def test_samtools_with_missing(self, env_mock, path_mock): path_mock.isfile.side_effect = lambda f: 'missing' not in f fake_env_variables = {'SRST2_SAMTOOLS': '/missing/samtools'} env_mock.get.side_effect = fake_env_variables.get samtools_exec = srst2.get_samtools_exec() self.assertEqual(samtools_exec, 'samtools')
def test_samtools_with_default(self, env_mock, path_mock): path_mock.isfile.side_effect = lambda f: 'missing' not in f fake_env_variables = {} env_mock.get.side_effect = fake_env_variables.get samtools_exec = srst2.get_samtools_exec() self.assertEqual(samtools_exec, 'samtools')