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

Example 6 with Issue

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

the class DocumentValidUtil method checkIssuesForErrors.

public static void checkIssuesForErrors(BioModel bioModel) {
    Vector<Issue> issueList = new Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    bioModel.gatherIssues(issueContext, issueList);
    checkIssuesForErrors(issueList);
}

Example 7 with Issue

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

the class Workflow method reportIssues.

public void reportIssues(ArrayList<Issue> issues, Severity minSeverity, boolean bExceptionOnError) {
    boolean bAbort = false;
    StringBuffer errorBuffer = new StringBuffer();
    for (Issue issue : issues) {
        if (issue.getSeverity().ordinal() >= minSeverity.ordinal()) {
            System.out.println("ISSUE: " + issue.toString());
        }
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            bAbort = true;
            errorBuffer.append(issue.getCategory() + ":" + issue.getMessage() + "  \n");
        }
    }
    if (bAbort && bExceptionOnError) {
        throw new RuntimeException(errorBuffer.toString());
    }
}

Example 8 with Issue

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

the class MolecularType method gatherIssues.

@Override
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.MolecularType, this);
    if (name == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Name of " + getDisplayType() + " is null", Issue.Severity.ERROR));
    } else if (name.equals("")) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Name of " + getDisplayType() + " is empty", Issue.Severity.ERROR));
    } else if (!name.equals(TokenMangler.fixTokenStrict(name))) {
        String msg = "Name of " + getDisplayType() + " is invalid";
        String tip = "Valid names must start with a letter or underscore and contain only letters, numbers and the '_' character (underscore)";
        issueList.add(new Issue(this, this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
    }
    if (componentList == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, getDisplayType() + " '" + getDisplayName() + MolecularComponent.typeName + "' List is null", Issue.Severity.ERROR));
    } else if (componentList.isEmpty()) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, getDisplayType() + " '" + getDisplayName() + MolecularComponent.typeName + "' List is empty", Issue.Severity.INFO));
    } else {
        for (MolecularComponent mc : componentList) {
            MolecularComponent[] mcList = getMolecularComponents(mc.getName());
            if (mcList.length > 1) {
                String msg = "Duplicate " + mc.getDisplayType() + " '" + mc.getDisplayName() + "' in the definition of the " + MolecularType.typeName + ".";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
            }
            String mcName = mc.getName();
            if (!mcName.equals(TokenMangler.fixTokenStrict(mcName))) {
                String msg = "Name of " + MolecularComponent.typeName + " " + mcName + " is invalid";
                String tip = "Valid names must start with a letter or underscore and contain only letters, numbers and the '_' character (underscore)";
                issueList.add(new Issue(this, mc, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
            }
            for (ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
                String csdName = csd.getName();
                if (!csdName.equals(TokenMangler.fixTokenStrict(csdName))) {
                    String msg = "Name of " + ComponentStateDefinition.typeName + " " + csdName + " is invalid";
                    String tip = "Valid names must start with a letter or underscore and contain only letters, numbers and the '_' character (underscore)";
                    issueList.add(new Issue(this, csd, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
                }
            }
        }
        for (MolecularComponent entity : componentList) {
            entity.gatherIssues(issueContext, issueList);
        }
    }
    if (!isAnchorAll() && getAnchors().isEmpty()) {
        String msg = getDisplayType() + " " + getDisplayName() + " must be anchored to at least one Structure.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
    }
}

