Source code for cowidev.variants.__main__

import os

from cowidev import PATHS
from cowidev.variants.etl import run_etl
from cowidev.variants.grapher import run_grapheriser, run_explorerizer, run_db_updater
from cowidev.variants._parser import _parse_args


FILE_DS = "s3://covid-19/internal/variants/covid-variants.csv"
FILE_SEQ_DS = "s3://covid-19/internal/variants/covid-sequencing.csv"
# FILE_DS = "covid-variants.csv"
# FILE_SEQ_DS = "covid-sequencing.csv"
# FILE_SEQ_DS = os.path.join(PATHS.DATA_DIR, "variants", "covid-sequencing.csv")
FILE_GRAPHER = os.path.join(PATHS.INTERNAL_GRAPHER_DIR, "COVID-19 - Variants.csv")
FILE_SEQ_GRAPHER = os.path.join(PATHS.INTERNAL_GRAPHER_DIR, "COVID-19 - Sequencing.csv")
FILE_EXPLORER = os.path.join(PATHS.DATA_INTERNAL_DIR, "megafile--variants.json")


[docs]def run_step(step: str): if step == "etl": run_etl() elif step == "grapher-file": # Filter by num_seq run_grapheriser() elif step == "explorer-file": # Filter by num_seq run_explorerizer() elif step == "grapher-db": run_db_updater()
if __name__ == "__main__": args = _parse_args() run_step(args.step)