int main(int argc, char *argv[])
{
// Parse the commandline options
// first argument is the SBML filename
// second argument is the endtime
// third argument is the step number
// fourth argument is the filename where the results are to be written
// fifth argument is the tmp directory (this is not needed)
// the rest of the arguments are species names for the result
try
{
// Create the root container.
CCopasiRootContainer::init(0, NULL, false);
}
catch (copasi::autoexcept &e)
{}
catch (copasi::option_error &e)
{}
if (argc < 5)
{
std::cout << "Usage: semantic-test-suite SBMLFILENAME ENDTIME STEPNUMBER OUTFILENAME TMPDIR SPECIESID1 SPECIESID2 ..." << std::endl;
exit(1);
}
char* pSBMLFilename = argv[1];
const char* pEndTime = argv[2];
const char* pStepNumber = argv[3];
char* pOutputFilename = argv[4];
//char* pTmpDirectory=argv[5];
char** pSBMLSpeciesIds = new char * [argc - 6];
unsigned int i, iMax = argc;
CTrajectoryTask* pTrajectoryTask = NULL;
std::string CWD = COptions::getPWD();
double endTime = strToDouble(pEndTime, &pEndTime);
double stepNumber = strToDouble(pStepNumber, &pStepNumber);
if (endTime == 0.0)
{
std::cerr << "Invalid endtime " << pEndTime << std::endl;
exit(1);
}
if (stepNumber == 0.0)
{
std::cerr << "Invalid step number " << pStepNumber << std::endl;
exit(1);
}
for (i = 6; i < iMax; ++i)
{
pSBMLSpeciesIds[i - 6] = argv[i];
//std::cout << "Copying pointer to " << argv[i] << "." << std::endl;
}
try
{
// Create the global data model.
CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
// Import the SBML File
pDataModel->importSBML(pSBMLFilename);
//pDataModel->getModel()->forceCompile();
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for SBML testsuite run");
pReport->setTaskType(CCopasiTask::timeCourse);
pReport->setIsTable(true);
std::vector<CRegisteredObjectName>* pTable = pReport->getTableAddr();
pTable->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));
iMax = iMax - 6;
const CCopasiVector<CMetab>& metabolites = pDataModel->getModel()->getMetabolites();
for (i = 0; i < iMax; ++i)
{
unsigned int j, jMax = metabolites.size();
for (j = 0; j < jMax; ++j)
{
if (metabolites[j]->getSBMLId() == pSBMLSpeciesIds[i])
{
pTable->push_back(metabolites[j]->getObject(CCopasiObjectName("Reference=Concentration"))->getCN());
//std::cout << "adding metabolite " << metabolites[j]->getObjectName() << " to report." << std::endl;
break;
}
}
if (j == jMax)
{
std::cerr << "Could not find a metabolite for the SBML id " << pSBMLSpeciesIds[i] << std::endl;
exit(1);
}
}
// create a trajectory task
pTrajectoryTask = new CTrajectoryTask();
pTrajectoryTask->getProblem()->setModel(pDataModel->getModel());
pTrajectoryTask->setScheduled(true);
pTrajectoryTask->getReport().setReportDefinition(pReport);
pTrajectoryTask->getReport().setTarget(CWD + "/" + pOutputFilename);
pTrajectoryTask->getReport().setAppend(false);
CTrajectoryProblem* pProblem = dynamic_cast<CTrajectoryProblem*>(pTrajectoryTask->getProblem());
pProblem->setStepNumber((const unsigned C_INT32)stepNumber);
pProblem->setDuration((const C_FLOAT64)endTime);
pProblem->setTimeSeriesRequested(true);
//pProblem->setInitialState(pDataModel->getModel()->getInitialState());
CTrajectoryMethod* pMethod = dynamic_cast<CTrajectoryMethod*>(pTrajectoryTask->getMethod());
pMethod->getParameter("Absolute Tolerance")->setValue(1.0e-20);
CCopasiVectorN< CCopasiTask > & TaskList = * pDataModel->getTaskList();
TaskList.remove("Time-Course");
TaskList.add(pTrajectoryTask, true);
// save the file for control purposes
std::string saveFilename = pSBMLFilename;
saveFilename = saveFilename.substr(0, saveFilename.length() - 4) + ".cps";
pDataModel->saveModel(saveFilename, NULL, true);
// Run the trajectory task
pTrajectoryTask->initialize(CCopasiTask::OUTPUT_UI, pDataModel, NULL);
pTrajectoryTask->process(true);
pTrajectoryTask->restore();
// create another report that will write to the directory where the input file came from
// this can be used for debugging
// create a trajectory task
pTrajectoryTask->getReport().setTarget(pOutputFilename);
pTrajectoryTask->initialize(CCopasiTask::OUTPUT_UI, pDataModel, NULL);
pTrajectoryTask->process(true);
pTrajectoryTask->restore();
}
catch (CCopasiException Exception)
{
std::cerr << Exception.getMessage().getText() << std::endl;
}
CCopasiRootContainer::destroy();
return 0;
}
/**
* Creates the data generators for SEDML.
