Search in sources :

Example 16 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class XmlReader method getSpeciesContextSpecs.

/**
 * This method returns a SpeciesContextSpec object from a XML representation.
 * Creation date: (4/26/2001 4:14:01 PM)
 * @return cbit.vcell.mapping.SpeciesContextSpec
 * @param param org.jdom.Element
 */
private void getSpeciesContextSpecs(List<Element> scsChildren, ReactionContext rxnContext, Model model) throws XmlParseException {
    for (int i = 0; i < scsChildren.size(); i++) {
        Element scsElement = scsChildren.get(i);
        SpeciesContextSpec specspec = null;
        // Get Atributes
        String speccontname = unMangle(scsElement.getAttributeValue(XMLTags.SpeciesContextRefAttrTag));
        boolean constant = Boolean.valueOf(scsElement.getAttributeValue(XMLTags.ForceConstantAttrTag)).booleanValue();
        // boolean enabledif = Boolean.valueOf(scsElement.getAttributeValue(XMLTags.EnableDiffusionAttrTag)).booleanValue();
        String spatialStr = scsElement.getAttributeValue(XMLTags.SpatialAttrTag);
        Boolean spatial = null;
        if (spatialStr != null) {
            spatial = Boolean.valueOf(spatialStr);
        }
        String bWellMixedStr = scsElement.getAttributeValue(XMLTags.WellMixedAttrTag);
        Boolean bWellMixed = null;
        if (bWellMixedStr != null) {
            bWellMixed = Boolean.valueOf(bWellMixedStr);
        }
        String bForceContinuousStr = scsElement.getAttributeValue(XMLTags.ForceContinuousAttrTag);
        Boolean bForceContinuous = null;
        if (bForceContinuousStr != null) {
            bForceContinuous = Boolean.valueOf(bForceContinuousStr);
        }
        // Retrieve reference
        SpeciesContext specref = model.getSpeciesContext(speccontname);
        if (specref == null) {
            throw new XmlParseException("The SpeciesContext " + speccontname + " refrence could not be resolved!");
        }
        // get SpeciesContextSpec from reactionContext & specRef
        specspec = rxnContext.getSpeciesContextSpec(specref);
        // set attributes
        specspec.setConstant(constant);
        // }
        if (spatial != null) {
            specspec.setWellMixed(!spatial);
        }
        if (bWellMixed != null) {
            specspec.setWellMixed(bWellMixed);
        }
        if (bForceContinuous != null) {
            specspec.setForceContinuous(bForceContinuous);
        }
        // set expressions
        // Initial
        String tempCon = scsElement.getChildText(XMLTags.InitialConcentrationTag, vcNamespace);
        String tempAmt = scsElement.getChildText(XMLTags.InitialAmountTag, vcNamespace);
        String temp = scsElement.getChildText(XMLTags.InitialTag, vcNamespace);
        try {
            if (// old model
            temp != null) {
                Expression expression = unMangleExpression(temp);
                specspec.getInitialConcentrationParameter().setExpression(expression);
                specspec.getInitialCountParameter().setExpression(null);
            } else // new model
            {
                if (// use concentration as initial condition
                tempCon != null) {
                    Expression expression = unMangleExpression(tempCon);
                    specspec.getInitialConcentrationParameter().setExpression(expression);
                    specspec.getInitialCountParameter().setExpression(null);
                } else if (// use number of particles as initial condition
                tempAmt != null) {
                    Expression expression = unMangleExpression(tempAmt);
                    specspec.getInitialCountParameter().setExpression(expression);
                    specspec.getInitialConcentrationParameter().setExpression(null);
                } else {
                    throw new XmlParseException("Unrecognizable initial condition when parsing VCML file.");
                }
            }
        // Expression expression = unMangleExpression(temp);
        // specspec.getInitialConditionParameter().setExpression(expression);
        } catch (ExpressionException e) {
            e.printStackTrace();
            throw new XmlParseException("An expressionException was fired when setting the InitilaconditionExpression " + temp + ", for a SpeciesContextSpec!", e);
        }
        // diffusion (if there is no diffusion information skip it)
