/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createTimeCourseTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
mpTimecourse = this->mpSEDMLDocument->createUniformTimeCourse();
mpTimecourse->setId(SEDMLUtils::getNextId("sim", mpSEDMLDocument->getNumSimulations()));
//presently SEDML only supports time course
CCopasiTask* pTask = (*dataModel.getTaskList())["Time-Course"];
CTrajectoryProblem* tProblem = static_cast<CTrajectoryProblem*>(pTask->getProblem());
mpTimecourse->setInitialTime(0.0);
mpTimecourse->setOutputStartTime(tProblem->getOutputStartTime());
mpTimecourse->setOutputEndTime(tProblem->getStepNumber()*tProblem->getStepSize());
mpTimecourse->setNumberOfPoints(tProblem->getStepNumber());
// set the correct KISAO Term
SedAlgorithm* alg = mpTimecourse->createAlgorithm();
if (pTask->getMethod()->getObjectName().find("Stochastic") != std::string::npos)
alg->setKisaoID("KISAO:0000241");
else
alg->setKisaoID("KISAO:0000019");
mpTimecourseTask = this->mpSEDMLDocument->createTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
mpTimecourseTask->setId(taskId);
mpTimecourseTask->setSimulationReference(mpTimecourse->getId());
mpTimecourseTask->setModelReference(modelId);
return taskId;
}
/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createSteadyStateTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
SedSteadyState *steady = this->mpSEDMLDocument->createSteadyState();
steady->setId(SEDMLUtils::getNextId("steady", mpSEDMLDocument->getNumSimulations()));
//presently SEDML only supports time course
CCopasiTask* pTask = (*dataModel.getTaskList())["Steady-State"];
CTrajectoryProblem* tProblem = static_cast<CTrajectoryProblem*>(pTask->getProblem());
// set the correct KISAO Term
SedAlgorithm* alg = steady->createAlgorithm();
alg->setKisaoID("KISAO:0000282");
SedTask *task = this->mpSEDMLDocument->createTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
task->setId(taskId);
task->setSimulationReference(steady->getId());
task->setModelReference(modelId);
return taskId;
}
LIBSEDML_CPP_NAMESPACE_USE
int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: create_sedml output-filename"
<< endl << endl;
return 2;
}
// create the document
SedDocument doc(1,3);
doc.setAnnotation("<test xmlns='http://test.org/test/annotation' attribute='test' />");
{
SedDataDescription* dataDesc = doc.createDataDescription();
dataDesc->setId("oscli");
dataDesc->setName("Oscli Timecourse data");
dataDesc->setSource("oscli.numl");
DimensionDescription* dimDesc = dataDesc->createDimensionDescription();
CompositeDescription* timeDesc = new CompositeDescription();
timeDesc->setIndexType("double");
timeDesc->setId("time");
timeDesc->setName("time");
CompositeDescription* speciesDesc = timeDesc->createCompositeDescription();
speciesDesc->setIndexType("string");
speciesDesc->setId("SpeciesIds");
speciesDesc->setName("SpeciesIds");
AtomicDescription* concentrationDesc = speciesDesc->createAtomicDescription();
concentrationDesc->setValueType("double");
concentrationDesc->setName("Concentrations");
dimDesc->appendAndOwn(timeDesc);
SedDataSource* dataSource = dataDesc->createDataSource();
dataSource->setId("dataS1");
SedSlice* slice = dataSource->createSlice();
slice->setReference("SpeciesIds");
slice->setValue("S1");
dataSource = dataDesc->createDataSource();
dataSource->setIndexSet("time");
}
{
// create a first model referencing an sbml file
SedModel *model = doc.createModel();
model->setId("model1");
model->setSource("file.xml");
model->setLanguage("urn:sedml:sbml");
// create a second model modifying a variable of that other sbml file
model = doc.createModel();
model->setId("model2");
model->setSource("model1");
model->setLanguage("urn:sedml:sbml");
// change a paramerter 'k' to 0.1
SedChangeAttribute* change = model->createChangeAttribute();
change->setTarget("/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='k']/@value");
change->setNewValue("0.1");
// remove species 's1'
SedRemoveXML* remove = model->createRemoveXML();
remove->setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
// add another species 's1' using addxml
SedAddXML* addXml = model->createAddXML();
addXml->setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies");
addXml->setNewXML(XMLNode::convertStringToXMLNode("<species xmlns='http://www.sbml.org/sbml/level2' id='S1' boundaryCondition='false' initialConcentration='0' compartment='compartment' />"));
// replace 's1' one more time by a better one
SedChangeXML* changeXML = model->createChangeXML();
changeXML->setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
changeXML->setNewXML(XMLNode::convertStringToXMLNode("<species xmlns='http://www.sbml.org/sbml/level2' id='S1' boundaryCondition='false' initialConcentration='10' compartment='compartment' />"));
// now for something tricky we want to update the initialConcentration of 'S2' to be
// half what it was in the original model
SedComputeChange* compute = model->createComputeChange();
compute->setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id="S2"]/@initialConcentration");
SedVariable *variable = compute->createVariable();
variable->setId("S2");
variable->setModelReference("model1");
variable->setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']");
compute->setMath(SBML_parseFormula("S2 / 2"));
}
// create simulation
SedUniformTimeCourse* tc = doc.createUniformTimeCourse();
tc->setId("sim1");
tc->setInitialTime(0.0);
tc->setOutputStartTime(0.0);
tc->setOutputEndTime(10.0);
tc->setNumberOfPoints(1000);
// need to set the correct KISAO Term
SedAlgorithm* alg = tc->createAlgorithm();
alg->setKisaoID("KISAO:0000019");
SedAlgorithmParameter* algParam = alg->createAlgorithmParameter();
algParam ->setNotes("<p xmlns='http://www.w3.org/1999/xhtml'>This is the absolute tolerance</p>");
algParam ->setKisaoID("KISAO:0000211");
algParam ->setValue("1e-12");
// add annotation
tc->setAnnotation("<test xmlns='http://test.org/test/simulation/annotation' attribute='uniform time course' />");
alg->setAnnotation("<test xmlns='http://test.org/test/simulation/annotation' attribute='algorithm' />");
// create one step
SedOneStep* step = doc.createOneStep();
step->setId("sim2");
step->setStep(0.1);
alg = step->createAlgorithm();
alg->setKisaoID("KISAO:0000019");
// create steady state
SedSteadyState* steady = doc.createSteadyState();
steady->setId("sim3");
alg = steady->createAlgorithm();
alg->setKisaoID("KISAO:0000282");
// create a task that uses the simulation and the model above
SedTask* task = doc.createTask();
task->setId("task1");
task->setModelReference("model1");
task->setSimulationReference("sim1");
task = doc.createTask();
task->setId("task2");
task->setModelReference("model1");
task->setSimulationReference("sim2");
SedRepeatedTask* repeat = doc.createRepeatedTask();
repeat->setId("task3");
repeat->setRangeId("index");
repeat->setResetModel(false);
SedUniformRange* index = repeat->createUniformRange();
index->setId("index");
index->setStart(0);
index->setEnd(10);
index->setNumberOfPoints(100);
index->setType("linear");
SedFunctionalRange* current = repeat->createFunctionalRange();
current->setId("current");
current->setRange("index");
current->setMath(SBML_parseFormula("piecewise(8, lt(index, 1), 0.1, and(geq(index, 4), lt(index, 6)), 8)"));
SedVectorRange* vrange = repeat->createVectorRange();
vrange->setId("vRange");
vrange->addValue(8);
vrange->addValue(4);
vrange->addValue(0.1);
SedSetValue* setValue = repeat->createTaskChange();
setValue->setTarget("/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='J0_v0']");
setValue->setRange("current");
setValue->setModelReference("model1");
setValue->setMath(SBML_parseFormula("current"));
SedSubTask* subTask = repeat->createSubTask();
subTask->setTask("task1");
subTask->setOrder(1);
// add a DataGenerator to hold the output for time
SedDataGenerator* dg = doc.createDataGenerator();
dg->setId("time");
dg->setName("time");
SedVariable* var = dg->createVariable();
var->setId("v0");
var->setName("time");
var->setTaskReference("task1");
var->setSymbol("urn:sedml:symbol:time");
dg->setMath(SBML_parseFormula("v0"));
// and one for S1
dg = doc.createDataGenerator();
dg->setId("S1");
dg->setName("S1");
var = dg->createVariable();
var->setId("v1");
var->setName("S1");
var->setTaskReference("task1");
var->setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
dg->setMath(SBML_parseFormula("v1"));
// add a report
SedReport* report = doc.createReport();
report->setId("r1");
report->setName("report 1");
SedDataSet* set = report->createDataSet();
set->setId("ds1");
set->setLabel("time");
set->setDataReference("time");
set = report->createDataSet();
set->setId("ds2");
set->setLabel("S1");
set->setDataReference("S1");
// add a 2d plot
SedPlot2D* plot = doc.createPlot2D();
plot->setId("p1");
plot->setName("S1 Timecourse");
SedCurve* curve = plot->createCurve();
curve->setId("c1");
curve->setName("S1");
curve->setLogX(false);
curve->setLogY(false);
curve->setXDataReference("time");
curve->setYDataReference("S1");
// add a 3D Plot
SedPlot3D* plot2 = doc.createPlot3D();
plot2->setId("p2");
plot2->setName("dunno");
SedSurface* surf = plot2->createSurface();
surf->setId("surf1");
surf->setName("S1");
surf->setLogX(false);
surf->setLogY(false);
surf->setLogZ(false);
surf->setXDataReference("time");
surf->setYDataReference("S1");
surf->setZDataReference("S1");
// write the document
writeSedML(&doc, argv[1]);
return 0;
}
