Running ./modules/csv_datasets.ipynb
Checking PEP8 compliance...
Running notebook...
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Executing: 61%|██████▏ | 19/31 [00:18<00:11, 1.03cell/s]
Traceback (most recent call last):
File "/opt/conda/bin/papermill", line 8, in <module>
sys.exit(papermill())
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1137, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1062, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 763, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
execute_notebook(
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [9]":
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/tmp/ipykernel_19481/3280160788.py in <module>
----> 1 dataset = CSVDataset(
2 filename=[filepath1, filepath2, filepath3],
3 row_indices=[[0, 2], 3], # load row: 0, 1, 3
4 col_names=["subject_id", "label", "ehr_1", "ehr_7", "meta_1"],
5 )
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/utils/deprecate_utils.py in _wrapper(*args, **kwargs)
208 warn_deprecated(argname, msg)
209
--> 210 return func(*args, **kwargs)
211
212 return _wrapper
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/dataset.py in __init__(self, src, row_indices, col_names, col_types, col_groups, transform, **kwargs)
1277 raise ValueError("`src` must be file path or pandas `DataFrame`.")
1278
-> 1279 data = convert_tables_to_dicts(
1280 dfs=dfs, row_indices=row_indices, col_names=col_names, col_types=col_types, col_groups=col_groups, **kwargs
1281 )
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/utils.py in convert_tables_to_dicts(dfs, row_indices, col_names, col_types, col_groups, **kwargs)
1117
1118 """
-> 1119 df = reduce(lambda l, r: pd.merge(l, r, **kwargs), ensure_tuple(dfs))
1120 # parse row indices
1121 rows: List[Union[int, str]] = []
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/utils.py in <lambda>(l, r)
1117
1118 """
-> 1119 df = reduce(lambda l, r: pd.merge(l, r, **kwargs), ensure_tuple(dfs))
1120 # parse row indices
1121 rows: List[Union[int, str]] = []
TypeError: merge() got an unexpected keyword argument 'filename'
Describe the bug