Example 1 with Model
use of org.jlibsedml.Model in project vcell by virtualcell.
the class SEDMLExporter method translateBioModelToSedML.
private void translateBioModelToSedML(String savePath) {
sbmlFilePathStrAbsoluteList.clear();
// models
try {
SimulationContext[] simContexts = vcBioModel.getSimulationContexts();
cbit.vcell.model.Model vcModel = vcBioModel.getModel();
// "urn:sedml:language:sbml";
String sbmlLanguageURN = SUPPORTED_LANGUAGE.SBML_GENERIC.getURN();
String bioModelName = TokenMangler.mangleToSName(vcBioModel.getName());
// String usrHomeDirPath = ResourceUtil.getUserHomeDir().getAbsolutePath();
// to get Xpath string for variables.
SBMLSupport sbmlSupport = new SBMLSupport();
// for model count, task subcount
int simContextCnt = 0;
// for dtaGenerator count.
int varCount = 0;
boolean bSpeciesAddedAsDataGens = false;
String sedmlNotesStr = "";
for (SimulationContext simContext : simContexts) {
String simContextName = simContext.getName();
// export all applications that are not spatial stochastic
if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch())) {
// to compute and set the sizes of the remaining structures.
if (!simContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
Structure structure = simContext.getModel().getStructure(0);
double structureSize = 1.0;
StructureMapping structMapping = simContext.getGeometryContext().getStructureMapping(structure);
StructureSizeSolver.updateAbsoluteStructureSizes(simContext, structure, structureSize, structMapping.getSizeParameter().getUnitDefinition());
}
// Export the application itself to SBML, with default overrides
String sbmlString = null;
int level = 2;
int version = 4;
boolean isSpatial = simContext.getGeometry().getDimension() > 0 ? true : false;
SimulationJob simJob = null;
// if (simContext.getGeometry().getDimension() > 0) {
// sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, true, simContext, null);
// } else {
// sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, false, simContext, null);
// }
//
// TODO: we need to salvage from the SBMLExporter info about the fate of local parameters
// some of them may stay as locals, some others may become globals
// Any of these, if used in a repeated task or change or whatever, needs to be used in a consistent way,
// that is, if a param becomes a global in SBML, we need to refer at it in SEDML as the same global
//
// We'll use:
// Map<Pair <String reaction, String param>, String global> - if local converted to global
// Set<Pair <String reaction, String param>> (if needed?) - if local stays local
//
// local to global translation map
Map<Pair<String, String>, String> l2gMap = null;
if (vcBioModel instanceof BioModel) {
try {
// check if model to be exported to SBML has units compatible with SBML default units (default units in SBML can be assumed only until SBML Level2)
ModelUnitSystem forcedModelUnitSystem = simContext.getModel().getUnitSystem();
if (level < 3 && !ModelUnitSystem.isCompatibleWithDefaultSBMLLevel2Units(forcedModelUnitSystem)) {
forcedModelUnitSystem = ModelUnitSystem.createDefaultSBMLLevel2Units();
}
// create new Biomodel with new (SBML compatible) unit system
BioModel modifiedBiomodel = ModelUnitConverter.createBioModelWithNewUnitSystem(simContext.getBioModel(), forcedModelUnitSystem);
// extract the simContext from new Biomodel. Apply overrides to *this* modified simContext
SimulationContext simContextFromModifiedBioModel = modifiedBiomodel.getSimulationContext(simContext.getName());
SBMLExporter sbmlExporter = new SBMLExporter(modifiedBiomodel, level, version, isSpatial);
sbmlExporter.setSelectedSimContext(simContextFromModifiedBioModel);
// no sim job
sbmlExporter.setSelectedSimulationJob(null);
sbmlString = sbmlExporter.getSBMLFile();
l2gMap = sbmlExporter.getLocalToGlobalTranslationMap();
} catch (ExpressionException | SbmlException e) {
e.printStackTrace(System.out);
throw new XmlParseException(e);
}
} else {
throw new RuntimeException("unsupported Document Type " + vcBioModel.getClass().getName() + " for SBML export");
}
String sbmlFilePathStrAbsolute = savePath + FileUtils.WINDOWS_SEPARATOR + bioModelName + "_" + simContextName + ".xml";
String sbmlFilePathStrRelative = bioModelName + "_" + simContextName + ".xml";
XmlUtil.writeXMLStringToFile(sbmlString, sbmlFilePathStrAbsolute, true);
sbmlFilePathStrAbsoluteList.add(sbmlFilePathStrRelative);
String simContextId = TokenMangler.mangleToSName(simContextName);
sedmlModel.addModel(new Model(simContextId, simContextName, sbmlLanguageURN, sbmlFilePathStrRelative));
// required for mathOverrides, if any
MathMapping mathMapping = simContext.createNewMathMapping();
MathSymbolMapping mathSymbolMapping = mathMapping.getMathSymbolMapping();
// create sedml simulation objects and tasks (mapping each sim with current simContext)
int simCount = 0;
String taskRef = null;
int overrideCount = 0;
for (Simulation vcSimulation : simContext.getSimulations()) {
List<DataGenerator> dataGeneratorsOfSim = new ArrayList<DataGenerator>();
// if simContext is non-spatial stochastic, check if sim is histogram
SolverTaskDescription simTaskDesc = vcSimulation.getSolverTaskDescription();
if (simContext.getGeometry().getDimension() == 0 && simContext.isStoch()) {
long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
if (numOfTrials > 1) {
String msg = "\n\t" + simContextName + " ( " + vcSimulation.getName() + " ) : export of non-spatial stochastic simulation with histogram option to SEDML not supported at this time.";
sedmlNotesStr += msg;
continue;
}
}
// create Algorithm and sedmlSimulation (UniformtimeCourse)
SolverDescription vcSolverDesc = simTaskDesc.getSolverDescription();
// String kiSAOIdStr = getKiSAOIdFromSimulation(vcSolverDesc); // old way of doing it, going directly to the web site
String kiSAOIdStr = vcSolverDesc.getKisao();
Algorithm sedmlAlgorithm = new Algorithm(kiSAOIdStr);
TimeBounds vcSimTimeBounds = simTaskDesc.getTimeBounds();
double startingTime = vcSimTimeBounds.getStartingTime();
String simName = vcSimulation.getName();
UniformTimeCourse utcSim = new UniformTimeCourse(TokenMangler.mangleToSName(simName), simName, startingTime, startingTime, vcSimTimeBounds.getEndingTime(), (int) simTaskDesc.getExpectedNumTimePoints(), sedmlAlgorithm);
// if solver is not CVODE, add a note to utcSim to indicate actual solver name
if (!vcSolverDesc.equals(SolverDescription.CVODE)) {
