Example 1 with Expression
use of cbit.vcell.parser.Expression 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 Expression
use of cbit.vcell.parser.Expression in project vcell by virtualcell.
the class SBMLImporter method addParameters.
/**
* addParameters : Adds global parameters from SBML model to VCell model. If
* expression for global parameter contains species, creates a conc_factor
* parameter (conversion from SBML - VCell conc units) and adds this factor
* to VC global params list, and replaces occurances of 'sp' with
* 'sp*concFactor' in original param expression.
*
* @throws PropertyVetoException
*/
protected void addParameters() throws Exception {
ListOf listofGlobalParams = sbmlModel.getListOfParameters();
if (listofGlobalParams == null) {
System.out.println("No Global Parameters");
return;
}
Model vcModel = vcBioModel.getSimulationContext(0).getModel();
ArrayList<ModelParameter> vcModelParamsList = new ArrayList<Model.ModelParameter>();
// create a hash of reserved symbols so that if there is any reserved
// symbol occurring as a global parameter in the SBML model,
// the hash can be used to check for reserved symbols, so that it will
// not be added as a global parameter in VCell,
// since reserved symbols cannot be used as other variables (species,
// structureSize, parameters, reactions, etc.).
HashSet<String> reservedSymbolHash = new HashSet<String>();
for (ReservedSymbol rs : vcModel.getReservedSymbols()) {
reservedSymbolHash.add(rs.getName());
}
ModelUnitSystem modelUnitSystem = vcModel.getUnitSystem();
for (int i = 0; i < sbmlModel.getNumParameters(); i++) {
Parameter sbmlGlobalParam = (Parameter) listofGlobalParams.get(i);
String paramName = sbmlGlobalParam.getId();
SpatialParameterPlugin spplugin = null;
if (bSpatial) {
// check if parameter id is x/y/z : if so, check if its
// 'spatialSymbolRef' child's spatial id and type are non-empty.
// If so, the parameter represents a spatial element.
// If not, throw an exception, since a parameter that does not
// represent a spatial element cannot have an id of x/y/z
spplugin = (SpatialParameterPlugin) sbmlGlobalParam.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
if (paramName.equals("x") || paramName.equals("y") || paramName.equals("z")) {
boolean bSpatialParam = (spplugin != null && spplugin.getParamType() instanceof SpatialSymbolReference);
// if (a) and (b) are true, continue with the next parameter
if (!bSpatialParam) {
throw new RuntimeException("Parameter '" + paramName + "' is not a spatial parameter : Cannot have a variable in VCell named '" + paramName + "' unless it is a spatial variable.");
} else {
// parameter to the list of vcell parameters.
continue;
}
}
}
//
// Get param value if set or get its expression from rule
//
// Check if param is defined by an assignment rule or initial
// assignment. If so, that value overrides the value existing in the
// param element.
// assignment rule, first
Expression valueExpr = getValueFromAssignmentRule(paramName);
if (valueExpr == null) {
if (sbmlGlobalParam.isSetValue()) {
double value = sbmlGlobalParam.getValue();
valueExpr = new Expression(value);
} else {
// if value for global param is not set and param has a rate
// rule, need to set an init value for param (else, there
// will be a problem in reaction which uses this parameter).
// use a 'default' initial value of '0'
valueExpr = new Expression(0.0);
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.Priority.LowPriority,
// "Parameter did not have an initial value, but has a rate rule specified. Using a default value of 0.0.");
}
}
if (valueExpr != null) {
// valueExpr will be changed
valueExpr = adjustExpression(valueExpr, vcModel);
}
// extension
if (bSpatial) {
VCAssert.assertTrue(spplugin != null, "invalid initialization logic");
ParameterType sbmlParamType = spplugin.getParamType();
SpeciesContext paramSpContext = null;
SpeciesContextSpec vcSpContextsSpec = null;
// Check for diffusion coefficient(s)
if (sbmlParamType instanceof DiffusionCoefficient) {
DiffusionCoefficient diffCoeff = (DiffusionCoefficient) sbmlParamType;
if (diffCoeff != null && diffCoeff.isSetVariable()) {
// get the var of diffCoeff; find appropriate spContext
// in vcell; set its diff param to param value.
