def make_sbgn(pysb_model, model_id):
pa = PysbAssembler()
pa.model = pysb_model
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
try:
sbgn_str = pa.export_model('sbgn')
except BngInterfaceError:
logger.error('Reaction network could not be generated for SBGN.')
return None
return sbgn_str
def make_sbgn(pysb_model, model_id):
pa = PysbAssembler()
pa.model = pysb_model
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
try:
sbgn_str = pa.export_model('sbgn')
except BngInterfaceError:
logger.error('Reaction network could not be generated for SBGN.')
return None
return sbgn_str
def post(self):
"""Assemble INDRA Statements and return PySB model string.
Parameters
----------
statements : list[indra.statements.Statement.to_json()]
A list of INDRA Statements to assemble.
export_format : str
The format to export into, for instance "kappa", "bngl",
"sbml", "matlab", "mathematica", "potterswheel". See
http://pysb.readthedocs.io/en/latest/modules/export/index.html
for a list of supported formats. In addition to the formats
supported by PySB itself, this method also provides "sbgn"
output.
Returns
-------
image or model
Assembled exported model. If export_format is kappa_im or kappa_cm,
image is returned. Otherwise model string is returned.
"""
args = request.json
stmts_json = args.get('statements')
export_format = args.get('export_format')
stmts = stmts_from_json(stmts_json)
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model()
try:
for m in pa.model.monomers:
pysb_assembler.set_extended_initial_condition(pa.model, m, 0)
except Exception as e:
logger.exception(e)
if not export_format:
model_str = pa.print_model()
elif export_format in ('kappa_im', 'kappa_cm'):
fname = 'model_%s.png' % export_format
root = os.path.dirname(os.path.abspath(fname))
graph = pa.export_model(format=export_format, file_name=fname)
with open(fname, 'rb') as fh:
data = 'data:image/png;base64,%s' % \
base64.b64encode(fh.read()).decode()
return {'image': data}
else:
try:
model_str = pa.export_model(format=export_format)
except Exception as e:
logger.exception(e)
model_str = ''
res = {'model': model_str}
return res
def assemble_model(stmts):
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model(policies='one_step')
pa.add_default_initial_conditions(100.0)
try:
targeted_agents = get_targeted_agents(stmts)
no_upstream_active_agents = get_no_upstream_active_agents(stmts)
except:
targeted_agents = []
no_upstream_active_agents = []
try:
chemical_agents = get_chemical_agents(stmts)
except:
chemical_agents = []
for m in model.monomers:
try:
if m.name in targeted_agents or m.name in no_upstream_active_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 50.0)
pysb_assembler.set_extended_initial_condition(model, m, 50.0)
elif m.name in chemical_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 10000.0)
else:
pysb_assembler.set_extended_initial_condition(model, m, 0)
except:
pysb_assembler.set_extended_initial_condition(model, m, 0)
# Tweak parameters
for param in model.parameters:
if 'kf' in param.name and 'bind' in param.name:
param.value = param.value * 100
return model
def assemble_model(stmts):
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model(policies='one_step')
pa.add_default_initial_conditions(100.0)
try:
targeted_agents = get_targeted_agents(stmts)
no_upstream_active_agents = get_no_upstream_active_agents(stmts)
except:
targeted_agents = []
no_upstream_active_agents = []
try:
chemical_agents = get_chemical_agents(stmts)
except:
chemical_agents = []
for m in model.monomers:
try:
if m.name in targeted_agents or m.name in no_upstream_active_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 50.0)
pysb_assembler.set_extended_initial_condition(model, m, 50.0)
elif m.name in chemical_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 10000.0)
else:
pysb_assembler.set_extended_initial_condition(model, m, 0)
except:
pysb_assembler.set_extended_initial_condition(model, m, 0)
# Tweak parameters
for param in model.parameters:
if 'kf' in param.name and 'bind' in param.name:
param.value = param.value * 100
return model
def assemble_pysb():
"""Assemble INDRA Statements and return PySB model string."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
export_format = body.get('export_format')
stmts = stmts_from_json(stmts_json)
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model()
try:
for m in pa.model.monomers:
pysb_assembler.set_extended_initial_condition(pa.model, m, 0)
except Exception as e:
logger.exception(e)
if not export_format:
model_str = pa.print_model()
elif export_format in ('kappa_im', 'kappa_cm'):
fname = 'model_%s.png' % export_format
root = os.path.dirname(os.path.abspath(fname))
graph = pa.export_model(format=export_format, file_name=fname)
with open(fname, 'rb') as fh:
data = 'data:image/png;base64,%s' % \
base64.b64encode(fh.read()).decode()
return {'image': data}
else:
try:
model_str = pa.export_model(format=export_format)
except Exception as e:
logger.exception(e)
model_str = ''
res = {'model': model_str}
return res
def draw_reaction_network(pysb_model, model_id):
"""Generate a PySB/BNG reaction network as a PNG file."""
try:
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
diagram_dot = render_reactions.run(pysb_model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
logger.error('Could not generate model diagram.')
logger.error(e)
return None
try:
fname_prefix = make_pic_name(model_id, 'rxn')
with open(fname_prefix + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(('dot -T png -o %s.png %s.dot' %
(fname_prefix, fname_prefix)).split(' '))
fname = fname_prefix + '.png'
except Exception as e:
logger.error('Could not save model diagram.')
logger.error(e)
return None
return fname
def assemble_pysb():
"""Assemble INDRA Statements and return PySB model string."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
export_format = body.get('export_format')
stmts = stmts_from_json(stmts_json)
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model()
try:
for m in pa.model.monomers:
pysb_assembler.set_extended_initial_condition(pa.model, m, 0)
except Exception as e:
logger.exception(e)
if not export_format:
model_str = pa.print_model()
elif export_format in ('kappa_im', 'kappa_cm'):
fname = 'model_%s.png' % export_format
root = os.path.dirname(os.path.abspath(fname))
graph = pa.export_model(format=export_format, file_name=fname)
with open(fname, 'rb') as fh:
data = 'data:image/png;base64,%s' % \
base64.b64encode(fh.read()).decode()
return {'image': data}
else:
try:
model_str = pa.export_model(format=export_format)
except Exception as e:
logger.exception(e)
model_str = ''
res = {'model': model_str}
return res
def draw_reaction_network(pysb_model, model_id):
"""Generate a PySB/BNG reaction network as a PNG file."""
try:
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
diagram_dot = render_reactions.run(pysb_model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
logger.error('Could not generate model diagram.')
logger.error(e)
return None
try:
fname_prefix = make_pic_name(model_id, 'rxn')
with open(fname_prefix + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(('dot -T png -o %s.png %s.dot' %
(fname_prefix, fname_prefix)).split(' '))
fname = fname_prefix + '.png'
except Exception as e:
logger.error('Could not save model diagram.')
logger.error(e)
return None
return fname