Examples with SimpleBoundsIssue cbit.vcell.model.SimpleBoundsIssue used on opensource projects

Example 1 with SimpleBoundsIssue

use of cbit.vcell.model.SimpleBoundsIssue in project vcell by virtualcell.

the class StructureMapping method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (11/1/2005 9:57:23 AM)
 * @param issueVector java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueVector) {
    // size parameter must be set to non zero value for new ode, and all stoch simulations.
    if (simulationContext != null) {
        Parameter sizeParam = null;
        if (simulationContext.getGeometry().getDimension() == 0) {
            sizeParam = getSizeParameter();
        } else {
            sizeParam = getUnitSizeParameter();
        }
        if (sizeParam != null) {
            if (sizeParam.getExpression() == null) {
                if (!simulationContext.getGeometryContext().isAllVolFracAndSurfVolSpecified()) {
                    issueVector.add(new Issue(this, issueContext, IssueCategory.StructureMappingSizeParameterNotSet, "Size parameter is not set.", Issue.SEVERITY_ERROR));
                }
            } else {
                try {
                    double val = sizeParam.getExpression().evaluateConstant();
                    if (val <= 0) {
                        issueVector.add(new Issue(this, issueContext, IssueCategory.StructureMappingSizeParameterNotPositive, "Size parameter is not positive.", Issue.SEVERITY_ERROR));
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace();
                    issueVector.add(new Issue(this, issueContext, IssueCategory.StructureMappingSizeParameterNotConstant, "Size parameter is not a constant.", Issue.SEVERITY_ERROR));
                }
            }
        }
    }
    // 
    for (int i = 0; fieldParameters != null && i < fieldParameters.length; i++) {
        RealInterval simpleBounds = parameterBounds[fieldParameters[i].getRole()];
        if (simpleBounds != null) {
            String parmName = fieldParameters[i].getNameScope().getName() + "." + fieldParameters[i].getName();
            issueVector.add(new SimpleBoundsIssue(fieldParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
        }
    }
    if (geometryClass == null) {
        issueVector.add(new Issue(this, issueContext, IssueCategory.StructureNotMapped, getStructure().getTypeName() + " " + getStructure().getName() + " is not mapped to a geometry subdomain.", Issue.SEVERITY_WARNING));
    }
    if (geometryClass != null && simulationContext.getGeometryContext().getGeometry().getDimension() > 0) {
        detectMappingConflictIssues(issueContext, issueVector, this);
    }
}

Example 2 with SimpleBoundsIssue

use of cbit.vcell.model.SimpleBoundsIssue in project vcell by virtualcell.

the class IssueManager method updateIssues0.

/**
 * @param immediate update now, skip check of {@link #LAST_DIRTY_MILLISECONDS}
 */
private void updateIssues0(boolean immediate) {
    if (vcDocument == null) {
        return;
    }
    if (!immediate) {
        if (dirtyTimestamp == 0) {
            return;
        }
        long elapsedTime = System.currentTimeMillis() - dirtyTimestamp;
        if (elapsedTime < LAST_DIRTY_MILLISECONDS) {
            return;
        }
    }
    try {
        VCDocumentDecorator decorator = VCDocumentDecorator.getDecorator(vcDocument);
        numErrors = 0;
        numWarnings = 0;
        ArrayList<Issue> oldIssueList = new ArrayList<Issue>(issueList);
        ArrayList<Issue> tempIssueList = new ArrayList<Issue>();
        IssueContext issueContext = new ManagerContext();
        decorator.gatherIssues(issueContext, tempIssueList);
        // vcDocument.gatherIssues(issueContext,tempIssueList);
        issueList = new ArrayList<Issue>();
        for (Issue issue : tempIssueList) {
            if (issue instanceof SimpleBoundsIssue) {
                continue;
            }
            issueList.add(issue);
            Severity severity = issue.getSeverity();
            if (severity == Issue.Severity.ERROR) {
                numErrors++;
            } else if (severity == Issue.Severity.WARNING) {
                numWarnings++;
            }
        }
        fireIssueEventListener(new IssueEvent(vcDocument, oldIssueList, issueList));
    // System.out.println("\n................... update performed .................." + System.currentTimeMillis());
    } finally {
        dirtyTimestamp = 0;
        if (bMoreTime) {
            setDirty();
            bMoreTime = false;
        }
    }
}

Example 3 with SimpleBoundsIssue

use of cbit.vcell.model.SimpleBoundsIssue 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 SimpleBoundsIssue

use of cbit.vcell.model.SimpleBoundsIssue in project vcell by virtualcell.

the class SpeciesContextSpec method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (11/1/2005 10:03:46 AM)
 * @param issueVector java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueVector) {
    issueContext = issueContext.newChildContext(ContextType.SpeciesContextSpec, this);
    // 
    for (int i = 0; i < fieldParameters.length; i++) {
        RealInterval simpleBounds = parameterBounds[fieldParameters[i].getRole()];
        if (simpleBounds != null) {
            String parmName = fieldParameters[i].getNameScope().getName() + "." + fieldParameters[i].getName();
            issueVector.add(new SimpleBoundsIssue(fieldParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
        }
    }
    if (bForceContinuous && !bConstant && getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() > 0)) {
        // if it's particle or constant we're good
        SpeciesContext sc = getSpeciesContext();
        ReactionContext rc = getSimulationContext().getReactionContext();
        ReactionSpec[] rsArray = rc.getReactionSpecs();
        for (ReactionSpec rs : rsArray) {
            if (!rs.isExcluded()) {
                // we only care about reactions which are not excluded
                // true if "this" is part of current reaction
                boolean iAmParticipant = false;
                // true if current reaction has at least a particle participant
                boolean haveParticle = false;
                ReactionStep step = rs.getReactionStep();
                for (ReactionParticipant p : step.getReactionParticipants()) {
                    if (p instanceof Product || p instanceof Reactant) {
                        SpeciesContextSpec candidate = rc.getSpeciesContextSpec(p.getSpeciesContext());
                        if (candidate == this) {
                            iAmParticipant = true;
                        } else if (!candidate.isForceContinuous() && !candidate.isConstant()) {
                            haveParticle = true;
                        }
                    }
                }
                if (iAmParticipant && haveParticle) {
                    String msg = "Continuous Species won't conserve mass in particle reaction " + rs.getReactionStep().getName() + ".";
                    String tip = "Mass conservation for reactions of binding between discrete and continuous species is handled approximately. <br>" + "To avoid any algorithmic approximation, which may produce undesired results, the user is advised to indicate <br>" + "the continuous species in those reactions as modifiers (i.e. 'catalysts') in the physiology.";
                    issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_WARNING));
                    // we issue warning as soon as we found the first reaction which satisfies criteria
                    break;
                }
            }
        }
    }
    if (!bForceContinuous && bConstant) {
        if (getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() > 0)) {
            String msg = "Clamped Species must be continuous rather than particles.";
            String tip = "If choose 'clamped', must also choose 'forceContinuous'";
            issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_ERROR));
        }
    }
    if (bForceContinuous && !bConstant) {
        if (getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() == 0)) {
            String msg = "Non-constant species is forced continuous, not supported for nonspatial stochastic applications.";
            issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
        }
    }
}