paramSpContext = vcModel.getSpeciesContext(diffCoeff.getVariable());
if (paramSpContext != null) {
vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
vcSpContextsSpec.getDiffusionParameter().setExpression(valueExpr);
}
// coeff parameter to the list of vcell parameters.
continue;
}
}
// Check for advection coefficient(s)
if (sbmlParamType instanceof AdvectionCoefficient) {
AdvectionCoefficient advCoeff = (AdvectionCoefficient) sbmlParamType;
if (advCoeff != null && advCoeff.isSetVariable()) {
// get the var of advCoeff; find appropriate spContext
// in vcell; set its adv param to param value.
paramSpContext = vcModel.getSpeciesContext(advCoeff.getVariable());
if (paramSpContext != null) {
vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
CoordinateKind coordKind = advCoeff.getCoordinate();
SpeciesContextSpecParameter param = null;
switch(coordKind) {
case cartesianX:
{
param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
break;
}
case cartesianY:
{
param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
break;
}
case cartesianZ:
{
param = vcSpContextsSpec.getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
break;
}
}
param.setExpression(valueExpr);
}
// coeff parameter to the list of vcell parameters.
continue;
}
}
// Check for Boundary condition(s)
if (sbmlParamType instanceof BoundaryCondition) {
BoundaryCondition bCondn = (BoundaryCondition) sbmlParamType;
if (bCondn != null && bCondn.isSetVariable()) {
// get the var of boundaryCondn; find appropriate
// spContext in vcell;
// set the BC param of its speciesContextSpec to param
// value.
paramSpContext = vcModel.getSpeciesContext(bCondn.getVariable());
if (paramSpContext == null) {
throw new RuntimeException("unable to process boundary condition for variable " + bCondn.getVariable());
}
StructureMapping sm = vcBioModel.getSimulationContext(0).getGeometryContext().getStructureMapping(paramSpContext.getStructure());
vcSpContextsSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(paramSpContext);
for (CoordinateComponent coordComp : getSbmlGeometry().getListOfCoordinateComponents()) {
if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMinimum().getSpatialId())) {
switch(coordComp.getType()) {
case cartesianX:
{
vcSpContextsSpec.getBoundaryXmParameter().setExpression(valueExpr);
}
case cartesianY:
{
vcSpContextsSpec.getBoundaryYmParameter().setExpression(valueExpr);
}
case cartesianZ:
{
vcSpContextsSpec.getBoundaryZmParameter().setExpression(valueExpr);
}
}
}
if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMaximum().getSpatialId())) {
switch(coordComp.getType()) {
case cartesianX:
{
vcSpContextsSpec.getBoundaryXpParameter().setExpression(valueExpr);
}
case cartesianY:
{
vcSpContextsSpec.getBoundaryYpParameter().setExpression(valueExpr);
}
case cartesianZ:
{
vcSpContextsSpec.getBoundaryZpParameter().setExpression(valueExpr);
}
}
}
}
continue;
}
}
// Check for Boundary condition(s)
if (sbmlParamType instanceof SpatialSymbolReference) {
SpatialSymbolReference spatialSymbolRef = (SpatialSymbolReference) sbmlParamType;
throw new RuntimeException("generic Spatial Symbol References not yet supported, unresolved spatial reference '" + spatialSymbolRef.getSpatialRef() + "'");
}
}
// doesn't exist.
if (vcModel.getModelParameter(paramName) == null) {
VCUnitDefinition glParamUnitDefn = sbmlUnitIdentifierHash.get(sbmlGlobalParam.getUnits());
// set it to TBD or check if it was dimensionless.
if (glParamUnitDefn == null) {
glParamUnitDefn = modelUnitSystem.getInstance_TBD();
}
// VCell : cannot add reserved symbol to model params.