String simNotesStr = "Actual Solver Name : '" + vcSolverDesc.getDisplayLabel() + "'.";
utcSim.addNote(createNotesElement(simNotesStr));
}
sedmlModel.addSimulation(utcSim);
// add SEDML tasks (map simulation to model:simContext)
// repeated tasks
MathOverrides mathOverrides = vcSimulation.getMathOverrides();
if (mathOverrides != null && mathOverrides.hasOverrides()) {
String[] overridenConstantNames = mathOverrides.getOverridenConstantNames();
String[] scannedConstantsNames = mathOverrides.getScannedConstantNames();
HashMap<String, String> scannedParamHash = new HashMap<String, String>();
HashMap<String, String> unscannedParamHash = new HashMap<String, String>();
for (String name : scannedConstantsNames) {
scannedParamHash.put(name, name);
}
for (String name : overridenConstantNames) {
if (!scannedParamHash.containsKey(name)) {
unscannedParamHash.put(name, name);
}
}
if (!unscannedParamHash.isEmpty() && scannedParamHash.isEmpty()) {
// only parameters with simple overrides (numeric/expression) no scans
// create new model with change for each parameter that has override; add simple task
String overriddenSimContextId = simContextId + "_" + overrideCount;
String overriddenSimContextName = simContextName + " modified";
Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
overrideCount++;
for (String unscannedParamName : unscannedParamHash.values()) {
SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
if (unscannedParamExpr.isNumeric()) {
// if expression is numeric, add ChangeAttribute to model created above
XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
sedModel.addChange(changeAttribute);
} else {
// non-numeric expression : add 'computeChange' to modified model
ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
ComputeChange computeChange = new ComputeChange(targetXpath, math);
String[] exprSymbols = unscannedParamExpr.getSymbols();
for (String symbol : exprSymbols) {
String symbolName = TokenMangler.mangleToSName(symbol);
SymbolTableEntry ste1 = vcModel.getEntry(symbol);
if (ste != null) {
if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
computeChange.addVariable(sedmlVar);
} else {
double doubleValue = 0.0;
if (ste1 instanceof ReservedSymbol) {
doubleValue = getReservedSymbolValue(ste1);
}
Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
computeChange.addParameter(sedmlParameter);
}
} else {
throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
}
}
sedModel.addChange(computeChange);
}
}
sedmlModel.addModel(sedModel);
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, sedModel.getId(), utcSim.getId());
sedmlModel.addTask(sedmlTask);
// to be used later to add dataGenerators : one set of DGs per model (simContext).
taskRef = taskId;
} else if (!scannedParamHash.isEmpty() && unscannedParamHash.isEmpty()) {
// only parameters with scans : only add 1 Task and 1 RepeatedTask
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
sedmlModel.addTask(sedmlTask);
String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
// TODO: temporary solution - we use as range here the first range
String scn = scannedConstantsNames[0];
String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
// to be used later to add dataGenerators - in our case it has to be the repeated task
taskRef = repeatedTaskId;
SubTask subTask = new SubTask("0", taskId);
rt.addSubtask(subTask);
for (String scannedConstName : scannedConstantsNames) {
ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
// list of Ranges, if sim is parameter scan.
if (constantArraySpec != null) {
Range r = null;
System.out.println(" " + constantArraySpec.toString());
if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
// ------ Uniform Range
r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
rt.addRange(r);
} else {
// ----- Vector Range
cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
ArrayList<Double> values = new ArrayList<Double>();
for (int i = 0; i < cs.length; i++) {
String value = cs[i].getExpression().infix();
values.add(Double.parseDouble(value));
}
r = new VectorRange(rangeId, values);
rt.addRange(r);
}
// list of Changes
SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
XPathTarget target = getTargetXPath(ste, l2gMap);
// ASTNode math1 = new ASTCi(r.getId()); // was scannedConstName
ASTNode math1 = Libsedml.parseFormulaString(r.getId());
SetValue setValue = new SetValue(target, r.getId(), simContextId);
setValue.setMath(math1);
rt.addChange(setValue);
} else {
throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
}
}
sedmlModel.addTask(rt);
} else {
// both scanned and simple parameters : create new model with change for each simple override; add RepeatedTask
// create new model with change for each unscanned parameter that has override
String overriddenSimContextId = simContextId + "_" + overrideCount;
String overriddenSimContextName = simContextName + " modified";
Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
overrideCount++;
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, overriddenSimContextId, utcSim.getId());
sedmlModel.addTask(sedmlTask);
// scanned parameters
String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
// TODO: temporary solution - we use as range here the first range
String scn = scannedConstantsNames[0];
String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
// to be used later to add dataGenerators - in our case it has to be the repeated task
taskRef = repeatedTaskId;
SubTask subTask = new SubTask("0", taskId);
rt.addSubtask(subTask);
for (String scannedConstName : scannedConstantsNames) {
ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
// list of Ranges, if sim is parameter scan.
if (constantArraySpec != null) {
Range r = null;
System.out.println(" " + constantArraySpec.toString());
if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
// ------ Uniform Range
r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
rt.addRange(r);
} else {
// ----- Vector Range
cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
ArrayList<Double> values = new ArrayList<Double>();
for (int i = 0; i < cs.length; i++) {
String value = cs[i].getExpression().infix() + ", ";
values.add(Double.parseDouble(value));
}
r = new VectorRange(rangeId, values);
rt.addRange(r);
}
// use scannedParamHash to store rangeId for that param, since it might be needed if unscanned param has a scanned param in expr.
