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)))
