/** * 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; }