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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>
#include <copasi/utilities/CCopasiException.h>
#include <sbml/SBMLTypes.h>
#include <sedml/SedTypes.h>
TEST_CASE("exporting sedml file with non-zero initial time", "[copasi][sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
dm->newModel(NULL, true);
auto * model = dm->getModel();
auto * r = model->createReaction("R1");
r->setReactionScheme("A -> B");
model->setInitialTime(10.0);
model->updateInitialValues(model->getInitialValueReference(), false);
auto & task = dynamic_cast<CTrajectoryTask&>((*dm->getTaskList())["Time-Course"]);
task.setScheduled(true);
auto * problem = dynamic_cast< CTrajectoryProblem * >(task.getProblem());
REQUIRE(problem != nullptr);
problem->setDuration(10);
problem->setStepNumber(100);
std::string sedml = dm->exportSEDMLToString(NULL, 1, 4);
REQUIRE(sedml.find("<uniformTimeCourse id=\"sim1\" initialTime=\"10") != std::string::npos);
// now lets try and read it back in ensuring that the initial time is being set.
model->setInitialTime(0.0);
model->updateInitialValues(model->getInitialValueReference(), false);
// also reset the task values, to see that hey are updated correctly
problem->setDuration(1);
problem->setStepNumber(10);
auto * doc = readSedMLFromString(sedml.c_str());
REQUIRE(doc->getNumErrors(LIBSEDML_SEV_ERROR) == 0);
auto * sim = dynamic_cast<SedUniformTimeCourse*>(doc->getSimulation(0));
REQUIRE(sim != nullptr);
SEDMLImporter imp;
imp.setDataModel(dm);
imp.initializeContent();
imp.setSEDMLDocument(doc);
imp.setCopasiModel(model);
imp.updateCopasiTaskForSimulation(sim, dm->getTaskList());
REQUIRE(problem->getDuration() == 10);
REQUIRE(problem->getStepNumber() == 100);
delete doc;
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("exporting sedml file with non-zero start time", "[copasi][sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
dm->newModel(NULL, true);
auto * model = dm->getModel();
auto * r = model->createReaction("R1");
r->setReactionScheme("A -> B");
auto & task = dynamic_cast< CTrajectoryTask & >((*dm->getTaskList())["Time-Course"]);
task.setScheduled(true);
auto * problem = dynamic_cast< CTrajectoryProblem * >(task.getProblem());
REQUIRE(problem != nullptr);
problem->setOutputStartTime(5);
problem->setDuration(10);
problem->setStepNumber(40);
std::string sedml = dm->exportSEDMLToString(NULL, 1, 4);
// also reset the task values, to see that hey are updated correctly
problem->setDuration(1);
problem->setStepNumber(10);
auto * doc = readSedMLFromString(sedml.c_str());
REQUIRE(doc->getNumErrors(LIBSEDML_SEV_ERROR) == 0);
auto * sim = dynamic_cast< SedUniformTimeCourse * >(doc->getSimulation(0));
REQUIRE(sim != nullptr);
REQUIRE(sim->getInitialTime() == 0);
REQUIRE(sim->getOutputStartTime() == 5);
REQUIRE(sim->getOutputEndTime() == 10);
REQUIRE(sim->getNumberOfPoints() == 20);
SEDMLImporter imp;
imp.setDataModel(dm);
imp.initializeContent();
imp.setSEDMLDocument(doc);
imp.setCopasiModel(model);
imp.updateCopasiTaskForSimulation(sim, dm->getTaskList());
REQUIRE(problem->getOutputStartTime() == 5);
REQUIRE(problem->getDuration() == 10);
REQUIRE(problem->getStepNumber() == 40);
delete doc;
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("convert sedml types and colors", "[copasi][sedml]")
{
REQUIRE(SEDMLUtils::argbToRgba("112233") == "#112233");
REQUIRE(SEDMLUtils::argbToRgba("#F0C800") == "#F0C800");
REQUIRE(SEDMLUtils::argbToRgba("#FFF0C800") == "#F0C800FF");
REQUIRE(SEDMLUtils::argbToRgba("FFF0C800") == "#F0C800FF");
