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

Example 1 with VCUnitEvaluator

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

the class Kinetics method resolveUndefinedUnits.

/**
 * Insert the method's description here.
 * Creation date: (4/13/2004 3:09:21 PM)
 */
public void resolveUndefinedUnits() {
    // 
    if (!bResolvingUnits) {
        bResolvingUnits = true;
        try {
            if (getReactionStep().getModel() != null) {
                ModelUnitSystem modelUnitSystem = getReactionStep().getModel().getUnitSystem();
                boolean bAnyTBDUnits = false;
                for (int i = 0; i < fieldKineticsParameters.length; i++) {
                    if (fieldKineticsParameters[i].getUnitDefinition() == null) {
                        // not ready to resolve units yet
                        return;
                    } else if (fieldKineticsParameters[i].getUnitDefinition().isTBD()) {
                        bAnyTBDUnits = true;
                    }
                }
                // 
                if (bAnyTBDUnits) {
                    VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(modelUnitSystem);
                    VCUnitDefinition[] vcUnitDefinitions = unitEvaluator.suggestUnitDefinitions(fieldKineticsParameters);
                    for (int i = 0; i < fieldKineticsParameters.length; i++) {
                        if (!fieldKineticsParameters[i].getUnitDefinition().isEquivalent(vcUnitDefinitions[i])) {
                            fieldKineticsParameters[i].setUnitDefinition(vcUnitDefinitions[i]);
                        }
                    }
                // System.out.println("successfully completed Kinetics.resolveUndefinedUnits() for ReactionStep '"+getReactionStep()+"'");
                }
            }
        } catch (Exception e) {
            if (lg.isEnabledFor(Level.WARN)) {
                lg.warn("Kinetics.resolveUndefinedUnits(): EXCEPTION: " + e.getMessage());
            }
        } finally {
            bResolvingUnits = false;
        }
    }
}

Example 2 with VCUnitEvaluator

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

the class Model method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 10:38:12 PM)
 * @param issueList java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.Model, this);
    // 
    try {
        for (ModelParameter modelParameter : fieldModelParameters) {
            Expression exp = modelParameter.getExpression();
            String[] symbols = exp.getSymbols();
            if (symbols != null) {
                String issueMsgPrefix = "Global parameter '" + modelParameter.getName() + "' ";
                for (int j = 0; j < symbols.length; j++) {
                    SymbolTableEntry ste = exp.getSymbolBinding(symbols[j]);
                    if (ste == null) {
                        issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined symbol '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                    } else if (ste instanceof SpeciesContext) {
                        if (!contains((SpeciesContext) ste)) {
                            issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined species '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        }
                    } else if (ste instanceof ModelParameter) {
                        if (!contains((ModelParameter) ste)) {
                            issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined global parameter '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        }
                    }
                }
            }
        }
        // 
        for (int i = 0; i < fieldModelParameters.length; i++) {
            try {
                VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(getUnitSystem());
                VCUnitDefinition paramUnitDef = fieldModelParameters[i].getUnitDefinition();
                VCUnitDefinition expUnitDef = unitEvaluator.getUnitDefinition(fieldModelParameters[i].getExpression());
                if (paramUnitDef == null) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "defined unit is null", Issue.SEVERITY_WARNING));
                } else if (expUnitDef == null) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "computed unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "unit is undefined (" + unitSystem.getInstance_TBD().getSymbol() + ")", Issue.SEVERITY_WARNING));
                } else if (!paramUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "unit mismatch, computed = [" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
                }
            } catch (VCUnitException e) {
                issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "units inconsistent: " + e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "units inconsistent: " + e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        issueList.add(new Issue(this, issueContext, IssueCategory.Units, "unexpected exception: " + e.getMessage(), Issue.SEVERITY_WARNING));
    }
    // 
    for (Structure struct : fieldStructures) {
        struct.gatherIssues(issueContext, issueList);
    }
    // 
    for (int i = 0; i < fieldReactionSteps.length; i++) {
        fieldReactionSteps[i].gatherIssues(issueContext, issueList);
    }
    // 
    // get issues from species contexts (species patterns)
    // 
    int seedSpeciesCount = 0;
    for (int i = 0; i < fieldSpeciesContexts.length; i++) {
        if (fieldSpeciesContexts[i].hasSpeciesPattern()) {
            seedSpeciesCount++;
        }
        fieldSpeciesContexts[i].gatherIssues(issueContext, issueList);
    }
    if (seedSpeciesCount == 0 && !rbmModelContainer.getReactionRuleList().isEmpty()) {
        String msg = "At least one seed species is required.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.WARNING));
    }
    // 
    // get issues for symbol name clashes (specifically structures with same voltage names or structure names)
    // 
    HashSet<SymbolTableEntry> steHashSet = new HashSet<SymbolTableEntry>();
    gatherLocalEntries(steHashSet);
    Iterator<SymbolTableEntry> iter = steHashSet.iterator();
    Hashtable<String, SymbolTableEntry> symbolHashtable = new Hashtable<String, SymbolTableEntry>();
    while (iter.hasNext()) {
        SymbolTableEntry ste = iter.next();
        SymbolTableEntry existingSTE = symbolHashtable.get(ste.getName());
        if (existingSTE != null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "model symbol \"" + ste.getName() + "\" is used within \"" + ste.getNameScope().getName() + "\" and \"" + existingSTE.getNameScope().getName() + "\"", Issue.SEVERITY_ERROR));
        } else {
            symbolHashtable.put(ste.getName(), ste);
        }
    }
    // 
    // gather issues for electrical topology (unspecified +ve or -ve features, or +ve feature == -ve feature
    // 
    getElectricalTopology().gatherIssues(issueContext, issueList);
    // 
    if (rbmModelContainer == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.InternalError, "Rbm Model Container is null", Issue.SEVERITY_WARNING));
    } else {
        rbmModelContainer.gatherIssues(issueContext, issueList);
    }
}

