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

Example 21 with ExpressionBindingException

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

the class GeometryContext method setDefaultUnitSizes.

private void setDefaultUnitSizes() throws PropertyVetoException {
    if (getGeometry().getDimension() > 0) {
        for (StructureMapping sm : fieldStructureMappings) {
            StructureMapping[] sms = getStructureMappings(sm.getGeometryClass());
            StructureMappingParameter unitSizeParameter = sm.getUnitSizeParameter();
            if (unitSizeParameter == null) {
                continue;
            }
            Expression exp = unitSizeParameter.getExpression();
            if (sm instanceof MembraneMapping) {
                // Membrane mapped to surface or subdomain, default to 1.0
                if (exp == null) {
                    try {
                        unitSizeParameter.setExpression(new Expression(1.0));
                    } catch (ExpressionBindingException e) {
                        e.printStackTrace();
                    }
                }
            } else if (sm instanceof FeatureMapping) {
                // Feature mapped to subdomain
                if (sm.getGeometryClass() instanceof SubVolume) {
                    if (sms != null && sms.length == 1) {
                        try {
                            unitSizeParameter.setExpression(new Expression(1.0));
                        } catch (ExpressionBindingException e) {
                            e.printStackTrace();
                        }
                    }
                } else {
                    if (exp == null) {
                        try {
                            unitSizeParameter.setExpression(new Expression(1.0));
                        } catch (ExpressionBindingException e) {
                            e.printStackTrace();
                        }
                    }
                }
            }
        }
    }
}

Example 22 with ExpressionBindingException

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

the class ParameterContext method resolveUndefinedUnits.

public void resolveUndefinedUnits() {
    // 
    if (!bResolvingUnits) {
        VCUnitSystem unitSystem = unitSystemProvider.getUnitSystem();
        try {
            bResolvingUnits = true;
            boolean bAnyTBDUnits = false;
            for (int i = 0; i < fieldParameters.length; i++) {
                if (fieldParameters[i].getUnitDefinition() == null) {
                    // not ready to resolve units yet
                    return;
                } else if (fieldParameters[i].getUnitDefinition().isTBD()) {
                    bAnyTBDUnits = true;
                }
            }
            // 
            if (bAnyTBDUnits) {
                VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(unitSystem);
                VCUnitDefinition[] vcUnitDefinitions = unitEvaluator.suggestUnitDefinitions(fieldParameters);
                for (int i = 0; i < fieldParameters.length; i++) {
                    if (!fieldParameters[i].getUnitDefinition().isEquivalent(vcUnitDefinitions[i])) {
                        fieldParameters[i].setUnitDefinition(vcUnitDefinitions[i]);
                    }
                }
            // System.out.println("successfully completed Kinetics.resolveUndefinedUnits() for ReactionStep '"+getReactionStep()+"'");
            }
        } catch (ExpressionBindingException e) {
            System.out.println("ParameterContext.resolveUndefinedUnits(): EXCEPTION: " + e.getMessage());
        } catch (Exception e) {
            System.out.println("ParameterContext.resolveUndefinedUnits(): EXCEPTION: " + e.getMessage());
        } finally {
            bResolvingUnits = false;
        }
    }
}

Example 23 with ExpressionBindingException

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

the class ParameterContext method cleanupParameters.

/**
 * This method was created in VisualAge.
 */
final void cleanupParameters() throws ExpressionException, PropertyVetoException {
    if (bReading) {
        return;
    }
    // 
    if (fieldParameters != null) {
        for (int i = 0; i < fieldParameters.length; i++) {
            if (parameterPolicy.isUserDefined(fieldParameters[i]) && !isReferenced(fieldParameters[i], 0)) {
                removeParameter(fieldParameters[i]);
                i--;
            }
        }
    }
    if (fieldProxyParameters != null) {
        for (int i = 0; i < fieldProxyParameters.length; i++) {
            if (!isReferenced(fieldProxyParameters[i], 0)) {
                removeProxyParameter(fieldProxyParameters[i]);
                i--;
            }
        }
    }
    for (int i = 0; fieldParameters != null && i < fieldParameters.length; i++) {
        Expression exp = fieldParameters[i].getExpression();
        if (exp != null) {
            try {
                exp.bindExpression(this);
            } catch (ExpressionBindingException e) {
                System.out.println("error binding expression '" + exp.infix() + "': " + e.getMessage());
            }
        }
    }
    resolveUndefinedUnits();
}

