def test_more_complex_archive(self):
archive_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'BIOMD0000000297.edited.omex')
config = get_config()
config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
config.VIZ_FORMATS = []
config.BUNDLE_OUTPUTS = True
config.KEEP_INDIVIDUAL_OUTPUTS = True
_, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname, config=config)
if log.exception:
raise log.exception
self.assertEqual(set(['reports.zip', 'reports.h5', 'ex1', 'ex2']).difference(set(os.listdir(self.dirname))), set())
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex1'))), set(['BIOMD0000000297.sedml']))
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex2'))), set(['BIOMD0000000297.sedml']))
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex1', 'BIOMD0000000297.sedml'))),
set(['two_species.csv', 'three_species.csv']))
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex2', 'BIOMD0000000297.sedml'))),
set(['one_species.csv', 'four_species.csv']))
archive = ArchiveReader().run(os.path.join(self.dirname, 'reports.zip'))
self.assertEqual(
sorted(file.archive_path for file in archive.files),
sorted([
'ex1/BIOMD0000000297.sedml/two_species.csv',
'ex1/BIOMD0000000297.sedml/three_species.csv',
'ex2/BIOMD0000000297.sedml/one_species.csv',
'ex2/BIOMD0000000297.sedml/four_species.csv',
]),
)
report = sedml_data_model.Report(
data_sets=[
sedml_data_model.DataSet(id='data_set_time_two_species', label='time'),
sedml_data_model.DataSet(id='data_set_Cln4', label='Cln4'),
sedml_data_model.DataSet(id='data_set_Swe13', label='Swe13'),
]
)
report_results = ReportReader().run(report, self.dirname,
'ex1/BIOMD0000000297.sedml/two_species',
format=report_data_model.ReportFormat.h5)
self.assertEqual(sorted(report_results.keys()), sorted(['data_set_time_two_species', 'data_set_Cln4', 'data_set_Swe13']))
numpy.testing.assert_allclose(report_results['data_set_time_two_species'], numpy.linspace(0., 1., 10 + 1))
def assert_outputs_created(self, dirname):
self.assertTrue(os.path.isfile(os.path.join(dirname, 'reports.h5')))
report = sedml_data_model.Report(data_sets=[
sedml_data_model.DataSet(id='time', label='time'),
])
report_results = ReportReader().run(
report,
dirname,
'simulation_1.sedml/simulation_1',
format=report_data_model.ReportFormat.h5)
self.assertEqual(len(report_results[report.data_sets[0].id]), 100 + 1)
numpy.testing.assert_almost_equal(
report_results[report.data_sets[0].id],
numpy.linspace(0., 100., 100 + 1),
)
for data_set_result in report_results.values():
self.assertFalse(numpy.any(numpy.isnan(data_set_result)))
def _build_sed_doc(self, algorithm=None):
if algorithm is None:
algorithm = sedml_data_model.Algorithm(
kisao_id='KISAO_0000019',
changes=[
sedml_data_model.AlgorithmParameterChange(
kisao_id='KISAO_0000211',
new_value='2e-8',
),
],
)
doc = sedml_data_model.SedDocument()
doc.models.append(
sedml_data_model.Model(
id='model_1',
source='model_1.bngl',
language=sedml_data_model.ModelLanguage.BNGL.value,
changes=[
sedml_data_model.ModelAttributeChange(
target='functions.gfunc.expression',
new_value='0.5*Atot^2/(10 + Atot^2)'),
sedml_data_model.ModelAttributeChange(
target='functions.gfunc().expression',
new_value='0.5*Atot^2/(10 + Atot^2)'),
sedml_data_model.ModelAttributeChange(
target='species.A().initialCount', new_value='4'),
sedml_data_model.ModelAttributeChange(
target='parameters.g1.value', new_value='18.0'),
],
))
doc.simulations.append(
sedml_data_model.UniformTimeCourseSimulation(
id='sim_1_time_course',
algorithm=algorithm,
initial_time=0.,
output_start_time=0.1,
output_end_time=0.2,
number_of_points=20,
))
doc.tasks.append(
sedml_data_model.Task(
id='task_1',
model=doc.models[0],
simulation=doc.simulations[0],
))
doc.data_generators.append(
sedml_data_model.DataGenerator(
id='data_gen_time',
variables=[
sedml_data_model.Variable(
id='var_time',
symbol=sedml_data_model.Symbol.time,
task=doc.tasks[0],
),
],
math='var_time',
))
doc.data_generators.append(
sedml_data_model.DataGenerator(
id='data_gen_A',
variables=[
sedml_data_model.Variable(
id='var_A',
target="species.A",
task=doc.tasks[0],
),
],
math='var_A',
))
doc.data_generators.append(
sedml_data_model.DataGenerator(
id='data_gen_B',
variables=[
sedml_data_model.Variable(
id='var_B',
target='species.B.count',
task=doc.tasks[0],
),
],
math='var_B',
))
doc.data_generators.append(
sedml_data_model.DataGenerator(
id='data_gen_GeneA_00',
variables=[
sedml_data_model.Variable(
id='var_GeneA_00',
target="molecules.GeneA_00()",
task=doc.tasks[0],
),
],
math='var_GeneA_00',
))
doc.data_generators.append(
sedml_data_model.DataGenerator(
id='data_gen_GeneA_01',
variables=[
sedml_data_model.Variable(
id='var_GeneA_01',
target="molecules.GeneA_01()",
task=doc.tasks[0],
),
],
math='var_GeneA_01',
))
doc.outputs.append(
sedml_data_model.Report(
id='report_1',
data_sets=[
sedml_data_model.DataSet(
id='data_set_time',
label='Time',
data_generator=doc.data_generators[0]),
sedml_data_model.DataSet(
id='data_set_A',
label='A',
data_generator=doc.data_generators[1]),
sedml_data_model.DataSet(
id='data_set_B',
label='B',
data_generator=doc.data_generators[2]),
sedml_data_model.DataSet(
id='data_set_GeneA_00',
label='GeneA_00',
data_generator=doc.data_generators[3]),
sedml_data_model.DataSet(
id='data_set_GeneA_01',
label='GeneA_01',
data_generator=doc.data_generators[4]),
],
))
append_all_nested_children_to_doc(doc)
return doc
def test_init_combine_archive_log(self):
archive = combine_data_model.CombineArchive(contents=[
combine_data_model.CombineArchiveContent(
location='./exp_2.sedml',
format=combine_data_model.CombineArchiveContentFormat.SED_ML,
master=False),
combine_data_model.CombineArchiveContent(
location='./exp_1.sedml',
format=combine_data_model.CombineArchiveContentFormat.SED_ML,
master=False),
])
exp_1 = sedml_data_model.SedDocument()
model_1 = sedml_data_model.Model(
id='model_1',
language=sedml_data_model.ModelLanguage.SBML.value,
source='./model.xml')
exp_1.models.append(model_1)
sim_1 = sedml_data_model.SteadyStateSimulation(
id='sim_1',
algorithm=sedml_data_model.Algorithm(kisao_id='KISAO_0000019'))
exp_1.simulations.append(sim_1)
task_1 = sedml_data_model.Task(id='task_1',
model=model_1,
simulation=sim_1)
task_2 = sedml_data_model.Task(id='task_2',
model=model_1,
simulation=sim_1)
exp_1.tasks.append(task_1)
exp_1.tasks.append(task_2)
data_gen_1 = sedml_data_model.DataGenerator(
id='data_gen_1',
math='param_1',
parameters=[sedml_data_model.Parameter(id='param_1', value=1.)])
