def test_thorough_json_file(self):
"""Test the round-trip through a node-link JSON file."""
sio = StringIO()
to_json_file(sialic_acid_graph, sio)
sio.seek(0)
graph = from_json_file(sio)
self.help_test_equal(graph)
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 save_model(self, path, output_format=None):
"""Save the :class:`pybel.BELGraph` using one of the outputs from
:py:mod:`pybel`
Parameters
----------
path : str
The path to output to
output_format : Optional[str]
Output format as ``cx``, ``pickle``, ``json`` or defaults to ``bel``
"""
if output_format == 'pickle':
pybel.to_pickle(self.model, path)
else:
with open(path, 'w') as fh:
if output_format == 'json':
pybel.to_json_file(self.model, fh)
elif output_format == 'cx':
pybel.to_cx_file(self.model, fh)
else: # output_format == 'bel':
pybel.to_bel(self.model, fh)
def save_model(self, path, output_format=None):
"""Save the :class:`pybel.BELGraph` using one of the outputs from
:py:mod:`pybel`
Parameters
----------
path : str
The path to output to
output_format : Optional[str]
Output format as ``cx``, ``pickle``, ``json`` or defaults to ``bel``
"""
if output_format == 'pickle':
pybel.to_pickle(self.model, path)
else:
with open(path, 'w') as fh:
if output_format == 'json':
pybel.to_json_file(self.model, fh)
elif output_format == 'cx':
pybel.to_cx_file(self.model, fh)
else: # output_format == 'bel':
pybel.to_bel(self.model, fh)
def test_thorough_json_file(self):
sio = StringIO()
to_json_file(self.thorough_graph, sio)
sio.seek(0)
graph = from_json_file(sio)
self.bel_thorough_reconstituted(graph)
def test_thorough_json_file(self):
sio = StringIO()
to_json_file(sialic_acid_graph, sio)
sio.seek(0)
graph = from_json_file(sio)
self.help_test_equal(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)