SedDataGenerator * createDataGenerator(
SedDocument* mpSEDMLDocument,
const std::string &sbmlId,
const std::string &targetXPathString,
const std::string& taskId,
size_t i,
size_t j)
{
SedDataGenerator *pPDGen = mpSEDMLDocument->createDataGenerator();
std::ostringstream idStrStream;
idStrStream << sbmlId;
idStrStream << "_";
idStrStream << j + 1;
pPDGen->setId(idStrStream.str());
pPDGen->setName(sbmlId);
SedVariable * pPVar = pPDGen->createVariable();
std::ostringstream idVarStrStream;
idVarStrStream << "p";
idVarStrStream << i + 1;
idVarStrStream << "_";
idVarStrStream << pPDGen->getName();
pPVar->setId(idVarStrStream.str());
pPVar->setTaskReference(taskId);
pPVar->setName(pPDGen->getName());
pPDGen->setMath(SBML_parseFormula(pPVar->getId().c_str()));
if (targetXPathString == SEDML_TIME_URN)
{
pPVar->setSymbol(targetXPathString);
}
else
{
pPVar->setTarget(targetXPathString);
}
return pPDGen;
}
/**
* Creates the data generators for SEDML.
*/
void CSEDMLExporter::createDataGenerators(CCopasiDataModel & dataModel, std::string & taskId)
{
const CModel* pModel = dataModel.getModel();
std::vector<std::string> stringsContainer; //split string container
if (pModel == NULL)
CCopasiMessage(CCopasiMessage::ERROR, "No model for this SEDML document. An SBML model must exist for every SEDML 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)
CCopasiMessage(CCopasiMessage::ERROR, "No plot definition for this SEDML document.");
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]);
bool xIsTime = objectX->getCN() == pTime->getCN();
if (pPlotItem->getChannels().size() >= 2)
objectY = dataModel.getDataObject(pPlotItem->getChannels()[1]);
const std::string& type = objectY->getObjectName();
std::string yAxis = objectY->getObjectDisplayName();
std::string targetXPathString = SEDMLUtils::getXPathAndName(yAxis, type,
pModel, dataModel);
if (targetXPathString.empty())
{
continue;
}
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
yAxis,
targetXPathString,
taskId,
i,
j
);
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->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());
}
}
}
}
/**
* 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());
}
}
}
}
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;
}