data_gen_2 = sedml_data_model.DataGenerator(
id='data_gen_2',
math='param_2',
parameters=[sedml_data_model.Parameter(id='param_2', value=2.)])
exp_1.data_generators.append(data_gen_1)
exp_1.data_generators.append(data_gen_2)
exp_1.outputs.append(
sedml_data_model.Report(
id='report_1',
data_sets=[
sedml_data_model.DataSet(id='data_set_1',
label='data_set_1',
data_generator=data_gen_1),
sedml_data_model.DataSet(id='data_set_2',
label='data_set_2',
data_generator=data_gen_2),
]))
exp_1.outputs.append(
sedml_data_model.Plot2D(
id='plot_2',
curves=[
sedml_data_model.Curve(
id='curve_1',
x_data_generator=data_gen_1,
y_data_generator=data_gen_1,
x_scale=sedml_data_model.AxisScale.log,
y_scale=sedml_data_model.AxisScale.log),
sedml_data_model.Curve(
id='curve_2',
x_data_generator=data_gen_2,
y_data_generator=data_gen_2,
x_scale=sedml_data_model.AxisScale.log,
y_scale=sedml_data_model.AxisScale.log),
]))
SedmlSimulationWriter().run(exp_1,
os.path.join(self.dirname, 'exp_1.sedml'),
validate_models_with_languages=False)
exp_2 = sedml_data_model.SedDocument()
model_2 = sedml_data_model.Model(
id='model_2',
language=sedml_data_model.ModelLanguage.SBML.value,
source='./model.xml')
exp_2.models.append(model_2)
sim_2 = sedml_data_model.SteadyStateSimulation(
id='sim_2',
algorithm=sedml_data_model.Algorithm(kisao_id='KISAO_0000019'))
exp_2.simulations.append(sim_2)
task_3 = sedml_data_model.Task(id='task_3',
model=model_2,
simulation=sim_2)
exp_2.tasks.append(task_3)
data_gen_3 = sedml_data_model.DataGenerator(
id='data_gen_3',
math='param_3',
parameters=[sedml_data_model.Parameter(id='param_3', value=1.)])
data_gen_4 = sedml_data_model.DataGenerator(
id='data_gen_4',
math='param_4',
parameters=[sedml_data_model.Parameter(id='param_4', value=2.)])
exp_2.data_generators.append(data_gen_3)
exp_2.data_generators.append(data_gen_4)
exp_2.outputs.append(sedml_data_model.Report(id='report_3'))
exp_2.outputs.append(sedml_data_model.Plot2D(id='plot_4'))
exp_2.outputs.append(
sedml_data_model.Plot3D(
id='plot_5',
surfaces=[
sedml_data_model.Surface(
id='surface_1',
x_data_generator=data_gen_3,
y_data_generator=data_gen_3,
z_data_generator=data_gen_4,
x_scale=sedml_data_model.AxisScale.log,
y_scale=sedml_data_model.AxisScale.log,
z_scale=sedml_data_model.AxisScale.log),
]))
SedmlSimulationWriter().run(exp_2,
os.path.join(self.dirname, 'exp_2.sedml'),
validate_semantics=False,
validate_models_with_languages=False)
status = utils.init_combine_archive_log(
archive,
self.dirname,
logged_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.Plot2D,
sedml_data_model.Plot3D,
sedml_data_model.DataSet,
sedml_data_model.Curve,
sedml_data_model.Surface,
),
supported_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.DataSet,
),
)
expected = {
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'sedDocuments': [
{
'location':
'exp_2.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_3',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None,
},
],
'outputs': [
{
'id': 'report_3',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'dataSets': []
},
{
'id': 'plot_4',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'curves': []
},
{
'id':
'plot_5',
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'surfaces': [
{
'id': 'surface_1',
'status': 'SKIPPED'
},
]
},
],
},
{
'location':
'exp_1.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_1',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
{
'id': 'task_2',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs': [
{
'id':
'report_1',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'dataSets': [
{
'id': 'data_set_1',
'status': 'QUEUED'
},
{
'id': 'data_set_2',
'status': 'QUEUED'
},
]
},
{
'id':
'plot_2',
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'curves': [
{
'id': 'curve_1',
'status': 'SKIPPED'
},
{
'id': 'curve_2',
'status': 'SKIPPED'
},
]
},
],
},
],
}
self.assertEqual(status.to_json()['sedDocuments'][1]['outputs'][1],
expected['sedDocuments'][1]['outputs'][1])
self.assertEqual(status.sed_documents['exp_1.sedml'].parent, status)
self.assertEqual(
status.sed_documents['exp_1.sedml'].tasks['task_1'].parent,
status.sed_documents['exp_1.sedml'])
self.assertEqual(
status.sed_documents['exp_1.sedml'].outputs['report_1'].parent,
status.sed_documents['exp_1.sedml'])
status = utils.init_combine_archive_log(archive, self.dirname)
for doc in status.sed_documents.values():
doc.status = data_model.Status.QUEUED
for task in doc.tasks.values():
task.status = data_model.Status.QUEUED
for output in doc.outputs.values():
output.status = data_model.Status.QUEUED
if isinstance(output, data_model.ReportLog):
els = output.data_sets
elif isinstance(output, data_model.Plot2DLog):
els = output.curves
elif isinstance(output, data_model.Plot3DLog):
els = output.surfaces
else:
raise ValueError(output.__class__)
for id in els.keys():
els[id] = data_model.Status.QUEUED
status.finalize()
self.assertEqual(
status.to_json(), {
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'sedDocuments': [
{
'location':
'exp_2.sedml',
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_3',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs': [
{
'id': 'report_3',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'dataSets': []
},
{
'id': 'plot_4',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'curves': []
},
{
'id':
'plot_5',
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'surfaces': [
{
'id': 'surface_1',
'status': 'SKIPPED'
},
]
},
],
},
