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CodeByDrescherCodeByDrescher
committedOct 15, 2024·
Added tests and fixed incorrect exception type
1 parent 086c05b commit 7d0e85c

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6 files changed

+90
-6
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6 files changed

+90
-6
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‎biosimulators_utils/sedml/utils.py

+3-1
Original file line numberDiff line numberDiff line change
@@ -559,7 +559,9 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
559559
attribute.set("size", change.new_value)
560560
elif type_suffix == "parameter" and attribute.get("value") is not None:
561561
attribute.set("value", change.new_value)
562-
elif (type_suffix == "reaction" and second_type_suffix == "parameter"
562+
elif (type_suffix == "reaction" and
563+
(second_type_suffix == "parameter" # SBML L1, L2
564+
or second_type_suffix == "localParameter") # SBML L3+
563565
and attribute.get("value") is not None): # Reaction parameter change
564566
attribute.set("value", change.new_value)
565567
else:

‎tests/fixtures/sbml-list-of-species.xml ‎tests/fixtures/sbml-list-of-species-lvl-2.xml

+22
Original file line numberDiff line numberDiff line change
@@ -18,5 +18,27 @@
1818
<parameter constant="false" id="parameter_1" name="Fe2GutQUant" value="1E-7" units="second">
1919
</parameter>
2020
</listOfParameters>
21+
<listOfReactions>
22+
<reaction metaid="COPASI127" id="lumen" name="01. StomachLumen -&gt; IntestineLumen" reversible="false" fast="false">
23+
<listOfReactants>
24+
<speciesReference species="Trim" stoichiometry="1" constant="true"/>
25+
</listOfReactants>
26+
<listOfProducts>
27+
<speciesReference species="Clb" stoichiometry="1" constant="true"/>
28+
</listOfProducts>
29+
<kineticLaw>
30+
<math xmlns="http://www.w3.org/1998/Math/MathML">
31+
<apply>
32+
<times/>
33+
<ci> k1 </ci>
34+
<ci> Trim </ci>
35+
</apply>
36+
</math>
37+
<listOfParameters>
38+
<parameter id="k1" name="k1" value="350"/>
39+
</listOfParameters>
40+
</kineticLaw>
41+
</reaction>
42+
</listOfReactions>
2143
</model>
2244
</sbml>

‎tests/fixtures/sbml-list-of-species-lvl-3.xml

+44
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,44 @@
1+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
2+
<sbml xmlns="http://www.sbml.org/sbml/level3/version1" level="3" version="1">
3+
<model id="Ciliberto2003_Morphogenesis" name="Ciliberto2003_Morphogenesis_Checkpoint">
4+
<listOfCompartments>
5+
<compartment id="compartment" size="1"/>
6+
</listOfCompartments>
7+
<listOfSpecies>
8+
<species compartment="compartment" id="Trim" initialConcentration="0.1" name="CDC28_Clb2_Sic1_Complex" sboTerm="SBO:0000296">
9+
</species>
10+
<species compartment="compartment" id="Clb" initialConcentration="0.1" name="Clb2" sboTerm="SBO:0000245">
11+
</species>
12+
<species compartment="compartment" id="Sic" initialConcentration="0.1" name="Sic1" sboTerm="SBO:0000245">
13+
</species>
14+
<species compartment="compartment" id="SpeciesToReplace" initialConcentration="0.0035491784" name="Sic1" sboTerm="SBO:0000245">
15+
</species>
16+
</listOfSpecies>
17+
<listOfParameters>
18+
<parameter constant="false" id="parameter_1" name="Fe2GutQUant" value="1E-7" units="second">
19+
</parameter>
20+
</listOfParameters>
21+
<listOfReactions>
22+
<reaction metaid="COPASI127" id="lumen" name="01. StomachLumen -&gt; IntestineLumen" reversible="false" fast="false">
23+
<listOfReactants>
24+
<speciesReference species="Trim" stoichiometry="1" constant="true"/>
25+
</listOfReactants>
26+
<listOfProducts>
27+
<speciesReference species="Clb" stoichiometry="1" constant="true"/>
28+
</listOfProducts>
29+
<kineticLaw>
30+
<math xmlns="http://www.w3.org/1998/Math/MathML">
31+
<apply>
32+
<times/>
33+
<ci> k1 </ci>
34+
<ci> Trim </ci>
35+
</apply>
36+
</math>
37+
<listOfLocalParameters>
38+
<localParameter id="k1" name="k1" value="350"/>
39+
</listOfLocalParameters>
40+
</kineticLaw>
41+
</reaction>
42+
</listOfReactions>
43+
</model>
44+
</sbml>

