def petab_problem(minimal_sbml_model): # pylint: disable=W0621
"""Test petab problem."""
# create test model
document, model = minimal_sbml_model
p = model.createParameter()
p.setId('fixedParameter1')
p.setName('FixedParameter1')
p = model.createParameter()
p.setId('observable_1')
p.setName('Observable 1')
measurement_df = pd.DataFrame(data={
OBSERVABLE_ID: ['obs1', 'obs2'],
OBSERVABLE_PARAMETERS: ['', 'p1;p2'],
NOISE_PARAMETERS: ['p3;p4', 'p5']
})
condition_df = pd.DataFrame(data={
CONDITION_ID: ['condition1', 'condition2'],
CONDITION_NAME: ['', 'Condition 2'],
'fixedParameter1': [1.0, 2.0]
}).set_index(CONDITION_ID)
parameter_df = pd.DataFrame(data={
PARAMETER_ID: ['dynamicParameter1', 'dynamicParameter2'],
PARAMETER_NAME: ['', '...'],
}).set_index(PARAMETER_ID)
observable_df = pd.DataFrame(data={
OBSERVABLE_ID: ['observable_1'],
OBSERVABLE_NAME: ['julius'],
OBSERVABLE_FORMULA: ['observable_1'],
NOISE_FORMULA: [1],
}).set_index(OBSERVABLE_ID)
with tempfile.TemporaryDirectory() as temp_dir:
sbml_file_name = Path(temp_dir, "model.xml")
libsbml.writeSBMLToFile(document, str(sbml_file_name))
measurement_file_name = Path(temp_dir, "measurements.tsv")
petab.write_measurement_df(measurement_df, measurement_file_name)
condition_file_name = Path(temp_dir, "conditions.tsv")
petab.write_condition_df(condition_df, condition_file_name)
parameter_file_name = Path(temp_dir, "parameters.tsv")
petab.write_parameter_df(parameter_df, parameter_file_name)
observable_file_name = Path(temp_dir, "observables.tsv")
petab.write_observable_df(observable_df, observable_file_name)
yield petab.Problem.from_files(
sbml_file=sbml_file_name,
measurement_file=measurement_file_name,
condition_file=condition_file_name,
parameter_file=parameter_file_name,
observable_files=observable_file_name)
def test_write_parameter_df():
"""Test parameters.write_parameter_df."""
parameter_df = pd.DataFrame(data={
PARAMETER_ID: ['par1', 'par2'],
PARAMETER_NAME: ['parname1', 'parname2'],
}).set_index(PARAMETER_ID)
with tempfile.NamedTemporaryFile(mode='w', delete=True) as fh:
file_name = fh.name
petab.write_parameter_df(parameter_df, file_name)
re_df = petab.get_parameter_df(file_name)
assert (parameter_df == re_df).all().all()
def test_write_parameter_df():
"""Test parameters.write_parameter_df."""
parameter_df = pd.DataFrame(data={
PARAMETER_ID: ['par1', 'par2'],
# Test utf8 characters
PARAMETER_NAME: ['ɑ', 'β'],
}).set_index(PARAMETER_ID)
with tempfile.TemporaryDirectory() as temp_dir:
file_name = Path(temp_dir) / "parameters.tsv"
petab.write_parameter_df(parameter_df, file_name)
re_df = petab.get_parameter_df(file_name)
assert (parameter_df == re_df).all().all()
def create_test_data(measurement_file_name, parameter_file_name, yaml_config,
yaml_file_name_test, model_output_dir, model_name,
hdf5_file_name):
"""Create some synthetic data to emulate a test set"""
test_measurement_file_name = \
"-testset".join(os.path.splitext(measurement_file_name))
test_parameter_file_name = \
"-testset".join(os.path.splitext(parameter_file_name))
# measurements
df = petab.get_measurement_df(measurement_file_name)
df.loc[df.observableParameters == 'scaling_x1_common', 'measurement'] = \
df.loc[df.observableParameters == 'scaling_x1_common', 'measurement'] \
* 2.0
df.loc[~df.observableParameters.isnull(), 'observableParameters'] = \
df.loc[~df.observableParameters.isnull(), 'observableParameters'] \
+ "_test"
petab.write_parameter_df(df, test_measurement_file_name)
# parameters
df = petab.get_parameter_df(parameter_file_name)