{
'location':
'exp_1.sedml',
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_1',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
{
'id': 'task_2',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs': [
{
'id':
'report_1',
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'dataSets': [
{
'id': 'data_set_1',
'status': 'SKIPPED'
},
{
'id': 'data_set_2',
'status': 'SKIPPED'
},
]
},
{
'id':
'plot_2',
'status':
'SKIPPED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'curves': [
{
'id': 'curve_1',
'status': 'SKIPPED'
},
{
'id': 'curve_2',
'status': 'SKIPPED'
},
]
},
],
},
],
})
status = utils.init_combine_archive_log(archive, self.dirname)
status.status = data_model.Status.RUNNING
for doc in status.sed_documents.values():
doc.status = data_model.Status.RUNNING
for task in doc.tasks.values():
task.status = data_model.Status.RUNNING
for output in doc.outputs.values():
output.status = data_model.Status.RUNNING
if isinstance(output, data_model.ReportLog):
els = output.data_sets
elif isinstance(output, data_model.Plot2DLog):
els = output.curves
elif isinstance(output, data_model.Plot3DLog):
els = output.surfaces
else:
raise ValueError(output.__class__)
for id in els.keys():
els[id] = data_model.Status.RUNNING
status.finalize()
self.assertEqual(
status.to_json(), {
'status':
'FAILED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'sedDocuments': [
{
'location':
'exp_2.sedml',
'status':
'FAILED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_3',
'status': 'FAILED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs': [
{
'id': 'report_3',
'status': 'FAILED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'dataSets': []
},
{
'id': 'plot_4',
'status': 'FAILED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'curves': []
},
{
'id':
'plot_5',
'status':
'FAILED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'surfaces': [
{
'id': 'surface_1',
'status': 'FAILED'
},
]
},
],
},
{
'location':
'exp_1.sedml',
'status':
'FAILED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_1',
'status': 'FAILED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
{
'id': 'task_2',
'status': 'FAILED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs': [
{
'id':
'report_1',
'status':
'FAILED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'dataSets': [
{
'id': 'data_set_1',
'status': 'FAILED'
},
{
'id': 'data_set_2',
'status': 'FAILED'
},
]
},
{
'id':
'plot_2',
'status':
'FAILED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'curves': [
{
'id': 'curve_1',
'status': 'FAILED'
},
{
'id': 'curve_2',
'status': 'FAILED'
},
]
},
],
},
],
})
# test logging subsets of possible features -- no data sets, curves, surfaces
status = utils.init_combine_archive_log(
archive,
self.dirname,
logged_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.Plot2D,
sedml_data_model.Plot3D,
),
supported_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.DataSet,
),
)
self.assertEqual(
status.to_json(), {
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'sedDocuments': [
{
'location':
'exp_2.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_3',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None,
},
],
'outputs': [
{
'id': 'report_3',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'dataSets': None
},
{
'id': 'plot_4',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'curves': None
},
{
'id': 'plot_5',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'surfaces': None
},
],
},
{
'location':
'exp_1.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_1',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
{
'id': 'task_2',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs': [
{
'id': 'report_1',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'dataSets': None
},
{
'id': 'plot_2',
'status': 'SKIPPED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'curves': None
},
],
},
],
})
# test logging subsets of possible features -- no plots
status = utils.init_combine_archive_log(
archive,
self.dirname,
logged_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
),
supported_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.DataSet,
),
)
self.assertEqual(
status.to_json(), {
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'sedDocuments': [
{
'location':
'exp_2.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_3',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None,
},
],
'outputs': [
{
'id': 'report_3',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'dataSets': None
},
],
},
{
'location':
'exp_1.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_1',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
{
'id': 'task_2',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs': [
{
'id': 'report_1',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'dataSets': None
},
],
},
],
})
# test logging subsets of possible features -- no outputs
status = utils.init_combine_archive_log(
archive,
self.dirname,
logged_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
),
supported_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.DataSet,
),
)
self.assertEqual(
status.to_json(), {
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'sedDocuments': [
{
'location':
'exp_2.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_3',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None,
},
],
'outputs':
None,
},
{
'location':
'exp_1.sedml',
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'tasks': [
{