if (scannedParamHash.get(scannedConstName).equals(scannedConstName)) {
// the hash was originally populated as <scannedParamName, scannedParamName>. Replace 'value' with rangeId for scannedParam
scannedParamHash.put(scannedConstName, r.getId());
}
// create setValue for scannedConstName
SymbolTableEntry ste2 = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
XPathTarget target1 = getTargetXPath(ste2, l2gMap);
ASTNode math1 = new ASTCi(scannedConstName);
SetValue setValue1 = new SetValue(target1, r.getId(), sedModel.getId());
setValue1.setMath(math1);
rt.addChange(setValue1);
} else {
throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
}
}
// for unscanned parameter overrides
for (String unscannedParamName : unscannedParamHash.values()) {
SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
if (unscannedParamExpr.isNumeric()) {
// if expression is numeric, add ChangeAttribute to model created above
XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
sedModel.addChange(changeAttribute);
} else {
// check for any scanned parameter in unscanned parameter expression
ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
String[] exprSymbols = unscannedParamExpr.getSymbols();
boolean bHasScannedParameter = false;
String scannedParamNameInUnscannedParamExp = null;
for (String symbol : exprSymbols) {
if (scannedParamHash.get(symbol) != null) {
bHasScannedParameter = true;
scannedParamNameInUnscannedParamExp = new String(symbol);
// @TODO check for multiple scannedParameters in expression.
break;
}
}
// (scanned parameter in expr) ? (add setValue for unscanned param in repeatedTask) : (add computeChange to modifiedModel)
if (bHasScannedParameter && scannedParamNameInUnscannedParamExp != null) {
// create setValue for unscannedParamName (which contains a scanned param in its expression)
SymbolTableEntry entry = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
XPathTarget target = getTargetXPath(entry, l2gMap);
String rangeId = scannedParamHash.get(scannedParamNameInUnscannedParamExp);
// @TODO: we have no range??
SetValue setValue = new SetValue(target, rangeId, sedModel.getId());
setValue.setMath(math);
rt.addChange(setValue);
} else {
// non-numeric expression : add 'computeChange' to modified model
XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
ComputeChange computeChange = new ComputeChange(targetXpath, math);
for (String symbol : exprSymbols) {
String symbolName = TokenMangler.mangleToSName(symbol);
SymbolTableEntry ste1 = vcModel.getEntry(symbol);
// ste1 could be a math parameter, hence the above could return null
if (ste1 == null) {
ste1 = simContext.getMathDescription().getEntry(symbol);
}
if (ste1 != null) {
if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
computeChange.addVariable(sedmlVar);
} else {
double doubleValue = 0.0;
if (ste1 instanceof ReservedSymbol) {
doubleValue = getReservedSymbolValue(ste1);
} else if (ste instanceof Function) {
try {
doubleValue = ste.getExpression().evaluateConstant();
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' used in '" + unscannedParamName + "' expression : ", e);
}
} else {
doubleValue = ste.getConstantValue();
}
// TODO: shouldn't be s1_init_uM which is a math symbol, should be s0 (so use the ste-something from above)
// TODO: revert to Variable, not Parameter
Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
computeChange.addParameter(sedmlParameter);
}
} else {
throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
}
}
sedModel.addChange(computeChange);
}
}
}
sedmlModel.addModel(sedModel);
sedmlModel.addTask(rt);
}
} else {
// no math overrides, add basic task.
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
sedmlModel.addTask(sedmlTask);
// to be used later to add dataGenerators : one set of DGs per model (simContext).
taskRef = taskId;
}
// add one dataGenerator for 'time' for entire SEDML model.
// (using the id of the first task in model for 'taskRef' field of var since
String timeDataGenPrefix = DATAGENERATOR_TIME_NAME + "_" + taskRef;
DataGenerator timeDataGen = sedmlModel.getDataGeneratorWithId(timeDataGenPrefix);
if (timeDataGen == null) {
// org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, sedmlModel.getTasks().get(0).getId(), VariableSymbol.TIME);
org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, taskRef, VariableSymbol.TIME);
ASTNode math = Libsedml.parseFormulaString(DATAGENERATOR_TIME_SYMBOL);
timeDataGen = new DataGenerator(timeDataGenPrefix, timeDataGenPrefix, math);
timeDataGen.addVariable(timeVar);
sedmlModel.addDataGenerator(timeDataGen);
dataGeneratorsOfSim.add(timeDataGen);
}
// add dataGenerators for species
// get species list from SBML model.
String dataGenIdPrefix = "dataGen_" + taskRef;
String[] varNamesList = SimSpec.fromSBML(sbmlString).getVarsList();
for (String varName : varNamesList) {
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(varName, varName, taskRef, sbmlSupport.getXPathForSpecies(varName));
ASTNode varMath = Libsedml.parseFormulaString(varName);
// "dataGen_" + varCount; - old code
String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(varName);
DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, varMath);
dataGen.addVariable(sedmlVar);
sedmlModel.addDataGenerator(dataGen);
dataGeneratorsOfSim.add(dataGen);
varCount++;
}
// add DataGenerators for output functions here
ArrayList<AnnotatedFunction> outputFunctions = simContext.getOutputFunctionContext().getOutputFunctionsList();
for (AnnotatedFunction annotatedFunction : outputFunctions) {
Expression functionExpr = annotatedFunction.getExpression();
ASTNode funcMath = Libsedml.parseFormulaString(functionExpr.infix());
// "dataGen_" + varCount; - old code
String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(annotatedFunction.getName());
DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, funcMath);
String[] functionSymbols = functionExpr.getSymbols();
for (String symbol : functionSymbols) {
String symbolName = TokenMangler.mangleToSName(symbol);
// try to get symbol from model, if null, try simContext.mathDesc
SymbolTableEntry ste = vcModel.getEntry(symbol);
if (ste == null) {
ste = simContext.getMathDescription().getEntry(symbol);
}
if (ste instanceof SpeciesContext || ste instanceof Structure || ste instanceof ModelParameter) {
XPathTarget targetXPath = getTargetXPath(ste, l2gMap);
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, targetXPath.getTargetAsString());
dataGen.addVariable(sedmlVar);
} else {
double value = 0.0;
if (ste instanceof Function) {
try {
value = ste.getExpression().evaluateConstant();
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' for output function '" + annotatedFunction.getName() + "'.", e);
}
} else {
value = ste.getConstantValue();
}
Parameter sedmlParameter = new Parameter(symbolName, symbolName, value);
dataGen.addParameter(sedmlParameter);
}
}
sedmlModel.addDataGenerator(dataGen);
dataGeneratorsOfSim.add(dataGen);
varCount++;
}
simCount++;
// ignoring output for spatial deterministic (spatial stochastic is not exported to SEDML) and non-spatial stochastic applications with histogram
if (!(simContext.getGeometry().getDimension() > 0)) {
// ignore Output (Plot2d) for non-spatial stochastic simulation with histogram.
