From a8f014aaeb91a71bf87bd5b961e2ee4317d16867 Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Thu, 11 Jul 2024 15:52:26 +0200 Subject: [PATCH] Remove DEFINED_CANCER_TYPES global variable --- scripts/importer/validateData.py | 4 +--- tests/unit_tests_validate_data.py | 2 -- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/scripts/importer/validateData.py b/scripts/importer/validateData.py index 3747b0bd..079479ba 100755 --- a/scripts/importer/validateData.py +++ b/scripts/importer/validateData.py @@ -70,7 +70,6 @@ DEFINED_SAMPLE_IDS = None DEFINED_SAMPLE_ATTRIBUTES = None PATIENTS_WITH_SAMPLES = None -DEFINED_CANCER_TYPES = None mutation_sample_ids = None mutation_file_sample_ids = set() sample_ids_panel_dict = {} @@ -5388,7 +5387,6 @@ def validate_study(study_dir, portal_instance, logger, relaxed_mode, strict_maf_ cancer_type_validators[0].validate() studydefined_cancer_types = ( cancer_type_validators[0].defined_cancer_types) - DEFINED_CANCER_TYPES = studydefined_cancer_types # next check the cancer type of the meta_study file if cbioportal_common.MetaFileTypes.STUDY not in validators_by_meta_type: @@ -5396,7 +5394,7 @@ def validate_study(study_dir, portal_instance, logger, relaxed_mode, strict_maf_ return if portal_instance.cancer_type_dict is not None and not ( study_cancer_type in portal_instance.cancer_type_dict or - study_cancer_type in DEFINED_CANCER_TYPES): + study_cancer_type in studydefined_cancer_types): logger.error( 'Cancer type of study is neither known to the portal nor defined ' 'in a cancer_type file', diff --git a/tests/unit_tests_validate_data.py b/tests/unit_tests_validate_data.py index f583f7e6..3089d33b 100755 --- a/tests/unit_tests_validate_data.py +++ b/tests/unit_tests_validate_data.py @@ -2297,12 +2297,10 @@ class StudyCompositionTestCase(LogBufferTestCase): def setUp(self): """Store validateData globals changed by running validate_study().""" super(StudyCompositionTestCase, self).setUp() - self.orig_defined_cancer_types = validateData.DEFINED_CANCER_TYPES self.orig_defined_sample_ids = validateData.DEFINED_SAMPLE_IDS def tearDown(self): """Restore the environment to before setUp() was called.""" - validateData.DEFINED_CANCER_TYPES = self.orig_defined_cancer_types validateData.DEFINED_SAMPLE_IDS = self.orig_defined_sample_ids super(StudyCompositionTestCase, self).tearDown()