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COPASI / data /tests /test_CDataHandler.cpp
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// Copyright (C) 2021 - 2024 by Pedro Mendes, Rector and Visitors of the
// 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>
#include <copasi/report/CDataHandler.h>
#include <copasi/output/COutputHandler.h>
TEST_CASE("1: load model, simulate, collect data", "[copasi][datahandler]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
SECTION("brusselator example")
{
REQUIRE(dm->loadModel(getTestFile("test-data/brusselator.cps"), NULL) == true);
// change the initial time
dm->getModel()->setInitialTime(20);
dm->getModel()->updateInitialValues(dm->getModel()->getInitialValueReference(), false);
dm->getModel()->forceCompile(NULL);
dm->getModel()->applyInitialValues();
CCopasiMessage::clearDeque();
CDataHandler inv_handler;
inv_handler.addDuringName({"CN=Root,Model=The Brusselator", dm}); // this should not work and give a warning during compile, and stop it
REQUIRE(inv_handler.compile({dm}) == false);
auto text = CCopasiMessage::getAllMessageText();
REQUIRE(text.find("CN=Root,Model=The Brusselator") != std::string::npos);
CCopasiMessage::clearDeque();
CDataHandler handler;
handler.addDuringName({"CN=Root,Model=The Brusselator,Reference=Time", dm});
handler.addDuringName({"CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[X],Reference=Concentration", dm});
handler.addDuringName({"CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[Y],Reference=Concentration", dm});
handler.addDuringName({"CN=Root,Model=The Brusselator,Vector=Reactions[R1],Reference=Flux", dm});
handler.addDuringName({"CN=Root,Model=The Brusselator,Vector=Reactions[R2],Reference=Flux", dm});
handler.addDuringName({"CN=Root,Model=The Brusselator,Vector=Reactions[R3],Reference=Flux", dm});
handler.addDuringName({"CN=Root,Model=The Brusselator,Vector=Reactions[R4],Reference=Flux", dm});
// add test to verify that array element references can be correctly resolved
handler.addDuringName({"CN=Root,Vector=TaskList[Metabolic Control Analysis],Method=MCA Method (Reder),Array=Scaled elasticities[(R1)][X]", dm});
auto& task = dynamic_cast<CTrajectoryTask&>((*dm->getTaskList())["Time-Course"]);
REQUIRE(task.initialize(CCopasiTask::OUTPUT_DURING, &handler, NULL) == true);
REQUIRE(task.process(true) == true);
REQUIRE(task.restore());
auto & data = handler.getDuringData();
REQUIRE(data.size() > 0);
REQUIRE(data[0].size() == 8);
{
REQUIRE(task.initialize(CCopasiTask::ONLY_TIME_SERIES, dm, NULL) == true);
REQUIRE(task.process(true) == true);
REQUIRE(task.restore());
auto & ts = task.getTimeSeries();
REQUIRE(data.size() > 0);
REQUIRE(ts.getTitle(0) == "Time");
REQUIRE(ts.getData(0, 0) == data[0][0]);
}
}
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("ensure that data handler with function evaluations can be compiled", "[copasi][datahandler]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
REQUIRE(dm->loadModel(getTestFile("test-data/brusselator.cps"), NULL) == true);
CDataHandler handler;
handler.addDuringName({"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations", dm});
handler.addDuringName({"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value", dm});
REQUIRE(handler.compile({dm}) == true);
// lets try whether it works now
auto& task = (*dm->getTaskList())["Optimization"];
task.setMethodType(CTaskEnum::Method::LevenbergMarquardt);
auto * problem = dynamic_cast< COptProblem * >(task.getProblem());
{
auto & item = problem->addOptItem(
{"CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=InitialConcentration", dm});
item.setLowerBound(0.0001);
item.setUpperBound(100);
item.setStartValue(0.5);
}
{
auto & item = problem->addOptItem({"CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Vector=Metabolites[B],Reference=InitialConcentration", dm});
item.setLowerBound(0.0001);
item.setUpperBound(100);
item.setStartValue(3);
}
std::stringstream exp;
exp << "<"
<< (dm->getModel()->getMetabolites()[0]).getConcentrationRateReference()->getStringCN()
<< ">";
problem->setObjectiveFunction(exp.str());
problem->setRandomizeStartValues(false);
problem->setSubtaskType(CTaskEnum::Task::timeCourse);
REQUIRE(task.initialize(CCopasiTask::OUTPUT_DURING, &handler, NULL));
REQUIRE(task.process(true));
auto data = handler.getDuringData();
dm->saveModel("opt.cps", NULL, true);
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("Test resolving of reactions with )", "[copasi][datahandler]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
REQUIRE(dm->loadModel(getTestFile("test-data/brusselator.cps"), NULL) == true);
auto * model = dm->getModel();
auto* reaction = model->createReaction("Reaction with spaces and (steps)");
reaction->setReactionScheme("A -> D");
model->compileIfNecessary(NULL);
// try and retrieve the reaction by display name:
auto fluxName = reaction->getFluxReference()->getObjectDisplayName();
auto* obj = dm->findObjectByDisplayName(fluxName);
REQUIRE(obj != nullptr);
CRootContainer::removeDatamodel(dm);
}