boolean bSimHasHistogram = false;
if (simContext.isStoch()) {
long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
if (numOfTrials > 1) {
// not histogram {
bSimHasHistogram = true;
}
}
if (!bSimHasHistogram) {
String plot2dId = "plot2d_" + TokenMangler.mangleToSName(vcSimulation.getName());
Plot2D sedmlPlot2d = new Plot2D(plot2dId, simContext.getName() + "plots");
sedmlPlot2d.addNote(createNotesElement("Plot of all variables and output functions from application '" + simContext.getName() + "' ; simulation '" + vcSimulation.getName() + "' in VCell model"));
List<DataGenerator> dataGenerators = sedmlModel.getDataGenerators();
String xDataRef = sedmlModel.getDataGeneratorWithId(DATAGENERATOR_TIME_NAME + "_" + taskRef).getId();
// add a curve for each dataGenerator in SEDML model
int curveCnt = 0;
for (DataGenerator dataGenerator : dataGeneratorsOfSim) {
// no curve for time, since time is xDateReference
if (dataGenerator.getId().equals(xDataRef)) {
continue;
}
String curveId = "curve_" + curveCnt++;
Curve curve = new Curve(curveId, curveId, false, false, xDataRef, dataGenerator.getId());
sedmlPlot2d.addCurve(curve);
}
sedmlModel.addOutput(sedmlPlot2d);
}
}
}
// end - for 'sims'
} else {
// end if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch()))
String msg = "\n\t" + simContextName + " : export of spatial stochastic (Smoldyn solver) applications to SEDML not supported at this time.";
sedmlNotesStr += msg;
}
// end : if-else simContext is not spatial stochastic
simContextCnt++;
}
// if sedmlNotesStr is not null, there were some applications that could not be exported to SEDML (eg., spatial stochastic). Create a notes element and add it to sedml Model.
if (sedmlNotesStr.length() > 0) {
sedmlNotesStr = "\n\tThe following applications in the VCell model were not exported to VCell : " + sedmlNotesStr;
sedmlModel.addNote(createNotesElement(sedmlNotesStr));
}
// error check : if there are no non-spatial deterministic applications (=> no models in SEDML document), complain.
if (sedmlModel.getModels().isEmpty()) {
throw new RuntimeException("No applications in biomodel to export to Sedml.");
}
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Error adding model to SEDML document : " + e.getMessage());
}
}
Also used :
Task(org.jlibsedml.Task)
SubTask(org.jlibsedml.SubTask)
RepeatedTask(org.jlibsedml.RepeatedTask)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
SpeciesContext(cbit.vcell.model.SpeciesContext)
ConstantArraySpec(cbit.vcell.solver.ConstantArraySpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
ChangeAttribute(org.jlibsedml.ChangeAttribute)
ComputeChange(org.jlibsedml.ComputeChange)
SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription)
SubTask(org.jlibsedml.SubTask)
AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)
Curve(org.jlibsedml.Curve)
SBMLExporter(org.vcell.sbml.vcell.SBMLExporter)
XmlParseException(cbit.vcell.xml.XmlParseException)
VectorRange(org.jlibsedml.VectorRange)
UniformRange(org.jlibsedml.UniformRange)
Range(org.jlibsedml.Range)
Algorithm(org.jlibsedml.Algorithm)
MathOverrides(cbit.vcell.solver.MathOverrides)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
DataGenerator(org.jlibsedml.DataGenerator)
MathMapping(cbit.vcell.mapping.MathMapping)
UniformTimeCourse(org.jlibsedml.UniformTimeCourse)
Plot2D(org.jlibsedml.Plot2D)
SbmlException(org.vcell.sbml.SbmlException)
VectorRange(org.jlibsedml.VectorRange)
SolverDescription(cbit.vcell.solver.SolverDescription)
ReservedSymbol(cbit.vcell.model.Model.ReservedSymbol)
StructureMapping(cbit.vcell.mapping.StructureMapping)
TimeBounds(cbit.vcell.solver.TimeBounds)
AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)
Function(cbit.vcell.math.Function)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ASTCi(org.jmathml.ASTCi)
RepeatedTask(org.jlibsedml.RepeatedTask)
ASTNode(org.jmathml.ASTNode)
Structure(cbit.vcell.model.Structure)
SimulationJob(cbit.vcell.solver.SimulationJob)
Pair(org.vcell.util.Pair)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MathSymbolMapping(cbit.vcell.mapping.MathSymbolMapping)
SbmlException(org.vcell.sbml.SbmlException)
TransformerException(javax.xml.transform.TransformerException)
XmlParseException(cbit.vcell.xml.XmlParseException)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
ParserConfigurationException(javax.xml.parsers.ParserConfigurationException)
SBMLSupport(org.jlibsedml.modelsupport.SBMLSupport)
Simulation(cbit.vcell.solver.Simulation)
Expression(cbit.vcell.parser.Expression)
BioModel(cbit.vcell.biomodel.BioModel)
UniformRange(org.jlibsedml.UniformRange)
BioModel(cbit.vcell.biomodel.BioModel)
Model(org.jlibsedml.Model)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
ProxyParameter(cbit.vcell.model.ProxyParameter)
Parameter(org.jlibsedml.Parameter)
XPathTarget(org.jlibsedml.XPathTarget)
SetValue(org.jlibsedml.SetValue)
Example 2 with Model
use of org.jlibsedml.Model in project vcell by virtualcell.
