diff --git a/biosimulators_utils/sedml/utils.py b/biosimulators_utils/sedml/utils.py index df22e7dc..7703f77c 100644 --- a/biosimulators_utils/sedml/utils.py +++ b/biosimulators_utils/sedml/utils.py @@ -559,7 +559,9 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non attribute.set("size", change.new_value) elif type_suffix == "parameter" and attribute.get("value") is not None: attribute.set("value", change.new_value) - elif (type_suffix == "reaction" and second_type_suffix == "parameter" + elif (type_suffix == "reaction" and + (second_type_suffix == "parameter" # SBML L1, L2 + or second_type_suffix == "localParameter") # SBML L3+ and attribute.get("value") is not None): # Reaction parameter change attribute.set("value", change.new_value) else: diff --git a/tests/fixtures/sbml-list-of-species.xml b/tests/fixtures/sbml-list-of-species-lvl-2.xml similarity index 57% rename from tests/fixtures/sbml-list-of-species.xml rename to tests/fixtures/sbml-list-of-species-lvl-2.xml index 03471f8f..ea467476 100644 --- a/tests/fixtures/sbml-list-of-species.xml +++ b/tests/fixtures/sbml-list-of-species-lvl-2.xml @@ -18,5 +18,27 @@ + + + + + + + + + + + + + k1 + Trim + + + + + + + + diff --git a/tests/fixtures/sbml-list-of-species-lvl-3.xml b/tests/fixtures/sbml-list-of-species-lvl-3.xml new file mode 100644 index 00000000..fb1b81ac --- /dev/null +++ b/tests/fixtures/sbml-list-of-species-lvl-3.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + Trim + + + + + + + + + + diff --git a/tests/model_lang/sbml/test_sbml_validation.py b/tests/model_lang/sbml/test_sbml_validation.py index 6016f0ea..8b505ca9 100644 --- a/tests/model_lang/sbml/test_sbml_validation.py +++ b/tests/model_lang/sbml/test_sbml_validation.py @@ -8,7 +8,7 @@ class ValidationTestCase(unittest.TestCase): FIXTURE_DIR = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures') def test(self): - errors, warnings, _ = validate_model(os.path.join(self.FIXTURE_DIR, 'sbml-list-of-species.xml')) + errors, warnings, _ = validate_model(os.path.join(self.FIXTURE_DIR, 'sbml-list-of-species-lvl-2.xml')) self.assertEqual(errors, []) self.assertEqual(warnings, []) diff --git a/tests/sedml/test_sedml_utils.py b/tests/sedml/test_sedml_utils.py index c616625d..3413cf6e 100644 --- a/tests/sedml/test_sedml_utils.py +++ b/tests/sedml/test_sedml_utils.py @@ -231,7 +231,8 @@ def test_get_variables_for_task(self): class ApplyModelChangesTestCase(unittest.TestCase): - FIXTURE_FILENAME = os.path.join(os.path.dirname(__file__), '../fixtures/sbml-list-of-species.xml') + FIXTURE_FILENAME = os.path.join(os.path.dirname(__file__), '../fixtures/sbml-list-of-species-lvl-2.xml') + FIXTURE_FILENAME_2 = os.path.join(os.path.dirname(__file__), '../fixtures/sbml-list-of-species-lvl-3.xml') def setUp(self): self.tmp_dir = tempfile.mkdtemp() @@ -668,7 +669,7 @@ def test_errors(self): 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') - self._attempt_change(change, self.FIXTURE_FILENAME, NotImplementedError) + self._attempt_change(change, self.FIXTURE_FILENAME, ValueError) change = data_model.ModelAttributeChange( target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:spesies[@id='Trim']", @@ -746,6 +747,21 @@ def test_errors(self): new_value='1.9') self._attempt_change(change, self.FIXTURE_FILENAME) + change = data_model.ModelAttributeChange( + target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='lumen']/sbml:kineticLaw" + "/sbml:listOfParameters/sbml:parameter[@id='k1']", + target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'}, + new_value='1.9') + self._attempt_change(change, self.FIXTURE_FILENAME) + + change = data_model.ModelAttributeChange( + target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='lumen']/sbml:kineticLaw" + "/sbml:listOfLocalParameters/sbml:localParameter[@id='k1']/@value", + target_namespaces={'sbml': 'http://www.sbml.org/sbml/level3/version1'}, + new_value='1.9') + self._attempt_change(change, self.FIXTURE_FILENAME_2) + + def _attempt_change(self, change: data_model.ModelChange, sbml_path: str, expected_exception: "type[BaseException] | tuple[type[BaseException], ...]" = None): et = etree.parse(sbml_path) diff --git a/tests/sedml/test_sedml_validation.py b/tests/sedml/test_sedml_validation.py index 3ef4c4b1..bc7eb9a9 100644 --- a/tests/sedml/test_sedml_validation.py +++ b/tests/sedml/test_sedml_validation.py @@ -828,7 +828,7 @@ def _validate_task(self, task, variables): return (errors, warnings) def test_validate_model_source_with_abs_path(self): - filename = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species.xml')) + filename = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species-lvl-2.xml')) errors, warnings = validation.validate_model_source(data_model.Model( source=filename, language=data_model.ModelLanguage.SBML), [], None, validate_models_with_languages=False) self.assertEqual(errors, []) @@ -851,7 +851,7 @@ def test_validate_model_source_with_url(self): def test_validate_model_with_language(self): # SBML - filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species.xml') + filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species-lvl-2.xml') validation.validate_model_with_language(filename, data_model.ModelLanguage.SBML) errors, warnings, _ = validation.validate_model_with_language(filename, '--not-supported--')