'id': 'task_1',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
{
'id': 'task_2',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'algorithm': None,
'simulatorDetails': None
},
],
'outputs':
None,
},
],
})
# test logging subsets of possible features -- no tasks or outputs
status = utils.init_combine_archive_log(
archive,
self.dirname,
logged_features=(sedml_data_model.SedDocument, ),
supported_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.DataSet,
),
)
self.assertEqual(
status.to_json(), {
'status':
'QUEUED',
'exception':
None,
'skipReason':
None,
'output':
None,
'duration':
None,
'sedDocuments': [
{
'location': 'exp_2.sedml',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'tasks': None,
'outputs': None,
},
{
'location': 'exp_1.sedml',
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'tasks': None,
'outputs': None,
},
],
})
# test logging subsets of possible features -- no SED documents
status = utils.init_combine_archive_log(
archive,
self.dirname,
logged_features=(),
supported_features=(
sedml_data_model.SedDocument,
sedml_data_model.Task,
sedml_data_model.Report,
sedml_data_model.DataSet,
),
)
self.assertEqual(
status.to_json(), {
'status': 'QUEUED',
'exception': None,
'skipReason': None,
'output': None,
'duration': None,
'sedDocuments': None,
})
def test(self):
model = data_model.Model(
id='model1',
name='Model1',
source='model.sbml',
language='urn:sedml:language:sbml',
changes=[
data_model.ModelAttributeChange(target='/sbml:sbml/sbml:model[id=\'a\']/@id', new_value='234'),
data_model.ModelAttributeChange(target='/sbml:sbml/sbml:model[id=\'b\']/@id', new_value='432'),
data_model.AddElementModelChange(target='/sbml:sbml/sbml:model[id=\'b\']/@id', new_elements='432'),
data_model.ReplaceElementModelChange(target='/sbml:sbml/sbml:model[id=\'b\']/@id', new_elements='432'),
data_model.RemoveElementModelChange(target='/sbml:sbml/sbml:model[id=\'b\']/@id'),
data_model.ComputeModelChange(
target='/sbml:sbml/sbml:model[id=\'b\']/@id',
parameters=[
data_model.Parameter(id='p_1', value=1.5),
data_model.Parameter(id='p_2', value=2.5),
],
variables=[
data_model.Variable(
id='v_1',
model=None,
target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='param_1']",
),
data_model.Variable(
id='v_1',
model=None,
target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='param_1']",
),
],
math='p_1 * v_1 + p_2 * v_2',
),
],
)
for var in model.changes[-1].variables:
var.model = model
ss_simulation = data_model.SteadyStateSimulation(
id='simulation1',
name='Simulation1',
algorithm=data_model.Algorithm(
kisao_id='KISAO_0000029',
changes=[
data_model.AlgorithmParameterChange(kisao_id='KISAO_0000001', new_value='1.234'),
]),
)
one_step_simulation = data_model.OneStepSimulation(
id='simulation1',
name='Simulation1',
algorithm=data_model.Algorithm(
kisao_id='KISAO_0000029',
changes=[
data_model.AlgorithmParameterChange(kisao_id='KISAO_0000001', new_value='1.234'),
]),
step=10.)
time_course_simulation = data_model.UniformTimeCourseSimulation(
id='simulation1',
name='Simulation1',
algorithm=data_model.Algorithm(
kisao_id='KISAO_0000029',
changes=[
data_model.AlgorithmParameterChange(kisao_id='KISAO_0000001', new_value='1.234'),
data_model.AlgorithmParameterChange(kisao_id='KISAO_0000002', new_value='4.321'),
]),
initial_time=10.,
output_start_time=20.,
output_end_time=30,
number_of_steps=10)
task = data_model.Task(id='task1', name='Task1', model=model, simulation=time_course_simulation)
for var in model.changes[-1].variables:
var.task = task
report = data_model.Report(
id='report1',
name='Report1',
data_sets=[
data_model.DataSet(
id='dataset1',
name='Dataset1',
label='Dataset-1',
data_generator=data_model.DataGenerator(
id='dataGen1',
name='DataGen1',
variables=[
data_model.Variable(
id='DataGenVar1', name='DataGenVar1', target='/sbml:sbml/sbml:model/@id', task=task, model=model)
],
parameters=[
data_model.Parameter(
id='DataGenParam1', name='DataGenParam1', value=2.)
],
math='DataGenVar1 - DataGenParam1',
)
),
],
)
plot2d = data_model.Plot2D(
name='Plot2D',
curves=[
data_model.Curve(
id='curve1', name='Curve1',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
x_data_generator=data_model.DataGenerator(
id='xDataGen1',
name='XDataGen1',
variables=[
data_model.Variable(
id='xDataGenVar1', name='XDataGenVar1', target='/sbml:sbml/sbml:model/@id', task=task, model=model)
],
parameters=[
data_model.Parameter(
id='xDataGenParam1', name='XDataGenParam1', value=2.)
],
math='xDataGenVar1 * xDataGenParam1',
),
y_data_generator=None,
),
data_model.Curve(
id='curve2', name='Curve2',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
x_data_generator=None,
y_data_generator=data_model.DataGenerator(
id='yDataGen1',
name='yDataGen1',
variables=[
data_model.Variable(
id='yDataGenVar1', name='YDataGenVar1', target='/sbml:sbml/sbml:model/@id', task=task, model=model)
],
parameters=[
data_model.Parameter(
id='yDataGenParam1', name='YDataGenParam1', value=2.)
],
math='yDataGenParam1 + YDataGenParam1',
),
),
]
)
plot3d = data_model.Plot3D(
name='Plot3D',
surfaces=[
data_model.Surface(
id='curve1', name='Curve1',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
z_scale=data_model.AxisScale.linear,
x_data_generator=data_model.DataGenerator(
id='xDataGen1',
name='XDataGen1',
variables=[
data_model.Variable(
id='xDataGenVar1', name='XDataGenVar1', target='/sbml:sbml/sbml:model/@id', task=task, model=model)
],
parameters=[
data_model.Parameter(
id='xDataGenParam1', name='XDataGenParam1', value=2.)
