def test_add_smoldyn_output_files_for_sed_variables(self):
filename = os.path.join(self.EXAMPLES_DIRNAME, 'S1_intro',
'bounce1.txt')
config = smoldyn.biosimulators.combine.read_smoldyn_simulation_configuration(
filename)
smoldyn.biosimulators.combine.disable_smoldyn_graphics_in_simulation_configuration(
config)
filename2 = os.path.join(self.dirname, 'config.txt')
smoldyn.biosimulators.combine.write_smoldyn_simulation_configuration(
config, filename2)
sim = smoldyn.biosimulators.combine.init_smoldyn_simulation_from_configuration_file(
filename2)
sim.setGraphics('none')
var = Variable(id='time', symbol=Symbol.time.value)
variable_output_cmd_map = smoldyn.biosimulators.combine.validate_variables(
[var])
smoldyn_output_files = smoldyn.biosimulators.combine.add_smoldyn_output_files_for_sed_variables(
self.dirname, [var], variable_output_cmd_map, sim)
self.assertEqual(set(smoldyn_output_files.keys()), set(['molcount']))
var.symbol = 'undefined'
with self.assertRaises(ValueError):
smoldyn.biosimulators.combine.validate_variables([var])
var.symbol = None
var.target = 'undefined '
with self.assertRaises(NotImplementedError):
smoldyn.biosimulators.combine.validate_variables([var])
def export_sed_doc(sed_doc_specs):
""" Export the specifications of SED-ML document to SED-ML
Args:
sed_doc_specs (``SedDocument``)
Returns:
:obj:`SedDocument`
"""
sed_doc = SedDocument(
level=sed_doc_specs['level'],
version=sed_doc_specs['version'],
)
# add styles to SED-ML document
style_id_map = {}
for style_spec in sed_doc_specs['styles']:
style = Style(
id=style_spec.get('id'),
name=style_spec.get('name', None),
)
sed_doc.styles.append(style)
style_id_map[style.id] = style
if style_spec.get('line', None) is not None:
style.line = LineStyle(
type=style_spec['line'].get('type', None),
color=style_spec['line'].get('color', None),
thickness=style_spec['line'].get('thickness', None),
)
if style_spec['line'].get('type', None) is not None:
style.line.type = LineStyleType[style_spec['line']['type']]
if style_spec['line'].get('color', None) is not None:
style.line.color = Color(style_spec['line']['color'])
if style_spec.get('marker', None) is not None:
style.marker = MarkerStyle(
type=style_spec['marker'].get('type', None),
size=style_spec['marker'].get('size', None),
line_color=style_spec['marker'].get('lineColor', None),
line_thickness=style_spec['marker'].get('lineThickness', None),
fill_color=style_spec['marker'].get('fillColor', None),
)
if style_spec['marker'].get('type', None) is not None:
style.marker.type = MarkerStyleType[style_spec['marker']
['type']]
if style_spec['marker'].get('lineColor', None) is not None:
style.marker.line_color = Color(
style_spec['marker']['lineColor'])
if style_spec['marker'].get('fillColor', None) is not None:
style.marker.fill_color = Color(
style_spec['marker']['fillColor'])
if style_spec.get('fill', None) is not None:
style.fill = FillStyle(color=style_spec['fill'].get('color',
None), )
if style_spec['fill'].get('color', None) is not None:
style.fill.color = Color(style_spec['fill']['color'])
for style_spec, style in zip(sed_doc_specs['styles'], sed_doc.styles):
if style_spec.get('base', None) is not None:
style.base = style_id_map.get(style_spec['base'], None)
if style.base is None:
raise BadRequestException(
title='Base style `{}` for style `{}` does not exist'.
