Added tests and fixed incorrect exception type

biosimulators · Oct 15, 2024 · 7d0e85c · 7d0e85c
1 parent 086c05b
commit 7d0e85c
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Showing 6 changed files with 90 additions and 6 deletions.
diff --git 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 → ...s/fixtures/sbml-list-of-species-lvl-2.xml b/tests/fixtures/sbml-list-of-species.xml → ...s/fixtures/sbml-list-of-species-lvl-2.xml
@@ -18,5 +18,27 @@
       <parameter constant="false" id="parameter_1" name="Fe2GutQUant" value="1E-7" units="second">
       </parameter>
     </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="COPASI127" id="lumen" name="01. StomachLumen  -&gt; IntestineLumen" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="Trim" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="Clb" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k1 </ci>
+              <ci> Trim </ci>
+            </apply>
+          </math>
+          <listOfParameters>
+            <parameter id="k1" name="k1" value="350"/>
+          </listOfParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
   </model>
 </sbml>
diff --git a/tests/fixtures/sbml-list-of-species-lvl-3.xml b/tests/fixtures/sbml-list-of-species-lvl-3.xml
@@ -0,0 +1,44 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1" level="3" version="1">
+  <model id="Ciliberto2003_Morphogenesis" name="Ciliberto2003_Morphogenesis_Checkpoint">
+    <listOfCompartments>
+      <compartment id="compartment" size="1"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species compartment="compartment" id="Trim" initialConcentration="0.1" name="CDC28_Clb2_Sic1_Complex" sboTerm="SBO:0000296">
+      </species>
+      <species compartment="compartment" id="Clb" initialConcentration="0.1" name="Clb2" sboTerm="SBO:0000245">
+      </species>
+      <species compartment="compartment" id="Sic" initialConcentration="0.1" name="Sic1" sboTerm="SBO:0000245">
+      </species>
+      <species compartment="compartment" id="SpeciesToReplace" initialConcentration="0.0035491784" name="Sic1" sboTerm="SBO:0000245">
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="false" id="parameter_1" name="Fe2GutQUant" value="1E-7" units="second">
+      </parameter>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="COPASI127" id="lumen" name="01. StomachLumen  -&gt; IntestineLumen" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="Trim" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="Clb" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k1 </ci>
+              <ci> Trim </ci>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="k1" name="k1" value="350"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git 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
@@ -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
@@ -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--')