REQUIRE(SEDMLUtils::argbToRgba("FFF0C800", false) == "F0C800FF");
REQUIRE(SEDMLUtils::argbToRgba("#FF0000", false) == "FF0000");
REQUIRE(SEDMLUtils::rgbaToArgb("112233") == "#112233");
REQUIRE(SEDMLUtils::rgbaToArgb("#F0C800") == "#F0C800");
REQUIRE(SEDMLUtils::rgbaToArgb("#F0C800FF") == "#FFF0C800");
REQUIRE(SEDMLUtils::rgbaToArgb("F0C800FF") == "#FFF0C800");
REQUIRE(SEDMLUtils::rgbaToArgb("F0C800FF", false) == "FFF0C800");
REQUIRE(SEDMLUtils::rgbaToArgb("#FF0000", false) == "FF0000");
REQUIRE(SEDMLUtils::lineTypeFromSed(SEDML_LINETYPE_SOLID) == (int) CPlotItem::LineStyle::Solid);
REQUIRE(SEDMLUtils::lineTypeFromSed(SEDML_LINETYPE_DASH) == (int) CPlotItem::LineStyle::Dashed);
REQUIRE(SEDMLUtils::lineTypeFromSed(SEDML_LINETYPE_DOT) == (int) CPlotItem::LineStyle::Dotted);
REQUIRE(SEDMLUtils::lineTypeToSed((int) CPlotItem::LineStyle::Solid) == SEDML_LINETYPE_SOLID);
REQUIRE(SEDMLUtils::lineTypeToSed((int) CPlotItem::LineStyle::Dashed) == SEDML_LINETYPE_DASH);
REQUIRE(SEDMLUtils::lineTypeToSed((int) CPlotItem::LineStyle::Dotted) == SEDML_LINETYPE_DOT);
REQUIRE(SEDMLUtils::symbolFromSed(SEDML_MARKERTYPE_CIRCLE) == (int) CPlotItem::SymbolType::Circle);
REQUIRE(SEDMLUtils::symbolFromSed(SEDML_MARKERTYPE_STAR) == (int) CPlotItem::SymbolType::Star);
REQUIRE(SEDMLUtils::symbolToSed((int) CPlotItem::SymbolType::Circle) == SEDML_MARKERTYPE_CIRCLE);
REQUIRE(SEDMLUtils::symbolToSed((int) CPlotItem::SymbolType::Star) == SEDML_MARKERTYPE_STAR);
REQUIRE(SEDMLUtils::symbolToSed((int) CPlotItem::SymbolType::LargeCross) == SEDML_MARKERTYPE_PLUS);
REQUIRE(SEDMLUtils::symbolToSed((int) CPlotItem::SymbolType::SmallCross) == SEDML_MARKERTYPE_PLUS);
REQUIRE(SEDMLUtils::symbolToSed((int) CPlotItem::SymbolType::Plus) == SEDML_MARKERTYPE_PLUS);
}
TEST_CASE("importing new curves and plots", "[copasi][sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
REQUIRE(
dm->importSEDML(
getTestFile("test-data/test_shaded_area_overlap_order.sedml")
) == true);
auto* plots = dm->getPlotDefinitionList();
REQUIRE(plots->size() == 1);
// test that we can export it again
std::string sedml = dm->exportSEDMLToString(NULL, 1, 4);
// export with sbml namespaces
CSEDMLExporter exp;
exp.setSBMLNamespaces(3, 1);
std::string sedmlwith_ns =
exp.exportModelAndTasksToString(*dm, "model.xml", 1, 4);
REQUIRE(sedmlwith_ns.find("http://www.sbml.org/sbml/level3/version1/core") != std::string::npos);
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("importing variables with terms", "[copasi][sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
REQUIRE(dm->importSEDML(getTestFile("test-data/concentration_amount.sedml")) == true);
auto * plots = dm->getPlotDefinitionList();
REQUIRE(plots->size() == 3);
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("export / import nested scan", "[copasi][sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
REQUIRE(dm->loadModel(getTestFile("test-data/NestedScan.cps"), NULL) == true);
auto sedml = dm->exportSEDMLToString(NULL, 1, 4);
auto * doc = readSedMLFromString(sedml.c_str());
REQUIRE(doc->getNumErrors(LIBSEDML_SEV_ERROR) == 0);
REQUIRE(doc->getDataGenerator("Rtot_1_task3") == NULL);
REQUIRE(doc->getDataGenerator("Rtot_1_task5") != NULL);
// the model has a timecourse, and a steady state scan with 3 variables, as such it should not be complex
REQUIRE(SedmlInfo(doc).isComplex() == false);
// if we had another time course then it should be complex
{
auto * task = doc->getTask(0)->clone();
task->setId("anotherTaks");
doc->getListOfTasks()->appendAndOwn(task);
REQUIRE(SedmlInfo(doc).isComplex() == true);