‎tests/model_lang/sbml/test_sbml_validation.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ class ValidationTestCase(unittest.TestCase):
88
FIXTURE_DIR = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures')
99

1010
def test(self):
11-
errors, warnings, _ = validate_model(os.path.join(self.FIXTURE_DIR, 'sbml-list-of-species.xml'))
11+
errors, warnings, _ = validate_model(os.path.join(self.FIXTURE_DIR, 'sbml-list-of-species-lvl-2.xml'))
1212
self.assertEqual(errors, [])
1313
self.assertEqual(warnings, [])
1414

‎tests/sedml/test_sedml_utils.py

+18-2
Original file line numberDiff line numberDiff line change
@@ -231,7 +231,8 @@ def test_get_variables_for_task(self):
231231

232232

233233
class ApplyModelChangesTestCase(unittest.TestCase):
234-
FIXTURE_FILENAME = os.path.join(os.path.dirname(__file__), '../fixtures/sbml-list-of-species.xml')
234+
FIXTURE_FILENAME = os.path.join(os.path.dirname(__file__), '../fixtures/sbml-list-of-species-lvl-2.xml')
235+
FIXTURE_FILENAME_2 = os.path.join(os.path.dirname(__file__), '../fixtures/sbml-list-of-species-lvl-3.xml')
235236

236237
def setUp(self):
237238
self.tmp_dir = tempfile.mkdtemp()
@@ -668,7 +669,7 @@ def test_errors(self):
668669
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:spesies[@id='Trim']/initialConcentration",
669670
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
670671
new_value='1.9')
671-
self._attempt_change(change, self.FIXTURE_FILENAME, NotImplementedError)
672+
self._attempt_change(change, self.FIXTURE_FILENAME, ValueError)
672673

673674
change = data_model.ModelAttributeChange(
674675
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:spesies[@id='Trim']",
@@ -746,6 +747,21 @@ def test_errors(self):
746747
new_value='1.9')
747748
self._attempt_change(change, self.FIXTURE_FILENAME)
748749

750+
change = data_model.ModelAttributeChange(
751+
target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='lumen']/sbml:kineticLaw"
752+
"/sbml:listOfParameters/sbml:parameter[@id='k1']",
753+
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level2/version4'},
754+
new_value='1.9')
755+
self._attempt_change(change, self.FIXTURE_FILENAME)
756+
757+
change = data_model.ModelAttributeChange(
758+
target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='lumen']/sbml:kineticLaw"
759+
"/sbml:listOfLocalParameters/sbml:localParameter[@id='k1']/@value",
760+
target_namespaces={'sbml': 'http://www.sbml.org/sbml/level3/version1'},
761+
new_value='1.9')
762+
self._attempt_change(change, self.FIXTURE_FILENAME_2)
763+
764+
749765
def _attempt_change(self, change: data_model.ModelChange, sbml_path: str,
750766
expected_exception: "type[BaseException] | tuple[type[BaseException], ...]" = None):
751767
et = etree.parse(sbml_path)

‎tests/sedml/test_sedml_validation.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -828,7 +828,7 @@ def _validate_task(self, task, variables):
828828
return (errors, warnings)
829829

830830
def test_validate_model_source_with_abs_path(self):
831-
filename = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species.xml'))
831+
filename = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species-lvl-2.xml'))
832832
errors, warnings = validation.validate_model_source(data_model.Model(
833833
source=filename, language=data_model.ModelLanguage.SBML), [], None, validate_models_with_languages=False)
834834
self.assertEqual(errors, [])
@@ -851,7 +851,7 @@ def test_validate_model_source_with_url(self):
851851

852852
def test_validate_model_with_language(self):
853853
# SBML
854-
filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species.xml')
854+
filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'sbml-list-of-species-lvl-2.xml')
855855
validation.validate_model_with_language(filename, data_model.ModelLanguage.SBML)
856856

857857
errors, warnings, _ = validation.validate_model_with_language(filename, '--not-supported--')

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