use of cbit.vcell.solver.Simulation in project vcell by virtualcell.
the class OdeFileWriter method createStateVariables.
private void createStateVariables() throws Exception {
Simulation simulation = simTask.getSimulation();
MathDescription mathDescription = simulation.getMathDescription();
SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
// get Ode's from MathDescription and create ODEStateVariables
Enumeration<Equation> enum1 = mathDescription.getSubDomains().nextElement().getEquations();
SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
while (enum1.hasMoreElements()) {
Equation equation = enum1.nextElement();
if (equation instanceof OdeEquation) {
fieldStateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
} else {
throw new MathException("encountered non-ode equation, unsupported");
}
}
// Get sensitivity variables
Variable[] variables = simSymbolTable.getVariables();
Vector<SensVariable> sensVariables = new Vector<SensVariable>();
Constant sensitivityParameter = solverTaskDescription.getSensitivityParameter();
if (sensitivityParameter != null) {
Constant origSensParam = sensitivityParameter;
Constant overriddenSensParam = (Constant) simSymbolTable.getVariable(origSensParam.getName());
for (int i = 0; i < variables.length; i++) {
if (variables[i] instanceof VolVariable) {
VolVariable volVariable = (VolVariable) variables[i];
SensVariable sv = new SensVariable(volVariable, overriddenSensParam);
sensVariables.addElement(sv);
}
}
}
if (rateSensitivity == null) {
rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
}
if (jacobian == null) {
jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
}
// get Jacobian and RateSensitivities from MathDescription and create SensStateVariables
for (int v = 0; v < sensVariables.size(); v++) {
fieldStateVariables.addElement(new SensStateVariable(sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
}
}
use of cbit.vcell.solver.Simulation in project vcell by virtualcell.
the class XmlHelper method applyOverridesForSBML.
/**
* applyOverrides: private method to apply overrides from the simulation in 'simJob' to simContext, if any.
* Start off by cloning biomodel, since all the references are required in cloned simContext and is
* best retained by cloning biomodel.
* @param bm - biomodel to be cloned
* @param sc - simulationContext to be cloned and overridden using math overrides in simulation
* @param simJob - simulationJob from where simulation with overrides is obtained.
* @return
*/
public static SimulationContext applyOverridesForSBML(BioModel bm, SimulationContext sc, SimulationJob simJob) {
SimulationContext overriddenSimContext = sc;
if (simJob != null) {
Simulation sim = simJob.getSimulation();
// need to clone Biomodel, simContext, etc. only if simulation has override(s)
try {
if (sim != null && sim.getMathOverrides().hasOverrides()) {
// BioModel clonedBM = (BioModel)BeanUtils.cloneSerializable(bm);
BioModel clonedBM = XMLToBioModel(new XMLSource(bioModelToXML(bm)));
clonedBM.refreshDependencies();
// get the simContext in cloned Biomodel that corresponds to 'sc'
SimulationContext[] simContexts = clonedBM.getSimulationContexts();
for (int i = 0; i < simContexts.length; i++) {
if (simContexts[i].getName().equals(sc.getName())) {
overriddenSimContext = simContexts[i];
break;
}
}
//
overriddenSimContext.getModel().refreshDependencies();
overriddenSimContext.refreshDependencies();
MathMapping mathMapping = overriddenSimContext.createNewMathMapping();
MathSymbolMapping msm = mathMapping.getMathSymbolMapping();
MathOverrides mathOverrides = sim.getMathOverrides();
String[] moConstNames = mathOverrides.getOverridenConstantNames();
for (int i = 0; i < moConstNames.length; i++) {
cbit.vcell.math.Constant overriddenConstant = mathOverrides.getConstant(moConstNames[i]);
// Expression overriddenExpr = mathOverrides.getActualExpression(moConstNames[i], 0);
Expression overriddenExpr = mathOverrides.getActualExpression(moConstNames[i], simJob.getJobIndex());
// The above constant (from mathoverride) is not the same instance as the one in the MathSymbolMapping hash.
