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

Example 86 with Issue

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

the class SBMLImporter method addReactionParticipants.

/**
 * addReactionParticipant : Adds reactants and products and modifiers to a
 * reaction. Input args are the sbml reaction, vc reaction This method was
 * created mainly to handle reactions where there are reactants and/or
 * products that appear multiple times in a reaction. Virtual Cell now
 * allows the import of such reactions.
 */
private void addReactionParticipants(org.sbml.jsbml.Reaction sbmlRxn, ReactionStep vcRxn) throws Exception {
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    // if (!(vcRxn instanceof FluxReaction)) {
    if (true) {
        // reactants in sbmlRxn
        HashMap<String, Integer> sbmlReactantsHash = new HashMap<String, Integer>();
        for (int j = 0; j < (int) sbmlRxn.getNumReactants(); j++) {
            SpeciesReference spRef = sbmlRxn.getReactant(j);
            String sbmlReactantSpId = spRef.getSpecies();
            if (sbmlModel.getSpecies(sbmlReactantSpId) != null) {
                // check
                // if
                // spRef
                // is in
                // sbml
                // model
                // If stoichiometry of speciesRef is not an integer, it is
                // not handled in the VCell at this time; no point going
                // further
                double stoichiometry = 0.0;
                if (level < 3) {
                    // for SBML models < L3, default
                    // stoichiometry is 1, if field is not
                    // set.
                    // default value of stoichiometry,
                    stoichiometry = 1.0;
                    // if not set.
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    }
                } else {
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    } else {
                        throw new SBMLImportException("This is a SBML level 3 model, stoichiometry is not set for the reactant '" + sbmlReactantSpId + "' and no default value can be assumed.");
                    // logger.sendMessage(VCLogger.Priority.HighPriority,
                    // VCLogger.ErrorType.ReactionError,
                    // "This is a SBML level 3 model, stoichiometry is not set for the reactant '"
                    // + spRef.getSpecies() +
                    // "' and no default value can be assumed.");
                    }
                }
                if (sbmlReactantsHash.get(sbmlReactantSpId) == null) {
                    // if sbmlReactantSpId is NOT in sbmlReactantsHash, add
                    // it with its stoichiometry
                    sbmlReactantsHash.put(sbmlReactantSpId, Integer.valueOf((int) stoichiometry));
                } else {
                    // if sbmlReactantSpId IS in sbmlReactantsHash, update
                    // its stoichiometry value to (existing-from-hash +
                    // stoichiometry) and put it back in hash
                    int intStoich = sbmlReactantsHash.get(sbmlReactantSpId).intValue();
                    intStoich += (int) stoichiometry;
                    sbmlReactantsHash.put(sbmlReactantSpId, Integer.valueOf(intStoich));
                }
            } else {
                // spRef is not in model, throw exception
                throw new SBMLImportException("Reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
            }
        // end - if (spRef is species in model)
        }
        // sbmlReactionParticipantsHash as reactants to vcRxn
        for (Entry<String, Integer> es : sbmlReactantsHash.entrySet()) {
            SpeciesContext speciesContext = vcModel.getSpeciesContext(es.getKey());
            int stoich = es.getValue();
            vcRxn.addReactant(speciesContext, stoich);
        }
        /*
			Iterator<String> sbmlReactantsIter = sbmlReactantsHash.keySet()
					.iterator();
			while (sbmlReactantsIter.hasNext()) {
				String sbmlReactantStr = sbmlReactantsIter.next();
				SpeciesContext speciesContext = vcModel
						.getSpeciesContext(sbmlReactantStr);
				int stoich = sbmlReactantsHash.get(sbmlReactantStr).intValue();
				((SimpleReaction) vcRxn).addReactant(speciesContext, stoich);
			}
			*/
        // products in sbmlRxn
        HashMap<String, Integer> sbmlProductsHash = new HashMap<String, Integer>();
        for (int j = 0; j < (int) sbmlRxn.getNumProducts(); j++) {
            SpeciesReference spRef = sbmlRxn.getProduct(j);
            String sbmlProductSpId = spRef.getSpecies();
            if (sbmlModel.getSpecies(sbmlProductSpId) != null) {
                /* check if spRef is in sbml model
					If stoichiometry of speciesRef is not an integer, it is
					not handled in the VCell at this time; no point going
					further */
                double stoichiometry = 0.0;
                if (level < 3) {
                    // for sBML models < L3, default
                    // stoichiometry is 1, if field is not
                    // set.
                    // default value of stoichiometry,
                    stoichiometry = 1.0;
                    // if not set.
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    }
                } else {
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    } else {
                        throw new SBMLImportException("This is a SBML level 3 model, stoichiometry is not set for the product '" + sbmlProductSpId + "' and no default value can be assumed.");
                    // logger.sendMessage(VCLogger.Priority.HighPriority,
                    // VCLogger.ErrorType.ReactionError,
                    // "This is a SBML level 3 model, stoichiometry is not set for the product '"
                    // + spRef.getSpecies() +
                    // "' and no default value can be assumed.");
                    }
                }
                if (sbmlProductsHash.get(sbmlProductSpId) == null) {
                    // if sbmlProductSpId is NOT in sbmlProductsHash, add it
                    // with its stoichiometry
                    sbmlProductsHash.put(sbmlProductSpId, Integer.valueOf((int) stoichiometry));
                } else {
                    // if sbmlProductSpId IS in sbmlProductsHash, update its
                    // stoichiometry value to (existing-value-from-hash +
                    // stoichiometry) and put it back in hash
                    int intStoich = sbmlProductsHash.get(sbmlProductSpId).intValue();
                    intStoich += (int) stoichiometry;
                    sbmlProductsHash.put(sbmlProductSpId, Integer.valueOf(intStoich));
                }
            } else {
                // spRef is not in model, throw exception
                throw new SBMLImportException("Product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
            }
        // end - if (spRef is species in model)
        }
        // as products to vcRxn
        for (Entry<String, Integer> es : sbmlProductsHash.entrySet()) {
            SpeciesContext speciesContext = vcModel.getSpeciesContext(es.getKey());
            int stoich = es.getValue();
            vcRxn.addProduct(speciesContext, stoich);
        }
    /*
			Iterator<String> sbmlProductsIter = sbmlProductsHash.keySet()
					.iterator();
			while (sbmlProductsIter.hasNext()) {
				String sbmlProductStr = sbmlProductsIter.next();
				SpeciesContext speciesContext = vcModel
						.getSpeciesContext(sbmlProductStr);
				int stoich = sbmlProductsHash.get(sbmlProductStr).intValue();
				((SimpleReaction) vcRxn).addProduct(speciesContext, stoich);
			}
			*/
    // proxy.addProducts(sbmlProductsHash);
    }
    // modifiers
    for (int j = 0; j < (int) sbmlRxn.getNumModifiers(); j++) {
        ModifierSpeciesReference spRef = sbmlRxn.getModifier(j);
        String sbmlSpId = spRef.getSpecies();
        if (sbmlModel.getSpecies(sbmlSpId) != null) {
            // check if this modifier species is preesent in vcRxn (could
            // have been added as reactamt/product/catalyst).
            // If alreay a catalyst in vcRxn, do nothing
            ArrayList<ReactionParticipant> vcRxnParticipants = getVCReactionParticipantsFromSymbol(vcRxn, sbmlSpId);
            SpeciesContext speciesContext = vcModel.getSpeciesContext(sbmlSpId);
            if (vcRxnParticipants == null || vcRxnParticipants.size() == 0) {
                // If not in reactionParticipantList of vcRxn, add as
                // catalyst.
                vcRxn.addCatalyst(speciesContext);
            } else {
                for (ReactionParticipant rp : vcRxnParticipants) {
                    if (rp instanceof Reactant || rp instanceof Product) {
                        // If already a reactant or product in vcRxn, add
                        // warning to localIssuesList, don't do anything
                        localIssueList.add(new Issue(speciesContext, issueContext, IssueCategory.SBMLImport_Reaction, "Species " + speciesContext.getName() + " was already added as a reactant and/or product to " + vcRxn.getName() + "; Cannot add it as a catalyst also.", Issue.SEVERITY_INFO));
                        break;
                    }
                }
            }
        } else {
            // spRef is not in model, throw exception
            throw new SBMLImportException("Modifier '" + sbmlSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
        }
    // end - if (spRef is species in model)
    }
// end - for modifiers
}

