def setup_class_hook(cls):
cls.study = create_study_from_dir('valid_study')
cls.tree_file = os.path.join(cls.temp_dir, 'treefile.json')
cls.json_data = tmtk.arborist.create_concept_tree(cls.study)
with open(cls.tree_file, 'w') as f:
f.write(cls.json_data)
def test_changes_clinical(self):
study = create_study_from_dir('valid_study')
json_data = self.json_data.replace('"text": "Characteristics"',
'"text": "Characteristic"')
json_data = json_data.replace('"text": "SW48"',
'"text": "SW48_MAPPED"')
tmtk.arborist.update_study_from_json(study, json_data)
self.assertEqual(9, len(study.Clinical.show_changes()))
def setup_class_hook(cls):
cls.study = create_study_from_dir('valid_study')
cls.tmp_batch_home = os.path.join(cls.temp_dir, 'batch_home')
options.transmart_batch_home = cls.tmp_batch_home
os.makedirs(cls.tmp_batch_home)
cls.properties_file = os.path.join(cls.tmp_batch_home, 'batchdb.properties')
cls.fake_jar = os.path.join(cls.tmp_batch_home, 'transmart-batch-fake.jar')
with open(cls.properties_file, 'w') as writer:
writer.write(properties_file)
with open(cls.fake_jar, 'w') as writer:
writer.write('')
def test_transmart_batch_mode_clinical_params(self):
params_ = ('MODIFIERS_FILE', 'TRIAL_VISITS_FILE', 'ONTOLOGY_MAP_FILE')
default = options.transmart_batch_mode
try:
options.transmart_batch_mode = True
limited_study = create_study_from_dir('incomplete')
for p in params_:
self.assertTrue(hasattr(self.study.Clinical.params, p))
self.assertFalse(hasattr(limited_study.Clinical.params, p))
self.assertTrue(limited_study.Clinical.validate())
limited_study = limited_study.write_to(self.temp_dir)
finally:
options.transmart_batch_mode = default
def setup_class_hook(cls):
cls.study = create_study_from_dir('TEST_ONTOLOGY')
cls.export = tmtk.toolbox.SkinnyExport(cls.study, cls.temp_dir)
cls.export.build_observation_fact()
def setup_class_hook(cls):
cls.study = create_study_from_dir('remap')
def setup_class_hook(cls):
cls.study = create_study_from_dir('valid_study')
cls.invalid_study = create_study_from_dir('invalid_study')
def setup_class_hook(cls):
cls.study = create_study_from_dir('incomplete')
def setUp(self):
self.study = create_study_from_dir('incomplete')
