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Exclude None from default_na_values list when reading csv files #1466

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merged 1 commit into from
Aug 17, 2023
Merged

Exclude None from default_na_values list when reading csv files #1466

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18 changes: 12 additions & 6 deletions workflow/tests/compare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,8 @@ def results(self, aggregate_column=None, aggregate_function=None, excludes=[], e
print("Warning: %s not found. Skipping..." % feature_file)
continue

base_df = pd.read_csv(base_file, index_col=0)
feature_df = pd.read_csv(feature_file, index_col=0)
base_df = read_csv(base_file, index_col=0)
feature_df = read_csv(feature_file, index_col=0)

base_df = self.intersect_rows(base_df, feature_df)
feature_df = self.intersect_rows(feature_df, base_df)
Expand Down Expand Up @@ -151,14 +151,14 @@ def visualize(self, aggregate_column=None, aggregate_function=None, display_colu
files.append(file)

if display_columns or aggregate_columns:
base_characteristics_df = pd.read_csv(
base_characteristics_df = read_csv(
os.path.join(
self.base_folder,
'results_characteristics.csv'),
index_col=0)[
display_columns +
aggregate_columns]
feature_characteristics_df = pd.read_csv(
feature_characteristics_df = read_csv(
os.path.join(
self.feature_folder,
'results_characteristics.csv'),
Expand Down Expand Up @@ -209,8 +209,8 @@ def remove_columns(cols):
print("Warning: %s not found. Skipping..." % feature_file)
continue

base_df = pd.read_csv(base_file, index_col=0)
feature_df = pd.read_csv(feature_file, index_col=0)
base_df = read_csv(base_file, index_col=0)
feature_df = read_csv(feature_file, index_col=0)

base_df = self.intersect_rows(base_df, feature_df)
feature_df = self.intersect_rows(feature_df, base_df)
Expand Down Expand Up @@ -334,6 +334,12 @@ def remove_columns(cols):
auto_open=False)


def read_csv(csv_file_path, **kwargs) -> pd.DataFrame:
default_na_values = pd._libs.parsers.STR_NA_VALUES
df = pd.read_csv(csv_file_path, na_values=list(default_na_values - {'None'}), keep_default_na=False, **kwargs)
return df


if __name__ == '__main__':

default_base_folder = 'workflow/tests/base_results'
Expand Down