Example 24 with ExpressionBindingException

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

the class AbstractMathMapping method getIdentifierSubstitutions.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
protected Expression getIdentifierSubstitutions(Expression origExp, VCUnitDefinition desiredExpUnitDef, GeometryClass geometryClass) throws ExpressionException, MappingException {
    String[] symbols = origExp.getSymbols();
    if (symbols == null) {
        return origExp;
    }
    VCUnitDefinition expUnitDef = null;
    try {
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(simContext.getModel().getUnitSystem());
        expUnitDef = unitEvaluator.getUnitDefinition(origExp);
        if (desiredExpUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', desiredUnits are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[null], observed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
        } else if (expUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', evaluated Units are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[null]", Issue.SEVERITY_WARNING));
        } else if (desiredExpUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        } else if (!desiredExpUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        }
    } catch (VCUnitException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (ExpressionException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (Exception e) {
        e.printStackTrace(System.out);
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    }
    Expression newExp = new Expression(origExp);
    // 
    // flatten user-defined functions
    // 
    FunctionInvocation[] functionInvocations = newExp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            return functionType == FunctionType.USERDEFINED;
        }
    });
    for (FunctionInvocation functionInvocation : functionInvocations) {
        if (functionInvocation.getSymbolTableFunctionEntry() instanceof Model.ModelFunction) {
            ModelFunction modelFunction = (ModelFunction) functionInvocation.getSymbolTableFunctionEntry();
            newExp.substituteInPlace(functionInvocation.getFunctionExpression(), modelFunction.getFlattenedExpression(functionInvocation));
        }
    }
    // 
    // then substitute Math symbols for Biological symbols.
    // 
    newExp.bindExpression(null);
    for (int i = 0; i < symbols.length; i++) {
        SymbolTableEntry ste = origExp.getSymbolBinding(symbols[i]);
        if (ste == null) {
            throw new ExpressionBindingException("symbol '" + symbols[i] + "' not bound");
        // ste = simContext.getGeometryContext().getModel().getSpeciesContext(symbols[i]);
        }
        if (ste != null) {
            String newName = getMathSymbol(ste, geometryClass);
            if (!newName.equals(symbols[i])) {
                newExp.substituteInPlace(new Expression(symbols[i]), new Expression(newName));
            }
        }
    }
    return newExp;
}

Example 25 with ExpressionBindingException

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

the class MathUtilities method substituteFunctions.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.parser.Expression
 * @param exp cbit.vcell.parser.Expression
 * @exception java.lang.Exception The exception description.
 */
public static Expression substituteFunctions(Expression exp, SymbolTable symbolTable) throws ExpressionException {
    Expression exp2 = new Expression(exp);
    // 
    // do until no more functions to substitute
    // 
    int count = 0;
    while (true) {
        if (count++ > 30) {
            throw new ExpressionBindingException("infinite loop in eliminating function nesting");
        }
        // 
        if (lg.isDebugEnabled()) {
            lg.debug("substituteFunctions() exp2 = '" + exp2 + "'");
        }
        Enumeration<Variable> enum1 = getRequiredVariablesExplicit(exp2, symbolTable);
        Vector<Variable> functionList = new Vector<Variable>();
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof Function) {
                functionList.addElement(var);
                if (lg.isDebugEnabled()) {
                    lg.debug("added " + var + " to function list");
                }
            }
        }
        // 
        if (functionList.size() == 0) {
            break;
        }
        // 
        for (int i = 0; i < functionList.size(); i++) {
            Function funct = (Function) functionList.elementAt(i);
            Expression functExp = new Expression(funct.getName() + ";");
            if (lg.isDebugEnabled()) {
                lg.debug("flattenFunctions(pass=" + count + "), substituting '" + funct.getExpression() + "' for function '" + functExp + "'");
            }
            exp2.substituteInPlace(functExp, new Expression(funct.getExpression()));
            if (lg.isDebugEnabled()) {
                lg.debug(".......substituted exp2 = '" + exp2 + "'");
            }
        }
    }
    // exp2 = exp2.flatten();
    exp2.bindExpression(symbolTable);
    return exp2;
}