def _get_statements(self):
import pybel
import requests
from indra.sources.bel import process_pybel_graph
logger.info('Processing CONIB from web')
url = 'https://github.com/pharmacome/conib/raw/master/conib' \
'/_cache.bel.nodelink.json'
res_json = requests.get(url).json()
graph = pybel.from_nodelink(res_json)
# Get INDRA statements
pbp = process_pybel_graph(graph)
# Fix and issue with PMID spaces
for stmt in pbp.statements:
for ev in stmt.evidence:
if ev.pmid:
ev.pmid = ev.pmid.strip()
if ev.text_refs.get('PMID'):
ev.text_refs['PMID'] = ev.text_refs['PMID'].strip()
logger.info('Expanding evidences and deduplicating')
filtered_stmts = [s for s in _expanded(pbp.statements)]
unique_stmts, _ = extract_duplicates(filtered_stmts,
KeyFunc.mk_and_one_ev_src)
return unique_stmts
def upload_json(connection: str,
user_id: int,
payload: Dict,
public: bool = False):
"""Receive and process a JSON serialized BEL graph.
:param connection: A connection to build the manager
:param user_id: the ID of the user to associate with the graph
:param payload: JSON dictionary for :func:`pybel.from_json`
:param public: Should the network be made public?
"""
manager = WebManager(connection=connection)
user = manager.get_user_by_id(user_id)
try:
graph = from_nodelink(payload)
except Exception:
celery_logger.exception('unable to parse JSON')
return -1
public = current_app.config.get('DISALLOW_PRIVATE') or public
try:
insert_graph(manager=manager, graph=graph, user=user, public=public)
except Exception:
celery_logger.exception('unable to insert graph')
manager.session.rollback()
return -2
return 0
def test_slushy_json(self):
graph_json = to_nodelink(self.slushy_graph)
graph = from_nodelink(graph_json)
self.bel_slushy_reconstituted(graph, check_warnings=False)
def test_thorough_json(self):
graph_json_dict = to_nodelink(self.thorough_graph)
graph = from_nodelink(graph_json_dict)
self.bel_thorough_reconstituted(graph)
def test_thorough_json(self):
"""Test the round-trip through node-link JSON."""
graph_json_dict = to_nodelink(sialic_acid_graph)
graph = from_nodelink(graph_json_dict)
self._help_test_equal(graph)
def test_slushy_json(self):
graph_json = to_nodelink(self.slushy_graph)
graph = from_nodelink(graph_json)
self.bel_slushy_reconstituted(graph)