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

Example 26 with Issue

use of org.vcell.util.Issue 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 27 with Issue

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

the class SimulationWarning method analyzeDiffusion.

/**
 * make sure diffusion expressions are constants, store for later use
 * @throws ExpressionException
 */
private static Map<MembraneSubDomain, List<DiffusionValue>> analyzeDiffusion(Simulation simulation, double timeStep, IssueContext issueContext, List<Issue> issueList) throws ExpressionException {
    Map<MembraneSubDomain, List<DiffusionValue>> diffusionValuesMap = new IdentityHashMap<>();
    diffusionValuesMap.clear();
    MutableDouble value = new MutableDouble();
    MathDescription cm = simulation.getMathDescription();
    Objects.requireNonNull(cm);
    MathDescription localMath = new MathDescription(cm);
    SimulationSymbolTable symTable = new SimulationSymbolTable(simulation, 0);
    Map<MembraneSubDomain, List<DiffusionValue>> dvMap = new HashMap<>();
    double maxDiffValue = Double.MIN_VALUE;
    List<DiffusionValue> diffusionList = new ArrayList<>();
    for (SubDomain sd : localMath.getSubDomainCollection()) {
        final boolean isMembrane = sd instanceof MembraneSubDomain;
        diffusionList.clear();
        for (ParticleProperties pp : sd.getParticleProperties()) {
            String name = pp.getVariable().getName();
            Expression diffExp = pp.getDiffusion();
            Expression flattened = MathUtilities.substituteFunctions(diffExp, symTable).flatten();
            if (isConstant(flattened, value)) {
                if (isMembrane) {
                    DiffusionValue dv = new DiffusionValue(name, value.doubleValue());
                    maxDiffValue = Math.max(maxDiffValue, dv.value);
                    diffusionList.add(dv);
                }
            } else {
                String s = "Smoldyn only supports constant diffusion, " + name + " is variable";
                Issue i = new Issue(simulation, issueContext, IssueCategory.SMOLYDN_DIFFUSION, s, s, Severity.ERROR);
                issueList.add(i);
            }
        }
        if (isMembrane && !diffusionList.isEmpty()) {
            dvMap.put((MembraneSubDomain) sd, diffusionList);
        }
    }
    diffusionValuesMap.putAll(dvMap);
    MeshSpecification ms = simulation.getMeshSpecification();
    Geometry g = ms.getGeometry();
    int dim = g.getDimension();
    double minDelta = Double.MAX_VALUE;
    switch(dim) {
        case 3:
            minDelta = Math.min(minDelta, ms.getDz(true));
        // fall-through
        case 2:
            minDelta = Math.min(minDelta, ms.getDy(true));
        // fall-through
        case 1:
            minDelta = Math.min(minDelta, ms.getDx(true));
            break;
        default:
            throw new RuntimeException("Invalid dimension " + dim + " for smoldyn solver");
    }
    double minArea = minDelta * minDelta / 2;
    double limit = PRECHECK_LIMIT_ADJUST * minArea / maxDiffValue;
    boolean warn = (timeStep > limit);
    if (lg.isDebugEnabled()) {
        lg.debug("Min delta " + minDelta + ", min area " + minArea + " time limit " + limit + " timeStep " + timeStep + " -> warn = " + warn);
    }
    if (warn) {
        String s = "Time step " + timeStep + " may be too large, performing further analysis ...";
        Issue i = new Issue(simulation, issueContext, IssueCategory.SMOLYDN_DIFFUSION, s, s, Severity.WARNING);
        issueList.add(i);
    }
    lg.debug("end of diffusion analysis");
    return diffusionValuesMap;
}

Example 28 with Issue

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

the class MathOverrides method hasUnusedOverrides.

public boolean hasUnusedOverrides() {
    ArrayList<Issue> issueList = new ArrayList<Issue>();
    IssueContext issueContext = new IssueContext(ContextType.Simulation, getSimulation(), null);
    gatherIssues(issueContext, issueList);
    for (Issue issue : issueList) {
        if (issue.getSeverity() == Issue.SEVERITY_ERROR && (issue.getCategory().equals(IssueCategory.Simulation_Override_NotFound) || issue.getCategory().equals(IssueCategory.Simulation_Override_NotSupported))) {
            return true;
        }
    }
    return false;
}

Example 29 with Issue

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

the class ModelOptimizationSpec method gatherIssues.

public void gatherIssues(IssueContext issueContext, java.util.List<Issue> issueList) {
    if (!hasSelectedParameters()) {
        issueList.add(new Issue(this, issueContext, IssueCategory.ParameterEstimationNoParameterSelected, "No parameters are selected for optimization.", Issue.SEVERITY_INFO));
    }
    boolean bExperimentalDataMapped = true;
    if (fieldReferenceDataMappingSpecs != null) {
        for (ReferenceDataMappingSpec rms : fieldReferenceDataMappingSpecs) {
            if (rms.getModelObject() == null) {
                bExperimentalDataMapped = false;
                break;
            }
        }
    }
    if (!bExperimentalDataMapped) {
        issueList.add(new Issue(this, issueContext, IssueCategory.ParameterEstimationRefereceDataNotMapped, "There is unmapped experimental data column.", Issue.SEVERITY_WARNING));
    }
    issueList.addAll(localIssueList);
}

Example 30 with Issue

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

the class OptimizationService method optimize.

public static OptimizationResultSet optimize(ParameterEstimationTask parameterEstimationTask) throws Exception {
    // if (OperatingSystemInfo.getInstance().isMac()){
    // throw new RuntimeException("parameter estimation not currently available on Mac\n\n   try Windows or Linux.\n\n   coming soon on Mac.");
    // }
    copasiOptCallbacks.reset();
    updateMath(parameterEstimationTask.getSimulationContext(), NetworkGenerationRequirements.ComputeFullStandardTimeout);
    StringBuffer issueText = new StringBuffer();
    java.util.Vector<Issue> issueList = new java.util.Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    parameterEstimationTask.gatherIssues(issueContext, issueList);
    boolean bFailed = false;
    for (int i = 0; i < issueList.size(); i++) {
        Issue issue = (Issue) issueList.elementAt(i);
        issueText.append(issue.getMessage() + "\n");
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            bFailed = true;
            break;
        }
    }
    if (bFailed) {
        throw new OptimizationException(issueText.toString());
    }
    parameterEstimationTask.refreshMappings();
    OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(new ParameterEstimationTaskSimulatorIDA(), parameterEstimationTask, copasiOptCallbacks, callback);
    return optResultSet;
}