        Element xmlDiffusionElement = scsElement.getChild(XMLTags.DiffusionTag, vcNamespace);
        if (xmlDiffusionElement != null) {
            temp = xmlDiffusionElement.getText();
            try {
                Expression expression = unMangleExpression(temp);
                specspec.getDiffusionParameter().setExpression(expression);
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new XmlParseException("An ExpressionException was fired when setting the diffusionExpression " + temp + " to a SpeciesContextSpec!", e);
            }
        }
        // Get Boundaries if any
        Element tempElement = scsElement.getChild(XMLTags.BoundariesTag, vcNamespace);
        if (tempElement != null) {
            try {
                // Xm
                temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm);
                if (temp != null) {
                    specspec.getBoundaryXmParameter().setExpression(unMangleExpression(temp));
                }
                // Xp
                temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp);
                if (temp != null) {
                    specspec.getBoundaryXpParameter().setExpression(unMangleExpression(temp));
                }
                // Ym
                temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm);
                if (temp != null) {
                    specspec.getBoundaryYmParameter().setExpression(unMangleExpression(temp));
                }
                // Yp
                temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp);
                if (temp != null) {
                    specspec.getBoundaryYpParameter().setExpression(unMangleExpression(temp));
                }
                // Zm
                temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm);
                if (temp != null) {
                    specspec.getBoundaryZmParameter().setExpression(unMangleExpression(temp));
                }
                // Zp
                temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp);
                if (temp != null) {
                    specspec.getBoundaryZpParameter().setExpression(unMangleExpression(temp));
                }
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new XmlParseException("An ExpressionException was fired when Setting the boundary Expression: " + unMangle(temp), e);
            }
        }
        // Get Velocities if any
        Element velocityE = scsElement.getChild(XMLTags.VelocityTag, vcNamespace);
        if (velocityE != null) {
            String tempStr = null;
            boolean dummyVel = true;
            try {
                tempStr = velocityE.getAttributeValue(XMLTags.XAttrTag);
                if (tempStr != null) {
                    // all velocity dimensions are optional.
                    specspec.getVelocityXParameter().setExpression(unMangleExpression(tempStr));
                    if (dummyVel) {
                        dummyVel = false;
                    }
                }
                tempStr = velocityE.getAttributeValue(XMLTags.YAttrTag);
                if (tempStr != null) {
                    specspec.getVelocityYParameter().setExpression(unMangleExpression(tempStr));
                    if (dummyVel) {
                        dummyVel = false;
                    }
                }
                tempStr = velocityE.getAttributeValue(XMLTags.ZAttrTag);
                if (tempStr != null) {
                    specspec.getVelocityZParameter().setExpression(unMangleExpression(tempStr));
                    if (dummyVel) {
                        dummyVel = false;
                    }
                }
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new XmlParseException("Error setting Velocity parameter for '" + specspec.getSpeciesContext().getName(), e);
            }
            if (dummyVel) {
                throw new XmlParseException("Void Velocity element found under PDE for: " + specspec.getSpeciesContext().getName());
            }
        }
    }
}
Also used : Expression(cbit.vcell.parser.Expression) Element(org.jdom.Element) SpeciesContext(cbit.vcell.model.SpeciesContext) SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec) ExpressionException(cbit.vcell.parser.ExpressionException)

Example 17 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class XmlReader method getBioEvents.

