log.info('selected catalog folder: %s' % catalog_folder) if config['actions']['transform']: try: transform = Transform(config, catalog_folder) transform.transform_data() except Exception as e: log.error(e) exit(1) else: log.info('data transformed succesfully') if config['actions']['upload']: if config['debug_mode']: # Data with errors is logged and skipped in debug mode. # Do not allow potentialy broken data to be uploaded to Molgenis. log.warn('upload is not allowed in debug mode') else: try: upload = Upload(config) upload.delete_molgenis_entities() upload.zip_transformed_data() upload.upload_transformed_data_zip() upload.set_entities_permissions() upload.set_entity_indexing_depth('lifelines_subsection_variable') except Exception as e: log.error(e) exit(1) log.info('execution time: %s' % (timedelta(seconds=time.time() - startTime)))