def test_completion_cluster_error(self): content = ERROR_MESSAGE self.mock_log( os.path.join(self.temp_output, MOCK_GENOME + '_diseased_genome', SUBCOMMAND.CLUSTER), content) result = checker.check_completion(self.temp_output) self.assertEqual(False, result)
def test_completion_validate_error(self): content = ERROR_MESSAGE self.mock_log( os.path.join(self.temp_output, MOCK_GENOME + '_diseased_genome', SUBCOMMAND.VALIDATE, 'batch-mock-1'), content) result = checker.check_completion(self.temp_output) self.assertEqual(False, result)
def test_completion_rerun_dir(self): content = "IndexError: list index out of range" log = 'batch-mock-1.log2' with open( os.path.join( os.path.join(self.temp_output, MOCK_GENOME + '_diseased_genome', SUBCOMMAND.ANNOTATE, 'batch-mock-1', log)), 'w') as f: f.write(content) print( os.path.join(self.temp_output, MOCK_GENOME + '_diseased_genome', SUBCOMMAND.ANNOTATE, 'batch-mock-1')) result = checker.check_completion(self.temp_output) self.assertEqual(True, result)
def test_completion_empty_dir(self): temp_output = tempfile.mkdtemp() result = checker.check_completion(temp_output) self.assertEqual(False, result) shutil.rmtree(temp_output)
def test_completion_pairing_error(self): content = ERROR_MESSAGE self.mock_log(os.path.join(self.temp_output, SUBCOMMAND.PAIR), content) result = checker.check_completion(self.temp_output) self.assertEqual(False, result)
def test_completion_incomplete_dir(self): shutil.rmtree(os.path.join(self.temp_output, SUBCOMMAND.SUMMARY)) mkdirs(os.path.join(self.temp_output, SUBCOMMAND.SUMMARY)) result = checker.check_completion(self.temp_output) self.assertEqual(False, result)
def test_completion_invalid_dir(self): result = checker.check_completion('') self.assertEqual(False, result)
def test_completion_valid_dir(self): result = checker.check_completion(self.temp_output) self.assertEqual(True, result)