def run():
logger = Configuration().get_logger(__name__)
try:
logger.info("Preparing machine learning data")
StagingTable().prepare()
PatientTable().prepare()
NetDataTable().prepare()
logger.info("Preparation of machine learning data complete")
except Exception as e:
message = "Failed to prepare machine learning data"
logger.exception(message, exc_info=e)
raise SystemExit(message)
def run():
logger = Configuration().get_logger(__name__)
try:
logger.info("Starting predicting_cancer_variants")
create_database_controller.run()
download_cancer_genomics_controller.run()
prepare_machine_learning_data_controller.run()
logger.info("predicting_cancer_variants complete")
except Exception as e:
message = "predicting_cancer_variants has failed"
logger.exception(message, exc_info=e)
raise SystemExit(message)
def run():
logger = Configuration().get_logger(__name__)
try:
logger.info("Creating tables")
StudiesTable().create()
CancerTable().create()
MolecularTable().create()
MutationTable().create()
GeneTable().create()
logger.info("Table creation complete")
except Exception as e:
message = "Failed to create tables"
logger.exception(message, exc_info=e)
raise SystemExit(message)
def run():
logger = Configuration().get_logger(__name__)
try:
logger.info(
"Downloading and storing data from large-scale online Cancer Genomics database cBioPortal.org"
)
StudiesDownloader().download_and_save_all_data()
GeneDownloader().download_and_save_all_data()
CancerDownloader().download_and_save_all_data()
MolecularDownloader().download_and_save_data_every_large_study()
MutationDownloader().download_and_save_data_every_large_study()
logger.info("Downloads complete")
except Exception as e:
message = "Failed to download and store data"
logger.exception(message, exc_info=e)
raise SystemExit(message)