Examples with Issue org.vcell.util.Issue used on opensource projects

Example 76 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class Structure method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    if (!fieldModel.getRbmModelContainer().getMolecularTypeList().isEmpty()) {
        if (!fieldName.equals(TokenMangler.fixTokenStrict(fieldName))) {
            String msg = "'" + fieldName + "' not legal identifier for rule-based modeling, try '" + TokenMangler.fixTokenStrict(fieldName) + "'.";
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
        }
    }
}

Example 77 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class ModelOptimizationMapping method computeOptimizationSpec.

/**
 * Insert the method's description here.
 * Creation date: (8/22/2005 9:26:52 AM)
 * @return cbit.vcell.opt.OptimizationSpec
 * @param modelOptimizationSpec cbit.vcell.modelopt.ModelOptimizationSpec
 */
MathSymbolMapping computeOptimizationSpec() throws MathException, MappingException {
    if (getModelOptimizationSpec().getReferenceData() == null) {
        System.out.println("no referenced data defined");
        return null;
    }
    OptimizationSpec optSpec = new OptimizationSpec();
    optSpec.setComputeProfileDistributions(modelOptimizationSpec.isComputeProfileDistributions());
    parameterMappings = null;
    // 
    // get original MathDescription (later to be substituted for local/global parameters).
    // 
    SimulationContext simContext = modelOptimizationSpec.getSimulationContext();
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription origMathDesc = null;
    mathSymbolMapping = null;
    try {
        origMathDesc = mathMapping.getMathDescription();
        mathSymbolMapping = mathMapping.getMathSymbolMapping();
    } catch (MatrixException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ModelException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    // create objective function (mathDesc and data)
    // 
    ReferenceData referenceData = getRemappedReferenceData(mathMapping);
    if (referenceData == null) {
        throw new RuntimeException("no referenced data defined");
    }
    // 
    // get parameter mappings
    // 
    ParameterMappingSpec[] parameterMappingSpecs = modelOptimizationSpec.getParameterMappingSpecs();
    Vector<ParameterMapping> parameterMappingList = new Vector<ParameterMapping>();
    Variable[] allVars = (Variable[]) BeanUtils.getArray(origMathDesc.getVariables(), Variable.class);
    for (int i = 0; i < parameterMappingSpecs.length; i++) {
        cbit.vcell.model.Parameter modelParameter = parameterMappingSpecs[i].getModelParameter();
        String mathSymbol = null;
        Variable mathVariable = null;
        if (mathSymbolMapping != null) {
            Variable variable = mathSymbolMapping.getVariable(modelParameter);
            if (variable != null) {
                mathSymbol = variable.getName();
            }
            if (mathSymbol != null) {
                mathVariable = origMathDesc.getVariable(mathSymbol);
            }
        }
        if (mathVariable != null) {
            if (parameterMappingSpecs[i].isSelected()) {
                if (parameterMappingSpecs[i].getHigh() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is smaller than its lower bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() > parameterMappingSpecs[i].getHigh()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getLow() < 0) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All lower bounds must not be negative.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getLow())) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Lower bounds must not be infinity.");
                }
                if (parameterMappingSpecs[i].getHigh() <= 0) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All upper bounds must be positive.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getHigh())) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Upper bounds must not be infinity.");
                }
            }
            double low = parameterMappingSpecs[i].isSelected() && parameterMappingSpecs[i].getLow() == 0 ? 1e-8 : parameterMappingSpecs[i].getLow();
            double high = parameterMappingSpecs[i].getHigh();
            double scale = Math.abs(parameterMappingSpecs[i].getCurrent()) < 1.0E-10 ? 1.0 : Math.abs(parameterMappingSpecs[i].getCurrent());
            double current = parameterMappingSpecs[i].getCurrent();
            low = Math.min(low, current);
            high = Math.max(high, current);
            Parameter optParameter = new Parameter(mathSymbol, low, high, scale, current);
            ParameterMapping parameterMapping = new ParameterMapping(modelParameter, optParameter, mathVariable);
            // 
            if (mathVariable instanceof Constant) {
                Constant origConstant = (Constant) mathVariable;
                for (int j = 0; j < allVars.length; j++) {
                    if (allVars[j].equals(origConstant)) {
                        if (parameterMappingSpecs[i].isSelected()) {
                            allVars[j] = new ParameterVariable(origConstant.getName());
                        } else {
                            allVars[j] = new Constant(origConstant.getName(), new Expression(optParameter.getInitialGuess()));
                        }
                        break;
                    }
                }
            }
            // 
            if (parameterMappingSpecs[i].isSelected()) {
                parameterMappingList.add(parameterMapping);
            }
        }
    }
    parameterMappings = (ParameterMapping[]) BeanUtils.getArray(parameterMappingList, ParameterMapping.class);
    try {
        origMathDesc.setAllVariables(allVars);
    } catch (ExpressionBindingException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    for (int i = 0; i < parameterMappings.length; i++) {
        optSpec.addParameter(parameterMappings[i].getOptParameter());
    }
    Vector<Issue> issueList = new Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    optSpec.gatherIssues(issueContext, issueList);
    for (int i = 0; i < issueList.size(); i++) {
        Issue issue = issueList.elementAt(i);
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            throw new RuntimeException(issue.getMessage());
        }
    }
    // 
    // 
    // 
    optimizationSpec = optSpec;
    return mathSymbolMapping;
}