if (!reservedSymbolHash.contains(paramName)) {
ModelParameter vcGlobalParam = vcModel.new ModelParameter(paramName, valueExpr, Model.ROLE_UserDefined, glParamUnitDefn);
if (paramName.length() > 64) {
// record global parameter name in annotation if it is
// longer than 64 characeters
vcGlobalParam.setDescription("Parameter Name : " + paramName);
}
vcModelParamsList.add(vcGlobalParam);
}
}
}
// end for - sbmlModel.parameters
vcModel.setModelParameters(vcModelParamsList.toArray(new ModelParameter[0]));
}
Also used :
ReservedSymbol(cbit.vcell.model.Model.ReservedSymbol)
ArrayList(java.util.ArrayList)
SpatialParameterPlugin(org.sbml.jsbml.ext.spatial.SpatialParameterPlugin)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
CoordinateKind(org.sbml.jsbml.ext.spatial.CoordinateKind)
ListOf(org.sbml.jsbml.ListOf)
HashSet(java.util.HashSet)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
CoordinateComponent(org.sbml.jsbml.ext.spatial.CoordinateComponent)
AdvectionCoefficient(org.sbml.jsbml.ext.spatial.AdvectionCoefficient)
ParameterType(org.sbml.jsbml.ext.spatial.ParameterType)
BioEventParameterType(cbit.vcell.mapping.BioEvent.BioEventParameterType)
DiffusionCoefficient(org.sbml.jsbml.ext.spatial.DiffusionCoefficient)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
SpatialSymbolReference(org.sbml.jsbml.ext.spatial.SpatialSymbolReference)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
Expression(cbit.vcell.parser.Expression)
BoundaryCondition(org.sbml.jsbml.ext.spatial.BoundaryCondition)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
Parameter(org.sbml.jsbml.Parameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
LocalParameter(org.sbml.jsbml.LocalParameter)
KineticsProxyParameter(cbit.vcell.model.Kinetics.KineticsProxyParameter)
UnresolvedParameter(cbit.vcell.model.Kinetics.UnresolvedParameter)
Example 3 with Expression
use of cbit.vcell.parser.Expression in project vcell by virtualcell.
the class SBMLImporter method addReactions.
/**
* addReactions:
*/
protected void addReactions(VCMetaData metaData) {
if (sbmlModel == null) {
throw new SBMLImportException("SBML model is NULL");
}
ListOf<Reaction> reactions = sbmlModel.getListOfReactions();
final int numReactions = reactions.size();
if (numReactions == 0) {
lg.info("No Reactions");
return;
}
// all reactions
ArrayList<ReactionStep> vcReactionList = new ArrayList<>();
// just the fast ones
ArrayList<ReactionStep> fastReactionList = new ArrayList<>();
Model vcModel = vcBioModel.getSimulationContext(0).getModel();
ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
try {
for (Reaction sbmlRxn : reactions) {
ReactionStep vcReaction = null;
String rxnName = sbmlRxn.getId();
boolean bReversible = true;
if (sbmlRxn.isSetReversible()) {
bReversible = sbmlRxn.getReversible();
}
// Check of reaction annotation is present; if so, does it have
// an embedded element (flux or simpleRxn).
// Create a fluxReaction or simpleReaction accordingly.
Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlRxn);
Structure reactionStructure = getReactionStructure(sbmlRxn, vcSpeciesContexts, sbmlImportRelatedElement);
if (sbmlImportRelatedElement != null) {
Element embeddedRxnElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, REACTION);
if (embeddedRxnElement != null) {
if (embeddedRxnElement.getName().equals(XMLTags.FluxStepTag)) {
// If embedded element is a flux reaction, set flux
// reaction's strucure, flux carrier, physicsOption
// from the element attributes.
String structName = embeddedRxnElement.getAttributeValue(XMLTags.StructureAttrTag);
CastInfo<Membrane> ci = SBMLHelper.getTypedStructure(Membrane.class, vcModel, structName);
if (!ci.isGood()) {
throw new SBMLImportException("Appears that the flux reaction is occuring on " + ci.actualName() + ", not a membrane.");
}
vcReaction = new FluxReaction(vcModel, ci.get(), null, rxnName, bReversible);
vcReaction.setModel(vcModel);
// Set the fluxOption on the flux reaction based on
// whether it is molecular, molecular & electrical,
// electrical.