],
math='xDataGenVar1 * xDataGenParam1',
),
y_data_generator=None,
z_data_generator=None,
),
data_model.Surface(
id='curve2',
name='Curve2',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
z_scale=data_model.AxisScale.log,
x_data_generator=None,
y_data_generator=None,
z_data_generator=data_model.DataGenerator(
id='zDataGen1',
name='zDataGen1',
variables=[
data_model.Variable(
id='zDataGenVar1', name='ZDataGenVar1', target='/sbml:sbml/sbml:model/@id', task=task, model=model)
],
parameters=[
data_model.Parameter(
id='zDataGenParam1', name='ZDataGenParam1', value=2.)
],
math='zDataGenParam1 / ZDataGenParam1',
),
),
]
)
document = data_model.SedDocument(
level=1,
version=3,
models=[model],
simulations=[ss_simulation, one_step_simulation, time_course_simulation],
tasks=[task],
data_generators=[plot2d.curves[0].x_data_generator],
outputs=[report, plot2d, plot3d],
metadata=Metadata(),
)
self.assertEqual(
ss_simulation.to_tuple(),
(
ss_simulation.id,
ss_simulation.name,
(
ss_simulation.algorithm.kisao_id,
(
(
ss_simulation.algorithm.changes[0].kisao_id,
ss_simulation.algorithm.changes[0].new_value,
),
),
),
)
)
self.assertEqual(
one_step_simulation.to_tuple(),
(
one_step_simulation.id,
one_step_simulation.name,
(
one_step_simulation.algorithm.kisao_id,
(
(
one_step_simulation.algorithm.changes[0].kisao_id,
one_step_simulation.algorithm.changes[0].new_value,
),
),
),
one_step_simulation.step
)
)
self.assertEqual(report.to_tuple()[0], report.id)
self.assertEqual(plot2d.to_tuple()[2][0][4], plot2d.curves[0].x_data_generator.id)
self.assertEqual(document.to_tuple(), (
document.level,
document.version,
(model.to_tuple(),),
tuple(none_sorted((ss_simulation.to_tuple(), one_step_simulation.to_tuple(), time_course_simulation.to_tuple()))),
(task.to_tuple(),),
(plot2d.curves[0].x_data_generator.to_tuple(),),
tuple(none_sorted((report.to_tuple(), plot2d.to_tuple(), plot3d.to_tuple()))),
document.metadata.to_tuple(),
))
change = model.changes[0]
change2 = copy.deepcopy(change)
self.assertTrue(change.is_equal(change2))
change2.target = None
self.assertFalse(change.is_equal(change2))
change = model.changes[-1]
change2 = copy.deepcopy(change)
self.assertTrue(change.is_equal(change2))
change2 = copy.deepcopy(change)
change2.target = None
self.assertFalse(change.is_equal(change2))
change2 = copy.deepcopy(change)
change2.parameters[0].value = -1
self.assertFalse(change.is_equal(change2))
change2 = copy.deepcopy(change)
change2.variables[0].id = 'variable_1'
self.assertFalse(change.is_equal(change2))
change2 = copy.deepcopy(change)
change2.variables[0].model.id = 'different_model'
self.assertFalse(change.is_equal(change2))
change2 = copy.deepcopy(change)
change2.math = 'x * y'
self.assertFalse(change.is_equal(change2))
model2 = copy.deepcopy(model)
self.assertTrue(model.is_equal(model2))
model2.id = None
self.assertFalse(model.is_equal(model2))
alg_change = time_course_simulation.algorithm.changes[0]
alg_change_2 = copy.deepcopy(alg_change)
self.assertTrue(alg_change.is_equal(alg_change_2))
alg_change_2.new_value = None
self.assertFalse(alg_change.is_equal(alg_change_2))
alg = time_course_simulation.algorithm
alg2 = copy.deepcopy(alg)
self.assertTrue(alg.is_equal(alg2))
alg2.kisao_id = None
self.assertFalse(alg.is_equal(alg2))
one_step_simulation_2 = copy.deepcopy(one_step_simulation)
self.assertTrue(one_step_simulation.is_equal(one_step_simulation_2))
one_step_simulation_2.step = -1.
self.assertFalse(one_step_simulation.is_equal(one_step_simulation_2))
time_course_simulation_2 = copy.deepcopy(time_course_simulation)
self.assertTrue(time_course_simulation.is_equal(time_course_simulation_2))
time_course_simulation_2.initial_time = -1.