the class XmlHelper method sedmlToBioModel.
public static VCDocument sedmlToBioModel(VCLogger transLogger, ExternalDocInfo externalDocInfo, SedML sedml, AbstractTask selectedTask) throws Exception {
if (sedml.getModels().isEmpty()) {
return null;
}
VCDocument doc = null;
try {
// extract the path only from the sedml file
String fullPath = FileUtils.getFullPath(externalDocInfo.getFile().getAbsolutePath());
// Namespace namespace = sedml.getNamespace();
// iterate through all the elements and show them at the console
List<org.jlibsedml.Model> mmm = sedml.getModels();
for (Model mm : mmm) {
System.out.println(mm.toString());
}
List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
for (org.jlibsedml.Simulation ss : sss) {
System.out.println(ss.toString());
}
List<AbstractTask> ttt = sedml.getTasks();
for (AbstractTask tt : ttt) {
System.out.println(tt.toString());
}
List<DataGenerator> ddd = sedml.getDataGenerators();
for (DataGenerator dd : ddd) {
System.out.println(dd.toString());
}
List<Output> ooo = sedml.getOutputs();
for (Output oo : ooo) {
System.out.println(oo.toString());
}
KisaoTerm sedmlKisao = null;
// this will become the vCell simulation
org.jlibsedml.Simulation sedmlSimulation = null;
// the "original" model referred to by the task
org.jlibsedml.Model sedmlOriginalModel = null;
String sedmlOriginalModelName = null;
if (selectedTask == null) {
// no task, just pick the Model and find its sbml file
sedmlOriginalModelName = SEDMLUtil.getName(mmm.get(0));
} else {
if (selectedTask instanceof Task) {
sedmlOriginalModel = sedml.getModelWithId(selectedTask.getModelReference());
sedmlSimulation = sedml.getSimulation(selectedTask.getSimulationReference());
} else if (selectedTask instanceof RepeatedTask) {
RepeatedTask rt = (RepeatedTask) selectedTask;
assert (rt.getSubTasks().size() == 1);
// first (and only) subtask
SubTask st = rt.getSubTasks().entrySet().iterator().next().getValue();
String taskId = st.getTaskId();
AbstractTask t = sedml.getTaskWithId(taskId);
// get model and simulation from subtask
sedmlOriginalModel = sedml.getModelWithId(t.getModelReference());
sedmlSimulation = sedml.getSimulation(t.getSimulationReference());
} else {
throw new RuntimeException("Unexpected task " + selectedTask);
}
sedmlOriginalModelName = sedmlOriginalModel.getId();
sedmlKisao = KisaoOntology.getInstance().getTermById(sedmlSimulation.getAlgorithm().getKisaoID());
}
// UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
// Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
// identify the vCell solvers that would match best the sedml solver kisao id
List<SolverDescription> solverDescriptions = new ArrayList<>();
for (SolverDescription sd : SolverDescription.values()) {
KisaoTerm solverKisaoTerm = KisaoOntology.getInstance().getTermById(sd.getKisao());
if (solverKisaoTerm == null) {
break;
}
boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
if (isExactlySame && !solverKisaoTerm.isObsolete()) {
// we make a list with all the solvers that match the kisao
solverDescriptions.add(sd);
}
}
// from the list of vcell solvers that match the sedml kisao we select the ones that have a matching time step
SolverDescription solverDescription = null;
for (SolverDescription sd : solverDescriptions) {
if (true) {
solverDescription = sd;
break;
}
}
// find out everything else we need about the application we're going to use,
// some of the info will be needed when we parse the sbml file
boolean bSpatial = false;
Application appType = Application.NETWORK_DETERMINISTIC;
Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
for (SolverDescription.SolverFeature sf : sfList) {
switch(sf) {
case Feature_Rulebased:
appType = Application.RULE_BASED_STOCHASTIC;
break;
case Feature_Stochastic:
appType = Application.NETWORK_STOCHASTIC;
break;
case Feature_Deterministic:
appType = Application.NETWORK_DETERMINISTIC;
break;
case Feature_Spatial:
bSpatial = true;
break;
default:
break;
}
}
// -------------------------------------------------------------------------------------------
// extract bioModel name from sedx (or sedml) file
String bioModelName = FileUtils.getBaseName(externalDocInfo.getFile().getAbsolutePath());
// if we have repeated task, we ignore them, we just use the normal resolvers for archive and changes
// once the application and simulation are built, we iterate through the repeated tasks and
// add math overrides to the simulation for each repeated task
ArchiveComponents ac = null;
if (externalDocInfo.getFile().getPath().toLowerCase().endsWith("sedx") || externalDocInfo.getFile().getPath().toLowerCase().endsWith("omex")) {
ac = Libsedml.readSEDMLArchive(new FileInputStream(externalDocInfo.getFile().getPath()));
}
ModelResolver resolver = new ModelResolver(sedml);
if (ac != null) {
resolver.add(new ArchiveModelResolver(ac));
}
resolver.add(new FileModelResolver());
resolver.add(new RelativeFileModelResolver(fullPath));
String newMdl = resolver.getModelString(sedmlOriginalModel);
// sbmlSource with all the changes applied
XMLSource sbmlSource = new XMLSource(newMdl);
doc = XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
BioModel bioModel = (BioModel) doc;
bioModel.setName(bioModelName);
// we already have an application loaded from the sbml file, with initial conditions and stuff
// which may be not be suitable because the sedml kisao may need a different app type
// so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
// the new application we're making from the old one
SimulationContext newSimulationContext = null;
if (bioModel.getSimulationContexts().length == 1) {
SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, sedmlOriginalModelName, bSpatial, appType);
bioModel.removeSimulationContext(oldSimulationContext);
bioModel.addSimulationContext(newSimulationContext);
} else {
// length == 0
newSimulationContext = bioModel.addNewSimulationContext(sedmlOriginalModelName, appType);
}
// making the new vCell simulation based on the sedml simulation
newSimulationContext.refreshDependencies();
MathMappingCallback callback = new MathMappingCallbackTaskAdapter(null);
newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
newSimulation.setName(SEDMLUtil.getName(sedmlSimulation));
// TODO: make sure that everything has proper names
// we check the repeated tasks, if any, and add to the list of math overrides
// if(selectedTask instanceof RepeatedTask) {
// for(Change change : ((RepeatedTask) selectedTask).getChanges()) {
// if(!(change instanceof SetValue)) {
// throw new RuntimeException("Only 'SetValue' changes are supported for repeated tasks.");
// }
// SetValue setValue = (SetValue)change;
// // TODO: extract target from XPath
// // ......