df.rename(index={
'scaling_x1_common': 'scaling_x1_common_test',
'offset_x2_batch_0': 'offset_x2_batch_0_test',
'offset_x2_batch_1': 'offset_x2_batch_1_test'
},
inplace=True)
petab.write_parameter_df(df, test_parameter_file_name)
# yaml
yaml_config[ptc.PARAMETER_FILE] = test_parameter_file_name
yaml_config[ptc.PROBLEMS][0][ptc.MEASUREMENT_FILES][0] = \
test_measurement_file_name
with open(yaml_file_name_test, 'w') as outfile:
yaml.dump(yaml_config, outfile, default_flow_style=False)
generate_hdf5_file(yaml_file=yaml_file_name_test,
model_output_dir=model_output_dir,
hdf5_file_name="-testset".join(
os.path.splitext(hdf5_file_name)),
model_name=model_name)
def write_problem(
test_id: int,
parameter_df: pd.DataFrame,
condition_dfs: Union[List[pd.DataFrame], pd.DataFrame],
observable_dfs: Union[List[pd.DataFrame], pd.DataFrame],
measurement_dfs: Union[List[pd.DataFrame], pd.DataFrame],
sbml_files: Union[List[str], str] = None,
) -> None:
"""Write problem to files.
Parameters
----------
test_id: Identifier of the test.
parameter_df: PEtab parameter table.
condition_dfs: PEtab condition tables.
observable_dfs: PEtab observable tables.
measurement_dfs: PEtab measurement tables.
sbml_files: PEtab SBML files. If None, then the default
petabtests.DEFAULT_MODEL_FILE is used.
"""
print(f"Writing case {test_id}...")
# convenience
if isinstance(condition_dfs, pd.DataFrame):
condition_dfs = [condition_dfs]
if isinstance(observable_dfs, pd.DataFrame):
observable_dfs = [observable_dfs]
if isinstance(measurement_dfs, pd.DataFrame):
measurement_dfs = [measurement_dfs]
if isinstance(sbml_files, str):
sbml_files = [sbml_files]
# id to string
id_str = test_id_str(test_id)
dir_ = os.path.join(CASES_DIR, id_str)
# petab yaml
config = {
FORMAT_VERSION:
petab.__format_version__,
PROBLEMS: [
{
SBML_FILES: [],
CONDITION_FILES: [],
MEASUREMENT_FILES: [],
OBSERVABLE_FILES: [],
},
]
}
# copy models
if sbml_files is None:
sbml_files = [DEFAULT_MODEL_FILE]
copied_sbml_files = []
for i_sbml, sbml_file in enumerate(sbml_files):
if len(sbml_files) == 1:
copied_sbml_file = '_model.xml'
else:
copied_sbml_file = f'_model{i_sbml}.xml'
copyfile(os.path.join(dir_, sbml_file),
os.path.join(dir_, copied_sbml_file))
copied_sbml_files.append(copied_sbml_file)
config[PROBLEMS][0][SBML_FILES] = copied_sbml_files
# write parameters
parameters_file = '_parameters.tsv'
petab.write_parameter_df(parameter_df, os.path.join(dir_, parameters_file))
config[PARAMETER_FILE] = parameters_file
# write conditions
_write_dfs_to_files(id_str, 'conditions', petab.write_condition_df,
condition_dfs, config[PROBLEMS][0][CONDITION_FILES])
# write observables
_write_dfs_to_files(id_str, 'observables', petab.write_observable_df,
observable_dfs, config[PROBLEMS][0][OBSERVABLE_FILES])
# write measurements
_write_dfs_to_files(id_str, 'measurements', petab.write_measurement_df,
measurement_dfs,
config[PROBLEMS][0][MEASUREMENT_FILES])
# validate petab yaml
petab.validate(config, path_prefix=dir_)
# write yaml
yaml_file = problem_yaml_name(test_id)
with open(os.path.join(dir_, yaml_file), 'w') as outfile:
yaml.dump(config, outfile, default_flow_style=False)
# validate written PEtab files
problem = petab.Problem.from_yaml(os.path.join(dir_, yaml_file))
petab.lint_problem(problem)
def test_combine_archive(minimal_sbml_model):
"""Test `create_combine_archive` and `Problem.from_combine`"""
# Create test files
document, _ = minimal_sbml_model
# Create tables with arbitrary content
measurement_df = pd.DataFrame(
data={
