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

Example 11 with Issue

use of org.vcell.util.Issue 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 12 with Issue

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

the class VolumeRegionObject method gatherIssues.

@Override
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    if (simulationContext.getGeometry().getGeometrySurfaceDescription() != null && simulationContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() != null) {
        GeometricRegion[] regions = simulationContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions();
        boolean bFound = false;
        for (GeometricRegion region : regions) {
            if (region instanceof VolumeGeometricRegion) {
                VolumeGeometricRegion vr = (VolumeGeometricRegion) region;
                if (getSubVolume() == vr.getSubVolume() && getRegionID() == vr.getRegionID()) {
                    bFound = true;
                    break;
                }
            }
        }
        if (!bFound) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "geometry missing volume region (subvolume " + subVolume.getName() + " region " + regionID + ")", Issue.Severity.ERROR));
        }
    }
}

Example 13 with Issue

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

the class BioEvent method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    // check all event assignment symbols
    if (eventAssignmentList != null) {
        for (EventAssignment ea : eventAssignmentList) {
            // the target of the event assignment
            SymbolTableEntry ste = simulationContext.getEntry(ea.getTarget().getName());
            // SymbolTableEntry ste = parameterContext.getEntry(ea.getTarget().getName());
            if (ste == null) {
                String msg = "Missing Parameter '" + ea.getTarget().getName() + "' used in BioEvent '" + name + "'.";
                String tip = "Remove the Action containing the missing parameter from the BioEvent '" + name + "'.";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
                // found one issue on this event assignment, we show it and go to next
                break;
            }
            // the expression of the event assignment
            Expression exp = ea.assignmentExpression;
            String[] symbols = exp.getSymbols();
            if (symbols != null) {
                boolean found = false;
                for (String symbol : symbols) {
                    ste = simulationContext.getEntry(symbol);
                    if (ste == null) {
                        String msg = "Missing Symbol '" + symbol + "' in Assignment Expression for BioEvent '" + name + "'.";
                        String tip = "Remove the Action containing the missing Symbol from the Assignment Expression of the BioEvent '" + name + "'.";
                        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
                        found = true;
                        break;
                    }
                }
                if (found == true) {
                    // found one issue on this event assignment, we show it and go to next
                    break;
                }
            }
        }
    } else {
        String msg = "No Action assigned to BioEvent '" + name + "'.";
        String tip = "Please assign an Action to the BioEvent '" + name + "'.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.WARNING));
    }
    // check all trigger condition symbols
    for (LocalParameter lp : getEventParameters()) {
        if (lp.getExpression() != null && lp.getExpression().getSymbols() != null) {
            String[] symbols = lp.getExpression().getSymbols();
            boolean found = false;
            for (String symbol : symbols) {
                SymbolTableEntry ste = simulationContext.getEntry(symbol);
                if (ste == null) {
                    String msg = "Missing Symbol '" + symbol + "' in the Trigger Condition for BioEvent '" + name + "'.";
                    String tip = "Remove the Action containing the missing Symbol from the Trigger Condition of the BioEvent '" + name + "'.";
                    issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
                    found = true;
                    break;
                }
            }
            if (found == true) {
                // found one issue with a parameter on this trigger condition, we show it and stop
                break;
            }
        }
    }
}

Example 14 with Issue

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

the class GHKKinetics method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 3:11:16 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 Product) {
            reactantCount++;
        }
        if (reactionParticipants[i] instanceof Reactant) {
            productCount++;
        }
    }
    if (reactantCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "GHK Kinetics must have exactly one reactant", Issue.SEVERITY_ERROR));
    }
    if (productCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "GHK Kinetics must have exactly one product", Issue.SEVERITY_WARNING));
    }
}

Example 15 with Issue

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

the class GeneralPermeabilityKinetics 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 Product) {
            reactantCount++;
        }
        if (reactionParticipants[i] instanceof Reactant) {
            productCount++;
        }
    }
    if (reactantCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "GeneralPermeability Kinetics must have exactly one reactant", Issue.SEVERITY_ERROR));
    }
    if (productCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "GeneralPermeability Kinetics must have exactly one product", Issue.SEVERITY_WARNING));
    }
}