def _custom_pb_assembly(stmts_list=None):
if stmts_list is None:
logger.info('No statements provided, downloading latest pa stmt dump')
stmts_list = get_latest_pa_stmt_dump()
# Filter bad statements
logger.info('Filtering out statements with bad position attribute')
filtered_stmts = []
for st in stmts_list:
try:
pos = getattr(st, 'position')
try:
if pos is not None and str(int(float(pos))) != pos:
continue
else:
filtered_stmts.append(st)
# Pos is not convertible to float
except ValueError:
continue
# Not a statement with a position attribute
except AttributeError:
filtered_stmts.append(st)
# Assemble Pybel model
logger.info('Assembling PyBEL model')
pb = PybelAssembler(stmts=filtered_stmts)
pb_model = pb.make_model()
return pb_model
def assemble_pybel(self):
"""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()
return pybel_model
def stmts_to_pybel_graph(stmts):
pba = PybelAssembler(stmts,
name='INDRA/REACH Fallahi Eval Model',
description='Automatically assembled model.',
version='0.0.1')
pba.make_model()
return pba.to_signed_graph()
def get_graph_from_statement(statement: Statement) -> BELGraph:
"""Convert an INDRA statement to a BEL graph."""
pba = PybelAssembler([statement])
try:
graph = pba.make_model()
except AttributeError: # something funny happening
logger.exception('problem making BEL graph from INDRA statements')
return BELGraph()
else:
return graph
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 assemble_pybel(stmts, out_file_prefix):
"""Return a PyBEL Assembler"""
stmts = ac.filter_belief(stmts, 0.95)
stmts = ac.filter_top_level(stmts)
pba = PybelAssembler(stmts,
name='INDRA/REACH Korkut Model',
description='Automatically assembled model of '
'cancer signaling.',
version='0.0.10')
pba.make_model()
pybel.to_bel_path(pba.model, out_file_prefix + '.bel')
with open(out_file_prefix, 'wt') as f:
pybel.to_json_file(pba.model, f)
url = 'https://pybel.scai.fraunhofer.de/api/receive'
headers = {'content-type': 'application/json'}
requests.post(url, json=pybel.to_json(pba.model), headers=headers)
def from_indra_statements(
stmts,
name: Optional[str] = None,
version: Optional[str] = None,
description: Optional[str] = None,
authors: Optional[str] = None,
contact: Optional[str] = None,
license: Optional[str] = None,
copyright: Optional[str] = None,
disclaimer: Optional[str] = None,
):
"""Import a model from :mod:`indra`.
:param List[indra.statements.Statement] stmts: A list of statements
:param name: The graph's name
:param version: The graph's version. Recommended to use `semantic versioning <http://semver.org/>`_ or
``YYYYMMDD`` format.
:param description: The description of the graph
:param authors: The authors of this graph
:param contact: The contact email for this graph
:param license: The license for this graph
:param copyright: The copyright for this graph
:param disclaimer: The disclaimer for this graph
:rtype: pybel.BELGraph
"""
from indra.assemblers.pybel import PybelAssembler
if authors is None:
authors = 'INDRA'
pba = PybelAssembler(
stmts=stmts,
name=name,
version=version,
description=description,
authors=authors,
contact=contact,
license=license,
copyright=copyright,
disclaimer=disclaimer,
)
graph = pba.make_model()
return graph
ActiveForm(elk1_p, 'transcription', True),
IncreaseAmount(elk1_tscript, fos),
Conversion(hk1, [glu], [g6p]),
Complex([egfr, grb2, sos1]),
Autophosphorylation(p38_tab1, 'Y', '100'),
Transphosphorylation(egfr_dimer, 'Y', '1173'),
]
ev = Evidence('assertion', 'assertion', 'assertion', 'assertion')
for stmt in stmts:
stmt.evidence = [ev]
model_description = 'Test of INDRA Statement assembly into PyBEL.'
print("Assembling to PyBEL...")
pba = PybelAssembler(stmts,
name='INDRA_PyBEL_test',
description=model_description,
version='0.0.22')
belgraph = pba.make_model()
# Write to BEL file
pybel.to_bel_path(belgraph, 'simple_pybel.bel')
# Upload to PyBEL web
with open('pybel_model.json', 'wt') as f:
pybel.to_json_file(pba.model, f)
url = 'https://pybel.scai.fraunhofer.de/api/receive'
headers = {'content-type': 'application/json'}
requests.post(url, json=pybel.to_json(pba.model), headers=headers)