public BioEvent[] getBioEvents(SimulationContext simContext, Element bioEventsElement) throws XmlParseException {
    Iterator<Element> bioEventsIterator = bioEventsElement.getChildren(XMLTags.BioEventTag, vcNamespace).iterator();
    Vector<BioEvent> bioEventsVector = new Vector<BioEvent>();
    while (bioEventsIterator.hasNext()) {
        Element bEventElement = (Element) bioEventsIterator.next();
        BioEvent newBioEvent = null;
        String name = unMangle(bEventElement.getAttributeValue(XMLTags.NameAttrTag));
        Element triggerElement = bEventElement.getChild(XMLTags.TriggerTag, vcNamespace);
        if (triggerElement != null && triggerElement.getText().length() > 0) {
            // 
            // read legacy VCell 5.3 style trigger and delay elements
            // 
            // <Trigger>(t>3.0)</Trigger>
            // <Delay UseValuesFromTriggerTime="true">3.0</Delay>     [optional]
            // 
            Expression triggerExpression = unMangleExpression(triggerElement.getText());
            // read <Delay>
            Expression delayDurationExpression = null;
            boolean useValuesFromTriggerTime = true;
            Element delayElement = bEventElement.getChild(XMLTags.DelayTag, vcNamespace);
            if (delayElement != null) {
                useValuesFromTriggerTime = Boolean.valueOf(delayElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue();
                delayDurationExpression = unMangleExpression((delayElement.getText()));
            }
            newBioEvent = new BioEvent(name, TriggerType.GeneralTrigger, useValuesFromTriggerTime, simContext);
            try {
                newBioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, triggerExpression);
                if (delayDurationExpression != null) {
                    newBioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayDurationExpression);
                }
            } catch (ExpressionBindingException | PropertyVetoException e) {
                e.printStackTrace();
                throw new XmlParseException("failed to read trigger or delay expressions in bioEvent " + name + ": " + e.getMessage(), e);
            }
        } else if (triggerElement != null && triggerElement.getText().length() == 0) {
            // 
            // read legacy first-pass VCell 5.4 style trigger and delay elements
            // 
            // <Trigger>
            // <TriggerParameters triggerClass="TriggerGeneral">
            // (t > 500.0)
            // </TriggerParameters>
            // </Trigger>
            // <Delay UseValuesFromTriggerTime="true">3.0</Delay>     [optional]
            // 
            final String TriggerParametersTag = "TriggerParameters";
            final String TriggerClassAttrTag = "triggerClass";
            final String TriggerClassAttrValue_TriggerGeneral = "TriggerGeneral";
            Element triggerParametersElement = triggerElement.getChild(TriggerParametersTag, vcNamespace);
            Expression triggerExpression = null;
            String triggerClass = triggerParametersElement.getAttributeValue(TriggerClassAttrTag);
            if (triggerClass.equals(TriggerClassAttrValue_TriggerGeneral)) {
                triggerExpression = unMangleExpression(triggerParametersElement.getText());
            } else {
                // not general trigger (just make it never happen, user will have to edit "t > -1")
                triggerExpression = Expression.relational(">", new Expression(simContext.getModel().getTIME(), simContext.getModel().getNameScope()), new Expression(-1.0));
            }
            // read <Delay>
            Expression delayDurationExpression = null;
            boolean useValuesFromTriggerTime = true;
            Element delayElement = bEventElement.getChild(XMLTags.DelayTag, vcNamespace);
            if (delayElement != null) {
                useValuesFromTriggerTime = Boolean.valueOf(delayElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue();
                delayDurationExpression = unMangleExpression((delayElement.getText()));
            }
            newBioEvent = new BioEvent(name, TriggerType.GeneralTrigger, useValuesFromTriggerTime, simContext);
            try {
                newBioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, triggerExpression);
                if (delayDurationExpression != null) {
                    newBioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayDurationExpression);
                }
            } catch (ExpressionBindingException | PropertyVetoException e) {
                e.printStackTrace();
                throw new XmlParseException("failed to read trigger or delay expressions in bioEvent " + name + ": " + e.getMessage(), e);
            }
        } else {
            // 
            // VCell 5.4 style bioevent parameters
            // 
            // 
            TriggerType triggerType = TriggerType.fromXmlName(bEventElement.getAttributeValue(XMLTags.BioEventTriggerTypeAttrTag));
            boolean bUseValuesFromTriggerTime = Boolean.parseBoolean(bEventElement.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag));
            newBioEvent = new BioEvent(name, triggerType, bUseValuesFromTriggerTime, simContext);
            Iterator<Element> paramElementIter = bEventElement.getChildren(XMLTags.ParameterTag, vcNamespace).iterator();
            ArrayList<LocalParameter> parameters = new ArrayList<LocalParameter>();
            boolean bHasGeneralTriggerParam = false;
            while (paramElementIter.hasNext()) {
                Element paramElement = paramElementIter.next();
                // Get parameter attributes
                String paramName = paramElement.getAttributeValue(XMLTags.NameAttrTag);
                Expression exp = unMangleExpression(paramElement.getText());
                String roleStr = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag);
                BioEventParameterType parameterType = BioEventParameterType.fromRoleXmlName(roleStr);
                if (parameterType == BioEventParameterType.GeneralTriggerFunction) {
                    bHasGeneralTriggerParam = true;
                }
                VCUnitDefinition unit = simContext.getModel().getUnitSystem().getInstance_TBD();
                String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                if (unitSymbol != null) {
                    unit = simContext.getModel().getUnitSystem().getInstance(unitSymbol);
                }
                parameters.add(newBioEvent.createNewParameter(paramName, parameterType, exp, unit));
