def main(force: bool, user: str, password: str):
"""Download and dump the INDRA 'rona graph."""
if not os.path.exists(GROUNDED_PATH) and not force:
if not os.path.exists(RAW_PATH) and not force:
click.echo('Getting EMMAA graph')
graph = pybel.from_emmaa('covid19')
pybel.dump(graph, RAW_PATH)
else:
click.echo('Loading EMMAA graph from path')
graph = pybel.load(RAW_PATH)
graph = pybel.grounding.ground(graph)
graph.summarize()
pybel.dump(graph, GROUNDED_PATH)
else:
graph = pybel.load(GROUNDED_PATH)
res = pybel.to_bel_commons(
graph=graph,
host='https://bel.labs.coronawhy.org',
user=user,
password=password,
)
click.secho(json.dumps(res.json(), indent=2))
def main():
"""Convert the Selventa graph to Hipathia."""
if not os.path.exists(PATH):
urlretrieve(URL, PATH)
if not os.path.exists(GROUNDED_PATH):
graph = pybel.load(PATH)
graph = pybel.grounding.ground(graph)
pybel.dump(graph, GROUNDED_PATH)
else:
graph = pybel.load(GROUNDED_PATH)
pybel.to_hipathia(graph, HERE)
def test_io(self):
with tempfile.TemporaryDirectory() as directory:
path = os.path.join(directory, 'ampk.bel.nodelink.json')
pybel.dump(pybel.examples.ampk_graph, path)
self.assertTrue(os.path.exists(path))
new_graph = pybel.load(path)
self.assertIsNotNone(new_graph)
def main():
"""Convert the AD graph to Hipathia."""
graph = pybel.load(PATH)
graph = pybel.grounding.ground(graph)
graphs = get_subgraphs_by_annotation(graph, annotation='Subgraph')
for name, graph in graphs.items():
graph.name = name
pybel.to_hipathia(graph, OUTPUT)
def get_graph(graph_name: str, force: bool = False) -> pybel.BELGraph:
"""Get the Selventa large corpus as a BEL Graph."""
url = f'https://github.com/cthoyt/selventa-knowledge/raw/master/selventa_knowledge/{graph_name}.bel'
cache_path = module.join(name=f'{graph_name}.bel.pickle')
if cache_path.exists() and not force:
return pybel.load(cache_path)
path = module.ensure(url=url, force=force)
graph = pybel.from_bel_script(path, citation_clearing=False)
pybel.dump(graph, path.as_posix())
return graph
def test_identifiable(self):
"""Test a BEL example for identifiability."""
bel_graph = pybel.load(BEL_EXAMPLE)
nxmg = bel_to_nxmg(bel_graph)
self.assertTrue(
is_identifiable(
nxmg,
P(
Variable('Severe Acute Respiratory Syndrome')
@ Variable('angiotensin II')),
))