def setUp(self): self.files_to_remove = [] self.dirs_to_remove = [] # Create example output directory tmp_dir = get_qiime_temp_dir() self.test_out = mkdtemp(dir=tmp_dir, prefix='core_qiime_analyses_test_', suffix='') self.dirs_to_remove.append(self.test_out) # Get input data self.test_data = get_test_data_fps() self.qiime_config = load_qiime_config() self.qiime_config['jobs_to_start'] = 2 self.qiime_config['seconds_to_sleep'] = 1 # suppress stderr during tests (one of the systems calls in the # workflow prints a warning, and we can't suppress that warning with # warnings.filterwarnings) here because it comes from within the code # executed through the system call. Found this trick here: # http://stackoverflow.com/questions/9949633/suppressing-print-as-stdout-python self.saved_stderr = sys.stderr sys.stderr = StringIO() # Define number of seconds a test can run for before timing out # and failing initiate_timeout(420)
def setUp(self): """ """ self.test_data = get_test_data_fps() self.files_to_remove = [] self.dirs_to_remove = [] # Create example output directory tmp_dir = get_qiime_temp_dir() self.test_out = mkdtemp(dir=tmp_dir, prefix='core_qiime_analyses_test_', suffix='') self.dirs_to_remove.append(self.test_out) self.qiime_config = load_qiime_config() self.params = parse_qiime_parameters(params_f1) # suppress stderr during tests (one of the systems calls in the # workflow prints a warning, and we can't suppress that warning with # warnings.filterwarnings) here because it comes from within the code # executed through the system call. Found this trick here: # http://stackoverflow.com/questions/9949633/suppressing-print-as-stdout-python self.saved_stderr = sys.stderr sys.stderr = StringIO() initiate_timeout(180)
def setUp(self): self.files_to_remove = [] self.dirs_to_remove = [] # Create example output directory tmp_dir = get_qiime_temp_dir() self.test_out = mkdtemp(dir=tmp_dir, prefix='core_qiime_analyses_test_', suffix='') self.dirs_to_remove.append(self.test_out) # Get input data self.test_data = get_test_data_fps() self.qiime_config = load_qiime_config() self.qiime_config['jobs_to_start'] = 2 self.qiime_config['seconds_to_sleep'] = 1 # suppress stderr during tests (one of the systems calls in the # workflow prints a warning, and we can't suppress that warning with # warnings.filterwarnings) here because it comes from within the code # executed through the system call. Found this trick here: # http://stackoverflow.com/questions/9949633/suppressing-print-as-stdout-python self.saved_stderr = sys.stderr sys.stderr = StringIO() # Define number of seconds a test can run for before timing out # and failing initiate_timeout(600)
def setUp(self): """ """ self.test_data = get_test_data_fps() self.files_to_remove = [] self.dirs_to_remove = [] # Create example output directory tmp_dir = get_qiime_temp_dir() self.test_out = mkdtemp(dir=tmp_dir, prefix='core_qiime_analyses_test_', suffix='') self.dirs_to_remove.append(self.test_out) self.qiime_config = load_qiime_config() self.params = parse_qiime_parameters({}) initiate_timeout(60)
def setUp(self): """ """ self.test_data = get_test_data_fps() self.files_to_remove = [] self.dirs_to_remove = [] # Create example output directory tmp_dir = get_qiime_temp_dir() self.test_out = mkdtemp(dir=tmp_dir, prefix='core_qiime_analyses_test_', suffix='') self.dirs_to_remove.append(self.test_out) self.qiime_config = load_qiime_config() self.params = parse_qiime_parameters([]) initiate_timeout(60)
def setUp(self): """ """ self.test_data = get_test_data_fps() self.files_to_remove = [] self.dirs_to_remove = [] # Create example output directory tmp_dir = get_qiime_temp_dir() self.test_out = mkdtemp(dir=tmp_dir, prefix='core_qiime_analyses_test_', suffix='') self.dirs_to_remove.append(self.test_out) self.qiime_config = load_qiime_config() self.params = parse_qiime_parameters([]) self.params_sortmerna = parse_qiime_parameters( ['pick_otus:otu_picking_method\tsortmerna']) self.params_sumaclust = parse_qiime_parameters( ['pick_otus:otu_picking_method\tsumaclust']) initiate_timeout(60)