            }
            if (!bHasGeneralTriggerParam) {
                parameters.add(newBioEvent.createNewParameter(BioEventParameterType.GeneralTriggerFunction.getDefaultName(), BioEventParameterType.GeneralTriggerFunction, // computed as needed
                null, simContext.getModel().getUnitSystem().getInstance_DIMENSIONLESS()));
            }
            try {
                newBioEvent.setParameters(parameters.toArray(new LocalParameter[0]));
            } catch (PropertyVetoException | ExpressionBindingException e) {
                e.printStackTrace();
                throw new XmlParseException("failed to read parameters in bioEvent " + name + ": " + e.getMessage(), e);
            }
        }
        ArrayList<BioEvent.EventAssignment> eventAssignmentList = new ArrayList<BioEvent.EventAssignment>();
        Iterator<Element> iter = bEventElement.getChildren(XMLTags.EventAssignmentTag, vcNamespace).iterator();
        while (iter.hasNext()) {
            Element eventAssignmentElement = iter.next();
            try {
                String varname = eventAssignmentElement.getAttributeValue(XMLTags.EventAssignmentVariableAttrTag);
                Expression assignExp = unMangleExpression(eventAssignmentElement.getText());
                SymbolTableEntry target = simContext.getEntry(varname);
                BioEvent.EventAssignment eventAssignment = newBioEvent.new EventAssignment(target, assignExp);
                eventAssignmentList.add(eventAssignment);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
        try {
            newBioEvent.setEventAssignmentsList(eventAssignmentList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace(System.out);
            throw new XmlParseException(e1);
        }
        try {
            newBioEvent.bind();
        } catch (ExpressionBindingException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
        bioEventsVector.add(newBioEvent);
    }
    return ((BioEvent[]) BeanUtils.getArray(bioEventsVector, BioEvent.class));
}
Also used : TriggerType(cbit.vcell.mapping.BioEvent.TriggerType) EventAssignment(cbit.vcell.math.Event.EventAssignment) Element(org.jdom.Element) ArrayList(java.util.ArrayList) ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException) ExpressionException(cbit.vcell.parser.ExpressionException) PropertyVetoException(java.beans.PropertyVetoException) LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry) Expression(cbit.vcell.parser.Expression) BioEventParameterType(cbit.vcell.mapping.BioEvent.BioEventParameterType) Iterator(java.util.Iterator) BioEvent(cbit.vcell.mapping.BioEvent) Vector(java.util.Vector)

Example 18 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class XmlReader method readParameters.

private void readParameters(List<Element> parameterElements, ParameterContext parameterContext, HashMap<String, ParameterRoleEnum> roleHash, ParameterRoleEnum userDefinedRole, HashSet<String> xmlRolesTagsToIgnore, Model model) throws XmlParseException {
    String contextName = parameterContext.getNameScope().getName();
    try {
        // 
        // prepopulate varHash with reserved symbols
        // 
        VariableHash varHash = new VariableHash();
        addResevedSymbols(varHash, model);
        // 
        for (Element xmlParam : parameterElements) {
            String parsedParamName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String parsedRoleString = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String parsedExpressionString = xmlParam.getText();
            // 
            if (xmlRolesTagsToIgnore.contains(parsedRoleString)) {
                varHash.removeVariable(parsedParamName);
                continue;
            }
            Expression paramExp = null;
            if (parsedExpressionString.trim().length() > 0) {
                paramExp = unMangleExpression(parsedExpressionString);
            }
            if (varHash.getVariable(parsedParamName) == null) {
                Domain domain = null;
                varHash.addVariable(new Function(parsedParamName, paramExp, domain));
            } else {
                if (model.getReservedSymbolByName(parsedParamName) != null) {
                    varHash.removeVariable(parsedParamName);
                    Domain domain = null;
                    varHash.addVariable(new Function(parsedParamName, paramExp, domain));
                }
            }
            // 
            // get the parameter for this xml role string
            // 
            ParameterRoleEnum paramRole = roleHash.get(parsedRoleString);
            if (paramRole == null) {
                throw new XmlParseException("parameter '" + parsedParamName + "' has unexpected role '" + parsedRoleString + "' in '" + contextName + "'");
            }
            // 
            if (paramRole != userDefinedRole) {
                LocalParameter paramWithSameRole = parameterContext.getLocalParameterFromRole(paramRole);
                if (paramWithSameRole == null) {
                    throw new XmlParseException("can't find parameter with role '" + parsedRoleString + "' in '" + contextName + "'");
                }
                // 
                if (!paramWithSameRole.getName().equals(parsedParamName)) {
                    // 
                    // first rename other parameters with same name
                    // 
                    LocalParameter paramWithSameNameButDifferentRole = parameterContext.getLocalParameterFromName(parsedParamName);
                    if (paramWithSameNameButDifferentRole != null) {
                        // 
                        // find available name
                        // 
                        int n = 0;
                        String newName = parsedParamName + "_" + n++;
                        while (parameterContext.getEntry(newName) != null) {
                            newName = parsedParamName + "_" + n++;
                        }
                        parameterContext.renameLocalParameter(parsedParamName, newName);
                    }
                    // 
                    // then rename parameter with correct role
                    // 
                    parameterContext.renameLocalParameter(paramWithSameRole.getName(), parsedParamName);
                }
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                Domain domain = null;
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
            parameterContext.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        // 
        // in topological order, add parameters to model (getting units also).
