def write_bel_export(df: pd.DataFrame):
"""Write BEL export."""
graph = BELGraph(name='Chemical Roles')
it = tqdm(df.dropna().values,
total=len(df.index),
desc='mapping to BEL',
unit_scale=True)
for source_db, source_id, source_name, modulation, target_type, target_db, target_id, target_name in it:
if target_type == 'molecular function':
continue
source = pybel.dsl.Abundance(
namespace=source_db,
identifier=source_id,
name=source_name,
)
target = _type_map[target_type](
namespace=target_db,
identifier=target_id,
name=target_name,
)
adder = _adders[modulation]
adder(graph, source, target, citation='', evidence='')
pybel.dump(graph,
os.path.join(EXPORT_DIRECTORY, 'export.bel.nodelink.json.gz'),
indent=2)
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(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 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 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 assemble_pybel(self, mode='local', bucket=EMMAA_BUCKET_NAME):
"""Assemble the model into PyBEL and return the assembled model."""
if not self.assembled_stmts:
self.run_assembly()
pba = PybelAssembler(self.assembled_stmts)
pybel_model = pba.make_model()
if mode == 's3' and 'pybel' in self.export_formats:
fname = f'pybel_{self.date_str}.bel.nodelink.json.gz'
pybel.dump(pybel_model, fname)
logger.info(f'Uploading {fname}')
client = get_s3_client(unsigned=False)
client.upload_file(fname, bucket, f'exports/{self.name}/{fname}')
return pybel_model
def main(force: bool):
"""Export CBN in several BEL formats."""
if not os.path.exists(HUMAN_PATH):
urlretrieve(HUMAN_URL, HUMAN_PATH)
full = BELGraph(name='CausalBioNet Human', version='2.0')
full_nodelink_path = os.path.join(BEL, 'human_2.0.bel.nodelink.json')
full_bel_path = os.path.join(BEL, 'human_2.0.bel.gz')
if os.path.exists(full_nodelink_path) and not force:
click.echo('already done!')
return sys.exit(0)
with zipfile.ZipFile(HUMAN_PATH) as human_zipfile:
for zf in human_zipfile.filelist:
name = zf.filename[:-len('.jgf')]
raw_path = os.path.join(HUMAN_PARTS,
f'{name}-raw.bel.nodelink.json')
grounded_path = os.path.join(HUMAN_PARTS,
f'{name}-grounded.bel.nodelink.json')
if os.path.exists(grounded_path) and not force:
continue
with human_zipfile.open(zf) as file:
graph = pybel.from_cbn_jgif_file(file)
print(zf)
pybel.dump(graph, raw_path, indent=2)
graph = pybel.grounding.ground(graph)
pybel.dump(graph, grounded_path, indent=2)
pybel.struct.add_annotation_value(graph,
'cbn_pathway',
name,
strict=False)
full += graph
pybel.dump(full, full_nodelink_path, indent=2)
pybel.dump(full, full_bel_path)
def test_invalid_io(self):
with tempfile.TemporaryDirectory() as directory:
path = os.path.join(directory, 'ampk.bel.invalid.json')
with self.assertRaises(InvalidExtensionError):
pybel.dump(pybel.examples.ampk_graph, path)
self.assertFalse(os.path.exists(path))
def bel(directory):
"""Write BEL export."""
import pybel
from .bel import get_bel
graph = get_bel()
pybel.dump(graph, os.path.join(directory, 'crog.bel.nodelink.json.gz'))
def write(manager: BELManagerMixin, output: str):
"""Write as BEL Script."""
graph = manager.to_bel()
click.echo(graph.summary_str())
pybel.dump(graph, output)
