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Adding more implicit ModelAttributeChange options (with more tests)
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@CodeByDrescher
CodeByDrescher committed Oct 4, 2024
1 parent a323d5e commit 7479d6a
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Showing 2 changed files with 45 additions and 16 deletions.
42 changes: 28 additions & 14 deletions biosimulators_utils/sedml/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -541,29 +541,38 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
xml_target_captures = regex.split(r"[\@|=]", xpath_captures[1])
xml_target_captures[2] = xml_target_captures[2][1:-1]
_, target_type, target_value = tuple(xml_target_captures)
xml_model_attribute = eval_xpath(model_etree, change.target, change.target_namespaces)
if validate_unique_xml_targets and len(xml_model_attribute) != 1:
xml_model_element = eval_xpath(model_etree, change.target, change.target_namespaces)
if validate_unique_xml_targets and len(xml_model_element) != 1:
raise ValueError(f'xpath {change.target} must match a single object')
xpath_tiers = [elem for elem in regex.split("/", xpath_captures[0]) if ":" in elem]
if len(xpath_tiers) == 0:
raise ValueError('No namespace is defined')
existing_namespace = regex.split(":", xpath_tiers[0])[0]
if change.target_namespaces.get(existing_namespace) is None:
raise ValueError(f'No namespace is defined with prefix `{existing_namespace}`')
element_type = regex.split(":", xpath_tiers[-1])
if len(element_type) != 2:
raise ValueError("Unexpected number of tokens in model element xpath")

namespace_prefix, type_suffix = tuple(element_type)
if change.target_namespaces.get(namespace_prefix) is None:
raise ValueError(f'No namespace is defined with prefix `{namespace_prefix}`')
# change value
for attribute in xml_model_attribute:
if attribute.get("initialConcentration") is not None:
for attribute in xml_model_element:
if type_suffix == "species" and attribute.get("initialConcentration") is not None:
attribute.set("initialConcentration", change.new_value)
elif type_suffix == "compartment" and attribute.get("size") is not None:
attribute.set("size", change.new_value)
elif type_suffix == "parameter" and attribute.get("value") is not None:
attribute.set("value", change.new_value)
else:
raise ValueError(f"SBML attribute to apply `{change.new_value}` to can not be figured out.")
change.model = model
non_xml_changes.append(change)
continue

elif isinstance(change, ComputeModelChange):
# get the values of model variables referenced by compute model changes
if variable_values is None:
model_etrees = {model.id: model_etree}
iter_variable_values = get_values_of_variable_model_xml_targets_of_model_change(change, sed_doc,
model_etrees,
working_dir)
iter_variable_values = \
get_values_of_variable_model_xml_targets_of_model_change(change, sed_doc, model_etrees, working_dir)
else:
iter_variable_values = variable_values

Expand Down Expand Up @@ -612,10 +621,15 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
# Second pass: changes that need to be interpreter-based:
for change in non_xml_changes:
if isinstance(change, ModelAttributeChange):

if not set_value_executer:
raise NotImplementedError(
'target ' + change.target + ' cannot be changed by XML manipulation, as the target '
'is not an attribute of a model element')
xpath_captures = regex.split(r"[\[|\]]", change.target)
if len(xpath_captures) != 3 or "@" not in xpath_captures[1] or xpath_captures[2] != "":
raise NotImplementedError(
'target ' + change.target + ' cannot be changed by XML manipulation, as the target '
'is not an attribute of a model element')
else:
raise ValueError(f"SBML attribute to apply `{change.new_value}` to can not be figured out.")
else:
set_value_executer(change.model, change.target, None, change.new_value, preprocessed_task)

Expand Down
19 changes: 17 additions & 2 deletions tests/sedml/test_sedml_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -681,11 +681,19 @@ def test_errors(self):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)

change = data_model.ModelAttributeChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']",
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:spesies[@id='Trim']",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_value='1.9')
et = etree.parse(self.FIXTURE_FILENAME)
with self.assertRaises(NotImplementedError):
with self.assertRaises(ValueError):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)

change = data_model.ModelAttributeChange(
target="/sbml/model/listOfSpecies/spesies[@id='Trim']",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_value='1.9')
et = etree.parse(self.FIXTURE_FILENAME)
with self.assertRaises(ValueError):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)

change = data_model.ModelAttributeChange(
Expand Down Expand Up @@ -740,6 +748,13 @@ def test_errors(self):
with self.assertRaisesRegex(ValueError, 'must match a single object'):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)

change = data_model.ModelAttributeChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_value='1.9')
et = etree.parse(self.FIXTURE_FILENAME)
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)

def test_apply_compute_model_change_new_value(self):
change = data_model.ComputeModelChange(
target="/model/parameter[@id='p1']/@value",
Expand Down

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