String fluxOptionStr = embeddedRxnElement.getAttributeValue(XMLTags.FluxOptionAttrTag);
if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularOnly)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_ONLY);
} else if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL);
} else if (fluxOptionStr.equals(XMLTags.FluxOptionElectricalOnly)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_ELECTRICAL_ONLY);
} else {
localIssueList.add(new Issue(vcReaction, issueContext, IssueCategory.SBMLImport_Reaction, "Unknown FluxOption : " + fluxOptionStr + " for SBML reaction : " + rxnName, Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.ReactionError,
// "Unknown FluxOption : " + fluxOptionStr +
// " for SBML reaction : " + rxnName);
}
} else if (embeddedRxnElement.getName().equals(XMLTags.SimpleReactionTag)) {
// if embedded element is a simple reaction, set
// simple reaction's structure from element
// attributes
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
}
} else {
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
}
} else {
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
}
// set annotations and notes on vcReactions[i]
sbmlAnnotationUtil.readAnnotation(vcReaction, sbmlRxn);
sbmlAnnotationUtil.readNotes(vcReaction, sbmlRxn);
// the limit on the reactionName length.
if (rxnName.length() > 64) {
String freeTextAnnotation = metaData.getFreeTextAnnotation(vcReaction);
if (freeTextAnnotation == null) {
freeTextAnnotation = "";
}
StringBuffer oldRxnAnnotation = new StringBuffer(freeTextAnnotation);
oldRxnAnnotation.append("\n\n" + rxnName);
metaData.setFreeTextAnnotation(vcReaction, oldRxnAnnotation.toString());
}
// Now add the reactants, products, modifiers as specified by
// the sbmlRxn
addReactionParticipants(sbmlRxn, vcReaction);
KineticLaw kLaw = sbmlRxn.getKineticLaw();
Kinetics kinetics = null;
if (kLaw != null) {
// Convert the formula from kineticLaw into MathML and then
// to an expression (infix) to be used in VCell kinetics
ASTNode sbmlRateMath = kLaw.getMath();
Expression kLawRateExpr = getExpressionFromFormula(sbmlRateMath);
Expression vcRateExpression = new Expression(kLawRateExpr);
// modifier (catalyst) to the reaction.
for (int k = 0; k < vcSpeciesContexts.length; k++) {
if (vcRateExpression.hasSymbol(vcSpeciesContexts[k].getName())) {
if ((vcReaction.getReactant(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getProduct(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getCatalyst(vcSpeciesContexts[k].getName()) == null)) {
// This means that the speciesContext is not a
// reactant, product or modifier : it has to be
// added to the VC Rxn as a catalyst
vcReaction.addCatalyst(vcSpeciesContexts[k]);
}
}
}
// set kinetics on VCell reaction
if (bSpatial) {
// if spatial SBML ('isSpatial' attribute set), create
// DistributedKinetics)
SpatialReactionPlugin ssrplugin = (SpatialReactionPlugin) sbmlRxn.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
// 'spatial'
if (ssrplugin != null && ssrplugin.getIsLocal()) {
kinetics = new GeneralKinetics(vcReaction);
} else {
kinetics = new GeneralLumpedKinetics(vcReaction);
}
} else {
kinetics = new GeneralLumpedKinetics(vcReaction);
}
// set kinetics on vcReaction
vcReaction.setKinetics(kinetics);
// If the name of the rate parameter has been changed by
// user, or matches with global/local param,
// it has to be changed.
resolveRxnParameterNameConflicts(sbmlRxn, kinetics, sbmlImportRelatedElement);
/**
* Now, based on the kinetic law expression, see if the rate
* is expressed in concentration/time or substance/time : If
* the compartment_id of the compartment corresponding to
* the structure in which the reaction takes place occurs in
* the rate law expression, it is in concentration/time;
* divide it by the compartment size and bring in the rate
* law as 'Distributed' kinetics. If not, the rate law is in
* substance/time; bring it in (as is) as 'Lumped' kinetics.
*/
ListOf<LocalParameter> localParameters = kLaw.getListOfLocalParameters();
for (LocalParameter p : localParameters) {
String paramName = p.getId();
KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
if (kineticsParameter == null) {
// add unresolved for now to prevent errors in kinetics.setParameterValue(kp,vcRateExpression) below
kinetics.addUnresolvedParameter(paramName);
}
}
KineticsParameter kp = kinetics.getAuthoritativeParameter();
if (lg.isDebugEnabled()) {
lg.debug("Setting " + kp.getName() + ": " + vcRateExpression.infix());
}
kinetics.setParameterValue(kp, vcRateExpression);
// If there are any global parameters used in the kinetics,
// and if they have species,
// check if the species are already reactionParticipants in
// the reaction. If not, add them as catalysts.
