def begin_pipeline(**kwargs):
print("begin_pipeline:")
s3_bucket = os.environ.get("S3_BUCKET", "")
folder_path = kwargs['dag_run'].conf.get('folder_path')
s3_file = kwargs['dag_run'].conf.get('s3_file')
uuid_mapping_file = kwargs['dag_run'].conf.get('uuid_mapping_file')
biobank_file = kwargs['dag_run'].conf.get('biobank_file')
mapping_file = kwargs['dag_run'].conf.get('mapping_file')
dp = DagPebbles()
download_key = dp.get_download_key(s3_bucket, folder_path, s3_file)
pipeline_state_args = {
"s3_bucket": s3_bucket,
"folder_path": folder_path,
"s3_file": s3_file,
"uuid_mapping_file": uuid_mapping_file,
"biobank_file": biobank_file,
"mapping_file": mapping_file,
"download_key": download_key
}
dp.save_pipeline_state(**pipeline_state_args)
kwargs["ti"].xcom_push(key="folder_path", value=folder_path)
kwargs["ti"].xcom_push(key="s3_file", value=s3_file)
kwargs["ti"].xcom_push(key="download_key", value=download_key)
kwargs["ti"].xcom_push(key="uuid_mapping_file", value=uuid_mapping_file)
kwargs["ti"].xcom_push(key="biobank_file", value=biobank_file)
kwargs["ti"].xcom_push(key="mapping_file", value=mapping_file)
def stage_custom_dmp_files(**kwargs):
print("stage_custom_dmp_files:")
dp = DagPebbles()
custom_log_file = kwargs['dag_run'].conf.get('custom_log_file')
custom_dmp_file = kwargs['dag_run'].conf.get('custom_dmp_file')
pipeline_args = {
"custom_log_file": custom_log_file,
"custom_dmp_file": custom_dmp_file
}
dp.save_pipeline_state(**pipeline_args)
dp.stage_custom_dmp_files(**pipeline_args)