self.assertFalse(time_course_simulation.is_equal(time_course_simulation_2))
task2 = copy.deepcopy(task)
self.assertTrue(task.is_equal(task2))
task2.id = None
self.assertFalse(task.is_equal(task2))
var = copy.deepcopy(report.data_sets[0].data_generator.variables[0])
var2 = copy.deepcopy(var)
self.assertTrue(var.is_equal(var2))
var2.target = None
self.assertFalse(var.is_equal(var2))
data_generator = copy.deepcopy(report.data_sets[0].data_generator)
data_generator_2 = copy.deepcopy(data_generator)
self.assertTrue(data_generator.is_equal(data_generator_2))
data_generator_2.variables = []
self.assertFalse(data_generator.is_equal(data_generator_2))
data_set = copy.deepcopy(report.data_sets[0])
data_set_2 = copy.deepcopy(data_set)
self.assertTrue(data_set.is_equal(data_set_2))
data_set_2.label = None
self.assertFalse(data_set.is_equal(data_set_2))
report2 = copy.deepcopy(report)
self.assertTrue(report.is_equal(report2))
report2.data_sets = []
self.assertFalse(report.is_equal(report2))
curve = copy.deepcopy(plot2d.curves[0])
curve2 = copy.deepcopy(curve)
self.assertTrue(curve.is_equal(curve2))
curve2.x_scale = None
self.assertFalse(curve.is_equal(curve2))
surface = copy.deepcopy(plot3d.surfaces[1])
surface2 = copy.deepcopy(surface)
self.assertTrue(surface.is_equal(surface2))
surface2.z_data_generator = None
self.assertFalse(surface.is_equal(surface2))
plot2d_2 = copy.deepcopy(plot2d)
self.assertTrue(plot2d.is_equal(plot2d_2))
plot2d_2.curves = []
self.assertFalse(plot2d.is_equal(plot2d_2))
plot3d_2 = copy.deepcopy(plot3d)
self.assertTrue(plot3d.is_equal(plot3d_2))
plot3d_2.name = None
self.assertFalse(plot3d.is_equal(plot3d_2))
document_2 = copy.deepcopy(document)
self.assertTrue(document.is_equal(document_2))
document_2.models = []
self.assertFalse(document.is_equal(document_2))
def _build_sed_doc(self, algorithm=None):
if algorithm is None:
algorithm = sedml_data_model.Algorithm(
kisao_id='KISAO_0000088',
changes=[
sedml_data_model.AlgorithmParameterChange(
kisao_id='KISAO_0000211',
new_value='1e-10',
),
],
)
doc = sedml_data_model.SedDocument()
doc.models.append(sedml_data_model.Model(
id='model_1',
source='model_1.xml',
language=sedml_data_model.ModelLanguage.SBML.value,
changes=[],
))
doc.simulations.append(sedml_data_model.UniformTimeCourseSimulation(
id='sim_1_time_course',
algorithm=algorithm,
initial_time=0.,
output_start_time=0.1,
output_end_time=0.2,
number_of_points=20,
))
doc.tasks.append(sedml_data_model.Task(
id='task_1',
model=doc.models[0],
simulation=doc.simulations[0],
))
doc.data_generators.append(sedml_data_model.DataGenerator(
id='data_gen_time',
variables=[
sedml_data_model.Variable(
id='var_time',
symbol=sedml_data_model.Symbol.time,
task=doc.tasks[0],
),
],
math='var_time',
))
doc.data_generators.append(sedml_data_model.DataGenerator(
id='data_gen_BE',
variables=[
sedml_data_model.Variable(
id='var_BE',
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE']",
target_namespaces=self.NAMESPACES,
task=doc.tasks[0],
),
],
math='var_BE',
))
doc.data_generators.append(sedml_data_model.DataGenerator(
id='data_gen_Cdh1',
variables=[
sedml_data_model.Variable(
id='var_Cdh1',
target='/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id="Cdh1"]',
target_namespaces=self.NAMESPACES,
task=doc.tasks[0],
),
],
math='var_Cdh1',
))
doc.data_generators.append(sedml_data_model.DataGenerator(
id='data_gen_Cdc20',
variables=[
sedml_data_model.Variable(
id='var_Cdc20',
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Cdc20']",
target_namespaces=self.NAMESPACES,
task=doc.tasks[0],
),
],
math='var_Cdc20',
))
doc.outputs.append(sedml_data_model.Report(
id='report_1',
data_sets=[
sedml_data_model.DataSet(id='data_set_time', label='Time', data_generator=doc.data_generators[0]),
sedml_data_model.DataSet(id='data_set_BE', label='BE', data_generator=doc.data_generators[1]),
sedml_data_model.DataSet(id='data_set_Cdh1', label='Cdh1', data_generator=doc.data_generators[2]),
sedml_data_model.DataSet(id='data_set_Cdc20', label='Cdc20', data_generator=doc.data_generators[3]),
],
))
append_all_nested_children_to_doc(doc)
return doc
def test_write_read(self):
shutil.copy(
os.path.join(os.path.dirname(__file__), '..', 'fixtures',
'BIOMD0000000075.xml'),
os.path.join(self.tmp_dir, 'model.sbml'))
model1 = data_model.Model(
id='model1',
name='Model1',
source='model.sbml',
language='urn:sedml:language:sbml',
changes=[
data_model.ModelAttributeChange(
target='/sbml:sbml/sbml:model[id=\'a\']/@id',
new_value='234'),
data_model.ModelAttributeChange(
target='/sbml:sbml/sbml:model[id=\'b\']/@id',
new_value='432'),
data_model.AddElementModelChange(
target=
'/sbml:sbml/sbml:model[id=\'b\']/sbml:listOfParameters',
new_elements=
'<sbml:parameter xmlns:sbml="http://www.sbml.org/sbml/level2/version3" id="new_parameter" value="1.0"/>'
),
data_model.AddElementModelChange(
target=
'/sbml:sbml/sbml:model[id=\'b\']/sbml:listOfParameters',
new_elements=
'<parameter id="new_parameter_1" value="1.0"/><parameter id="new_parameter_2" value="1.0"/>'
),
data_model.ReplaceElementModelChange(
target=
'/sbml:sbml/sbml:model[id=\'b\']/sbml:listOfParameters/sbml:parameter[@id=\'p1\']',
new_elements='<parameter id="p1" value="1.0"/>'),
data_model.ReplaceElementModelChange(
target=
'/sbml:sbml/sbml:model[id=\'b\']/sbml:listOfParameters/sbml:parameter[@id=\'p1\']',
new_elements=
'<parameter id="p1" value="1.0"/><parameter id="p1" value="1.0"/>'
),
data_model.RemoveElementModelChange(
target=
'/sbml:sbml/sbml:model[id=\'b\']/sbml:listOfParameters/sbml:parameter[@id=\'p1\']',
),
data_model.ComputeModelChange(
target=
'/sbml:sbml/sbml:model[id=\'b\']/sbml:listOfParameters/sbml:parameter[@id=\'p1\']',
parameters=[
data_model.Parameter(id='a', value=1.5),
data_model.Parameter(id='b', value=2.25),
],
variables=[
data_model.Variable(
id='x',
target='variable_target_x',
),
data_model.Variable(
id='y',
target='variable_target_y',
),
],
math='a * x + b * y',
),
],
)
for var in model1.changes[-1].variables:
var.model = model1
model2 = data_model.Model(
id='model2',
name='Model2',
source='model.sbml',
language='urn:sedml:language:sbml',
changes=[
data_model.ModelAttributeChange(
target='/sbml:sbml/sbml:model[id=\'a\']/@id',
new_value='234',
),
data_model.ModelAttributeChange(
target='/sbml:sbml/sbml:model[id=\'b\']/@id',
new_value='432'),
],
)
ss_simulation = data_model.SteadyStateSimulation(
id='simulation1',
name='Simulation1',
algorithm=data_model.Algorithm(
kisao_id='KISAO_0000019',
changes=[
data_model.AlgorithmParameterChange(
kisao_id='KISAO_0000211', new_value='1.234'),
]),
)
one_step_simulation = data_model.OneStepSimulation(
id='simulation2',
name='Simulation2',
algorithm=data_model.Algorithm(
kisao_id='KISAO_0000019',
changes=[
data_model.AlgorithmParameterChange(
kisao_id='KISAO_0000211', new_value='1.234'),
]),
step=10.)