format(style_spec['base'], style.id),
instance=ValueError('Style does not exist'),
)
# add models to SED-ML document
model_id_map = {}
for model_spec in sed_doc_specs['models']:
model = Model(
id=model_spec.get('id'),
name=model_spec.get('name', None),
language=model_spec.get('language'),
source=model_spec.get('source'),
)
sed_doc.models.append(model)
model_id_map[model.id] = model
for change_spec in model_spec['changes']:
if change_spec['_type'] == 'SedModelAttributeChange':
change = ModelAttributeChange(
new_value=change_spec.get('newValue'), )
elif change_spec['_type'] == 'SedAddElementModelChange':
change = AddElementModelChange(
new_elements=change_spec.get('newElements'), )
elif change_spec['_type'] == 'SedReplaceElementModelChange':
change = ReplaceElementModelChange(
new_elements=change_spec.get('newElements'), )
elif change_spec['_type'] == 'SedRemoveElementModelChange':
change = RemoveElementModelChange()
elif change_spec['_type'] == 'SedComputeModelChange':
change = ComputeModelChange(
parameters=[],
variables=[],
math=change_spec.get('math'),
)
for parameter_spec in change_spec.get('parameters', []):
change.parameters.append(
Parameter(
id=parameter_spec.get('id'),
name=parameter_spec.get('name', None),
value=parameter_spec.get('value'),
))
for variable_spec in change_spec.get('variables', []):
change.variables.append(
Variable(
id=variable_spec.get('id'),
name=variable_spec.get('name', None),
model=variable_spec.get('model', None),
target=variable_spec.get('target',
{}).get('value', None),
target_namespaces={
namespace['prefix']: namespace['uri']
for namespace in variable_spec.get(
'target', {}).get('namespaces', [])
},
symbol=variable_spec.get('symbol', None),
task=variable_spec.get('task', None),
))
else:
raise BadRequestException(
title='Changes of type `{}` are not supported'.format(
change_spec['_type']),
instance=NotImplementedError('Invalid change'))
change.target = change_spec.get('target').get('value')
for ns in change_spec.get('target').get('namespaces', []):
change.target_namespaces[ns.get('prefix', None)] = ns['uri']
model.changes.append(change)
# add simulations to SED-ML document
simulation_id_map = {}
for sim_spec in sed_doc_specs['simulations']:
if sim_spec['_type'] == 'SedOneStepSimulation':
sim = OneStepSimulation(
id=sim_spec.get('id'),
name=sim_spec.get('name', None),
step=sim_spec.get('step'),
)
elif sim_spec['_type'] == 'SedSteadyStateSimulation':
sim = SteadyStateSimulation(
id=sim_spec.get('id'),
name=sim_spec.get('name', None),
)
elif sim_spec['_type'] == 'SedUniformTimeCourseSimulation':
sim = UniformTimeCourseSimulation(
id=sim_spec.get('id'),
name=sim_spec.get('name', None),
initial_time=sim_spec.get('initialTime'),
output_start_time=sim_spec.get('outputStartTime'),
output_end_time=sim_spec.get('outputEndTime'),
number_of_steps=sim_spec.get('numberOfSteps'),
)
else:
raise BadRequestException(
title='Simulations of type `{}` are not supported'.format(
sim_spec['_type']),
instance=NotImplementedError('Invalid simulation')
) # pragma: no cover: unreachable due to schema validation
alg_spec = sim_spec.get('algorithm')
sim.algorithm = Algorithm(kisao_id=alg_spec.get('kisaoId'))
for change_spec in alg_spec.get('changes'):
sim.algorithm.changes.append(
AlgorithmParameterChange(
kisao_id=change_spec.get('kisaoId'),
new_value=change_spec.get('newValue'),
))
sed_doc.simulations.append(sim)
simulation_id_map[sim.id] = sim
# add tasks to SED-ML document
task_id_map = {}
for task_spec in sed_doc_specs['tasks']:
if task_spec['_type'] == 'SedTask':
model_id = task_spec.get('model')
sim_id = task_spec.get('simulation')
model = model_id_map.get(model_id, None)
sim = simulation_id_map.get(sim_id, None)
if not model:
raise BadRequestException(
title='Model `{}` for task `{}` does not exist'.format(
model_id, task_spec.get('id')),
instance=ValueError('Model does not exist'),
)
if not sim:
raise BadRequestException(
title='Simulation `{}` for task `{}` does not exist'.
format(sim_id, task_spec.get('id')),
instance=ValueError('Simulation does not exist'),
)
task = Task(
id=task_spec.get('id'),
name=task_spec.get('name', None),
model=model,
simulation=sim,
)
else:
# TODO: support repeated tasks
raise BadRequestException(
title='Tasks of type `{}` are not supported'.format(
task_spec['_type']),
instance=NotImplementedError('Invalid task')
) # pragma: no cover: unreachable due to schema validation
sed_doc.tasks.append(task)
task_id_map[task.id] = task
# add data generators to SED-ML document
data_gen_id_map = {}
for data_gen_spec in sed_doc_specs['dataGenerators']:
data_gen = DataGenerator(
id=data_gen_spec.get('id'),
name=data_gen_spec.get('name', None),
math=data_gen_spec.get('math'),
)
for var_spec in data_gen_spec['variables']:
task_id = var_spec.get('task')
task = task_id_map.get(task_id, None)
if not task:
raise BadRequestException(
title='Task `{}` for variable `{}` does not exist'.format(
task_id, var_spec.get('id')),
instance=ValueError('Task does not exist'),
)
var = Variable(
id=var_spec.get('id'),
name=var_spec.get('name', None),
task=task,
symbol=var_spec.get('symbol', None),
)
target_spec = var_spec.get('target', None)
if target_spec:
var.target = target_spec['value']
for ns in target_spec.get('namespaces', []):
var.target_namespaces[ns.get('prefix', None)] = ns['uri']
data_gen.variables.append(var)
sed_doc.data_generators.append(data_gen)
data_gen_id_map[data_gen.id] = data_gen
# add outputs to SED-ML document
for output_spec in sed_doc_specs['outputs']:
if output_spec['_type'] == 'SedReport':
output = Report(
id=output_spec.get('id'),
name=output_spec.get('name', None),
)
for data_set_spec in output_spec['dataSets']:
data_gen_id = data_set_spec['dataGenerator']
data_gen = data_gen_id_map.get(data_gen_id, None)
if not data_gen:
raise BadRequestException(
title=
'Data generator `{}` for output `{}` does not exist'.
