Commit 3dfa160f authored by Chris Jewell's avatar Chris Jewell
Browse files

Updated utility scripts to incorporate change to Tier data download.

parent 87abe7b1
......@@ -2,9 +2,9 @@
# Enqueues COVID-19 pipelines
CASES_FILE="data/Anonymised Combined Line List 20201228.csv"
DATE_LOW="2020-10-01"
DATE_HIGH="2020-12-25"
CASES_FILE="data/Anonymised Combined Line List 20210104.csv"
DATE_LOW="2020-10-09"
DATE_HIGH="2021-01-01"
TEMPLATE_CONFIG=template_config.yaml
......@@ -14,7 +14,7 @@ switch-gpu
for PILLAR in both 1
do
for CASE_DATE_TYPE in specimen report
for CASE_DATE_TYPE in specimen
do
RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}
JOB_NAME="covid_${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}"
......
......@@ -58,7 +58,7 @@ for key in ["reported_cases", "commute_volume", "case_date_type", "pillar"]:
config["data"][key] = val
if args.inference_period is not None:
config["settings"]["inference_period"] = [str(x) for x in args.inference_period]
config["Global"]["inference_period"] = [str(x) for x in args.inference_period]
for key in ["results_dir"]:
val = getattr(args, key)
......
......@@ -166,15 +166,11 @@ if __name__ == "__main__":
config = yaml.load(f, Loader=yaml.FullLoader)
inference_period = [
np.datetime64(x) for x in config["settings"]["inference_period"]
np.datetime64(x) for x in config["Global"]["inference_period"]
]
# Load covariate data
covar_data = model_spec.read_covariates(
config["data"],
date_low=inference_period[0],
date_high=inference_period[1],
)
covar_data = model_spec.read_covariates(config)
# Load posterior file
posterior_path = os.path.join(
......
......@@ -65,13 +65,11 @@ with open(args.config, "r") as f:
config = yaml.load(f, Loader=yaml.FullLoader)
inference_period = [
np.datetime64(x) for x in config["settings"]["inference_period"]
np.datetime64(x) for x in config["Global"]["inference_period"]
]
# Load covariate data
covar_data = model_spec.read_covariates(
config["data"], date_low=inference_period[0], date_high=inference_period[1]
)
covar_data = model_spec.read_covariates(config)
# Load posterior file
posterior = h5py.File(
......
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