OBSERVABLE_ID: ['obs1', 'obs2'],
OBSERVABLE_PARAMETERS: ['', 'p1;p2'],
NOISE_PARAMETERS: ['p3;p4', 'p5']
})
condition_df = pd.DataFrame(
data={
CONDITION_ID: ['condition1', 'condition2'],
CONDITION_NAME: ['', 'Condition 2'],
'fixedParameter1': [1.0, 2.0]
})
condition_df.set_index(CONDITION_ID, inplace=True)
parameter_df = pd.DataFrame(
data={
PARAMETER_ID: ['dynamicParameter1', 'dynamicParameter2'],
PARAMETER_NAME: ['', '...'],
})
parameter_df.set_index(PARAMETER_ID, inplace=True)
observable_df = pd.DataFrame(
data={
OBSERVABLE_ID: ['observable_1'],
OBSERVABLE_FORMULA: ['observable_1'],
NOISE_FORMULA: [1],
})
observable_df.set_index(OBSERVABLE_ID, inplace=True)
sbml_file_name = 'model.xml'
measurement_file_name = 'measurements.tsv'
condition_file_name = 'conditions.tsv'
parameter_file_name = 'parameters.tsv'
observable_file_name = 'observables.tsv'
yaml_file_name = 'test.yaml'
yaml_config = {
FORMAT_VERSION:
petab.__format_version__,
PARAMETER_FILE:
parameter_file_name,
PROBLEMS: [{
SBML_FILES: [sbml_file_name],
MEASUREMENT_FILES: [measurement_file_name],
CONDITION_FILES: [condition_file_name],
OBSERVABLE_FILES: [observable_file_name]
}]
}
with tempfile.TemporaryDirectory(prefix='petab_test_combine_archive') \
as tempdir:
# Write test data
petab.write_sbml(document, os.path.join(tempdir, sbml_file_name))
petab.write_measurement_df(
measurement_df, os.path.join(tempdir, measurement_file_name))
petab.write_parameter_df(parameter_df,
os.path.join(tempdir, parameter_file_name))
petab.write_observable_df(observable_df,
os.path.join(tempdir, observable_file_name))
petab.write_condition_df(condition_df,
os.path.join(tempdir, condition_file_name))
petab.write_yaml(yaml_config, os.path.join(tempdir, yaml_file_name))
archive_file_name = os.path.join(tempdir, 'test.omex')
# Create COMBINE archive
petab.create_combine_archive(os.path.join(tempdir, yaml_file_name),
archive_file_name,
family_name="Tester")
# Read COMBINE archive
problem = petab.Problem.from_combine(archive_file_name)
assert problem.parameter_df is not None
assert problem.condition_df is not None
assert problem.measurement_df is not None
assert problem.observable_df is not None
PARAMETER_NAME: parameter_dict0['name'],
PARAMETER_SCALE: LIN,
NOMINAL_VALUE: 1,
ESTIMATE: 0,
}
else:
raise NotImplementedError(parameter_dict0['id'])
parameter_dicts.append(parameter_dict)
## Noise
parameter_dicts.append({
PARAMETER_ID: noise,
PARAMETER_NAME: noise,
PARAMETER_SCALE: LOG10,
LOWER_BOUND: '1e-12',
UPPER_BOUND: '1e3',
NOMINAL_VALUE: 0.1,
ESTIMATE: 1,
})
condition_df = petab.get_condition_df(
pd.DataFrame({CONDITION_ID: [condition_id]}))
observable_df = petab.get_observable_df(pd.DataFrame(observable_dicts))
measurement_df = petab.get_measurement_df(pd.DataFrame(measurement_dicts))
parameter_df = petab.get_parameter_df(pd.DataFrame(parameter_dicts))
petab.write_condition_df(condition_df, 'output/petab/conditions.tsv')
petab.write_observable_df(observable_df, 'output/petab/observables.tsv')
petab.write_measurement_df(measurement_df, 'output/petab/measurements.tsv')
petab.write_parameter_df(parameter_df, 'output/petab/parameters.tsv')
shutil.copy('input/petab_problem.yaml', 'output/petab/petab_problem.yaml')
def write_problem(test_id: int,
parameter_df: pd.DataFrame,
condition_dfs: Union[List[pd.DataFrame], pd.DataFrame],
observable_dfs: Union[List[pd.DataFrame], pd.DataFrame],
measurement_dfs: Union[List[pd.DataFrame], pd.DataFrame],
model_files: Union[List[str], str],
format_: str = 'sbml') -> None:
"""Write problem to files.
