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Update create_pickles_locally() #1688

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Update create_pickles_locally() #1688

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7 changes: 4 additions & 3 deletions src/tlo/analysis/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -511,13 +511,13 @@ def format_gbd(gbd_df: pd.DataFrame):
return gbd_df


def create_pickles_locally(scenario_output_dir, compressed_file_name_prefix=None):
def create_pickles_locally(scenario_output_dir, compressed_file_name_prefix=None, level: int = logging.INFO):
"""For a run from the Batch system that has not resulted in the creation of the pickles, reconstruct the pickles
locally."""

def turn_log_into_pickles(logfile):
print(f"Opening {logfile}")
outputs = parse_log_file(logfile)
outputs = parse_log_file(logfile, level)
for key, output in outputs.items():
if key.startswith("tlo."):
print(f" - Writing {key}.pickle")
Expand All @@ -541,7 +541,8 @@ def uncompress_and_save_logfile(compressed_file) -> Path:
logfile = [x for x in os.listdir(run_folder) if x.endswith('.log')][0]
else:
compressed_file_name = [
x for x in os.listdir(run_folder) if x.startswith(compressed_file_name_prefix)
x for x in os.listdir(run_folder) if x.startswith(compressed_file_name_prefix) and
x.endswith('.log.gz')
][0]
logfile = uncompress_and_save_logfile(Path(run_folder) / compressed_file_name)

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