def test_sbml_import_structured_model():
model_from_sbml(_sbml_location('test_sbml_structured_SBML'), atomize=True)
def test_sbml_import_flat_model():
model_from_sbml(_sbml_location('test_sbml_flat_SBML'))
def test_sbml_import_flat_model():
model_from_sbml(_sbml_location('test_sbml_flat_SBML'))
def test_sbml_import_structured_model():
model_from_sbml(_sbml_location('test_sbml_structured_SBML'), atomize=True)
def data_to_json(value, widget):
"""
Generate a json file from the data passed to the widget
Parameters
----------
value: pysb.Model, pysb.SimulationResult, str
Value passed to the widget that is going to be visualized
widget: Widget
Widget instance
Returns
-------
"""
if is_pysb_model(value):
from pyvipr.pysb_viz.static_viz import PysbStaticViz
viz = PysbStaticViz(value)
jsondata = static_data(viz, widget)
return jsondata
elif is_pysb_sim(value):
from pyvipr.pysb_viz.dynamic_viz import PysbDynamicViz
viz = PysbDynamicViz(value, widget.sim_idx, widget.cmap)
jsondata = dynamic_data(viz, widget)
return jsondata
elif isinstance(value, str):
file_extension = os.path.splitext(value)[1]
if file_extension in ['.bngl', '.sbml', '.xml'] and widget.type_of_viz != 'sbgn_xml'\
or value.startswith('BIOMD'):
try:
from pysb.importers.sbml import model_from_sbml, model_from_biomodels
from pysb.importers.bngl import model_from_bngl
except ImportError:
raise Exception(
'PySB must be installed to visualize models from files')
from pyvipr.pysb_viz.static_viz import PysbStaticViz
if file_extension == '.bngl':
model = model_from_bngl(value)
elif file_extension in ['.sbml', '.xml']:
model = model_from_sbml(value)
elif value.startswith('BIOMD'):
model = model_from_biomodels(value)
viz = PysbStaticViz(model)
jsondata = static_data(viz, widget)
return jsondata
elif file_extension == '.graphml' or widget.type_of_viz == 'sbgn_xml':
with open(value, 'r') as file:
data = file.read().replace('\n', '')
return data
elif file_extension == '.json':
import json
with open(value, 'r') as file:
data = file.read().replace('\n', '')
jsondata = json.loads(data)
return jsondata
elif file_extension == '.sif':
with open(value, 'r') as file:
data = file.read()
data = data.rstrip('\n')
return data
# elif file_extension == '.ka':
# subprocess.run(['truml', '-k', value])
# bngl_model_path = re.sub('ka', 'bngl', value)
# model = model_from_bngl(bngl_model_path)
# os.remove(bngl_model_path)
else:
raise ValueError('Format not supported')
elif is_tellurium_model(value):
if widget.type_of_viz.startswith('dynamic'):
from pyvipr.tellurium_viz.dynamic_viz import TelluriumDynamicViz
viz = TelluriumDynamicViz(value, widget.cmap)
jsondata = dynamic_data(viz, widget)
else:
from pyvipr.tellurium_viz.static_viz import TelluriumStaticViz
viz = TelluriumStaticViz(value)
jsondata = static_data(viz, widget)
return jsondata
elif isinstance(
value,
(nx.DiGraph, nx.Graph, nx.MultiDiGraph, nx.MultiGraph, dict)):
from pyvipr.network_viz.network_viz import NetworkViz
viz = NetworkViz(value)
if widget.type_of_viz:
jsondata = getattr(viz, widget.type_of_viz)()
else:
jsondata = value
return jsondata
elif is_ecell_model(value):
try:
from pysb.importers.sbml import model_from_sbml
except ImportError:
raise Exception(
'PySB must be installed to visualize models from files')
from pyvipr.pysb_viz.static_viz import PysbStaticViz
import tempfile
ecell4 = sys.modules['ecell4']
f_sbml = tempfile.NamedTemporaryFile(suffix='.sbml')
# In ecell4 species don't have initial conditions as attributes. Hence, the
# initial conditions are passed as a dictionary to the save_sbml function.
# If no initial conditions are passed ecell4 sets the initial condition of the
# species to 0, and PySB throws an error when the initial condition of all the species
# are zero. For visualization purposes we then set the initial conditions to 1.
y0 = {sp.serial(): 1 for sp in value.list_species()}
ecell4.util.ports.save_sbml(f_sbml.name, value, y0=y0)
model = model_from_sbml(f_sbml.name)
viz = PysbStaticViz(model)
jsondata = static_data(viz, widget)
return jsondata
elif is_pysces_model(value):
try:
from pysb.importers.sbml import model_from_sbml
except ImportError:
raise Exception(
'PySB must be installed to visualize models from files')
from pyvipr.pysb_viz.static_viz import PysbStaticViz
import tempfile
# Note: Importing a pysces model to sbml doesn't work in python 3.7
pysces = sys.modules['pysces']
f_sbml = tempfile.NamedTemporaryFile(suffix='.xml')
pysces.interface.writeMod2SBML(value, f_sbml.name)
model = model_from_sbml(f_sbml.name)
viz = PysbStaticViz(model)
jsondata = static_data(viz, widget)
return jsondata
else:
raise TypeError(
'Only pysb Model, pysb SimulationResult, tellurium Model, '
'PySCeS Model, and networkx graphs are supported')