// //
// String target = "s0"; // for now we just use a hardcoded thing
// ConstantArraySpec cas;
// Range range = ((RepeatedTask) selectedTask).getRange(setValue.getRangeReference());
// if(range instanceof UniformRange) {
// cas = ConstantArraySpec.createIntervalSpec(target, ((UniformRange) range).getStart(), ((UniformRange) range).getEnd(),
// range.getNumElements(), ((UniformRange) range).getType() == UniformRange.UniformType.LOG ? true : false);
// } else if(range instanceof VectorRange) {
// // List<String> constants = new ArrayList<> ();
// // for(int i=0; i<range.getNumElements(); i++) {
// // constants.add(new Constant(i+"", new Expression(range.getElementAt(i))));
// // }
// // cas = ConstantArraySpec.createListSpec(target, constants);
//
// } else {
// throw new RuntimeException("Only 'Uniform Range' and 'Vector Range' are supported at this time.");
// }
//
// }
// }
// we identify the type of sedml simulation (uniform time course, etc)
// and set the vCell simulation parameters accordingly
SolverTaskDescription simTaskDesc = newSimulation.getSolverTaskDescription();
TimeBounds timeBounds = new TimeBounds();
TimeStep timeStep = new TimeStep();
double outputTimeStep = 0.1;
if (sedmlSimulation instanceof UniformTimeCourse) {
// we translate initial time to zero, we provide output for the duration of the simulation
// because we can't select just an interval the way the SEDML simulation can
double initialTime = ((UniformTimeCourse) sedmlSimulation).getInitialTime();
double outputStartTime = ((UniformTimeCourse) sedmlSimulation).getOutputStartTime();
double outputEndTime = ((UniformTimeCourse) sedmlSimulation).getOutputEndTime();
double outputNumberOfPoints = ((UniformTimeCourse) sedmlSimulation).getNumberOfPoints();
outputTimeStep = (outputEndTime - outputStartTime) / outputNumberOfPoints;
timeBounds = new TimeBounds(0, outputEndTime - initialTime);
} else if (sedmlSimulation instanceof OneStep) {
// for anything other than UniformTimeCourse we just ignore
} else if (sedmlSimulation instanceof SteadyState) {
} else {
}
OutputTimeSpec outputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
simTaskDesc.setTimeBounds(timeBounds);
simTaskDesc.setTimeStep(timeStep);
simTaskDesc.setOutputTimeSpec(outputTimeSpec);
newSimulation.setSolverTaskDescription(simTaskDesc);
bioModel.addSimulation(newSimulation);
newSimulation.refreshDependencies();
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("Unable to initialize bioModel for the given selection.");
}
return doc;
}
Also used :
Task(org.jlibsedml.Task)
RepeatedTask(org.jlibsedml.RepeatedTask)
SimulationTask(cbit.vcell.messaging.server.SimulationTask)
AbstractTask(org.jlibsedml.AbstractTask)
SubTask(org.jlibsedml.SubTask)
ArrayList(java.util.ArrayList)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
FileModelResolver(org.jlibsedml.execution.FileModelResolver)
RelativeFileModelResolver(org.vcell.sedml.RelativeFileModelResolver)
ModelResolver(org.jlibsedml.execution.ModelResolver)
SteadyState(org.jlibsedml.SteadyState)
OutputTimeSpec(cbit.vcell.solver.OutputTimeSpec)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription)
SubTask(org.jlibsedml.SubTask)
VCDocument(org.vcell.util.document.VCDocument)
MathMappingCallback(cbit.vcell.mapping.SimulationContext.MathMappingCallback)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
FileInputStream(java.io.FileInputStream)
KisaoTerm(org.jlibsedml.modelsupport.KisaoTerm)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
DataGenerator(org.jlibsedml.DataGenerator)
UniformTimeCourse(org.jlibsedml.UniformTimeCourse)
Application(cbit.vcell.mapping.SimulationContext.Application)
AbstractTask(org.jlibsedml.AbstractTask)
SolverDescription(cbit.vcell.solver.SolverDescription)
RelativeFileModelResolver(org.vcell.sedml.RelativeFileModelResolver)
OneStep(org.jlibsedml.OneStep)
TimeBounds(cbit.vcell.solver.TimeBounds)
TimeStep(cbit.vcell.solver.TimeStep)
ArchiveComponents(org.jlibsedml.ArchiveComponents)
RepeatedTask(org.jlibsedml.RepeatedTask)
Output(org.jlibsedml.Output)
MathMappingCallbackTaskAdapter(cbit.vcell.mapping.MathMappingCallbackTaskAdapter)
FileModelResolver(org.jlibsedml.execution.FileModelResolver)
RelativeFileModelResolver(org.vcell.sedml.RelativeFileModelResolver)
SimulationContext(cbit.vcell.mapping.SimulationContext)
XMLStreamException(javax.xml.stream.XMLStreamException)
SbmlException(org.vcell.sbml.SbmlException)
SBMLException(org.sbml.jsbml.SBMLException)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
Simulation(cbit.vcell.solver.Simulation)
Model(org.jlibsedml.Model)
BioModel(cbit.vcell.biomodel.BioModel)
MathModel(cbit.vcell.mathmodel.MathModel)
BioModel(cbit.vcell.biomodel.BioModel)
Model(org.jlibsedml.Model)
Example 3 with Model
use of org.jlibsedml.Model in project vcell by virtualcell.
the class ModelCyclesDetector method validate.
