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Attempting to get rid of duplication
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@CodeByDrescher
CodeByDrescher committed Oct 4, 2024
1 parent 3071ead commit 0f5be30
Showing 1 changed file with 32 additions and 71 deletions.
103 changes: 32 additions & 71 deletions tests/sedml/test_sedml_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -456,34 +456,10 @@ def test_add_multiple_elements_to_single_target_with_different_namespace_prefix(

species = et.xpath("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species",
namespaces=get_namespaces_with_prefixes(namespaces))
num_species = len(species)
species_ids = set([s.get('id') for s in species])

# apply changes
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
num_species = len(species) + 2
species_ids = set([s.get('id') for s in species]) | {'NewSpecies1', 'NewSpecies2'}

# check changes applied
xpath_evaluator = etree.XPathEvaluator(et, namespaces=get_namespaces_with_prefixes(namespaces))
species = xpath_evaluator("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species")
self.assertEqual(len(species), num_species + 2)
self.assertEqual(set([s.get('id') for s in species]), species_ids | set(['NewSpecies1', 'NewSpecies2']))

# check that changes can be written/read from file
doc = data_model.SedDocument(
models=[
data_model.Model(
id='model',
language='language',
source='source',
changes=[change],
),
]
)

filename = os.path.join(self.tmp_dir, 'test.sedml')
io.SedmlSimulationWriter().run(doc, filename)
doc2 = io.SedmlSimulationReader().run(filename)
self.assertTrue(doc2.is_equal(doc))
self._apply_namespace_changes_and_evaluate_equality(change, et, num_species, namespaces, species_ids)

####################
# Incorrect namespace
Expand All @@ -508,6 +484,10 @@ def test_add_multiple_elements_to_single_target_with_different_namespace_prefix(
num_species = len(species)
species_ids = set([s.get('id') for s in species])

self._apply_namespace_changes_and_evaluate_equality(change, et, num_species, namespaces, species_ids)

def _apply_namespace_changes_and_evaluate_equality(self, change: data_model.ModelChange, et, num_species: int,
namespaces: dict, species_ids: "set[str]"):
# apply changes
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)

Expand Down Expand Up @@ -676,123 +656,104 @@ def test_errors(self):
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_value='1.9')
et = etree.parse(self.FIXTURE_FILENAME)
with self.assertRaises(NotImplementedError):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME, NotImplementedError)

change = data_model.ModelAttributeChange(
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(ValueError):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)

self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

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

change = data_model.ModelAttributeChange(
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(ValueError):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

change = data_model.ModelAttributeChange(
target="/:sbml/:model/:listOfSpecies/:species[@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(etree.XPathEvalError):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME, etree.XPathEvalError)

change = data_model.ModelAttributeChange(
target="/sbml/model/listOfSpecies/species[@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)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

change = data_model.ModelAttributeChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species/@initialConcentration",
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)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

namespaces = {'sbml': 'http://www.sbml.org/sbml/level2/version4'}
change = data_model.ModelAttributeChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@sbml2:initialConcentration",
target_namespaces=namespaces,
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)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

namespaces['sbml2'] = 'http://www.sbml.org/sbml/level2/version4'
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME)

change = data_model.AddElementModelChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_elements='<')
et = etree.parse(self.FIXTURE_FILENAME)
with self.assertRaisesRegex(ValueError, 'invalid XML'):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

change = data_model.AddElementModelChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_elements='1.9')
et = etree.parse(self.FIXTURE_FILENAME)
with self.assertRaisesRegex(ValueError, 'must match a single object'):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

change = data_model.ReplaceElementModelChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_elements='<')
et = etree.parse(self.FIXTURE_FILENAME)
with self.assertRaisesRegex(ValueError, 'invalid XML'):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

change = data_model.ReplaceElementModelChange(
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species",
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
new_elements='1.9')
et = etree.parse(self.FIXTURE_FILENAME)
with self.assertRaisesRegex(ValueError, 'must match a single object'):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)

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)
self._attempt_change(change, self.FIXTURE_FILENAME)

change = data_model.ModelAttributeChange(
target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']",
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)
self._attempt_change(change, self.FIXTURE_FILENAME)

change = data_model.ModelAttributeChange(
target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='parameter_1']",
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)
self._attempt_change(change, self.FIXTURE_FILENAME)

def _attempt_change(self, change: data_model.ModelChange, sbml_path: str,
expected_exception: "type[BaseException] | tuple[type[BaseException], ...]" = None):
et = etree.parse(sbml_path)
if expected_exception is not None:
with self.assertRaises(expected_exception):
utils.apply_changes_to_xml_model(data_model.Model(changes=[change]), et, None, None)
else:
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(
Expand Down

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