format(data_gen_id, output_spec.get('id')),
instance=ValueError('Data generator does not exist'),
)
data_set = DataSet(
id=data_set_spec.get('id'),
name=data_set_spec.get('name', None),
label=data_set_spec.get('label', None),
data_generator=data_gen,
)
output.data_sets.append(data_set)
elif output_spec['_type'] == 'SedPlot2D':
output = Plot2D(
id=output_spec.get('id'),
name=output_spec.get('name', None),
)
for curve_spec in output_spec['curves']:
x_data_gen_id = curve_spec['xDataGenerator']
y_data_gen_id = curve_spec['yDataGenerator']
style_id = curve_spec.get('style', None)
x_data_gen = data_gen_id_map.get(x_data_gen_id, None)
y_data_gen = data_gen_id_map.get(y_data_gen_id, None)
style = style_id_map.get(style_id, None)
if not x_data_gen:
raise BadRequestException(
title=
'X data generator `{}` for curve `{}` does not exist'.
format(x_data_gen_id, output_spec.get('id')),
instance=ValueError('Data generator does not exist'),
)
if not y_data_gen:
raise BadRequestException(
title=
'Y data generator `{}` for curve `{}` does not exist'.
format(y_data_gen_id, output_spec.get('id')),
instance=ValueError('Data generator does not exist'),
)
if style_id is not None and style is None:
raise BadRequestException(
title='Style `{}` for curve `{}` does not exist'.
format(style_id, output_spec.get('id')),
instance=ValueError('Style does not exist'),
)
curve = Curve(
id=curve_spec.get('id'),
name=curve_spec.get('name', None),
x_data_generator=x_data_gen,
y_data_generator=y_data_gen,
x_scale=AxisScale[output_spec['xScale']],
y_scale=AxisScale[output_spec['yScale']],
style=style,
)
output.curves.append(curve)
elif output_spec['_type'] == 'SedPlot3D':
output = Plot3D(
id=output_spec.get('id'),
name=output_spec.get('name', None),
)
for surface_spec in output_spec['surfaces']:
x_data_gen_id = surface_spec['xDataGenerator']
y_data_gen_id = surface_spec['yDataGenerator']
z_data_gen_id = surface_spec['zDataGenerator']
style_id = surface_spec.get('style', None)
x_data_gen = data_gen_id_map.get(x_data_gen_id, None)
y_data_gen = data_gen_id_map.get(y_data_gen_id, None)
z_data_gen = data_gen_id_map.get(z_data_gen_id, None)
style = style_id_map.get(style_id, None)
if not x_data_gen:
raise BadRequestException(
title=
'X data generator `{}` for surface `{}` does not exist'
.format(x_data_gen_id, output_spec.get('id')),
instance=ValueError('Data generator does not exist'),
)
if not y_data_gen:
raise BadRequestException(
title=
'Y data generator `{}` for surface `{}` does not exist'
.format(y_data_gen_id, output_spec.get('id')),
instance=ValueError('Data generator does not exist'),
)
if not z_data_gen:
raise BadRequestException(
title=
'X data generator `{}` for surface `{}` does not exist'
.format(z_data_gen_id, output_spec.get('id')),
instance=ValueError('Data generator does not exist'),
)
if style_id is not None and style is None:
raise BadRequestException(
title='Style `{}` for surface `{}` does not exist'.
format(style_id, output_spec.get('id')),
instance=ValueError('Style does not exist'),
)
surface = Surface(
id=surface_spec.get('id'),
name=surface_spec.get('name', None),
x_data_generator=x_data_gen,
y_data_generator=y_data_gen,
z_data_generator=z_data_gen,
x_scale=AxisScale[output_spec['xScale']],
y_scale=AxisScale[output_spec['yScale']],
z_scale=AxisScale[output_spec['zScale']],
style=style,
)
output.surfaces.append(surface)
else:
raise BadRequestException(
title='Outputs of type `{}` are not supported'.format(
output_spec['_type']),
instance=NotImplementedError('Invalid output')
) # pragma: no cover: unreachable due to schema validation
sed_doc.outputs.append(output)
# deserialize references
model_map = {}
for model in sed_doc.models:
model_map[model.id] = model
task_map = {}
for task in sed_doc.tasks:
task_map[task.id] = task
for model in sed_doc.models:
for change in model.changes:
if isinstance(change, ComputeModelChange):
for variable in change.variables:
if variable.model:
variable.model = model_map[variable.model]
if variable.task:
variable.task = task_map[variable.task]
return sed_doc