diff --git a/scripts/importer/validateData.py b/scripts/importer/validateData.py index eb5a0392..3747b0bd 100755 --- a/scripts/importer/validateData.py +++ b/scripts/importer/validateData.py @@ -3386,7 +3386,7 @@ def checkLine(self, data): sample_ids_panel_dict[sample_id] = data[self.mutation_stable_id_index - 1] # Sample ID has been removed from list, so subtract 1 position. if data[self.mutation_stable_id_index - 1] != 'NA': - if sample_id not in mutation_sample_ids: + if mutation_sample_ids is not None and sample_id not in mutation_sample_ids: self.logger.error('Sample ID has mutation gene panel, but is not in the sequenced case list', extra={'line_number': self.line_number, 'cause': sample_id}) diff --git a/tests/test_data/study_es_0_inc/cna_long/meta_cna_discrete_long.txt b/tests/test_data/study_es_0_inc/cna_long/meta_cna_discrete_long.txt index df6ccdae..d1ce3813 100644 --- a/tests/test_data/study_es_0_inc/cna_long/meta_cna_discrete_long.txt +++ b/tests/test_data/study_es_0_inc/cna_long/meta_cna_discrete_long.txt @@ -6,4 +6,3 @@ show_profile_in_analysis_tab: true profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. profile_name: Putative copy-number alterations from GISTIC data_filename: data_cna_discrete_long.txt -gene_panel: TSTGNPNLCNADS diff --git a/tests/test_data/study_es_0_inc/meta_mutations_extended.txt b/tests/test_data/study_es_0_inc/meta_mutations_extended.txt index 9215c831..94df92aa 100644 --- a/tests/test_data/study_es_0_inc/meta_mutations_extended.txt +++ b/tests/test_data/study_es_0_inc/meta_mutations_extended.txt @@ -8,4 +8,3 @@ profile_name: Mutations data_filename: data_mutations_extended.maf swissprot_identifier: name namespaces: Zygosity -gene_panel: TSTGNPNLMUTEXT diff --git a/tests/test_data/study_es_0_inc/meta_treatment_ic50.txt b/tests/test_data/study_es_0_inc/meta_treatment_ic50.txt index ced1af7d..edc5ef22 100644 --- a/tests/test_data/study_es_0_inc/meta_treatment_ic50.txt +++ b/tests/test_data/study_es_0_inc/meta_treatment_ic50.txt @@ -10,4 +10,3 @@ show_profile_in_analysis_tab: true pivot_threshold_value: 0.1 value_sort_order: ASC generic_entity_meta_properties: NAME,DESCRIPTION,URL -gene_panel: TSTGNPNLGENASS