        // note that all pre-defined parameters already have the correct names
        // here we set expressions on pre-defined parameters and add user-defined parameters
        // 
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = model.getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < parameterElements.size(); j++) {
                    Element tempParam = (Element) parameterElements.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                LocalParameter tempParam = parameterContext.getLocalParameterFromName(paramFunction.getName());
                if (tempParam == null) {
                    tempParam = parameterContext.addLocalParameter(paramFunction.getName(), new Expression(0.0), userDefinedRole, unit, userDefinedRole.getDescription());
                    parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
                } else {
                    if (tempParam.getExpression() != null) {
                        // if the expression is null, it should remain null.
                        parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
                    }
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (PropertyVetoException | ExpressionException | MathException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for '" + contextName + "': " + e.getMessage(), e);
    }
}
Also used : FilamentVariable(cbit.vcell.math.FilamentVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) InsideVariable(cbit.vcell.math.InsideVariable) VolVariable(cbit.vcell.math.VolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) PointVariable(cbit.vcell.math.PointVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) VariableHash(cbit.vcell.math.VariableHash) Element(org.jdom.Element) ExpressionException(cbit.vcell.parser.ExpressionException) LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter) PropertyVetoException(java.beans.PropertyVetoException) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) Function(cbit.vcell.math.Function) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) Expression(cbit.vcell.parser.Expression) MathException(cbit.vcell.math.MathException) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) Domain(cbit.vcell.math.Variable.Domain) ParameterRoleEnum(cbit.vcell.mapping.ParameterContext.ParameterRoleEnum) ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)

Example 19 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class XmlReader method getParticleJumpProcess.

private ParticleJumpProcess getParticleJumpProcess(Element param, MathDescription md) throws XmlParseException {
    // name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    ProcessSymmetryFactor processSymmetryFactor = null;
    Attribute symmetryFactorAttr = param.getAttribute(XMLTags.ProcessSymmetryFactorAttrTag);
    if (symmetryFactorAttr != null) {
        processSymmetryFactor = new ProcessSymmetryFactor(Double.parseDouble(symmetryFactorAttr.getValue()));
    }
    // selected particle
    List<ParticleVariable> varList = new ArrayList<ParticleVariable>();
    Iterator<Element> iterator = param.getChildren(XMLTags.SelectedParticleTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        String varname = unMangle(tempelement.getAttributeValue(XMLTags.NameAttrTag));
        Variable var = md.getVariable(varname);
        if (!(var instanceof ParticleVariable)) {
            throw new XmlParseException("Not a ParticleVariable in ParticleJumpProcess.");
        }
        varList.add((ParticleVariable) var);
    }
    // probability rate
    JumpProcessRateDefinition jprd = null;
    // for old models
    Element pb = param.getChild(XMLTags.ParticleProbabilityRateTag, vcNamespace);
    if (pb != null) {
        Expression exp = unMangleExpression(pb.getText());
        jprd = new MacroscopicRateConstant(exp);
    } else // for new models
    {
        pb = param.getChild(XMLTags.MacroscopicRateConstantTag, vcNamespace);
        if (// jump process rate defined by macroscopic rate constant
        pb != null) {
            Expression exp = unMangleExpression(pb.getText());
            jprd = new MacroscopicRateConstant(exp);