/**
* @see ISedMLValidator
*/
public List<SedMLError> validate() throws XMLException {
List<SedMLError> errs = new ArrayList<SedMLError>();
List<Model> models = sedml.getModels();
for (Model model : models) {
String src = model.getSource();
String id = model.getId();
Set<String> ids = new HashSet<String>();
ids.add(id);
while (sedml.getModelWithId(src) != null) {
String newID = sedml.getModelWithId(src).getId();
if (ids.contains(newID)) {
int line = getLineNumberOfError(SEDMLTags.MODEL_TAG, model);
errs.add(new SedMLError(line, "Cycles detected in source references for model " + newID + " and " + sedml.getModelWithId(newID).getSource(), ERROR_SEVERITY.ERROR));
return errs;
} else {
ids.add(newID);
src = sedml.getModelWithId(src).getSource();
}
}
}
return errs;
}
Also used :
SedMLError(org.jlibsedml.SedMLError)
ArrayList(java.util.ArrayList)
Model(org.jlibsedml.Model)
HashSet(java.util.HashSet)
Example 4 with Model
use of org.jlibsedml.Model in project vcell by virtualcell.
the class StandaloneSEDMLTest method doit.
public static void doit(File archiveFile) throws Exception {
ArchiveComponents ac = null;
ac = Libsedml.readSEDMLArchive(new FileInputStream(archiveFile));
SEDMLDocument sedmlDoc = ac.getSedmlDocuments().get(0);
SedML sedml = sedmlDoc.getSedMLModel();
if (sedml == null || sedml.getModels().isEmpty()) {
throw new RuntimeException("sedml null or empty");
}
ModelResolver resolver = new ModelResolver(sedml);
// resolver.add(new FileModelResolver());
resolver.add(new ArchiveModelResolver(ac));
resolver.add(new BioModelsModelsRetriever());
resolver.add(new URLResourceRetriever());
// resolver.add(new RelativeFileModelResolver(FileUtils.getFullPath(archiveFile.getAbsolutePath())));
//
// iterate through all the elements and show them at the console
//
List<org.jlibsedml.Model> mmm = sedml.getModels();
for (Model mm : mmm) {
System.out.println(mm.toString());
}
List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
for (org.jlibsedml.Simulation ss : sss) {
System.out.println(ss.toString());
}
List<AbstractTask> ttt = sedml.getTasks();
for (AbstractTask tt : ttt) {
System.out.println(tt.toString());
}
List<DataGenerator> ddd = sedml.getDataGenerators();
for (DataGenerator dd : ddd) {
System.out.println(dd.toString());
}
List<Output> ooo = sedml.getOutputs();
for (Output oo : ooo) {
System.out.println(oo.toString());
}
//
// extract models referenced in tasks.
//
KisaoOntology kisaoInstance = KisaoOntology.getInstance();
// HashMap<String,Model> flattenedModels = new HashMap<String, Model>();
List<AbstractTask> taskList = sedml.getTasks();
for (AbstractTask task : taskList) {
String modelReference = task.getModelReference();
org.jlibsedml.Model sedmlOriginalModel = sedml.getModelWithId(modelReference);
String sbmlModelString = resolver.getModelString(sedmlOriginalModel);
// sbmlSource with all the changes applied
XMLSource sbmlSource = new XMLSource(sbmlModelString);
org.jlibsedml.Simulation sedmlSimulation = sedml.getSimulation(task.getSimulationReference());
Algorithm algorithm = sedmlSimulation.getAlgorithm();
KisaoTerm sedmlKisao = kisaoInstance.getTermById(algorithm.getKisaoID());
//
// try to find a VCell solverDescription to match the Kisao term
//
// UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
// Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
// identify the vCell solvers that would match best the sedml solver kisao id
List<SolverDescription> solverDescriptions = new ArrayList<>();
for (SolverDescription sd : SolverDescription.values()) {
KisaoTerm solverKisaoTerm = kisaoInstance.getTermById(sd.getKisao());
if (solverKisaoTerm == null) {
break;
}
boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
if (isExactlySame && !solverKisaoTerm.isObsolete()) {
// we make a list with all the solvers that match the kisao
solverDescriptions.add(sd);
}
}
if (solverDescriptions.isEmpty()) {
throw new RuntimeException("cannot find the solverDescription with exact match for Kisao term '" + sedmlKisao + "'");
}
// choose first one
SolverDescription solverDescription = solverDescriptions.get(0);
// find out everything else we need about the application we're going to use,
// some of the info will be needed when we parse the sbml file
boolean bSpatial = false;
Application appType = Application.NETWORK_DETERMINISTIC;
Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
for (SolverDescription.SolverFeature sf : sfList) {
switch(sf) {
case Feature_Rulebased:
appType = Application.RULE_BASED_STOCHASTIC;
break;
case Feature_Stochastic:
appType = Application.NETWORK_STOCHASTIC;
break;
case Feature_Deterministic:
appType = Application.NETWORK_DETERMINISTIC;
break;
case Feature_Spatial:
bSpatial = true;
break;
default:
break;
}
}
BioModel bioModel = (BioModel) XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
//
// we already have an application loaded from the sbml file, with initial conditions and stuff
// which may be not be suitable because the sedml kisao may need a different app type
// so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
//
// the new application we're making from the old one
SimulationContext newSimulationContext = null;
if (bioModel.getSimulationContexts().length == 1) {
SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
String newSCName = bioModel.getFreeSimulationContextName();
newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, newSCName, bSpatial, appType);
