def test_absolute_path(self, atacseq_piface_data, path_config_file, tmpdir,
pipe_path, expected_path_base, atac_pipe_name):
""" Absolute path regardless of variables works as pipeline path. """
exp_path = os.path.join(tmpdir.strpath, expected_path_base,
atac_pipe_name)
piface = ProtocolInterface(path_config_file)
_, obs_path, _ = piface.finalize_pipeline_key_and_paths(atac_pipe_name)
assert exp_path == obs_path
def test_warns_about_nonexistent_pipeline_script_path(
self, atacseq_piface_data, path_config_file, tmpdir, pipe_path,
atac_pipe_name):
""" Nonexistent, resolved pipeline script path generates warning. """
name_log_file = "temp-test-log.txt"
path_log_file = os.path.join(tmpdir.strpath, name_log_file)
temp_hdlr = logging.FileHandler(path_log_file, mode='w')
fmt = logging.Formatter(DEV_LOGGING_FMT)
temp_hdlr.setFormatter(fmt)
temp_hdlr.setLevel(logging.WARN)
models._LOGGER.handlers.append(temp_hdlr)
pi = ProtocolInterface(path_config_file)
pi.finalize_pipeline_key_and_paths(atac_pipe_name)
with open(path_log_file, 'r') as logfile:
loglines = logfile.readlines()
assert 1 == len(loglines)
logmsg = loglines[0]
assert "WARN" in logmsg and pipe_path in logmsg
def test_non_dot_relpath_becomes_absolute(self, atacseq_piface_data,
path_config_file, tmpdir,
pipe_path, atac_pipe_name):
""" Relative pipeline path is made absolute when requested by key. """
# TODO: constant-ify "path" and "ATACSeq.py", as well as possibly "pipelines"
# and "protocol_mapping" section names of PipelineInterface
exp_path = os.path.join(tmpdir.strpath, pipe_path, atac_pipe_name)
piface = ProtocolInterface(path_config_file)
_, obs_path, _ = piface.finalize_pipeline_key_and_paths(atac_pipe_name)
assert exp_path == obs_path
def test_no_path(self, atacseq_piface_data, path_config_file,
atac_pipe_name):
""" Without explicit path, pipeline is assumed parallel to config. """
piface = ProtocolInterface(path_config_file)
# The pipeline is assumed to live alongside its configuration file.
config_dirpath = os.path.dirname(path_config_file)
expected_pipe_path = os.path.join(config_dirpath, atac_pipe_name)
_, full_pipe_path, _ = \
piface.finalize_pipeline_key_and_paths(atac_pipe_name)
assert expected_pipe_path == full_pipe_path
def test_relpath_with_dot_becomes_absolute(self, tmpdir, atac_pipe_name,
atacseq_piface_data):
""" Leading dot drops from relative path, and it's made absolute. """
path_parts = ["relpath", "to", "pipelines", atac_pipe_name]
sans_dot_path = os.path.join(*path_parts)
pipe_path = os.path.join(".", sans_dot_path)
atacseq_piface_data[atac_pipe_name]["path"] = pipe_path
exp_path = os.path.join(tmpdir.strpath, sans_dot_path)
path_config_file = _write_config_data(
protomap={ATAC_PROTOCOL_NAME: atac_pipe_name},
conf_data=atacseq_piface_data,
dirpath=tmpdir.strpath)
piface = ProtocolInterface(path_config_file)
_, obs_path, _ = piface.finalize_pipeline_key_and_paths(atac_pipe_name)
# Dot may remain in path, so assert equality of absolute paths.
assert os.path.abspath(exp_path) == os.path.abspath(obs_path)