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Fix SQLite build using all CSV files #1788

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merged 3 commits into from
Aug 25, 2024
Merged

Fix SQLite build using all CSV files #1788

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72fa263
remove files if they are not in the set of mimic tables
alistairewj Aug 25, 2024
2cd3360
remove specifying format of date
alistairewj Aug 25, 2024
f925c03
print files which are ignored
alistairewj Aug 25, 2024
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11 changes: 10 additions & 1 deletion mimic-iv/buildmimic/sqlite/import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@
def process_dataframe(df: pd.DataFrame, subjects: t.Optional[t.List[int]] = None) -> pd.DataFrame:
for c in df.columns:
if c.endswith('time') or c.endswith('date'):
df[c] = pd.to_datetime(df[c], format='ISO8601')
df[c] = pd.to_datetime(df[c])

if subjects is not None and 'subject_id' in df:
df = df.loc[df['subject_id'].isin(subjects)]
Expand Down Expand Up @@ -96,6 +96,15 @@ def main():
print(f"Missing tables: {missing_tables}")
sys.exit()

# subselect to only tables in the above list
ignored_files = set([f for f, t in zip(data_files, tablenames) if t not in _MIMIC_TABLES])
data_files = [f for f, t in zip(data_files, tablenames) if t in _MIMIC_TABLES]
tablenames = [t for t in tablenames if t in _MIMIC_TABLES]
print(f"Importing {len(tablenames)} files.")

if ignored_files:
print(f"Ignoring {len(ignored_files)} files: {ignored_files}")

pt = None
subjects = None
if args.limit > 0:
Expand Down
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