How to use

FileIndex$TransformedFile

in

org.opencb.opencga.core.models

private long getTransformedFileIdFromOriginal(File file) throws CatalogException {
  long transformedFile = file.getIndex() != null && file.getIndex().getTransformedFile() != null
      ? file.getIndex().getTransformedFile().getId()
      : -1;
  if (transformedFile == -1) {
    logger.error("This code should never be executed. Every vcf file containing the transformed status should have"
        + " a registered transformed file");
    throw new CatalogException("Internal error. No transformed file could be found for file " + file.getUid());
  }
  return transformedFile;
}

        && file.getIndex().getTransformedFile().getId() != transformedFile.getUid());
FileIndex index = vcf.getIndex();
if (index.getTransformedFile() == null) {
  index.setTransformedFile(new FileIndex.TransformedFile(transformedFile.getUid(), json.getUid()));

public boolean hasTransformedFile(FileIndex index) {
  return index.getTransformedFile() != null && index.getTransformedFile().getId() > 0;
}

assertEquals(inputFile.getUid(), relatedFiles.get(0).getFileId());
assertEquals(transformedFile.getUid(), inputFile.getIndex().getTransformedFile().getId());

assertNotNull(inputFile.getIndex().getTransformedFile());
String transformedFileId = catalogManager.getFileManager().get(studyId, new Query(FileDBAdaptor.QueryParams.UID.key(),
    inputFile.getIndex().getTransformedFile().getId()), new QueryOptions(), sessionId).first().getId();