diff --git a/mimic-iv/buildmimic/sqlite/import.py b/mimic-iv/buildmimic/sqlite/import.py index f99abd21..02b4f0b3 100644 --- a/mimic-iv/buildmimic/sqlite/import.py +++ b/mimic-iv/buildmimic/sqlite/import.py @@ -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)] @@ -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: