/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createScanTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
// need L1V2 to export repeated tasks
if (mpSEDMLDocument->getVersion() != 2) return "";
CScanTask* pTask = dynamic_cast<CScanTask*>((*dataModel.getTaskList())["Scan"]);
if (pTask == NULL) return "";
CScanProblem* pProblem = dynamic_cast<CScanProblem*>(pTask->getProblem());
size_t numItems = pProblem->getNumberOfScanItems();
if (numItems == 0)
return "";
if (pProblem->getSubtask() != CCopasiTask::steadyState &&
pProblem->getSubtask() != CCopasiTask::timeCourse)
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI only allows the export of time course or steady state scans.");
return "";
}
std::string subTaskId;
if (pProblem->getSubtask() == CCopasiTask::steadyState)
{
subTaskId = createSteadyStateTask(dataModel, modelId);
}
else
{
subTaskId = mpTimecourseTask->getId();
}
SedRepeatedTask* task = mpSEDMLDocument->createRepeatedTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
task->setId(taskId);
task->setResetModel(!pProblem->getContinueFromCurrentState());
// craete ranges / changes
for (size_t i = 0; i < numItems; ++i)
{
CCopasiParameterGroup* current = pProblem->getScanItem(i);
CScanProblem::Type type = (CScanProblem::Type)(*current->getParameter("Type")->getValue().pUINT);
// ignore random items
if (type == CScanProblem::SCAN_RANDOM)
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI cannot export random scan items, they will be ignored.");
continue;
}
int numSteps = (*current->getParameter("Number of steps")->getValue().pUINT);
// handle repeats
if (type == CScanProblem::SCAN_REPEAT)
{
SedUniformRange *range = task->createUniformRange();
range->setId(SEDMLUtils::getNextId("range", task->getNumRanges()));
range->setStart(0);
range->setEnd(numSteps);
range->setNumberOfPoints(numSteps);
range->setType("linear");
if (task->isSetRangeId())
task->setRangeId(range->getId());
continue;
}
// handle scans
if (type == CScanProblem::SCAN_LINEAR)
{
double min = (*current->getParameter("Minimum")->getValue().pDOUBLE);
double max = (*current->getParameter("Maximum")->getValue().pDOUBLE);
bool log = (*current->getParameter("log")->getValue().pBOOL);
SedUniformRange *range = task->createUniformRange();
range->setId(SEDMLUtils::getNextId("range", task->getNumRanges()));
range->setStart(min);
range->setEnd(max);
range->setNumberOfPoints(numSteps);
range->setType(log ? "log" : "linear");
const CRegisteredObjectName& cn = (*current->getParameter("Object")->getValue().pCN);
std::string xpath = SEDMLUtils::getXPathForObject(*static_cast<const CCopasiObject*>(dataModel.getObject(cn)));
if (xpath.empty())
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI cannot export the selected scan object, it will be ignored.");
continue;
}
SedSetValue *change = task->createTaskChange();
change->setModelReference(modelId);
if (xpath == SEDML_TIME_URN)
{
change->setSymbol(xpath);
}
else
{
change->setTarget(xpath);
}
change->setRange(range->getId());
change->setMath(SBML_parseFormula(range->getId().c_str()));
continue;
}
}
if (!task->isSetRangeId() && task->getNumRanges() > 0)
task->setRangeId(task->getRange(0)->getId());
// create subtask
SedSubTask* subTask = task->createSubTask();
subTask->setOrder(1);
subTask->setTask(subTaskId);
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;
}