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COPASI / data /tests /ModelLoading.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.
// BEGIN: Copyright
// END: Copyright
// BEGIN: License
// Licensed under the Artistic License 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
// https://opensource.org/licenses/Artistic-2.0
// END: License
#include "catch.hpp"
#include <limits>
#include <copasi/core/CRootContainer.h>
#include <copasi/CopasiDataModel/CDataModel.h>
#include <copasi/utilities/CDirEntry.h>
#include <copasi/CopasiTypes.h>
extern std::string getTestFile(const std::string & fileName);
TEST_CASE("Load model", "[COPASI]")
{
CDataModel * pDataModel = CRootContainer::addDatamodel();
REQUIRE(pDataModel != nullptr);
// Loading from file
REQUIRE(pDataModel->loadFromFile(getTestFile("test-data/brusselator.gps")) == true);
REQUIRE(pDataModel->loadFromFile(getTestFile("test-data/brusselator.cps")) == true);
REQUIRE(pDataModel->loadFromFile(getTestFile("test-data/brusselator.xml")) == true);
REQUIRE(pDataModel->loadFromFile(getTestFile("test-data/brusselator.sedml")) == true);
REQUIRE(pDataModel->loadFromFile(getTestFile("test-data/brusselator.omex")) == true);
std::stringstream FileContent;
{
FileContent.str("");
std::ifstream File(getTestFile("test-data/brusselator.gps"));
FileContent << File.rdbuf();
}
REQUIRE(pDataModel->loadFromString(FileContent.str()) == true);
{
FileContent.str("");
std::ifstream File(getTestFile("test-data/brusselator.cps"));
FileContent << File.rdbuf();
}
REQUIRE(pDataModel->loadFromString(FileContent.str(), CDirEntry::dirName(getTestFile("test-data/brusselator.cps"))) == true);
{
FileContent.str("");
std::ifstream File(getTestFile("test-data/brusselator.xml"));
FileContent << File.rdbuf();
}
REQUIRE(pDataModel->loadFromString(FileContent.str()) == true);
{
FileContent.str("");
std::ifstream File(getTestFile("test-data/brusselator.sedml"));
FileContent << File.rdbuf();
}
REQUIRE(pDataModel->loadFromString(FileContent.str(), CDirEntry::dirName(getTestFile("test-data/brusselator.sedml"))) == true);
{
FileContent.str("");
std::ifstream File(getTestFile("test-data/brusselator.omex"));
FileContent << File.rdbuf();
}
#ifndef WIN32
// this test fails on Windows as the archive created is invalid
// so skipping this test there for now
REQUIRE(pDataModel->loadFromString(FileContent.str()) == true);
#endif
CRootContainer::removeDatamodel(pDataModel);
}
TEST_CASE("Update Model", "[COPASI]")
{
CDataModel * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
std::string test_file = getTestFile("test-data/Issue3050.cps");
REQUIRE(dm->loadModel(test_file, NULL) == true);
auto * model = dm->getModel();
model->applyInitialValues();
auto& x = model->getModelValues()["x"];
auto & y = model->getModelValues()["y"];
REQUIRE(x.getInitialValue() == 1);
REQUIRE(y.getInitialValue() == 1);
auto & optimization = (*dm->getTaskList())["Optimization"];
REQUIRE(optimization.isUpdateModel());
// executing the optimization task should set x and y to the specified values
auto * optProblem = dynamic_cast< COptProblem * >(optimization.getProblem());
REQUIRE(optProblem->getOptItem(0).getStartValue() == 2);
REQUIRE(optProblem->getOptItem(1).getStartValue() == 2);
optimization.initialize(CCopasiTask::OUTPUT_SE, NULL, NULL);
optimization.process(true);
optimization.restore();
REQUIRE(x.getInitialValue() == 2);
REQUIRE(y.getInitialValue() == 2);
// reset the values again
x.setInitialValue(1);
y.setInitialValue(1);
model->updateInitialValues(CCore::Framework::Concentration, false);
model->applyInitialValues();
REQUIRE(x.getInitialValue() == 1);
REQUIRE(y.getInitialValue() == 1);
auto & scan = (*dm->getTaskList())["Scan"];
REQUIRE(scan.isUpdateModel());
scan.initialize(CCopasiTask::OUTPUT_SE, NULL, NULL);
scan.process(true);
scan.restore();
// now this should also be 2
REQUIRE(x.getInitialValue() == 2);
REQUIRE(y.getInitialValue() == 2);
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("Species ODE expressions", "[COPASI][multiple_models]")
{
CDataModel * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
std::string test_file = getTestFile("test-data/Issue3221.cps");
REQUIRE(dm->loadModel(test_file, NULL) == true);
CDataModel * dm2 = CRootContainer::addDatamodel();
dm2->newModel(NULL, true);
dm2->getModel()->setObjectName("empty");
auto * model = dm->getModel();
model->applyInitialValues();
auto & species = model->getCompartments()["compartment"].getMetabolites()["c"];
std::string expression = species.getExpression();
REQUIRE(expression.find("Model=New Model") != std::string::npos);
CRootContainer::removeDatamodel(dm);
CRootContainer::removeDatamodel(dm2);
}