Example 78 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class HMM_IRRKinetics method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 3:23:27 PM)
 * @return cbit.util.Issue[]
 */
@Override
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    super.gatherIssues(issueContext, issueList);
    // 
    // check for correct number of reactants
    // 
    ReactionParticipant[] reactionParticipants = getReactionStep().getReactionParticipants();
    int reactantCount = 0;
    for (int i = 0; i < reactionParticipants.length; i++) {
        if (reactionParticipants[i] instanceof Reactant) {
            reactantCount++;
        }
    }
    if (reactantCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "HMM_IRRKinetics must have exactly one reactant", Issue.SEVERITY_ERROR));
    }
}

Example 79 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class HMM_REVKinetics method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 3:26:54 PM)
 * @return cbit.util.Issue[]
 */
@Override
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    super.gatherIssues(issueContext, issueList);
    // 
    // check for correct number of reactants and products
    // 
    int reactantCount = 0;
    int productCount = 0;
    ReactionParticipant[] reactionParticipants = getReactionStep().getReactionParticipants();
    for (int i = 0; i < reactionParticipants.length; i++) {
        if (reactionParticipants[i] instanceof Reactant) {
            reactantCount++;
        }
        if (reactionParticipants[i] instanceof Product) {
            productCount++;
        }
    }
    if (reactantCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "HMM Reversible Kinetics must have exactly one reactant", Issue.SEVERITY_ERROR));
    }
    if (productCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "HMM Reversible Kinetics must have exactly one product", Issue.SEVERITY_ERROR));
    }
}

Example 80 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class Kinetics method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 2:53:13 PM)
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.ModelProcessDynamics, this);
    // 
    for (int i = 0; fieldUnresolvedParameters != null && i < fieldUnresolvedParameters.length; i++) {
        issueList.add(new Issue(fieldUnresolvedParameters[i], issueContext, IssueCategory.UnresolvedParameter, "Unresolved parameter '" + fieldUnresolvedParameters[i].getName() + "' in reaction '" + reactionStep.getName() + "'", Issue.SEVERITY_ERROR));
    }
    // 
    for (int i = 0; fieldKineticsParameters != null && i < fieldKineticsParameters.length; i++) {
        if (fieldKineticsParameters[i].getRole() == ROLE_UserDefined) {
            try {
                if (!isReferenced(fieldKineticsParameters[i], 0)) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.KineticsUnreferencedParameter, "Unreferenced Kinetic Parameter '" + fieldKineticsParameters[i].getName() + "' in reaction '" + reactionStep.getName() + "'", Issue.SEVERITY_WARNING));
                }
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.KineticsExpressionError, "error resolving expression " + e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ModelException e) {
                issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.CyclicDependency, "cyclic dependency in the parameter definitions", Issue.SEVERITY_ERROR));
            }
        }
    }
    // 
    if (fieldKineticsParameters != null) {
        for (KineticsParameter kineticsParameter : fieldKineticsParameters) {
            if (kineticsParameter.getExpression() == null) {
                issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.KineticsExpressionMissing, "expression is missing", Issue.SEVERITY_INFO));
            } else {
                Expression exp = kineticsParameter.getExpression();
                String[] symbols = exp.getSymbols();
                String issueMessagePrefix = "Kinetic parameter '" + kineticsParameter.getName() + "' in reaction '" + getReactionStep().getName() + "' ";
                if (symbols != null) {
                    for (int j = 0; j < symbols.length; j++) {
                        SymbolTableEntry ste = exp.getSymbolBinding(symbols[j]);
                        if (ste instanceof KineticsProxyParameter) {
                            ste = ((KineticsProxyParameter) ste).getTarget();
                        }
                        if (ste == null) {
                            issueList.add(new Issue(kineticsParameter, 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(kineticsParameter, issueContext, IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined species '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                            }
                            if (reactionStep.countNumReactionParticipants((SpeciesContext) ste) == 0) {
                                issueList.add(new Issue(kineticsParameter, 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(kineticsParameter, 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 (KineticsParameter kineticsParameter : fieldKineticsParameters) {
            String name = kineticsParameter.getName();
            SymbolTableEntry ste = getReactionStep().getNameScope().getExternalEntry(name, getReactionStep());
            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 + " in reaction " + getReactionStep().getName();
                issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
            }
        }
    }
    try {
        // 
        // determine unit consistency for each expression
        // 
        ModelUnitSystem modelUnitSystem = getReactionStep().getModel().getUnitSystem();
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(modelUnitSystem);
        for (int i = 0; i < fieldKineticsParameters.length; i++) {
            try {
                VCUnitDefinition paramUnitDef = fieldKineticsParameters[i].getUnitDefinition();
                VCUnitDefinition expUnitDef = unitEvaluator.getUnitDefinition(fieldKineticsParameters[i].getExpression());
                if (paramUnitDef == null) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "defined unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "undefined unit " + modelUnitSystem.getInstance_TBD().getSymbol(), Issue.SEVERITY_WARNING));
                } else if (expUnitDef == null) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "computed unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD() || (!paramUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD())) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "inconsistent units, defined=[" + fieldKineticsParameters[i].getUnitDefinition().getSymbol() + "], computed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
                }
            } catch (VCUnitException e) {
                issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    } catch (Throwable e) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.Units, "unexpected exception: " + e.getMessage(), Issue.SEVERITY_INFO));
    }
    // 
    for (int i = 0; i < fieldKineticsParameters.length; i++) {
        RealInterval simpleBounds = bounds[fieldKineticsParameters[i].getRole()];
        if (simpleBounds != null) {
            String parmName = reactionStep.getNameScope().getName() + "." + fieldKineticsParameters[i].getName();
            issueList.add(new SimpleBoundsIssue(fieldKineticsParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
        }
    }
}