def upload_cbn_dir(dir_path, manager):
"""Uploads CBN data to edge store
:param str dir_path: Directory full of CBN JGIF files
:param pybel.Manager manager:
"""
t = time.time()
for jfg_path in os.listdir(dir_path):
if not jfg_path.endswith('.jgf'):
continue
path = os.path.join(dir_path, jfg_path)
log.info('opening %s', path)
with open(path) as f:
cbn_jgif_dict = json.load(f)
graph = pybel.from_cbn_jgif(cbn_jgif_dict)
out_path = os.path.join(dir_path, jfg_path.replace('.jgf', '.bel'))
with open(out_path, 'w') as o:
pybel.to_bel(graph, o)
strip_annotations(graph)
enrich_pubmed_citations(manager=manager, graph=graph)
pybel.to_database(graph, manager=manager)
log.info('')
log.info('done in %.2f', time.time() - t)
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_json_file(self.model, fh)
elif output_format == 'cx':
pybel.to_cx_file(self.model, fh)
else: # output_format == 'bel':
pybel.to_bel(self.model, fh)
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_json_file(self.model, fh)
elif output_format == 'cx':
pybel.to_cx_file(self.model, fh)
else: # output_format == 'bel':
pybel.to_bel(self.model, fh)
def main(file):
"""Provide BEL Statements from BEL graph."""
df = get_equivalences_df()
graph = build_equivalences_graph(df)
pybel.to_bel(graph, file)
def main():
"""Provide BEL Statements from BEL graph."""
df = get_relations_df()
graph = build_relations_graph(df)
with open("famplex.bel", "w") as file:
to_bel(graph, file)
def to_bel_file(self, file):
graph = self.to_bel_graph()
pybel.to_bel(graph, file=file)
