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

Example 46 with Issue

use of org.vcell.util.Issue 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));
        }
    }
}

Example 47 with Issue

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

the class StructureMapping method detectMappingConflictIssues.

private static void detectMappingConflictIssues(IssueContext issueContext, List<Issue> issueVector, StructureMapping ours) {
    if (ours.getGeometryClass() == null) {
        return;
    }
    final String ourStructureName = ours.getStructure().getName();
    final String ourStructureTypeName = ours.getStructure().getTypeName();
    final String ourSubdomainName = ours.getGeometryClass().getName();
    SimulationContext sc = ours.simulationContext;
    // list of incompatible structures mapped to the same subdomain, correctly built but not used
    String incompatibilityList = "";
    boolean incompatibilityFound = false;
    StructureMapping[] structureMappings = sc.getGeometryContext().getStructureMappings();
    for (StructureMapping theirs : structureMappings) {
        if (ours == theirs) {
            // don't compare ours with itself
            continue;
        }
        if (theirs.getGeometryClass() == null) {
            // 'theirs' is unmapped but some others may be, keep looking
            continue;
        }
        final String theirSubdomainName = theirs.getGeometryClass().getName();
        if (!ourSubdomainName.equals(theirSubdomainName)) {
            // we don't care if mapped to another subdomain
            continue;
        }
        String incompatibleStructure = findMappingBoundaryConflict(ours, theirs);
        if (incompatibleStructure != null) {
            if (incompatibilityFound) {
                incompatibilityList += ", ";
            }
            incompatibilityList += incompatibleStructure;
            incompatibilityFound = true;
        }
    }
    if (!incompatibilityList.isEmpty()) {
        // TODO: modify StructureMappingTableRenderer to customize the way issues are being rendered
        String message = "Subdomain '" + ourSubdomainName + "' boundary conditions (e.g. for X-, X+...) must match.";
        String tooltip = "Can't mix Flux and Value on the same column (e.g. X-, X+...) for multiple Structures mapped to the same Subdomain.";
        issueVector.add(new Issue(ours, issueContext, IssueCategory.SubVolumeVerificationError, message, tooltip, Issue.Severity.ERROR));
    }
}

Example 48 with Issue

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

the class SurfaceRegionObject method gatherIssues.

@Override
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    if (simulationContext.getGeometry().getGeometrySurfaceDescription() != null) {
        GeometricRegion[] regions = simulationContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions();
        boolean bFound = false;
        if (regions != null) {
            for (GeometricRegion region : regions) {
                if (region instanceof SurfaceGeometricRegion) {
                    SurfaceGeometricRegion sr = (SurfaceGeometricRegion) region;
                    if (sr.getAdjacentGeometricRegions() != null && sr.getAdjacentGeometricRegions().length == 2) {
                        VolumeGeometricRegion vr1 = (VolumeGeometricRegion) sr.getAdjacentGeometricRegions()[0];
                        VolumeGeometricRegion vr2 = (VolumeGeometricRegion) sr.getAdjacentGeometricRegions()[1];
                        if (vr1.getSubVolume() == insideSubVolume && vr1.getRegionID() == insideRegionID && vr2.getSubVolume() == outsideSubVolume && vr2.getRegionID() == outsideRegionID) {
                            bFound = true;
                        }
                        if (vr1.getSubVolume() == outsideSubVolume && vr1.getRegionID() == outsideRegionID && vr2.getSubVolume() == insideSubVolume && vr2.getRegionID() == insideRegionID) {
                            bFound = true;
                        }
                    }
                }
            }
        }
        if (!bFound) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "could not find corresponding surface region in geometry", Issue.Severity.ERROR));
        }
    }
}

Example 49 with Issue

use of org.vcell.util.Issue 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 50 with Issue

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

the class GeometryContext method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (11/1/2005 9:48:55 AM)
 * @param issueList java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.Geometry, getGeometry());
    GeometrySpec geometrySpec = getGeometry().getGeometrySpec();
    if (geometrySpec != null) {
        geometrySpec.gatherIssues(issueContext, getGeometry(), issueList);
    }
    for (int i = 0; fieldStructureMappings != null && i < fieldStructureMappings.length; i++) {
        fieldStructureMappings[i].gatherIssues(issueContext, issueList);
    }
    for (GeometryClass gc : fieldGeometry.getGeometryClasses()) {
        Structure[] structuresFromGeometryClass = getStructuresFromGeometryClass(gc);
        if (structuresFromGeometryClass == null || structuresFromGeometryClass.length == 0) {
            UnmappedGeometryClass unmappedGeometryClass = new UnmappedGeometryClass(gc);
            Issue issue = new Issue(unmappedGeometryClass, issueContext, IssueCategory.GeometryClassNotMapped, "Subdomain '" + gc.getName() + "' is not mapped to any physiological structure.", Issue.SEVERITY_WARNING);
            issueList.add(issue);
        }
    }
    if (getSimulationContext().isStoch() && getGeometry().getDimension() != 0 && getGeometry().getDimension() != 3) {
        Issue issue = new Issue(this, issueContext, IssueCategory.Smoldyn_Geometry_3DWarning, "VCell spatial stochastic models only support 3D geometry.", Issue.SEVERITY_ERROR);
        issueList.add(issue);
    }
}