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fix: corrected handling of XPP ODE files
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@jonrkarr
jonrkarr committed Feb 25, 2022
1 parent e0744a1 commit 35ea3f4
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Showing 6 changed files with 307 additions and 118 deletions.
2 changes: 1 addition & 1 deletion biosimulators_utils/_version.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = '0.1.162'
__version__ = '0.1.163'
43 changes: 28 additions & 15 deletions biosimulators_utils/model_lang/xpp/data_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,46 +11,54 @@
SIMULATION_METHOD_KISAO_MAP = {
'rungekutta': {
'kisao_id': 'KISAO_0000032',
'parameters': {}
'parameters': {
'dt': 'KISAO_0000483',
}
},
'discrete': {
'kisao_id': 'KISAO_0000029',
'parameters': {
'seed': 'KISAO_0000488'
'seed': 'KISAO_0000488',
}
},
'euler': {
'kisao_id': 'KISAO_0000030',
'parameters': {}
'parameters': {
'dt': 'KISAO_0000483',
}
},
'backeul': {
'kisao_id': 'KISAO_0000031',
'parameters': {}
'parameters': {
'dt': 'KISAO_0000483',
}
},
'adams': {
'kisao_id': 'KISAO_0000279',
'parameters': {}
'parameters': {
'dt': 'KISAO_0000483',
}
},
'gear': {
'kisao_id': 'KISAO_0000288',
'parameters': {
'dtmin': 'KISAO_0000485',
'dtmax': 'KISAO_0000467',
'toler': 'KISAO_0000597'
'toler': 'KISAO_0000597',
}
},
'5dp': {
'kisao_id': 'KISAO_0000087',
'parameters': {
'toler': 'KISAO_0000209',
'atoler': 'KISAO_0000211'
'atoler': 'KISAO_0000211',
}
},
'83dp': {
'kisao_id': 'KISAO_0000436',
'parameters': {
'toler': 'KISAO_0000209',
'atoler': 'KISAO_0000211'
'atoler': 'KISAO_0000211',
}
},
'2rb': {
Expand All @@ -59,7 +67,7 @@
'toler': 'KISAO_0000209',
'atoler': 'KISAO_0000211',
'bandlo': 'KISAO_0000480',
'bandup': 'KISAO_0000479'
'bandup': 'KISAO_0000479',
}
},
'cvode': {
Expand All @@ -68,7 +76,7 @@
'toler': 'KISAO_0000209',
'atoler': 'KISAO_0000211',
'bandlo': 'KISAO_0000480',
'bandup': 'KISAO_0000479'
'bandup': 'KISAO_0000479',
}
},
'qualrk': {
Expand All @@ -79,29 +87,34 @@
'dtmax': 'KISAO_0000467',
'newt_iter': 'KISAO_0000665',
'newt_tol': 'KISAO_0000565',
'jac_eps': 'KISAO_0000666'
'jac_eps': 'KISAO_0000666',
}
},
'modeuler': {
'kisao_id': 'KISAO_0000301',
'parameters': {}
'parameters': {
'dt': 'KISAO_0000483',
}
},
'ymp': {
'kisao_id': 'KISAO_0000367',
'parameters': {}
'parameters': {
'dt': 'KISAO_0000483',
}
},
'volterra': {
'kisao_id': 'KISAO_0000664',
'parameters': {
'vmaxpts': 'KISAO_0000667'
'vmaxpts': 'KISAO_0000667',
'dt': 'KISAO_0000483',
}
},
'stiff': {
'kisao_id': 'KISAO_0000668',
'parameters': {
'dtmin': 'KISAO_0000485',
'dtmax': 'KISAO_0000467',
'toler': 'KISAO_0000597'
'toler': 'KISAO_0000597',
}
}
}
76 changes: 42 additions & 34 deletions biosimulators_utils/model_lang/xpp/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
def get_parameters_variables_outputs_for_simulation(model_filename, model_language, simulation_type, algorithm_kisao_id=None,
set_filename=None, parameter_filename=None, initial_conditions_filename=None,
change_level=SedDocument, native_ids=False, native_data_types=False,
config=None):
config=None, max_number_of_steps=None):
""" Get the possible observables for a simulation of a model
Args:
Expand All @@ -43,6 +43,7 @@ def get_parameters_variables_outputs_for_simulation(model_filename, model_langua
for the variable of an associated SED-ML data generator
native_data_types (:obj:`bool`, optional): whether to return new_values in their native data types
config (:obj:`Config`, optional): whether to fail on missing includes
max_number_of_steps (:obj:`int`, optional): maximum number of steps to record
Returns:
:obj:`list` of :obj:`ModelAttributeChange`: possible attributes of a model that can be changed and their default values
Expand All @@ -67,24 +68,27 @@ def get_parameters_variables_outputs_for_simulation(model_filename, model_langua
# parameters
params = []

for key, val in model['parameters'].items():
for key, val in (model.get('parameters', None) or {}).items():
params.append(ModelAttributeChange(
id=key if native_ids else 'parameter_{}'.format(key),
name=None if native_ids else 'Value of parameter "{}"'.format(key),
target='{}'.format(key),
new_value=val if native_data_types else str(val),
))

for key, val in model['initial_conditions'].items():
params.append(ModelAttributeChange(
id=key if native_ids else 'initial_condition_{}'.format(key),
name=None if native_ids else 'Initial condition of "{}"'.format(key),
target='{}'.format(key),
new_value=val if native_data_types else str(val),
))
aux_var_ids = [key.upper() for key in (model.get('auxiliary_variables', None) or {}).keys()]
for key, val in (model.get('initial_conditions', None) or {}).items():
if key.upper() not in aux_var_ids:
params.append(ModelAttributeChange(
id=key if native_ids else 'initial_condition_{}'.format(key),
name=None if native_ids else 'Initial condition of "{}"'.format(key),
target='{}'.format(key),
new_value=val if native_data_types else str(val),
))

