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 upload_jgf_directory(directory: str, manager: Manager):
"""Upload CBN data to edge store."""
if not (os.path.exists(directory) and os.path.isdir(directory)):
logger.warning('directory does not exist: %s', directory)
return
t = time.time()
for path in iter_jgf(directory):
gpickle_path = get_jgf_corresponding_gpickle_path(path)
if os.path.exists(gpickle_path):
graph = from_pickle(gpickle_path)
strip_annotations(graph)
else:
with open(path) as f:
cbn_jgif_dict = json.load(f)
graph = pybel.from_cbn_jgif(cbn_jgif_dict)
strip_annotations(graph)
to_pickle(graph, gpickle_path)
try:
insert_graph(manager, graph, public=True, use_tqdm=True)
except OperationalError:
manager.session.rollback()
logger.info('could not insert %s', graph)
logger.info('done in %.2f seconds', time.time() - t)
def test_jgif_interchange(self):
"""Tests data from CBN"""
with open(test_jgif_path) as f:
graph_jgif_dict = json.load(f)
graph = from_cbn_jgif(graph_jgif_dict)
self.assertEqual(jgif_expected_nodes, set(graph))
for u, v, d in jgif_expected_edges:
self.assert_has_edge(graph, u, v, **d)
# TODO test more thoroughly?
export_jgif = to_jgif(graph)
self.assertIsInstance(export_jgif, dict)
def process_cbn_jgif_file(file_name):
"""Return a PybelProcessor by processing a CBN JGIF JSON file.
Parameters
----------
file_name : str
The path to a CBN JGIF JSON file.
Returns
-------
bp : PybelProcessor
A PybelProcessor object which contains INDRA Statements in
bp.statements.
"""
with open(file_name, 'r') as jgf:
return process_pybel_graph(pybel.from_cbn_jgif(json.load(jgf)))
def process_cbn_jgif_file(file_name):
"""Return a PybelProcessor by processing a CBN JGIF JSON file.
Parameters
----------
file_name : str
The path to a CBN JGIF JSON file.
Returns
-------
bp : PybelProcessor
A PybelProcessor object which contains INDRA Statements in
bp.statements.
"""
with open(file_name, 'r') as jgf:
return process_pybel_graph(pybel.from_cbn_jgif(json.load(jgf)))
def main():
"""Convert all CBN graphs to Hipathia."""
if not os.path.exists(PATH):
urlretrieve(URL, PATH)
if not os.path.exists(SOURCE):
with zipfile.ZipFile(PATH) as file:
file.extractall(SOURCE)
for filename in tqdm(os.listdir(SOURCE)):
path = os.path.join(SOURCE, filename)
with open(path) as f:
cbn_jgif_dict = json.load(f)
graph = pybel.from_cbn_jgif(cbn_jgif_dict)
graph = pybel.grounding.ground(graph)
pybel.to_hipathia(graph, OUTPUT)