File size: 4,004 Bytes
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// University of Virginia, University of Heidelberg, and University
// of Connecticut School of Medicine.
// All rights reserved.
#include "catch.hpp"
extern std::string getTestFile(const std::string& fileName);
#include <copasi/CopasiTypes.h>
bool verify_cn(const CDataModel* dm, const std::string& cn)
{
auto* ref = dm->getObject({cn });
if (ref == NULL)
return false;
auto resolved = ref->getStringCN();
if (resolved.find("not found") != std::string::npos)
return false;
return true;
}
TEST_CASE("1: loading example files, and resolve CNs", "[copasi]")
{
auto* dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
SECTION("brusselator example")
{
REQUIRE(dm->loadModel(getTestFile("test-data/brusselator.cps"), NULL) == true);
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Reference=InitialVolume"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Reference=Rate"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Reference=Volume"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=InitialParticleNumber"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=ParticleNumber"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=ParticleNumberRate"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=Rate"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=Concentration"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=InitialConcentration"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Array=Stoichiometry(ann)[0][0]"));
REQUIRE(verify_cn(dm, "CN=Root,Model=The Brusselator,Array=Stoichiometry(ann)[X][(R1)]"));
REQUIRE(verify_cn(dm, "CN=Root,Vector=TaskList[Sensitivities],Problem=Sensitivities,Array=Sensitivities array[0][0]"));
REQUIRE(verify_cn(dm, "CN=Root,Vector=TaskList[Sensitivities],Problem=Sensitivities,Array=Sensitivities array[\\[X\\]][(R1).k1]"));
}
SECTION("simple_v3_event")
{
REQUIRE(dm->loadModel(getTestFile("test-data/simple_v3_event.cps"), NULL) == true);
REQUIRE(verify_cn(dm, "CN=Root,Model=New Model,Vector=Compartments[compartment],Reference=InitialVolume"));
REQUIRE(verify_cn(dm, "CN=Root,Vector=TaskList[Sensitivities],Problem=Sensitivities,Array=Sensitivities array[\\[C\\]][Values\\[X\\].InitialValue]"));
// switch the sensitivity setup
auto* task = dynamic_cast<CSensTask*>(&((*dm->getTaskList())["Sensitivities"]));
REQUIRE(task != nullptr);
auto* prob = dynamic_cast<CSensProblem*>(task->getProblem());
REQUIRE(prob != nullptr);
REQUIRE(prob->getNumberOfVariables() == 2);
prob->setTargetFunctions({CObjectLists::NON_CONST_METAB_NUMBERS });
prob->changeVariables(0, {CObjectLists::ALL_LOCAL_PARAMETER_VALUES });
prob->changeVariables(1, {CObjectLists::EMPTY_LIST });
task->updateMatrices();
auto* ref = dynamic_cast<const CArrayElementReference*>(dm->getObject(CCommonName("CN=Root,Vector=TaskList[Sensitivities],Problem=Sensitivities,Array=Sensitivities array[A.ParticleNumber][(reaction).k1]")));
auto* obj = (double*)ref->getValuePointer();
auto cn = ref->getCN();
REQUIRE(verify_cn(dm, "CN=Root,Vector=TaskList[Sensitivities],Problem=Sensitivities,Array=Sensitivities array[A.ParticleNumber][(reaction).k1]"));
auto registeredCN = cn;
registeredCN.sanitizeObjectNames();
REQUIRE(cn == registeredCN);
}
CRootContainer::removeDatamodel(dm);
}
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