bioModel.addSimulationContext(newSimulationContext);
bioModel.removeSimulationContext(oldSimulationContext);
} else {
newSimulationContext = bioModel.addNewSimulationContext("App1", appType);
}
//
// making the new vCell simulation based on the sedml simulation
//
newSimulationContext.refreshDependencies();
MathMappingCallback callback = new MathMappingCallbackTaskAdapter(progressListener);
newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
newSimulation.setName(sedmlSimulation.getName());
bioModel.addSimulation(newSimulation);
// and set the vCell simulation parameters accordingly
if (sedmlSimulation instanceof UniformTimeCourse) {
} else if (sedmlSimulation instanceof OneStep) {
} else if (sedmlSimulation instanceof SteadyState) {
} else {
}
System.out.println(XmlHelper.bioModelToXML(bioModel));
}
}
Also used :
AbstractTask(org.jlibsedml.AbstractTask)
SolverDescription(cbit.vcell.solver.SolverDescription)
ArrayList(java.util.ArrayList)
OneStep(org.jlibsedml.OneStep)
ModelResolver(org.jlibsedml.execution.ModelResolver)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
SteadyState(org.jlibsedml.SteadyState)
SedML(org.jlibsedml.SedML)
ArchiveComponents(org.jlibsedml.ArchiveComponents)
Output(org.jlibsedml.Output)
MathMappingCallbackTaskAdapter(cbit.vcell.mapping.MathMappingCallbackTaskAdapter)
MathMappingCallback(cbit.vcell.mapping.SimulationContext.MathMappingCallback)
BioModelsModelsRetriever(org.jlibsedml.modelsupport.BioModelsModelsRetriever)
SimulationContext(cbit.vcell.mapping.SimulationContext)
Algorithm(org.jlibsedml.Algorithm)
FileInputStream(java.io.FileInputStream)
KisaoTerm(org.jlibsedml.modelsupport.KisaoTerm)
Simulation(cbit.vcell.solver.Simulation)
URLResourceRetriever(org.jlibsedml.modelsupport.URLResourceRetriever)
KisaoOntology(org.jlibsedml.modelsupport.KisaoOntology)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
Model(org.jlibsedml.Model)
SEDMLDocument(org.jlibsedml.SEDMLDocument)
DataGenerator(org.jlibsedml.DataGenerator)
BioModel(cbit.vcell.biomodel.BioModel)
BioModel(cbit.vcell.biomodel.BioModel)
Model(org.jlibsedml.Model)
UniformTimeCourse(org.jlibsedml.UniformTimeCourse)
XMLSource(cbit.vcell.xml.XMLSource)
Application(cbit.vcell.mapping.SimulationContext.Application)
Example 5 with Model
use of org.jlibsedml.Model in project vcell by virtualcell.
the class AbstractSedmlExecutor method runSimulations.
/**
* Main method for running simulations
*
* @return A non-null Map<AbstractTask, IRawSedmlSimulationResults>
*/
public final Map<AbstractTask, IRawSedmlSimulationResults> runSimulations() {
failureMessages.clear();
log.debug("Running simulations");
Map<AbstractTask, IRawSedmlSimulationResults> res = new HashMap<AbstractTask, IRawSedmlSimulationResults>();
Set<AbstractTask> tasksToExecute = new HashSet<AbstractTask>();
if (task != null) {
tasksToExecute.add(task);
} else {
tasksToExecute = findTasks(output);
}
if (tasksToExecute.isEmpty()) {
addStatus(new ExecutionStatusElement(null, NO_TASKS_ERROR, ExecutionStatusType.ERROR));
return res;
}
log.debug("Got a task to execute");
for (AbstractTask t : tasksToExecute) {
if (!getSimulatableTasks().contains(t)) {
addStatus(new ExecutionStatusElement(null, NO_SIMULATABLE_TASK_ERROR1 + t.getId() + NO_SIMULATABLE_TASK_ERROR2, ExecutionStatusType.ERROR));
return res;
}
}
for (AbstractTask task : tasksToExecute) {
Model m = sedml.getModelWithId(task.getModelReference());
if (!supportsLanguage(m.getLanguage())) {
addStatus(new ExecutionStatusElement(null, LANGUAGE_NOT_SUPPORTED_ERROR + m.getLanguage(), ExecutionStatusType.ERROR));
return res;
}
log.debug("language {} is OK", m.getLanguage());
String changedModel = modelResolver.getModelString(m);
log.debug("Changed modell is {}", changedModel);
if (changedModel == null) {
addStatus(new ExecutionStatusElement(null, modelResolver.getMessage(), ExecutionStatusType.ERROR));
}
log.debug("Ready to execute");
IRawSedmlSimulationResults results = executeSimulation(changedModel, (UniformTimeCourse) sedml.getSimulation(task.getSimulationReference()));
if (results == null) {
addStatus(new ExecutionStatusElement(null, "Simulation failed during execution: " + task.getSimulationReference() + " with model: " + task.getModelReference(), ExecutionStatusType.ERROR));
// return res;
}
log.debug("Results are {}", results);
res.put(task, results);
}
return res;
}
Also used :
AbstractTask(org.jlibsedml.AbstractTask)
HashMap(java.util.HashMap)
Model(org.jlibsedml.Model)
HashSet(java.util.HashSet)
Aggregations
Model (org.jlibsedml.Model)7
ArrayList (java.util.ArrayList)6
BioModel (cbit.vcell.biomodel.BioModel)5
SimulationContext (cbit.vcell.mapping.SimulationContext)5
DataGenerator (org.jlibsedml.DataGenerator)5
UniformTimeCourse (org.jlibsedml.UniformTimeCourse)5
ExpressionException (cbit.vcell.parser.ExpressionException)4
IOException (java.io.IOException)4
AbstractTask (org.jlibsedml.AbstractTask)4
Algorithm (org.jlibsedml.Algorithm)4
RepeatedTask (org.jlibsedml.RepeatedTask)4
SubTask (org.jlibsedml.SubTask)4
Task (org.jlibsedml.Task)4
SbmlException (org.vcell.sbml.SbmlException)4
MathMappingCallbackTaskAdapter (cbit.vcell.mapping.MathMappingCallbackTaskAdapter)3
Application (cbit.vcell.mapping.SimulationContext.Application)3
MathMappingCallback (cbit.vcell.mapping.SimulationContext.MathMappingCallback)3
Simulation (cbit.vcell.solver.Simulation)3
SolverDescription (cbit.vcell.solver.SolverDescription)3
MathMapping (cbit.vcell.mapping.MathMapping)2