time_course_simulation = data_model.UniformTimeCourseSimulation(
id='simulation3',
name='Simulation3',
algorithm=data_model.Algorithm(
kisao_id='KISAO_0000019',
changes=[
data_model.AlgorithmParameterChange(
kisao_id='KISAO_0000209', new_value='1.234'),
data_model.AlgorithmParameterChange(
kisao_id='KISAO_0000211', new_value='4.321'),
]),
initial_time=10.,
output_start_time=20.,
output_end_time=30,
number_of_steps=10)
task1 = data_model.Task(id='task1',
name='Task1',
model=model1,
simulation=time_course_simulation)
task2 = data_model.Task(id='task2',
name='Task2',
model=model2,
simulation=time_course_simulation)
task3 = data_model.RepeatedTask(
id='task3',
name='Task3',
reset_model_for_each_iteration=True,
changes=[],
sub_tasks=[
data_model.SubTask(task=task1, order=1),
data_model.SubTask(task=task2, order=2),
],
ranges=[
data_model.UniformRange(
id='range1',
start=10.,
end=20.,
number_of_steps=4,
type=data_model.UniformRangeType.linear),
data_model.UniformRange(id='range2',
start=10.,
end=20.,
number_of_steps=4,
type=data_model.UniformRangeType.log),
data_model.VectorRange(id='range3',
values=[3., 5., 7., 11., 13.]),
],
)
task3.ranges.append(
data_model.FunctionalRange(
id='range4',
range=task3.ranges[0],
parameters=[
data_model.Parameter(
id='x2',
value=2.0,
),
],
variables=[
data_model.Variable(
id='y2',
model=model1,
target=
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:Parameter[@id='param_1']",
),
],
math='{} * {} + {}'.format(task3.ranges[0].id, 'x2', 'y2'),
), )
task3.range = task3.ranges[1]
task3.changes.append(
data_model.SetValueComputeModelChange(
model=model1,
target=
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='p1']",
range=task3.ranges[0],
parameters=[],
variables=[],
math='range1',
), )
task3.changes.append(
data_model.SetValueComputeModelChange(
model=model1,
target=
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='p1']",
range=task3.ranges[0],
parameters=[],
variables=[
data_model.Variable(
id='range1_var1',
model=model1,
target=
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='p1']",
)
],
math='range1 * range1_var1',
), )
task3.changes.append(
data_model.SetValueComputeModelChange(
model=model1,
target=
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='p1']",
range=task3.ranges[0],
parameters=[
data_model.Parameter(id='range1_p1', value=2.5),
],
variables=[],
math='range1 * range1_p1',
), )
report = data_model.Report(
id='report1',
name='Report1',
data_sets=[
data_model.DataSet(
id='dataset1',
name='Dataset1',
label='Dataset-1',
data_generator=data_model.DataGenerator(
id='dataGen1',
name='DataGen1',
variables=[
data_model.Variable(
id='DataGenVar1',
name='DataGenVar1',
target='/sbml:sbml/sbml:model/@id',
task=task1,
)
],
parameters=[
data_model.Parameter(id='DataGenParam1',
name='DataGenParam1',
value=2.)
],
math='DataGenVar1 - DataGenParam1',
)),
],
)
plot2d = data_model.Plot2D(
id='plot2d',
name='Plot2D',
curves=[
data_model.Curve(
id='curve1',
name='Curve1',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
x_data_generator=data_model.DataGenerator(
id='xDataGen2',
name='XDataGen2',
variables=[
data_model.Variable(id='xDataGenVar1',
name='XDataGenVar1',
symbol='urn:sedml:symbol:time',
task=task2)
],
parameters=[
data_model.Parameter(id='xDataGenParam1',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar1 * xDataGenParam1',
),
y_data_generator=data_model.DataGenerator(
id='yDataGen3',
name='yDataGen3',
variables=[
data_model.Variable(
id='xDataGenVar2',
name='XDataGenVar1',
target='/sbml:sbml/sbml:model/@id',
task=task2,
)
],
parameters=[
data_model.Parameter(id='xDataGenParam2',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar2 * xDataGenParam2',
),
),
data_model.Curve(
id='curve2',
name='Curve2',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
x_data_generator=data_model.DataGenerator(
id='yDataGen4',
name='yDataGen4',
variables=[
data_model.Variable(
id='yDataGenVar1',
target='/sbml:sbml/sbml:model/@id',
task=task1,
)
],
parameters=[
data_model.Parameter(id='YDataGenParam1', value=2.)