KineticsProxyParameter[] kpps = kinetics.getProxyParameters();
for (int j = 0; j < kpps.length; j++) {
if (kpps[j].getTarget() instanceof ModelParameter) {
ModelParameter mp = (ModelParameter) kpps[j].getTarget();
HashSet<String> refSpeciesNameHash = new HashSet<String>();
getReferencedSpeciesInExpr(mp.getExpression(), refSpeciesNameHash);
java.util.Iterator<String> refSpIterator = refSpeciesNameHash.iterator();
while (refSpIterator.hasNext()) {
String spName = refSpIterator.next();
org.sbml.jsbml.Species sp = sbmlModel.getSpecies(spName);
ArrayList<ReactionParticipant> rpArray = getVCReactionParticipantsFromSymbol(vcReaction, sp.getId());
if (rpArray == null || rpArray.size() == 0) {
// This means that the speciesContext is not
// a reactant, product or modifier : it has
// to be added as a catalyst
vcReaction.addCatalyst(vcModel.getSpeciesContext(sp.getId()));
}
}
}
}
// model - local params cannot be defined by rules.
for (LocalParameter param : localParameters) {
String paramName = param.getId();
Expression exp = new Expression(param.getValue());
String unitString = param.getUnits();
VCUnitDefinition paramUnit = sbmlUnitIdentifierHash.get(unitString);
if (paramUnit == null) {
paramUnit = vcModelUnitSystem.getInstance_TBD();
}
// check if sbml local param is in kinetic params list;
// if so, add its value.
boolean lpSet = false;
KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
if (kineticsParameter != null) {
if (lg.isDebugEnabled()) {
lg.debug("Setting local " + kineticsParameter.getName() + ": " + exp.infix());
}
kineticsParameter.setExpression(exp);
kineticsParameter.setUnitDefinition(paramUnit);
lpSet = true;
} else {
UnresolvedParameter ur = kinetics.getUnresolvedParameter(paramName);
if (ur != null) {
kinetics.addUserDefinedKineticsParameter(paramName, exp, paramUnit);
lpSet = true;
}
}
if (!lpSet) {
// check if it is a proxy parameter (specifically,
// speciesContext or model parameter (structureSize
// too)).
KineticsProxyParameter kpp = kinetics.getProxyParameter(paramName);
// and units to local param values
if (kpp != null && kpp.getTarget() instanceof ModelParameter) {
kinetics.convertParameterType(kpp, false);
kineticsParameter = kinetics.getKineticsParameter(paramName);
kinetics.setParameterValue(kineticsParameter, exp);
kineticsParameter.setUnitDefinition(paramUnit);
}
}
}
} else {
// sbmlKLaw was null, so creating a GeneralKinetics with 0.0
// as rate.
kinetics = new GeneralKinetics(vcReaction);
}
// end - if-else KLaw != null
// set the reaction kinetics, and add reaction to the vcell
// model.