# simulation
sim_method_id = model['simulation_method'].get('meth', 'rungekutta').lower()
simulation_method = model.get('simulation_method', None) or {}
sim_method_id = simulation_method.get('meth', 'rungekutta').lower()
sim_method_props = SIMULATION_METHOD_KISAO_MAP[sim_method_id]
sim_method_kisao_id = sim_method_props['kisao_id']

Expand All @@ -95,26 +99,33 @@ def get_parameters_variables_outputs_for_simulation(model_filename, model_langua
)
)

t_0 = float(model['simulation_method'].get('t0', 0.))
t_output_start = float(model['simulation_method'].get('trans', t_0))
duration = float(model['simulation_method'].get('total', 20.))
d_t = float(model['simulation_method'].get('dt', 0.05))
n_jmp = float(model['simulation_method'].get('njmp', 1))
t_0 = float(simulation_method.get('t0', 0.))
t_output_start = float(simulation_method.get('trans', t_0))
duration = float(simulation_method.get('total', 20.))
d_t = float(simulation_method.get('dt', 0.05))
n_jmp = int(float(simulation_method.get('njmp', 1)))

if 'dt' not in sim_method_props['parameters']:
n_jmp = simulation_method['njmp'] = 1

sim.initial_time = t_0
sim.output_start_time = t_output_start
sim.output_end_time = t_0 + duration
sim.number_of_steps = (sim.output_end_time - sim.output_start_time) / (d_t * n_jmp)
sim.number_of_steps = round(sim.number_of_steps)

for key, val in model['simulation_method'].items():
if max_number_of_steps is not None and sim.number_of_steps > max_number_of_steps:
n_jmp = simulation_method['njmp'] = round(n_jmp * sim.number_of_steps / max_number_of_steps)
sim.number_of_steps = (sim.output_end_time - sim.output_start_time) / (d_t * n_jmp)
sim.number_of_steps = round(sim.number_of_steps)

for key, val in simulation_method.items():
param_kisao_id = sim_method_props['parameters'].get(key, None)
if param_kisao_id:
sim.algorithm.changes.append(AlgorithmParameterChange(kisao_id=param_kisao_id,
new_value=float(val) if native_data_types else val))

# observables
var_ids = set()
vars = []

time_variable = Variable(
Expand All @@ -124,37 +135,34 @@ def get_parameters_variables_outputs_for_simulation(model_filename, model_langua
)
vars.append(time_variable)

for key in model['initial_conditions'].keys():
for key in (model.get('initial_conditions', None) or {}).keys():
var = Variable(
id=key if native_ids else 'dynamics_{}'.format(key),
name=None if native_ids else 'Dynamics of "{}"'.format(key),
target=key,
)
if var.id not in var_ids:
var_ids.add(var.id)
vars.append(var)
vars.append(var)

for key in model['auxiliary_variables'].keys():
for key in (model.get('auxiliary_variables', None) or {}).keys():
var = Variable(
id=key if native_ids else 'dynamics_{}'.format(key),
id=key if native_ids else 'dynamics_aux_{}'.format(key),
name=None if native_ids else 'Dynamics of "{}"'.format(key),
target=key,
)
if var.id not in var_ids:
var_ids.add(var.id)
vars.append(var)
vars.append(var)

# plots
if 'elements' in model['plot']:
ode_plot = model.get('plot', None) or {}
if 'elements' in ode_plot:
plot_type = Plot2D
for i_element in sorted(model['plot']['elements'].keys()):
element = model['plot']['elements'][i_element]
for i_element in sorted(ode_plot['elements'].keys()):
element = ode_plot['elements'][i_element]
if 'z' in element:
plot_type = Plot3D
break

for i_element in sorted(model['plot']['elements'].keys()):
element = model['plot']['elements'][i_element]
for i_element in sorted(ode_plot['elements'].keys()):
element = ode_plot['elements'][i_element]
if 'x' not in element:
element['x'] = 'T' # what XPP uses as the default

Expand All @@ -167,7 +175,7 @@ def get_parameters_variables_outputs_for_simulation(model_filename, model_langua

data_generators = {}
for var in vars:
data_generators[var.target or 'T'] = DataGenerator(
data_generators[(var.target or 'T').upper()] = DataGenerator(
id='data_generator_{}'.format(var.target),
name=var.target,
variables=[var],
Expand All @@ -176,8 +184,8 @@ def get_parameters_variables_outputs_for_simulation(model_filename, model_langua

plot = plot_type(id='plot')

for i_element in sorted(model['plot']['elements'].keys()):
element = model['plot']['elements'][i_element]
for i_element in sorted(ode_plot['elements'].keys()):
element = ode_plot['elements'][i_element]

if plot_type == Plot2D:
plot.curves.append(Curve(
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