def process_genomic_water_line():
"""
Entrypoint, executed as a cron job
"""
genomic_set_id = genomic_set_file_handler.read_genomic_set_from_bucket()
if genomic_set_id is not None:
logging.info('Read input genomic set file successfully.')
dao = GenomicSetDao()
validation.validate_and_update_genomic_set_by_id(genomic_set_id, dao)
genomic_set = dao.get(genomic_set_id)
if genomic_set.genomicSetStatus == GenomicSetStatus.VALID:
genomic_biobank_menifest_handler\
.create_and_upload_genomic_biobank_manifest_file(genomic_set_id)
logging.info(
'Validation passed, generate biobank manifest file successfully.'
)
else:
logging.info('Validation failed.')
genomic_set_file_handler.create_genomic_set_status_result_file(
genomic_set_id)
else:
logging.info('No file found or nothing read from genomic set file')
genomic_biobank_menifest_handler.process_genomic_manifest_result_file_from_bucket(
)
genomic_center_menifest_handler.process_genotyping_manifest_files()
def create_genomic_set_status_result_file(genomic_set_id):
set_dao = GenomicSetDao()
genomic_set = set_dao.get(genomic_set_id)
_create_and_upload_result_file(genomic_set)