From 83d6f98be26d111bcd44ce38d90ebf42fab6c79c Mon Sep 17 00:00:00 2001 From: Amanda Birmingham Date: Fri, 22 Nov 2024 17:45:56 -0800 Subject: [PATCH] Add back in remove_internals option --- qiimp/src/metadata_extender.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/qiimp/src/metadata_extender.py b/qiimp/src/metadata_extender.py index b382a0c..f4e64a3 100644 --- a/qiimp/src/metadata_extender.py +++ b/qiimp/src/metadata_extender.py @@ -39,6 +39,7 @@ # (Per Antonio 10/28/24, this is a reserved name for Qiita and may not be # in the metadata). + def get_reserved_cols(raw_metadata_df, study_specific_config_dict, study_specific_transformers_dict=None): validate_required_columns_exist( @@ -148,7 +149,7 @@ def write_metadata_results( def write_extended_metadata_from_df( raw_metadata_df, study_specific_config_dict, out_dir, out_name_base, - study_specific_transformers_dict=None, sep="\t", + study_specific_transformers_dict=None, sep="\t", remove_internals=True, suppress_empty_fails=False, internal_col_names=None): metadata_df, validation_msgs_df = _extend_metadata_df( @@ -157,14 +158,16 @@ def write_extended_metadata_from_df( write_metadata_results( metadata_df, validation_msgs_df, out_dir, out_name_base, - sep, suppress_empty_fails, internal_col_names) + sep=sep, remove_internals=remove_internals, + suppress_empty_fails=suppress_empty_fails, + internal_col_names=internal_col_names) return metadata_df def write_extended_metadata( - raw_metadata_fp, study_specific_config_fp, - out_dir, out_name_base, sep="\t", suppress_empty_fails=False): + raw_metadata_fp, study_specific_config_fp, out_dir, out_name_base, + sep="\t", remove_internals=True, suppress_empty_fails=False): # extract the extension from the raw_metadata_fp file path extension = os.path.splitext(raw_metadata_fp)[1] @@ -186,6 +189,7 @@ def write_extended_metadata( extended_df = write_extended_metadata_from_df( raw_metadata_df, study_specific_config_dict, out_dir, out_name_base, sep=sep, + remove_internals=remove_internals, suppress_empty_fails=suppress_empty_fails) return extended_df