kinetics.resolveUndefinedUnits();
// System.out.println("ADDED SBML REACTION : \"" + rxnName +
// "\" to VCModel");
vcReactionList.add(vcReaction);
if (sbmlRxn.isSetFast() && sbmlRxn.getFast()) {
fastReactionList.add(vcReaction);
}
}
// end - for vcReactions
ReactionStep[] array = vcReactionList.toArray(new ReactionStep[vcReactionList.size()]);
vcModel.setReactionSteps(array);
final ReactionContext rc = vcBioModel.getSimulationContext(0).getReactionContext();
for (ReactionStep frs : fastReactionList) {
final ReactionSpec rs = rc.getReactionSpec(frs);
rs.setReactionMapping(ReactionSpec.FAST);
}
} catch (ModelPropertyVetoException mpve) {
throw new SBMLImportException(mpve.getMessage(), mpve);
} catch (Exception e1) {
e1.printStackTrace(System.out);
throw new SBMLImportException(e1.getMessage(), e1);
}
}
Also used :
Issue(org.vcell.util.Issue)
ArrayList(java.util.ArrayList)
FluxReaction(cbit.vcell.model.FluxReaction)
SpeciesContext(cbit.vcell.model.SpeciesContext)
GeneralKinetics(cbit.vcell.model.GeneralKinetics)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
ReactionContext(cbit.vcell.mapping.ReactionContext)
HashSet(java.util.HashSet)
KineticsProxyParameter(cbit.vcell.model.Kinetics.KineticsProxyParameter)
ReactionSpec(cbit.vcell.mapping.ReactionSpec)
ModelPropertyVetoException(cbit.vcell.model.ModelPropertyVetoException)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
ReactionStep(cbit.vcell.model.ReactionStep)
Kinetics(cbit.vcell.model.Kinetics)
GeneralKinetics(cbit.vcell.model.GeneralKinetics)
GeneralLumpedKinetics(cbit.vcell.model.GeneralLumpedKinetics)
KineticLaw(org.sbml.jsbml.KineticLaw)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
Element(org.jdom.Element)
UnresolvedParameter(cbit.vcell.model.Kinetics.UnresolvedParameter)
GeneralLumpedKinetics(cbit.vcell.model.GeneralLumpedKinetics)
ASTNode(org.sbml.jsbml.ASTNode)
Membrane(cbit.vcell.model.Membrane)
Structure(cbit.vcell.model.Structure)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
SpatialReactionPlugin(org.sbml.jsbml.ext.spatial.SpatialReactionPlugin)
SimpleReaction(cbit.vcell.model.SimpleReaction)
Reaction(org.sbml.jsbml.Reaction)
SimpleReaction(cbit.vcell.model.SimpleReaction)
FluxReaction(cbit.vcell.model.FluxReaction)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
XMLStreamException(javax.xml.stream.XMLStreamException)
SbmlException(org.vcell.sbml.SbmlException)
IOException(java.io.IOException)
PropertyVetoException(java.beans.PropertyVetoException)
SBMLException(org.sbml.jsbml.SBMLException)
ModelPropertyVetoException(cbit.vcell.model.ModelPropertyVetoException)
ExpressionException(cbit.vcell.parser.ExpressionException)
LocalParameter(org.sbml.jsbml.LocalParameter)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
Example 4 with Expression
use of cbit.vcell.parser.Expression in project vcell by virtualcell.
the class SBMLImporter method addCompartments.
protected void addCompartments(VCMetaData metaData) {
if (sbmlModel == null) {
throw new SBMLImportException("SBML model is NULL");
}
ListOf listofCompartments = sbmlModel.getListOfCompartments();
if (listofCompartments == null) {
throw new SBMLImportException("Cannot have 0 compartments in model");
}
// Using a vector here - since there can be SBML models with only
// features and no membranes.
// Hence keeping the datastructure flexible.
List<Structure> structList = new ArrayList<Structure>();
java.util.HashMap<String, Structure> structureNameMap = new java.util.HashMap<String, Structure>();
try {
int structIndx = 0;
// First pass - create the structures
for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
org.sbml.jsbml.Compartment compartment = (org.sbml.jsbml.Compartment) listofCompartments.get(i);
String compartmentName = compartment.getId();
if (!compartment.isSetSpatialDimensions() || compartment.getSpatialDimensions() == 3) {
Feature feature = new Feature(compartmentName);
structList.add(structIndx, feature);
structureNameMap.put(compartmentName, feature);
} else if (compartment.getSpatialDimensions() == 2) {
// spatial dimensions is set (see clause above)
Membrane membrane = new Membrane(compartmentName);
structList.add(structIndx, membrane);
structureNameMap.put(compartmentName, membrane);
} else {
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.CompartmentError, "Cannot deal with spatial dimension : " + compartment.getSpatialDimensions() + " for compartments at this time.");
throw new SBMLImportException("Cannot deal with spatial dimension : " + compartment.getSpatialDimensions() + " for compartments at this time");
}
structIndx++;
sbmlAnnotationUtil.readAnnotation(structList.get(i), compartment);
sbmlAnnotationUtil.readNotes(structList.get(i), compartment);
}
// Second pass - connect the structures
Model model = vcBioModel.getSimulationContext(0).getModel();
for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
org.sbml.jsbml.Compartment sbmlCompartment = (org.sbml.jsbml.Compartment) listofCompartments.get(i);
String outsideCompartmentId = null;
if (sbmlCompartment.getOutside() != null && sbmlCompartment.getOutside().length() > 0) {
// compartment.getOutside returns the Sid of the 'outside'
// compartment, so get the compartment from model.
