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_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()
if not export_format:
model_str = pa.print_model()
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_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 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
