SQLite import for mimic3 gives mixed column type warning

Prerequisites

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  • Checked the online documentation: https://mimic.mit.edu/
  • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=

Description

While trying to import mimic3 into SQLite with import.py, I get the following error:

Starting processing DATETIMEEVENTS.csv.gz
mimic-code/mimic-iii/buildmimic/sqlite/import.py:25: DtypeWarning: Columns (13) have mixed types. Specify dtype option on import or set low_memory=False.
  for chunk in pd.read_csv(f, index_col="ROW_ID", chunksize=CHUNKSIZE):
...
Starting processing INPUTEVENTS_CV.csv.gz
/home/armando/projects/mimic-code/mimic-iii/buildmimic/sqlite/import.py:25: DtypeWarning: Columns (20,21) have mixed types. Specify dtype option on import or set low_memory=False.
  for chunk in pd.read_csv(f, index_col="ROW_ID", chunksize=CHUNKSIZE):
...
Starting processing NOTEEVENTS.csv.gz
/home/armando/projects/mimic-code/mimic-iii/buildmimic/sqlite/import.py:25: DtypeWarning: Columns (4,5) have mixed types. Specify dtype option on import or set low_memory=False.
  for chunk in pd.read_csv(f, index_col="ROW_ID", chunksize=CHUNKSIZE):
...
Starting processing CHARTEVENTS.csv.gz
/home/armando/projects/mimic-code/mimic-iii/buildmimic/sqlite/import.py:25: DtypeWarning: Columns (13) have mixed types. Specify dtype option on import or set low_memory=False.
  for chunk in pd.read_csv(f, index_col="ROW_ID", chunksize=CHUNKSIZE):
...

mimic-iii/buildmimic/sqlite/import.py の pandas read_csv 呼び出しから始め、指定された CSV ファイルをインポートする際の DtypeWarning を再現します。報告された列を調査し、混在する値に対する意図された処理を判断してから、SQLite のインポートがこれらの警告なしに完了することを確認します。