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)
Beispiel #2
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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)