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Minor fixes in MIMIC_example #224

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merged 2 commits into from
Nov 12, 2024
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Minor fixes in MIMIC_example #224

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1ab0e72
Read input files even if mimic subdirs are symbolic links
prenc Nov 12, 2024
069b2b9
Use the proper read function
prenc Nov 12, 2024
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6 changes: 3 additions & 3 deletions MIMIC-IV_Example/pre_MEDS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,7 +229,7 @@ def main(cfg: DictConfig):
)
exit(0)

all_fps = list(input_dir.glob("**/*.*"))
all_fps = list(input_dir.rglob("*/*.*"))
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Allows to properly find files if subdirs are symbolic links


dfs_to_load = {}
seen_fps = {}
Expand Down Expand Up @@ -299,9 +299,9 @@ def main(cfg: DictConfig):

logger.info(f"Loading {str(df_to_load_fp.resolve())} for manipulating other dataframes...")
if df_to_load_fp.suffix in [".csv.gz"]:
df = read_fn(df_to_load_fp, columns=cols)
df = df_to_load_read_fn(df_to_load_fp, columns=cols)
else:
df = read_fn(df_to_load_fp)
df = df_to_load_read_fn(df_to_load_fp)
logger.info(f" Loaded in {datetime.now() - st}")

for fp in fps:
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