],
math='yDataGenVar1 + YDataGenParam1',
),
y_data_generator=data_model.DataGenerator(
id='yDataGen5',
name='yDataGen5',
variables=[
data_model.Variable(
id='yDataGenVar2',
target='/sbml:sbml/sbml:model/@id',
task=task1,
)
],
parameters=[
data_model.Parameter(id='YDataGenParam2',
value=2.),
],
math='yDataGenVar2 + YDataGenParam2',
),
),
])
plot3d = data_model.Plot3D(
id='plot3d',
name='Plot3D',
surfaces=[
data_model.Surface(
id='surface1',
name='Surface1',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
z_scale=data_model.AxisScale.linear,
x_data_generator=data_model.DataGenerator(
id='xDataGen6',
name='XDataGen6',
variables=[
data_model.Variable(
id='xDataGenVar3',
name='XDataGenVar2',
target='/sbml:sbml/sbml:model/@id',
task=task2,
)
],
parameters=[
data_model.Parameter(id='xDataGenParam3',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar3 * xDataGenParam3',
),
y_data_generator=data_model.DataGenerator(
id='xDataGen8',
name='XDataGen8',
variables=[
data_model.Variable(
id='xDataGenVar4',
name='XDataGenVar2',
target='/sbml:sbml/sbml:model/@id',
task=task2,
)
],
parameters=[
data_model.Parameter(id='xDataGenParam4',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar4 * xDataGenParam4',
),
z_data_generator=data_model.DataGenerator(
id='xDataGen9',
name='XDataGen9',
variables=[
data_model.Variable(
id='xDataGenVar5',
name='XDataGenVar2',
target='/sbml:sbml/sbml:model/@id',
task=task2,
)
],
parameters=[
data_model.Parameter(id='xDataGenParam5',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar5 * xDataGenParam5',
),
),
data_model.Surface(
id='surface2',
name='Surface2',
x_scale=data_model.AxisScale.linear,
y_scale=data_model.AxisScale.log,
z_scale=data_model.AxisScale.log,
x_data_generator=data_model.DataGenerator(
id='xDataGen10',
name='XDataGen10',
variables=[
data_model.Variable(
id='xDataGenVar6',
name='XDataGenVar2',
target='/sbml:sbml/sbml:model/@id',
task=task2,
)
],
parameters=[
data_model.Parameter(id='xDataGenParam6',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar6 * xDataGenParam6',
),
y_data_generator=data_model.DataGenerator(
id='xDataGen11',
name='XDataGen11',
variables=[
data_model.Variable(
id='xDataGenVar7',
name='XDataGenVar2',
target='/sbml:sbml/sbml:model/@id',
task=task2,
)
],
parameters=[
data_model.Parameter(id='xDataGenParam7',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar7 * xDataGenParam7',
),
z_data_generator=data_model.DataGenerator(
id='xDataGen12',
name='XDataGen12',
variables=[
data_model.Variable(
id='xDataGenVar8',
name='XDataGenVar2',
target='/sbml:sbml/sbml:model/@id',
task=task2,
)
],
parameters=[
data_model.Parameter(id='xDataGenParam8',
name='XDataGenParam1',
value=2.)
],
math='xDataGenVar8 * xDataGenParam8',
),
),
])
now = datetime.datetime(2020,
1,
2,
1,
2,
3,
tzinfo=dateutil.tz.tzutc())
document = data_model.SedDocument(
level=1,
version=3,
models=[model1],
simulations=[time_course_simulation],
tasks=[task1],
data_generators=([d.data_generator for d in report.data_sets]),
outputs=[report],
metadata=Metadata(
description="description",
tags=['tag-1', 'tag-2'],
authors=[
Person(given_name='first',
other_name='middle',
family_name='last'),
],
references=ExternalReferences(
identifiers=None,
citations=[
Citation(title='creative title',
authors='Author-1 & Author-2',
journal='major journal',
volume='10',
issue='20',
pages='30-40',
year=2020,
identifiers=[
Identifier(
namespace="doi",
id='10.0/1.0',
url="https://doi.org/10.0/1.0"),
])
]),
license=OntologyTerm(
namespace='SPDX',
id='MIT',
url='https://spdx.org/licenses/MIT.html',
),
created=now,
updated=now,
),
)
self._set_target_namespaces(document)
filename = os.path.join(self.tmp_dir, 'test.xml')
io.SedmlSimulationWriter().run(document, filename)
document2 = io.SedmlSimulationReader().run(filename)
self.assertTrue(document.is_equal(document2))
document = data_model.SedDocument(
level=1,
version=3,
models=[model1, model2],
simulations=[
ss_simulation, one_step_simulation, time_course_simulation
],
tasks=[task1, task2, task3],
data_generators=([d.data_generator for d in report.data_sets] +
[c.x_data_generator for c in plot2d.curves] +
[c.y_data_generator for c in plot2d.curves] +
[s.x_data_generator for s in plot3d.surfaces] +
[s.y_data_generator for s in plot3d.surfaces] +
[s.z_data_generator for s in plot3d.surfaces]),
outputs=[report, plot2d, plot3d],
metadata=Metadata(
description="description",
license=OntologyTerm(
namespace='SPDX',
id='MIT',
url='https://spdx.org/licenses/MIT.html',
),
),
)
self._set_target_namespaces(document)
filename = os.path.join(self.tmp_dir, 'test.xml')
io.SedmlSimulationWriter().run(document, filename)
document2 = io.SedmlSimulationReader().run(filename)
self.assertTrue(document.is_equal(document2))
document2.metadata.license.namespace = None
document2.metadata.license.url = None
io.SedmlSimulationWriter().run(document2, filename)
document3 = io.SedmlSimulationReader().run(filename)
self.assertTrue(document2.is_equal(document3))
document3.metadata = None
io.SedmlSimulationWriter().run(document3, filename)
document4 = io.SedmlSimulationReader().run(filename)
self.assertTrue(document4.is_equal(document3))
document.models[0].changes[
2].new_elements = '<parameter id="new_parameter" value="1.0/>'
document.models[0].changes[
4].new_elements = '<parameter id="new_parameter" value="1.0"/>'
with self.assertRaisesRegex(ValueError, 'invalid XML'):
io.SedmlSimulationWriter().run(document, filename)
document.models[0].changes[
2].new_elements = '<parameter id="new_parameter" value="1.0"/>'
document.models[0].changes[
4].new_elements = '<parameter id="new_parameter" value="1.0/>'
with self.assertRaisesRegex(ValueError, 'invalid XML'):
io.SedmlSimulationWriter().run(document, filename)