*/
void CSEDMLExporter::createDataGenerators(CCopasiDataModel & dataModel,
std::string & taskId,
CCopasiTask* task)
{
const CModel* pModel = dataModel.getModel();
std::vector<std::string> stringsContainer; //split string container
if (pModel == NULL)
CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No model for this SED-ML document. An SBML model must exist for every SED-ML document.");
SedPlot2D* pPSedPlot;
SedCurve* pCurve; // = pPSedPlot->createCurve();
//create generator for special varibale time
const CCopasiObject* pTime = static_cast<const CCopasiObject *>(dataModel.getModel()->getObject(CCopasiObjectName("Reference=Time")));
SedDataGenerator *pTimeDGenp = this->mpSEDMLDocument->createDataGenerator();
pTimeDGenp->setId("time");
pTimeDGenp->setName(pTime->getObjectName());
SedVariable *pTimeVar = pTimeDGenp->createVariable();
pTimeVar->setId("var_time");
pTimeVar->setTaskReference(taskId);
pTimeVar->setSymbol(SEDML_TIME_URN);
pTimeDGenp->setMath(SBML_parseFormula(pTimeVar->getId().c_str()));
size_t i, imax = dataModel.getPlotDefinitionList()->size();
SedDataGenerator *pPDGen;
if (imax == 0 && (task == NULL || task->getReport().getTarget().empty()))
CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No plot/report definition for this SED-ML document.");
// export report
if (task != NULL && !task->getReport().getTarget().empty())
{
CReportDefinition* def = task->getReport().getReportDefinition();
if (def != NULL)
{
SedReport* pReport = mpSEDMLDocument->createReport();
std::string name = def->getObjectName();
SEDMLUtils::removeCharactersFromString(name, "[]");
//
pReport->setId(SEDMLUtils::getNextId("report", mpSEDMLDocument->getNumOutputs()));
pReport->setName(name);
std::vector<CRegisteredObjectName> header = *def->getHeaderAddr();
std::vector<CRegisteredObjectName> body =
def->isTable() ? *def->getTableAddr() :
*def->getBodyAddr();
int dsCount = 0;
for (size_t i = 0; i < body.size(); ++i)
{
CRegisteredObjectName& current = body[i];
if (current == def->getSeparator().getCN()) continue;
CCopasiObject *object = dataModel.getDataObject(current);
if (object == NULL) continue;
const std::string& typeX = object->getObjectName();
std::string xAxis = object->getObjectDisplayName();
std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
pModel, dataModel);
if (object->getCN() == pTime->getCN())
pPDGen = pTimeDGenp;
else
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
xAxis,
targetXPathStringX,
taskId,
i,
0
);
SedDataSet* pDS = pReport->createDataSet();
pDS->setId(SEDMLUtils::getNextId("ds", ++dsCount));
if (def->isTable())
{
CCopasiObject *headerObj = NULL;
if (header.size() > i)
headerObj = dataModel.getDataObject(header[i]);
else
headerObj = dataModel.getDataObject(body[i]);
if (headerObj != NULL)
pDS->setLabel(headerObj->getObjectDisplayName());
else
pDS->setLabel(xAxis);
}
else
pDS->setLabel(xAxis);
pDS->setDataReference(pPDGen->getId());
}
}
}
// export plots
for (i = 0; i < imax; i++)
{
pPSedPlot = this->mpSEDMLDocument->createPlot2D();
const CPlotSpecification* pPlot = (*dataModel.getPlotDefinitionList())[i];
std::string plotName = pPlot->getObjectName();
SEDMLUtils::removeCharactersFromString(plotName, "[]");
pPSedPlot->setId(SEDMLUtils::getNextId("plot", mpSEDMLDocument->getNumOutputs()));
pPSedPlot->setName(plotName);
size_t j, jmax = pPlot->getItems().size();
for (j = 0; j < jmax; j++)
{
const CPlotItem* pPlotItem = pPlot->getItems()[j];
CCopasiObject *objectX, *objectY;
if (pPlotItem->getChannels().size() >= 1)
{
objectX = dataModel.getDataObject(pPlotItem->getChannels()[0]);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s', as it has no data channel.", pPlotItem->getObjectName().c_str());
continue;
}
if (objectX == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as it cannot be resolved.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[0].c_str());
continue;
}
bool xIsTime = objectX->getCN() == pTime->getCN();
if (pPlotItem->getChannels().size() >= 2)
{
objectY = dataModel.getDataObject(pPlotItem->getChannels()[1]);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s', as it has only 1 data channel.", pPlotItem->getObjectName().c_str());
continue;
}
if (objectY == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as it cannot be resolved.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[1].c_str());
continue;
}
const std::string& type = objectY->getObjectName();
std::string yAxis = objectY->getObjectDisplayName();
std::string sbmlId = yAxis;
std::string targetXPathString = SEDMLUtils::getXPathAndName(sbmlId, type,
pModel, dataModel);
if (targetXPathString.empty())
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as no xpath expression for it could be generated.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[1].c_str());
continue;
}
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
sbmlId,
targetXPathString,
taskId,
i,
j
);
pPDGen->setName(yAxis);
pCurve = pPSedPlot->createCurve();
std::ostringstream idCurveStrStream;
idCurveStrStream << "p";
idCurveStrStream << i + 1;
idCurveStrStream << "_curve_";
idCurveStrStream << j + 1;
pCurve->setId(idCurveStrStream.str());
pCurve->setLogX(pPlot->isLogX());
pCurve->setLogY(pPlot->isLogY());
pCurve->setName(yAxis);
pCurve->setYDataReference(pPDGen->getId());
if (xIsTime)
{
pCurve->setXDataReference(pTimeDGenp->getId());
}
else
{
const std::string& typeX = objectX->getObjectName();
std::string xAxis = objectX->getObjectDisplayName();
std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
pModel, dataModel);
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
xAxis,
targetXPathStringX,
taskId,
i,
j
);
pCurve->setXDataReference(pPDGen->getId());
}
}
}
}