Example 3 with VCUnitEvaluator

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

the class ParameterContext method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList, ParameterRoleEnum userDefinedRole) {
    // 
    for (int i = 0; fieldUnresolvedParameters != null && i < fieldUnresolvedParameters.length; i++) {
        issueList.add(new Issue(fieldUnresolvedParameters[i], issueContext, IssueCategory.UnresolvedParameter, "Unresolved parameter '" + fieldUnresolvedParameters[i].getName(), Issue.SEVERITY_ERROR));
    }
    // 
    for (int i = 0; fieldParameters != null && i < fieldParameters.length; i++) {
        if (fieldParameters[i].getRole() == userDefinedRole) {
            try {
                if (!isReferenced(fieldParameters[i], 0)) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.KineticsUnreferencedParameter, "Unreferenced Kinetic Parameter '" + fieldParameters[i].getName(), Issue.SEVERITY_WARNING));
                }
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.KineticsExpressionError, "error resolving expression " + e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    }
    // 
    if (fieldParameters != null) {
        for (LocalParameter parameter : this.fieldParameters) {
            if (parameter.getExpression() == null) {
                issueList.add(new Issue(parameter, issueContext, IssueCategory.KineticsExpressionMissing, "expression is missing", Issue.SEVERITY_INFO));
            } else {
                Expression exp = parameter.getExpression();
                String[] symbols = exp.getSymbols();
                String issueMessagePrefix = "parameter '" + parameter.getName() + "' ";
                if (symbols != null) {
                    for (int j = 0; j < symbols.length; j++) {
                        SymbolTableEntry ste = exp.getSymbolBinding(symbols[j]);
                        if (ste instanceof LocalProxyParameter) {
                            ste = ((LocalProxyParameter) ste).getTarget();
                        }
                        if (ste == null) {
                            issueList.add(new Issue(parameter, issueContext, IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined symbol '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        // } else if (ste instanceof SpeciesContext) {
                        // if (!getReactionStep().getModel().contains((SpeciesContext)ste)) {
                        // issueList.add(new Issue(parameter,issueContext,IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined species '"+symbols[j]+"'",Issue.SEVERITY_ERROR));
                        // }
                        // if (reactionStep.countNumReactionParticipants((SpeciesContext)ste) == 0){
                        // issueList.add(new Issue(parameter,issueContext,IssueCategory.KineticsExpressionNonParticipantSymbol, issueMessagePrefix + "references species context '"+symbols[j]+"', but it is not a reactant/product/catalyst of this reaction",Issue.SEVERITY_WARNING));
                        // }
                        // } else if (ste instanceof ModelParameter) {
                        // if (!getReactionStep().getModel().contains((ModelParameter)ste)) {
                        // issueList.add(new Issue(parameter,issueContext,IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined global parameter '"+symbols[j]+"'",Issue.SEVERITY_ERROR));
                        // }
                        }
                    }
                }
            }
        }
        // looking for local param which masks a global and issueing a warning
        for (LocalParameter parameter : fieldParameters) {
            String name = parameter.getName();
            SymbolTableEntry ste = nameScope.getExternalEntry(name, this);
            String steName;
            if (ste != null) {
                if (ste instanceof Displayable) {
                    steName = ((Displayable) ste).getDisplayType() + " " + ste.getName();
                } else {
                    steName = ste.getClass().getSimpleName() + " " + ste.getName();
                }
                String msg = steName + " is overriden by a local parameter " + name;
                issueList.add(new Issue(parameter, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
            }
        }
    }
    try {
        // 
        // determine unit consistency for each expression
        // 
        VCUnitSystem unitSystem = unitSystemProvider.getUnitSystem();
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(unitSystem);
        for (int i = 0; i < fieldParameters.length; i++) {
            if (fieldParameters[i].getExpression() == null) {
                continue;
            }
            try {
                VCUnitDefinition paramUnitDef = fieldParameters[i].getUnitDefinition();
                VCUnitDefinition expUnitDef = unitEvaluator.getUnitDefinition(fieldParameters[i].getExpression());
                if (paramUnitDef == null) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "defined unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "undefined unit " + unitSystem.getInstance_TBD().getSymbol(), Issue.SEVERITY_WARNING));
                } else if (expUnitDef == null) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "computed unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD() || (!paramUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD())) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "inconsistent units, defined=[" + fieldParameters[i].getUnitDefinition().getSymbol() + "], computed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
                }
            } catch (VCUnitException e) {
                issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    } catch (Throwable e) {
        issueList.add(new Issue(parameterPolicy.getIssueSource(), issueContext, IssueCategory.Units, "unexpected exception: " + e.getMessage(), Issue.SEVERITY_INFO));
    }
    // 
    for (int i = 0; i < fieldParameters.length; i++) {
        RealInterval simpleBounds = parameterPolicy.getConstraintBounds(fieldParameters[i].getRole());
        if (simpleBounds != null) {
            String parmName = fieldParameters[i].getName();
            issueList.add(new SimpleBoundsIssue(fieldParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
        }
    }
}

Example 4 with VCUnitEvaluator

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

the class MathMapping_4_8 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, StructureMapping structureMapping) 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);
    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, structureMapping);
            if (!newName.equals(symbols[i])) {
                newExp.substituteInPlace(new Expression(symbols[i]), new Expression(newName));
            }
        }
    }
    return newExp;
}

Example 5 with VCUnitEvaluator

use of cbit.vcell.parser.VCUnitEvaluator 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;
        }
    }
}