        } else // jump process rate defined by binding radius
        {
            pb = param.getChild(XMLTags.InteractionRadiusTag, vcNamespace);
            if (pb != null) {
                Expression exp = unMangleExpression(pb.getText());
                jprd = new InteractionRadius(exp);
            }
        }
    }
    // add actions
    List<Action> actionList = new ArrayList<Action>();
    iterator = param.getChildren(XMLTags.ActionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            actionList.add(getAction(tempelement, md));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        } catch (ExpressionException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    ParticleJumpProcess jump = new ParticleJumpProcess(name, varList, jprd, actionList, processSymmetryFactor);
    return jump;
}
Also used : JumpProcessRateDefinition(cbit.vcell.math.JumpProcessRateDefinition) Action(cbit.vcell.math.Action) FilamentVariable(cbit.vcell.math.FilamentVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) InsideVariable(cbit.vcell.math.InsideVariable) VolVariable(cbit.vcell.math.VolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) PointVariable(cbit.vcell.math.PointVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) InteractionRadius(cbit.vcell.math.InteractionRadius) Attribute(org.jdom.Attribute) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) Element(org.jdom.Element) ParticleJumpProcess(cbit.vcell.math.ParticleJumpProcess) ArrayList(java.util.ArrayList) ExpressionException(cbit.vcell.parser.ExpressionException) ProcessSymmetryFactor(cbit.vcell.math.ParticleJumpProcess.ProcessSymmetryFactor) Expression(cbit.vcell.parser.Expression) MathException(cbit.vcell.math.MathException) MacroscopicRateConstant(cbit.vcell.math.MacroscopicRateConstant)

Example 20 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class XmlReader method getRbmReactionRule.

private ReactionRule getRbmReactionRule(Element reactionRuleElement, Model newModel) throws XmlParseException {
    String n = reactionRuleElement.getAttributeValue(XMLTags.NameAttrTag);
    if (n == null || n.isEmpty()) {
        System.out.println("XMLReader: getRbmReactionRule: name is missing.");
        return null;
    }
    try {
        boolean reversible = Boolean.valueOf(reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleReversibleTag));
        // get 1st structure if attribute missing
        String structureName = reactionRuleElement.getAttributeValue(XMLTags.StructureAttrTag, newModel.getStructures()[0].getName());
        Structure structure = newModel.getStructure(structureName);
        ReactionRule reactionRule = new ReactionRule(newModel, n, structure, reversible);
        // we ignore this, name and label are the same thing for now
        String reactionRuleLabel = reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleLabelTag);
        // 
        // old style kinetics placed parameter values as attributes
        // look for attributes named ("MassActionKf","MassActionKr","MichaelisMentenKcat","MichaelisMentenKm","SaturableKs","SaturableVmax")
        String[] oldKineticsAttributes = new String[] { XMLTags.RbmMassActionKfAttrTag_DEPRECATED, XMLTags.RbmMassActionKrAttrTag_DEPRECATED, XMLTags.RbmMichaelisMentenKcatAttrTag_DEPRECATED, XMLTags.RbmMichaelisMentenKmAttrTag_DEPRECATED, XMLTags.RbmSaturableKsAttrTag_DEPRECATED, XMLTags.RbmSaturableVmaxAttrTag_DEPRECATED };
        boolean bOldKineticsFound = false;
        for (String oldKineticsAttribute : oldKineticsAttributes) {
            if (reactionRuleElement.getAttribute(oldKineticsAttribute) != null) {
                bOldKineticsFound = true;
            }
        }
        if (bOldKineticsFound) {
            readOldRbmKineticsAttributes(reactionRuleElement, reactionRule);
        } else {
            Element kineticsElement = reactionRuleElement.getChild(XMLTags.KineticsTag, vcNamespace);
            if (kineticsElement != null) {
                String kineticLawTypeString = kineticsElement.getAttributeValue(XMLTags.KineticsTypeAttrTag);
                RbmKineticLaw.RateLawType rateLawType = null;