// Hence retreive the correct instance from mathSymbolMapping (mathMapping -> mathDescription) and use it to
// retrieve its value (symbolTableEntry) from hash.
cbit.vcell.math.Variable overriddenVar = msm.findVariableByName(overriddenConstant.getName());
cbit.vcell.parser.SymbolTableEntry[] stes = msm.getBiologicalSymbol(overriddenVar);
if (stes == null) {
throw new NullPointerException("No matching biological symbol for : " + overriddenConstant.getName());
}
if (stes.length > 1) {
throw new RuntimeException("Cannot have more than one mapping entry for constant : " + overriddenConstant.getName());
}
if (stes[0] instanceof Parameter) {
Parameter param = (Parameter) stes[0];
if (param.isExpressionEditable()) {
if (param instanceof Kinetics.KineticsParameter) {
// Kinetics param has to be set separately for the integrity of the kinetics object
Kinetics.KineticsParameter kinParam = (Kinetics.KineticsParameter) param;
ReactionStep[] rs = overriddenSimContext.getModel().getReactionSteps();
for (int j = 0; j < rs.length; j++) {
if (rs[j].getNameScope().getName().equals(kinParam.getNameScope().getName())) {
rs[j].getKinetics().setParameterValue(kinParam, overriddenExpr);
}
}
} else if (param instanceof cbit.vcell.model.ExpressionContainer) {
// If it is any other editable param, set its expression with the
((cbit.vcell.model.ExpressionContainer) param).setExpression(overriddenExpr);
}
}
}
// end - if (stes[0] is Parameter)
}
// end - for moConstNames
}
// end if (sim has MathOverrides)
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Could not apply overrides from simulation to application parameters : " + e.getMessage());
}
}
// end if (simJob != null)
return overriddenSimContext;
}
use of cbit.vcell.solver.Simulation in project vcell by virtualcell.
the class XmlHelper method XMLToSim.
public static Simulation XMLToSim(String xmlString) throws XmlParseException {
Simulation sim = null;
Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
try {
if (xmlString == null || xmlString.length() == 0) {
throw new XmlParseException("Invalid xml for Simulation: " + xmlString);
}
// default parser and no validation
Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
Element simElement = root.getChild(XMLTags.SimulationTag, ns);
Element mdElement = root.getChild(XMLTags.MathDescriptionTag, ns);
Element geomElement = root.getChild(XMLTags.GeometryTag, ns);
XmlReader reader = new XmlReader(true, ns);
Geometry geom = null;
if (geomElement != null) {
geom = reader.getGeometry(geomElement);
}
MathDescription md = reader.getMathDescription(mdElement, geom);
sim = reader.getSimulation(simElement, md);
} catch (Exception pve) {
pve.printStackTrace();
throw new XmlParseException("Unable to parse simulation string.", pve);
}
sim.refreshDependencies();
return sim;
}
use of cbit.vcell.solver.Simulation in project vcell by virtualcell.
the class XmlHelper method XMLToSimTask.
public static SimulationTask XMLToSimTask(String xmlString) throws XmlParseException, ExpressionException {
Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
try {
if (xmlString == null || xmlString.length() == 0) {
throw new XmlParseException("Invalid xml for Simulation: " + xmlString);
}
// default parser and no validation
Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
if (!root.getName().equals(SimulationTask_tag)) {
throw new RuntimeException("expecting top level element to be " + SimulationTask_tag);
}
int taskId = Integer.parseInt(root.getAttributeValue(TaskId_attr));
int jobIndex = Integer.parseInt(root.getAttributeValue(JobIndex_attr));
String computeResource = root.getChildTextTrim(ComputeResource_tag, ns);
List<?> children = root.getChildren(FieldFunctionIdentifierSpec_tag, ns);
ArrayList<FieldDataIdentifierSpec> fdisArrayList = new ArrayList<FieldDataIdentifierSpec>();
for (Object child : children) {
if (child instanceof Element) {
String fdisText = ((Element) child).getTextTrim();
FieldDataIdentifierSpec fdis = FieldDataIdentifierSpec.fromCSVString(fdisText);
fdisArrayList.add(fdis);
}
}
FieldDataIdentifierSpec[] fdisArray = fdisArrayList.toArray(new FieldDataIdentifierSpec[0]);
Element simElement = root.getChild(XMLTags.SimulationTag, ns);
Element mdElement = root.getChild(XMLTags.MathDescriptionTag, ns);
Element geomElement = root.getChild(XMLTags.GeometryTag, ns);
XmlReader reader = new XmlReader(true, ns);
Geometry geom = null;
if (geomElement != null) {
geom = reader.getGeometry(geomElement);
}
MathDescription md = reader.getMathDescription(mdElement, geom);
Simulation sim = reader.getSimulation(simElement, md);
sim.refreshDependencies();
SimulationJob simJob = new SimulationJob(sim, jobIndex, fdisArray);
SimulationTask simTask = new SimulationTask(simJob, taskId, computeResource);
return simTask;
} catch (Exception pve) {
pve.printStackTrace();
throw new XmlParseException("Unable to parse simulation string.", pve);
}
}
use of cbit.vcell.solver.Simulation 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;
}
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