}
delete doc;
// now import
SedmlImportOptions opts;
opts.setSkipModelImport(true);
dm->importSEDMLFromString(sedml, "", NULL, true, &opts);
REQUIRE(dynamic_cast< CScanProblem * >(dm->getTaskList()->operator[]("Scan").getProblem())->getNumberOfScanItems() == 3);
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("Export different plot styles", "[copasi][sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
REQUIRE(dm->loadModel(getTestFile("test-data/brusselator.cps"), NULL) == true);
auto * m = dm->getModel();
REQUIRE(m != NULL);
// export sbml so we have sbml ids
std::string sbml = dm->exportSBMLToString(NULL, 3, 1);
// export sedml
std::string sedml = dm->exportSEDMLToString(NULL, 1, 4);
auto * doc = readSedMLFromString(sedml.c_str());
REQUIRE(doc->getNumErrors(LIBSEDML_SEV_ERROR) == 0);
delete doc;
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("generating variables with terms", "[copasi][sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
REQUIRE(dm->loadModel(getTestFile("test-data/brusselator.cps"), NULL) == true);
auto * m = dm->getModel();
auto * pMV = m->createModelValue("g_mv", 1);
// export to sbml so we have sbml ids for everything
std::string sbml = dm->exportSBMLToString(NULL, 3, 1);
{
REQUIRE(VariableInfo(m).getSymbol() == SEDML_TIME_URN);
REQUIRE(VariableInfo(m->getValueReference()).getSymbol() == SEDML_TIME_URN);
}
{
REQUIRE(VariableInfo(&m->getCompartments()[0]).getXpath() == "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']");
REQUIRE(VariableInfo(m->getCompartments()[0].getRateReference()).getTerm() == SEDML_KISAO_RATE);
}
{
REQUIRE(VariableInfo(&m->getMetabolites()[0]).getXpath() == "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='X']");
REQUIRE(VariableInfo(m->getMetabolites()[0].getConcentrationReference()).getTerm() == SEDML_KISAO_CONCENTRATION);
REQUIRE(VariableInfo(m->getMetabolites()[0].getValueReference()).getTerm() == SEDML_KISAO_PARTICLENUMBER);
REQUIRE(VariableInfo(m->getMetabolites()[0].getConcentrationRateReference()).getTerm() == SEDML_KISAO_CONCENTRATION_RATE);
REQUIRE(VariableInfo(m->getMetabolites()[0].getRateReference()).getTerm() == SEDML_KISAO_PARTICLE_RATE);
}
{
REQUIRE(VariableInfo(&m->getModelValues()[0]).getXpath() == "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='g_mv']");
REQUIRE(VariableInfo(m->getModelValues()[0].getRateReference()).getTerm() == SEDML_KISAO_RATE);
}
{
REQUIRE(VariableInfo(&m->getReactions()[0]).getXpath() == "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R1']");
REQUIRE(VariableInfo(m->getReactions()[0].getFluxReference()).getTerm() == SEDML_KISAO_FLUX);
REQUIRE(VariableInfo(m->getReactions()[0].getParameterObjects("k1").at(0)).getXpath() == "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R1']/sbml:kineticLaw/sbml:listOfParameters/sbml:parameter[@id='k1']");
}
CRootContainer::removeDatamodel(dm);
}
TEST_CASE("importing document with remote model should fail", "[copasi][sedml]")
{
// generate sedml
auto* doc = new SedDocument(1, 4);
auto* model = doc->createModel();
model->setId("model");
model->setLanguage("urn:sedml:language:sbml");
model->setSource("urn:miriam:biomodels.db:BIOMD0000000005");
auto sedml = writeSedMLToStdString(doc);
delete doc;
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
try
{
dm->importSEDMLFromString(sedml, "", NULL, true);
}
catch (const CCopasiException& e)
{
REQUIRE(e.getMessage().getText().find("remote") != std::string::npos);
}
CRootContainer::removeDatamodel(dm);
}
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