def to_indra_statements(self, *args, **kwargs):
"""Dump as a list of INDRA statements.
:rtype: List[indra.Statement]
"""
graph = self.to_bel(*args, **kwargs)
return to_indra_statements(graph)
def get_indra_statements(
self,
directory: str,
use_cached: bool = True) -> List['indra.statements.Statement']:
"""Get INDRA statements for the graph."""
return pybel.to_indra_statements(
self.get_graph(directory, use_cached=use_cached))
def get_graph(
self,
directory: Optional[str] = None,
use_cached: bool = True,
use_tqdm: bool = True,
) -> BELGraph:
"""Get the graph from all sources."""
if directory is None:
if self.directory is None:
raise ValueError
directory = self.directory
pickle_path = os.path.join(directory, f'{self.name}.bel.pickle')
if use_cached and os.path.exists(pickle_path):
return pybel.from_pickle(pickle_path)
rv = union(self.get_graphs(use_tqdm=use_tqdm))
self.metadata.update(rv)
pybel.to_pickle(rv, pickle_path)
nodelink_path = os.path.join(directory,
f'{self.name}.bel.nodelink.json')
pybel.to_json_path(rv, nodelink_path)
sif_path = os.path.join(directory, f'{self.name}.bel.sif')
pybel.to_sif_path(rv, sif_path)
gsea_path = os.path.join(directory, f'{self.name}.bel.gmt')
pybel.to_gsea_path(rv, gsea_path)
graphml_path = os.path.join(directory, f'{self.name}.bel.graphml')
pybel.to_graphml(rv, graphml_path)
try:
statements = pybel.to_indra_statements(rv)
except ImportError:
pass
else:
indra_path = os.path.join(directory, f'{self.name}.indra.pickle')
with open(indra_path, 'wb') as file:
pickle.dump(statements, file)
try:
from pybel_cx import to_cx_file
except ImportError:
pass
else:
cx_path = os.path.join(directory, f'{self.name}.bel.cx.json')
with open(cx_path, 'w') as file:
to_cx_file(rv, file)
try:
from pybel_tools.assembler.html import to_html
except ImportError:
pass
else:
html_path = os.path.join(directory, 'index.html')
with open(html_path, 'w') as file:
print(to_html(rv), file=file)
return rv
def iterate_indra_statements(**kwargs
) -> Iterable['indra.statements.Statement']:
"""Iterate over INDRA statements for the universe."""
for _, _, graph in iterate_universe_graphs(**kwargs):
yield from pybel.to_indra_statements(graph)