outsideCompartmentId = sbmlCompartment.getOutside();
} else {
Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlCompartment);
if (sbmlImportRelatedElement != null) {
Element embeddedVCellElement = sbmlImportRelatedElement.getChild(OUTSIDE_COMP_NAME, Namespace.getNamespace(SBMLUtils.SBML_VCELL_NS));
if (embeddedVCellElement != null) {
outsideCompartmentId = embeddedVCellElement.getAttributeValue(XMLTags.NameTag);
}
}
}
if (outsideCompartmentId != null) {
Compartment outsideCompartment = sbmlModel.getCompartment(outsideCompartmentId);
Structure outsideStructure = (Structure) structureNameMap.get(outsideCompartment.getId());
Structure struct = (Structure) structureNameMap.get(sbmlCompartment.getId());
struct.setSbmlParentStructure(outsideStructure);
}
}
// set the structures in vc vcBioModel.getSimulationContext(0)
Structure[] structures = structList.toArray(new Structure[structList.size()]);
model.setStructures(structures);
// Third pass thro' the list of compartments : set the sizes on the
// structureMappings - can be done only after setting
// the structures on vcBioModel.getSimulationContext(0).
boolean allSizesSet = true;
for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
org.sbml.jsbml.Compartment compartment = (org.sbml.jsbml.Compartment) listofCompartments.get(i);
String compartmentName = compartment.getId();
if (!compartment.isSetSize()) {
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// TranslationMessage.COMPARTMENT_ERROR,
// "compartment "+compartmentName+" size is not set in SBML document.");
allSizesSet = false;
} else {
double size = compartment.getSize();
// Check if size is specified by a rule
Expression sizeExpr = getValueFromAssignmentRule(compartmentName);
if (sizeExpr != null && !sizeExpr.isNumeric()) {
// We are NOT handling compartment sizes with assignment
// rules/initial Assignments that are NON-numeric at
// this time ...
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.CompartmentError, "compartment " + compartmentName + " size has an assignment rule which is not a numeric value, cannot handle it at this time.");
}
// check if it is specified by initial assignment
if (sizeExpr == null) {
InitialAssignment compInitAssgnment = sbmlModel.getInitialAssignment(compartmentName);
if (compInitAssgnment != null) {
sizeExpr = getExpressionFromFormula(compInitAssgnment.getMath());
}
}
if (sizeExpr != null && !sizeExpr.isNumeric()) {
// We are NOT handling compartment sizes with assignment
// rules/initial Assignments that are NON-numeric at
// this time ...
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.CompartmentError, "compartment " + compartmentName + " size has an initial assignment which is not a numeric value, cannot handle it at this time.");
}
// from 'size' attribute,
if (sizeExpr == null) {
sizeExpr = new Expression(size);
}
// Now set the size of the compartment.
Structure struct = model.getStructure(compartmentName);
StructureMapping.StructureMappingParameter mappingParam = vcBioModel.getSimulationContext(0).getGeometryContext().getStructureMapping(struct).getSizeParameter();
mappingParam.setExpression(sizeExpr);
}
}
// size is set
if (allSizesSet) {
StructureSizeSolver.updateRelativeStructureSizes(vcBioModel.getSimulationContext(0));
}
} catch (Exception e) {
e.printStackTrace(System.out);
throw new SBMLImportException("Error adding Feature to vcModel " + e.getMessage(), e);
}
}
Also used :
HashMap(java.util.HashMap)
Compartment(org.sbml.jsbml.Compartment)
Element(org.jdom.Element)
ArrayList(java.util.ArrayList)
Feature(cbit.vcell.model.Feature)
StructureMapping(cbit.vcell.mapping.StructureMapping)
ListOf(org.sbml.jsbml.ListOf)
Membrane(cbit.vcell.model.Membrane)
Structure(cbit.vcell.model.Structure)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
XMLStreamException(javax.xml.stream.XMLStreamException)
SbmlException(org.vcell.sbml.SbmlException)
IOException(java.io.IOException)
PropertyVetoException(java.beans.PropertyVetoException)
SBMLException(org.sbml.jsbml.SBMLException)
ModelPropertyVetoException(cbit.vcell.model.ModelPropertyVetoException)
ExpressionException(cbit.vcell.parser.ExpressionException)
InitialAssignment(org.sbml.jsbml.InitialAssignment)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
Compartment(org.sbml.jsbml.Compartment)
Example 5 with Expression
use of cbit.vcell.parser.Expression in project vcell by virtualcell.
