Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix crash when infering units #284

Merged
merged 1 commit into from
Nov 30, 2022
Merged

Fix crash when infering units #284

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 26 additions & 0 deletions src/sbml/conversion/test/TestInferUnitsConverter.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -392,6 +392,31 @@ START_TEST (test_infer_localParam_fromReaction)
END_TEST


START_TEST (test_infer_reaction_with_4_params_func_call)
{
string filename(TestDataDirectory);
filename += "inferUnits-4.xml";

SBMLDocument* d = readSBMLFromFile(filename.c_str());

fail_unless(d != NULL);

SBMLInferUnitsConverter * units = new SBMLInferUnitsConverter();

units->setDocument(d);

fail_unless (units->convert() == LIBSBML_OPERATION_SUCCESS);

// TO DO infer units using the function formula
// fail_unless(d->getModel()->getParameter("k1")->isSetUnits() == true);
// fail_unless(d->getModel()->getParameter("k1")->getUnits() == "unitSid_0");

delete units;
delete d;
}
END_TEST


Suite *
create_suite_TestInferUnitsConverter (void)
{
Expand All @@ -409,6 +434,7 @@ create_suite_TestInferUnitsConverter (void)
tcase_add_test(tcase, test_infer_baseUnit_fromMath);
tcase_add_test(tcase, test_infer_fromReaction);
tcase_add_test(tcase, test_infer_localParam_fromReaction);
tcase_add_test(tcase, test_infer_reaction_with_4_params_func_call);

suite_add_tcase(suite, tcase);

Expand Down
82 changes: 82 additions & 0 deletions src/sbml/conversion/test/test-data/inferUnits-4.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,82 @@
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="ea71b239_15b6_4fa3_a76f_dd6c414eede6" version="4">
<model id="MODEL1212210000" metaid="f4425bc4_80db_4c1c_b889_aae600e0ce20" name="Smith2013 - Regulation of Insulin Signalling by Oxidative Stress">
<listOfFunctionDefinitions>
<functionDefinition id="function_1" metaid="_0b927bb6_7666_4bab_9a62_1bb488a2950b" name="Function for R1f_1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> InR </ci>
</bvar>
<bvar>
<ci> Ins </ci>
</bvar>
<bvar>
<ci> cellsurface </ci>
</bvar>
<bvar>
<ci> extracellular </ci>
</bvar>
<bvar>
<ci> k1 </ci>
</bvar>
<apply>
<times/>
<ci> k1 </ci>
<ci> Ins </ci>
<ci> extracellular </ci>
<ci> InR </ci>
<ci> cellsurface </ci>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
<compartment constant="true" id="extracellular" metaid="_33c764a6_3a3f_4ef0_8617_010e61aaadc6" name="extracellular" sboTerm="SBO:0000290" size="8.3E-12" spatialDimensions="3">
</compartment>
<compartment constant="true" id="cellsurface" metaid="_3998f93a_7adc_4437_90cb_86503740c79e" name="cellsurface" outside="extracellular" sboTerm="SBO:0000290" size="6.4E-14" spatialDimensions="3">
</compartment>
<compartment constant="true" id="cytoplasm" metaid="_546b89ee_5e8b_4791_875c_73de58897f5e" name="cytoplasm" outside="cellsurface" sboTerm="SBO:0000290" size="1.65E-11" spatialDimensions="3">
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="true" compartment="extracellular" constant="true" hasOnlySubstanceUnits="false" id="Ins" initialAmount="0" metaid="_820723ff_e05b_49d4_b9bd_b025befd02dc" name="Ins">
</species>
<species boundaryCondition="false" compartment="cellsurface" constant="false" hasOnlySubstanceUnits="false" id="InR" initialAmount="90000" metaid="d8602ba9_77a8_4307_ab2d_280bbcc14b67" name="InR">
</species>
<species boundaryCondition="false" compartment="cellsurface" constant="false" hasOnlySubstanceUnits="false" id="Ins_InR" initialAmount="0" metaid="_9672349d_f3af_4c17_8def_526d82171d04" name="Ins_InR">
</species>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="k1" metaid="_2ad1244a_ce86_42ed_9222_df283a1c56a5" name="k1" value="2E-5"/>
</listOfParameters>
<listOfReactions>
<reaction id="R1f" metaid="b644817b_aa91_4732_9b17_f83803035b63" name="R1f" reversible="false">
<listOfReactants>
<speciesReference metaid="_652747b2_354c_407c_9dee_9680991fa150" species="Ins" stoichiometry="1"/>
<speciesReference metaid="_725a5142_9442_4c37_908f_aeea73cdae7d" species="InR" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="cc7fe296_cb4a_401f_ac8c_64cedf7f36d2" species="Ins_InR" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="_0d4998c7_4bc9_4fa7_85b8_9fa7250d6151" species="InR"/>
<modifierSpeciesReference metaid="a8a2b586_05fe_478f_a9e7_66a5ff911afe" species="Ins"/>
</listOfModifiers>
<kineticLaw metaid="_1d9b134e_3620_4ad0_8872_400169c862ca">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> function_1 </ci>
<ci> InR </ci>
<ci> Ins </ci>
<ci> cellsurface </ci>
<ci> extracellular </ci>
<ci> k1 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
5 changes: 4 additions & 1 deletion src/sbml/units/UnitFormulaFormatter.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -377,7 +377,10 @@ UnitFormulaFormatter::getUnitDefinitionFromFunction(const ASTNode * node,

if(node->getType() == AST_FUNCTION)
{
const FunctionDefinition *fd =
// The function name get lost by ASTNode::reduceToBinary when it has more
// than one parameter. So we need to check we have a name before calling
// model->getFunctionDefinition to avoid crashing.
const FunctionDefinition *fd = node->getName() == NULL ? NULL :
avandecreme marked this conversation as resolved.
Show resolved Hide resolved
model->getFunctionDefinition(node->getName());
if (fd && fd->isSetMath())
{
Expand Down