                if (XMLTags.RbmKineticTypeMassAction.equals(kineticLawTypeString)) {
                    rateLawType = RateLawType.MassAction;
                } else if (XMLTags.RbmKineticTypeMichaelisMenten.equals(kineticLawTypeString)) {
                    rateLawType = RateLawType.MichaelisMenten;
                } else if (XMLTags.RbmKineticTypeSaturable.equals(kineticLawTypeString)) {
                    rateLawType = RateLawType.Saturable;
                } else {
                    throw new RuntimeException("unexpected rate law type " + kineticLawTypeString);
                }
                reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, rateLawType));
                List<Element> parameterElements = kineticsElement.getChildren(XMLTags.ParameterTag, vcNamespace);
                HashMap<String, ParameterRoleEnum> roleHash = new HashMap<String, ParameterContext.ParameterRoleEnum>();
                roleHash.put(XMLTags.RbmMassActionKfRole, RbmKineticLawParameterType.MassActionForwardRate);
                roleHash.put(XMLTags.RbmMassActionKrRole, RbmKineticLawParameterType.MassActionReverseRate);
                roleHash.put(XMLTags.RbmMichaelisMentenKcatRole, RbmKineticLawParameterType.MichaelisMentenKcat);
                roleHash.put(XMLTags.RbmMichaelisMentenKmRole, RbmKineticLawParameterType.MichaelisMentenKm);
                roleHash.put(XMLTags.RbmSaturableVmaxRole, RbmKineticLawParameterType.SaturableVmax);
                roleHash.put(XMLTags.RbmSaturableKsRole, RbmKineticLawParameterType.SaturableKs);
                roleHash.put(XMLTags.RbmUserDefinedRole, RbmKineticLawParameterType.UserDefined);
                HashSet<String> xmlRolesToIgnore = new HashSet<String>();
                xmlRolesToIgnore.add(XMLTags.RbmRuleRateRole);
                ParameterContext parameterContext = reactionRule.getKineticLaw().getParameterContext();
                readParameters(parameterElements, parameterContext, roleHash, RbmKineticLawParameterType.UserDefined, xmlRolesToIgnore, newModel);
            }
        }
        Element e1 = reactionRuleElement.getChild(XMLTags.RbmReactantPatternsListTag, vcNamespace);
        getRbmReactantPatternsList(e1, reactionRule, newModel);
        Element e2 = reactionRuleElement.getChild(XMLTags.RbmProductPatternsListTag, vcNamespace);
        getRbmProductPatternsList(e2, reactionRule, newModel);
        reactionRule.checkMatchConsistency();
        return reactionRule;
    } catch (PropertyVetoException | ExpressionException ex) {
        ex.printStackTrace(System.out);
        throw new RuntimeException("failed to parse kinetics for reaction rule '" + n + "': " + ex.getMessage(), ex);
    }
}
Also used : ReactionRule(cbit.vcell.model.ReactionRule) HashMap(java.util.HashMap) Element(org.jdom.Element) RbmKineticLaw(cbit.vcell.model.RbmKineticLaw) ExpressionException(cbit.vcell.parser.ExpressionException) PropertyVetoException(java.beans.PropertyVetoException) ParameterContext(cbit.vcell.mapping.ParameterContext) RateLawType(cbit.vcell.model.RbmKineticLaw.RateLawType) Structure(cbit.vcell.model.Structure) ParameterRoleEnum(cbit.vcell.mapping.ParameterContext.ParameterRoleEnum) HashSet(java.util.HashSet)

Aggregations

ExpressionException (cbit.vcell.parser.ExpressionException)199 Expression (cbit.vcell.parser.Expression)138 MathException (cbit.vcell.math.MathException)58 PropertyVetoException (java.beans.PropertyVetoException)51 DataAccessException (org.vcell.util.DataAccessException)34 ArrayList (java.util.ArrayList)32 Variable (cbit.vcell.math.Variable)30 IOException (java.io.IOException)29 Element (org.jdom.Element)26 ExpressionBindingException (cbit.vcell.parser.ExpressionBindingException)25 MappingException (cbit.vcell.mapping.MappingException)24 Function (cbit.vcell.math.Function)24 Vector (java.util.Vector)24 ModelException (cbit.vcell.model.ModelException)23 SolverException (cbit.vcell.solver.SolverException)23 CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)22 VCUnitDefinition (cbit.vcell.units.VCUnitDefinition)21 Constant (cbit.vcell.math.Constant)20 MathDescription (cbit.vcell.math.MathDescription)19 Structure (cbit.vcell.model.Structure)18