the class SBMLImporter method addAssignmentRules.
/**
* addAssignmentRules : Adds Assignment Rules from the SBML document
* Assignment rules are allowed (initial concentration of species; parameter
* definitions, etc.
*/
protected void addAssignmentRules() throws Exception {
if (sbmlModel == null) {
throw new SBMLImportException("SBML model is NULL");
}
ListOf listofRules = sbmlModel.getListOfRules();
if (listofRules == null) {
System.out.println("No Rules specified");
return;
}
for (int i = 0; i < sbmlModel.getNumRules(); i++) {
Rule rule = (org.sbml.jsbml.Rule) listofRules.get(i);
if (rule instanceof AssignmentRule) {
// Get the assignment rule and store it in the hashMap.
AssignmentRule assignmentRule = (AssignmentRule) rule;
Expression assignmentRuleMathExpr = getExpressionFromFormula(assignmentRule.getMath());
String assgnRuleVar = assignmentRule.getVariable();
// check if assignment rule is for species. If so, check if
// expression has x/y/z term. This is not allowed for
// non-spatial models in vcell.
org.sbml.jsbml.Species ruleSpecies = sbmlModel.getSpecies(assgnRuleVar);
if (ruleSpecies != null) {
if (assignmentRuleMathExpr != null) {
Model vcModel = vcBioModel.getSimulationContext(0).getModel();
if (!bSpatial) {
if (assignmentRuleMathExpr.hasSymbol(vcModel.getX().getName()) || assignmentRuleMathExpr.hasSymbol(vcModel.getY().getName()) || assignmentRuleMathExpr.hasSymbol(vcModel.getZ().getName())) {
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, "An assignment rule for species " + ruleSpecies.getId() + " contains " + RESERVED_SPATIAL + " variable(s) (x,y,z), this is not allowed for a non-spatial model in VCell");
}
}
}
}
assignmentRulesHash.put(assignmentRule.getVariable(), assignmentRuleMathExpr);
}
}
// end - for i : rules
}
Also used :
Expression(cbit.vcell.parser.Expression)
AssignmentRule(org.sbml.jsbml.AssignmentRule)
ListOf(org.sbml.jsbml.ListOf)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
AlgebraicRule(org.sbml.jsbml.AlgebraicRule)
Rule(org.sbml.jsbml.Rule)
AssignmentRule(org.sbml.jsbml.AssignmentRule)
RateRule(org.sbml.jsbml.RateRule)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
Aggregations
Expression (cbit.vcell.parser.Expression)596
ExpressionException (cbit.vcell.parser.ExpressionException)190
PropertyVetoException (java.beans.PropertyVetoException)88
VCUnitDefinition (cbit.vcell.units.VCUnitDefinition)78
SymbolTableEntry (cbit.vcell.parser.SymbolTableEntry)74
Variable (cbit.vcell.math.Variable)71
ArrayList (java.util.ArrayList)68
ExpressionBindingException (cbit.vcell.parser.ExpressionBindingException)66
MathException (cbit.vcell.math.MathException)61
SpeciesContext (cbit.vcell.model.SpeciesContext)61
Model (cbit.vcell.model.Model)60
Vector (java.util.Vector)59
VolVariable (cbit.vcell.math.VolVariable)55
KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)54
Element (org.jdom.Element)50
ModelParameter (cbit.vcell.model.Model.ModelParameter)49
Function (cbit.vcell.math.Function)44
Structure (cbit.vcell.model.Structure)44
BioModel (cbit.vcell.biomodel.BioModel)43
Constant (cbit.vcell.math.Constant)43