Example 87 with Issue

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

the class DocumentValidUtil method checkIssuesForErrors.

public static void checkIssuesForErrors(SimulationContext simulationContext, boolean bIgnoreMathDescription) {
    Vector<Issue> issueList = new Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    simulationContext.getModel().gatherIssues(issueContext, issueList);
    simulationContext.gatherIssues(issueContext, issueList, bIgnoreMathDescription);
    checkIssuesForErrors(issueList);
}

Example 88 with Issue

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

the class KenworthyTest method main.

public static void main(String[] args) {
    if (args.length != 2) {
        System.out.println("expecting 2 arguments");
        System.out.println("usage: java " + Workflow.class.getSimpleName() + " workingdir workflowInputFile");
        System.out.println("workingdir example: " + "D:\\developer\\eclipse\\workspace\\VCell_5.4_vmicro\\datadir");
        System.out.println("workflowInputFile example: " + "D:\\developer\\eclipse\\workspace\\VCell_5.4_vmicro\\workflow1.txt");
        System.exit(1);
    }
    try {
        // PropertyLoader.loadProperties();
        // workflowInputFile "C:\\developer\\eclipse\\workspace\\VCell_5.3_vmicro\\workflow1.txt"
        File workingDirectory = new File(args[0]);
        LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
        Repository repository = new MemoryRepository();
        // String workflowLanguageText = BeanUtils.readBytesFromFile(new File(args[1]), null);
        // Workflow workflow = Workflow.parse(localWorkspace, workflowLanguageText);
        System.err.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using hard-coded example instead <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<");
        File vfrapFile = new File("D:\\Developer\\eclipse\\workspace_refactor\\VCell_5.4_vmicro\\3D_FRAP_2_ZProjection_Simulation1.vfrap");
        // Workflow workflow = getVFrapSimpleExample(workingDirectory, vfrapFile);
        // Workflow workflow = getFakeDataExample(workingDirectory);
        Workflow workflow = getInteractiveModelWorkflow(repository, workingDirectory);
        TaskContext taskContext = new TaskContext(workflow, repository, localWorkspace);
        ArrayList<Issue> issues = new ArrayList<Issue>();
        IssueContext issueContext = new IssueContext();
        workflow.gatherIssues(issueContext, issues);
        // WorkflowJGraphProxy workflowJGraphProxy = new WorkflowJGraphProxy(workflow);
        // displayWorkflowGraphJGraphX(workflowJGraphProxy);
        WorkflowUtilities.displayWorkflowGraph(workflow);
        WorkflowUtilities.displayWorkflowTable(taskContext);
        workflow.reportIssues(issues, Issue.SEVERITY_INFO, true);
        // 
        // execute the workflow
        // 
        workflow.compute(taskContext, new WorkflowUtilities.Progress());
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}