From 83c9181870b0aac2647ea7d0fcb7ef67872414c6 Mon Sep 17 00:00:00 2001 From: danlu1 Date: Thu, 14 Nov 2024 22:49:06 +0000 Subject: [PATCH] revert to use check_col_and_values --- genie_registry/assay.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/genie_registry/assay.py b/genie_registry/assay.py index 3d14203f..fcca0452 100644 --- a/genie_registry/assay.py +++ b/genie_registry/assay.py @@ -178,7 +178,7 @@ def _validate(self, assay_info_df): read_group_dict = process_functions.get_gdc_data_dictionary("read_group") read_group_headers = read_group_dict["properties"] - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "is_paired_end", [True, False], @@ -188,7 +188,7 @@ def _validate(self, assay_info_df): warning += warn total_error += error - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "library_selection", read_group_headers["library_selection"]["enum"], @@ -198,7 +198,7 @@ def _validate(self, assay_info_df): warning += warn total_error += error - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "library_strategy", ["Targeted Sequencing", "WXS"], @@ -208,7 +208,7 @@ def _validate(self, assay_info_df): warning += warn total_error += error - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "platform", read_group_headers["platform"]["enum"], @@ -220,7 +220,7 @@ def _validate(self, assay_info_df): instrument_model = read_group_headers["instrument_model"]["enum"] instrument_model.extend(["Illumina NovaSeq 6000", None]) - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "instrument_model", instrument_model, @@ -256,7 +256,7 @@ def _validate(self, assay_info_df): "3'Flank", None, ] - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "variant_classifications", variant_classes, @@ -319,7 +319,7 @@ def _validate(self, assay_info_df): "gene_padding is by default 10 if not specified.\n" ) - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "calling_strategy", ["tumor_only", "tumor_normal", "plasma_normal"], @@ -354,7 +354,7 @@ def _validate(self, assay_info_df): "intragenic_cna", "structural_variants", ] - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "alteration_types", alteration_types, @@ -366,7 +366,7 @@ def _validate(self, assay_info_df): total_error += error preservation_technique = ["FFPE", "fresh_frozen", "NA"] - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "preservation_technique", preservation_technique, @@ -378,7 +378,7 @@ def _validate(self, assay_info_df): total_error += error coverage = ["hotspot_regions", "coding_exons", "introns", "promoters"] - warn, error = process_functions.check_column_and_values_row_specific( + warn, error = process_functions.check_col_and_values( assay_info_df, "coverage", coverage,