Make validation of study_es_0_inc data to pass

cBioPortal · May 28, 2024 · e8bbb34 · e8bbb34
1 parent 4070e68
commit e8bbb34
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Showing 4 changed files with 1 addition and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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