Examples with ExpressionBindingException cbit.vcell.parser.ExpressionBindingException used on opensource projects

Example 1 with ExpressionBindingException

use of cbit.vcell.parser.ExpressionBindingException 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));
}

Example 2 with ExpressionBindingException

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

the class SpeciesContextSpec method initializeForSpatial.

public void initializeForSpatial() {
    if (getDiffusionParameter() != null && getDiffusionParameter().getExpression() != null && getDiffusionParameter().getExpression().isZero()) {
        Expression e = null;
        ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
        VCUnitDefinition micronsqpersecond = modelUnitSystem.getInstance("um2.s-1");
        if (speciesContext.getStructure() instanceof Feature) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(10, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else if (speciesContext.getStructure() instanceof Membrane) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(0.1, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(1.0, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        }
        try {
            getDiffusionParameter().setExpression(e);
        } catch (ExpressionBindingException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Error while initializing diffusion rate, " + e1.getMessage());
        }
    }
}

Example 3 with ExpressionBindingException

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

the class MathMapping_4_8 method substituteGlobalParameters.

private Expression substituteGlobalParameters(Expression exp) throws ExpressionException {
    Expression exp2 = new Expression(exp);
    // 
    // do until no more globals to substitute
    // 
    int count = 0;
    ModelParameter[] modelParams = simContext.getModel().getModelParameters();
    while (true) {
        if (count++ > 30) {
            throw new ExpressionBindingException("infinite loop in eliminating function nesting");
        }
        // 
        // get all symbols (identifiers), make list of globals used
        // 
        String[] symbols = exp2.getSymbols();
        Vector<ModelParameter> globalsVector = new Vector<ModelParameter>();
        if (symbols != null) {
            for (int i = 0; i < symbols.length; i++) {
                for (int j = 0; j < modelParams.length; j++) {
                    if (symbols[i].equals(modelParams[j].getName())) {
                        globalsVector.addElement(modelParams[j]);
                    }
                }
            }
        }
        // 
        if (globalsVector.size() == 0) {
            break;
        }
        // 
        for (int i = 0; i < globalsVector.size(); i++) {
            ModelParameter mp = globalsVector.elementAt(i);
            Expression mpExp = new Expression(mp.getName() + ";");
            exp2.substituteInPlace(mpExp, new Expression(mp.getExpression()));
        }
    }
    exp2.bindExpression(simContext.getModel());
    return exp2;
}

Example 4 with ExpressionBindingException

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

the class AbstractMathMapping method substituteGlobalParameters.

private Expression substituteGlobalParameters(Expression exp) throws ExpressionException {
    Expression exp2 = new Expression(exp);
    // 
    // do until no more globals to substitute
    // 
    int count = 0;
    ModelParameter[] modelParams = simContext.getModel().getModelParameters();
    while (true) {
        if (count++ > 30) {
            throw new ExpressionBindingException("infinite loop in eliminating function nesting");
        }
        // 
        // get all symbols (identifiers), make list of globals used
        // 
        String[] symbols = exp2.getSymbols();
        Vector<ModelParameter> globalsVector = new Vector<ModelParameter>();
        if (symbols != null) {
            for (int i = 0; i < symbols.length; i++) {
                for (int j = 0; j < modelParams.length; j++) {
                    if (symbols[i].equals(modelParams[j].getName())) {
                        globalsVector.addElement(modelParams[j]);
                    }
                }
            }
        }
        // 
        if (globalsVector.size() == 0) {
            break;
        }
        // 
        for (int i = 0; i < globalsVector.size(); i++) {
            ModelParameter mp = globalsVector.elementAt(i);
            Expression mpExp = new Expression(mp.getName());
            exp2.substituteInPlace(mpExp, mp.getExpression());
        }
    }
    // exp2.bindExpression(simContext.getModel());
    return exp2;
}

Example 5 with ExpressionBindingException

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

the class BioEvent method refreshDependencies.

public void refreshDependencies() {
    removePropertyChangeListener(this);
    addPropertyChangeListener(this);
    parameterContext.removePropertyChangeListener(this);
    parameterContext.addPropertyChangeListener(this);
    parameterContext.refreshDependencies();
    for (EventAssignment eventAssignment : eventAssignmentList) {
        try {
            eventAssignment.rebind();
        } catch (ExpressionBindingException e) {
            e.printStackTrace();
            throw new RuntimeException("failed to bind expression for assignment in event " + getName() + ": " + e.getMessage(), e);
        }
    }
}