def test_thorough_json_file(self):
"""Test the round-trip through a node-link JSON file."""
sio = StringIO()
to_nodelink_file(sialic_acid_graph, sio)
sio.seek(0)
graph = from_nodelink_file(sio)
self._help_test_equal(graph)
def get_graph(
self,
use_cached: bool = True,
use_tqdm: bool = False,
tqdm_kwargs: Optional[Mapping[str, Any]] = None,
) -> BELGraph:
"""Get the BEL graph from all sheets in this repository.
.. warning:: This BEL graph isn't pre-filled with namespace and annotation URLs.
"""
if use_cached and os.path.exists(self._cache_json_path):
return pybel.from_nodelink_gz(self._cache_json_path)
graph = BELGraph()
if self.metadata is not None:
self.metadata.update(graph)
logger.info('streamlining parser')
bel_parser = BELParser(graph)
paths = list(self.iterate_sheets_paths())
if use_tqdm:
_tqdm_kwargs = dict(desc=f'Sheets in {self.directory}')
if tqdm_kwargs:
_tqdm_kwargs.update(tqdm_kwargs)
paths = tqdm(list(paths), **_tqdm_kwargs)
for path in paths:
graph.path = path
try:
df = pd.read_excel(path)
except LookupError as exc:
logger.warning(f'Error opening {path}: {exc}')
continue
# Check columns in DataFrame exist
if not _check_curation_template_columns(df):
logger.warning(f'^ above columns in {path} were missing')
continue
process_df(bel_parser=bel_parser,
df=df,
use_tqdm=use_tqdm,
tqdm_kwargs=dict(desc=f'Reading {path}'))
if self.prior is not None: # assign edges to sub-graphs
prior = self.get_prior()
assign_subgraphs(graph=graph, prior=prior)
pybel.to_nodelink_file(graph,
self._cache_json_path,
indent=2,
sort_keys=True)
return graph
def save_model(self, path, output_format=None):
"""Save the :class:`pybel.BELGraph` using one of the outputs from
:py:mod:`pybel`
Parameters
----------
path : str
The path to output to
output_format : Optional[str]
Output format as ``cx``, ``pickle``, ``json`` or defaults to ``bel``
"""
if output_format == 'pickle':
pybel.to_pickle(self.model, path)
else:
with open(path, 'w') as fh:
if output_format == 'json':
pybel.to_nodelink_file(self.model, fh)
elif output_format == 'cx':
pybel.to_cx_file(self.model, fh)
else: # output_format == 'bel':
pybel.to_bel_script(self.model, fh)
def test_thorough_json_file(self):
sio = StringIO()
to_nodelink_file(self.thorough_graph, sio)
sio.seek(0)
graph = from_nodelink_file(sio)
self.bel_thorough_reconstituted(graph)