Parameters
----------
test_id: Identifier of the test.
parameter_df: PEtab parameter table.
condition_dfs: PEtab condition tables.
observable_dfs: PEtab observable tables.
measurement_dfs: PEtab measurement tables.
model_files: PEtab SBML/PySB files.
format: Model format (SBML/PySB)
"""
print(f"Writing case {test_id} {format_} ...")
# convenience
if isinstance(condition_dfs, pd.DataFrame):
condition_dfs = [condition_dfs]
if isinstance(observable_dfs, pd.DataFrame):
observable_dfs = [observable_dfs]
if isinstance(measurement_dfs, pd.DataFrame):
measurement_dfs = [measurement_dfs]
if isinstance(model_files, str):
model_files = [model_files]
# id to string
dir_ = case_dir(test_id, format_)
# petab yaml
config = {
FORMAT_VERSION:
petab.__format_version__,
PROBLEMS: [
{
SBML_FILES: [],
CONDITION_FILES: [],
MEASUREMENT_FILES: [],
OBSERVABLE_FILES: [],
},
]
}
if format_ == 'sbml':
suffix = '.xml'
else:
suffix = '.py'
# copy models
copied_model_files = []
for i_sbml, model_file in enumerate(model_files):
if len(model_files) == 1:
copied_model_file = f'_model{suffix}'
else:
copied_model_file = f'_model{i_sbml}{suffix}'
copyfile(os.path.join(dir_, model_file),
os.path.join(dir_, copied_model_file))
copied_model_files.append(copied_model_file)
config[PROBLEMS][0][SBML_FILES] = copied_model_files
# write parameters
parameters_file = '_parameters.tsv'
petab.write_parameter_df(parameter_df, os.path.join(dir_, parameters_file))
config[PARAMETER_FILE] = parameters_file
# write conditions
_write_dfs_to_files(dir_, 'conditions', petab.write_condition_df,
condition_dfs, config[PROBLEMS][0][CONDITION_FILES])
# write observables
_write_dfs_to_files(dir_, 'observables', petab.write_observable_df,
observable_dfs, config[PROBLEMS][0][OBSERVABLE_FILES])
# write measurements
_write_dfs_to_files(dir_, 'measurements', petab.write_measurement_df,
measurement_dfs,
config[PROBLEMS][0][MEASUREMENT_FILES])
# validate petab yaml
petab.validate(config, path_prefix=dir_)
# write yaml
yaml_file = problem_yaml_name(test_id)
with open(os.path.join(dir_, yaml_file), 'w') as outfile:
yaml.dump(config, outfile, default_flow_style=False)
# validate written PEtab files
problem = petab.Problem.from_yaml(os.path.join(dir_, yaml_file))
petab.lint_problem(problem)
}).set_index([OBSERVABLE_ID])
parameter_df = pd.DataFrame(
data={
PARAMETER_ID: ['k1', 'k2'],
PARAMETER_SCALE: [LOG] * 2,
LOWER_BOUND: [1e-5] * 2,
UPPER_BOUND: [1e5] * 2,
NOMINAL_VALUE: [k1, k2],
ESTIMATE: [1, 1],
}).set_index(PARAMETER_ID)
petab.write_condition_df(condition_df, "conditions.tsv")
petab.write_measurement_df(measurement_df, "measurements.tsv")
petab.write_observable_df(observable_df, "observables.tsv")
petab.write_parameter_df(parameter_df, "parameters.tsv")
yaml_config = {
FORMAT_VERSION:
1,
PARAMETER_FILE:
"parameters.tsv",
PROBLEMS: [{
SBML_FILES: ["model_conversion_reaction.xml"],
CONDITION_FILES: ["conditions.tsv"],
MEASUREMENT_FILES: ["measurements.tsv"],
OBSERVABLE_FILES: ["observables.tsv"]
}]
}
petab.write_yaml(yaml_config, "conversion_reaction.yaml")