Example 9 with Issue

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

the class SimulationContext method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueVector, boolean bIgnoreMathDescription) {
    // issueContext = issueContext.newChildContext(ContextType.SimContext, this);
    if (applicationType.equals(Application.RULE_BASED_STOCHASTIC)) {
        for (ReactionRuleSpec rrs : getReactionContext().getReactionRuleSpecs()) {
            if (rrs.isExcluded()) {
                continue;
            }
            ReactionRule rr = rrs.getReactionRule();
            if (rr.getReactantPatterns().size() > 2) {
                String message = "NFSim doesn't support more than 2 reactants within a reaction rule.";
                issueVector.add(new Issue(rr, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
            if (rr.isReversible() && rr.getProductPatterns().size() > 2) {
                String message = "NFSim doesn't support more than 2 products within a reversible reaction rule.";
                issueVector.add(new Issue(rr, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
        }
        for (ReactionSpec rrs : getReactionContext().getReactionSpecs()) {
            if (rrs.isExcluded()) {
                continue;
            }
            ReactionStep rs = rrs.getReactionStep();
            if (rs.getNumReactants() > 2) {
                String message = "NFSim doesn't support more than 2 reactants within a reaction step.";
                issueVector.add(new Issue(rs, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
            if (rs.isReversible() && rs.getNumProducts() > 2) {
                String message = "NFSim doesn't support more than 2 products within a reversible reaction step.";
                issueVector.add(new Issue(rs, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
        }
        // we give warning when we have plain reactions with participants with patterns;
        // making rules from these may result in inconsistent interpretation for the constant rates
        boolean isParticipantWithPattern = false;
        for (ReactionSpec rrs : getReactionContext().getReactionSpecs()) {
            if (rrs.isExcluded()) {
                continue;
            }
            ReactionStep rs = rrs.getReactionStep();
            for (Reactant r : rs.getReactants()) {
                if (r.getSpeciesContext().hasSpeciesPattern()) {
                    isParticipantWithPattern = true;
                    break;
                }
            }
            if (isParticipantWithPattern) {
                break;
            }
            for (Product p : rs.getProducts()) {
                if (p.getSpeciesContext().hasSpeciesPattern()) {
                    isParticipantWithPattern = true;
                    break;
                }
            }
            if (isParticipantWithPattern) {
                break;
            }
        }
        if (isParticipantWithPattern) {
            String message = SimulationContext.rateWarning2;
            String tooltip = SimulationContext.rateWarning;
            issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, tooltip, Issue.Severity.WARNING));
        }
        for (Structure struct : getModel().getStructures()) {
            String name = struct.getName();
            if (!name.equals(TokenMangler.fixTokenStrict(name))) {
                String msg = "'" + name + "' not legal identifier for rule-based stochastic applications, try '" + TokenMangler.fixTokenStrict(name) + "'.";
                issueVector.add(new Issue(struct, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
            }
        }
    }
    if (fieldBioEvents != null) {
        for (BioEvent bioEvent : fieldBioEvents) {
            bioEvent.gatherIssues(issueContext, issueVector);
        }
    }
    if (spatialObjects != null) {
        for (SpatialObject spatialObject : spatialObjects) {
            spatialObject.gatherIssues(issueContext, issueVector);
        }
    }
    if (spatialProcesses != null) {
        for (SpatialProcess spatialProcess : spatialProcesses) {
            spatialProcess.gatherIssues(issueContext, issueVector);
        }
    }
    if (applicationType.equals(Application.NETWORK_DETERMINISTIC) && getModel().getRbmModelContainer().getMolecularTypeList().size() > 0) {
        // we're going to use network transformer to flatten (or we already did)
        if (isInsufficientIterations()) {
            issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, IssueInsufficientIterations, Issue.Severity.WARNING));
        }
        if (isInsufficientMaxMolecules()) {
            issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, IssueInsufficientMolecules, Issue.Severity.WARNING));
        }
    }
    getReactionContext().gatherIssues(issueContext, issueVector);
    getGeometryContext().gatherIssues(issueContext, issueVector);
    if (fieldAnalysisTasks != null) {
        for (AnalysisTask analysisTask : fieldAnalysisTasks) {
            analysisTask.gatherIssues(issueContext, issueVector);
        }
    }
    getOutputFunctionContext().gatherIssues(issueContext, issueVector);
    getMicroscopeMeasurement().gatherIssues(issueContext, issueVector);
    if (getMathDescription() != null && !bIgnoreMathDescription) {
        getMathDescription().gatherIssues(issueContext, issueVector);
    }
    if (networkConstraints == null) {
    // issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, "Network Constraints is null", Issue.Severity.ERROR));
    } else {
        networkConstraints.gatherIssues(issueContext, issueVector);
    }
}

Example 10 with Issue

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

the class SimulationContext method gatherIssueForMathOverride.

@Override
public Issue gatherIssueForMathOverride(IssueContext issueContext, Simulation simulation, String overriddenConstantName) {
    issueContext = issueContext.newChildContext(ContextType.SimContext, this);
    ReservedSymbol reservedSymbol = getModel().getReservedSymbolByName(overriddenConstantName);
    if (reservedSymbol != null && reservedSymbol.getRole() == ReservedSymbolRole.KMOLE) {
        String msg = "overriding unit factor KMOLE is no longer supported, unit conversion has been completely redesigned";
        return new Issue(simulation, issueContext, Issue.IssueCategory.Simulation_Override_NotSupported, msg, Severity.ERROR);
    }
    if (reservedSymbol != null && reservedSymbol.getRole() == ReservedSymbolRole.N_PMOLE) {
        String msg = "overriding unit factor N_PMOLE is no longer supported, unit conversion has been completely redesigned";
        return new Issue(simulation, issueContext, Issue.IssueCategory.Simulation_Override_NotSupported, msg, Severity.ERROR);
    }
    return null;
}