelineResult> etlResults, String expectedStatus) throws CatalogException {
  for (StoragePipelineResult etlResult : etlResults) {
    File input = catalogManager.getFileManager().get(studyId, new Query(FileDBAdaptor.QueryParams.URI.key(),
        etlResult.getInput()), null, sessionId).first();
    String indexedFileId;
    if (input.getRelatedFiles().isEmpty()) {
      indexedFileId = input.getId();
    } else {
      long indexedFileUid = input.getRelatedFiles().get(0).getFileId();
      indexedFileId = catalogManager.getFileManager().get(studyId, new Query(FileDBAdaptor.QueryParams.UID.key(),
          indexedFileUid), new QueryOptions(), sessionId).first().getId();
    }
    assertEquals(expectedStatus, catalogManager.getFileManager().get(studyId, indexedFileId, null, sessionId).first().getIndex().getStatus().getName());
    System.out.println("etlResult = " + etlResult);
  }
}

    .collect(Collectors.toList());
assertEquals(1, relatedFiles.size());
assertEquals(inputFile.getUid(), relatedFiles.get(0).getFileId());