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

Example 6 with IssueContext

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

the class OptimizationService method optimize.

public static OptimizationResultSet optimize(ParameterEstimationTask parameterEstimationTask) throws Exception {
    // if (OperatingSystemInfo.getInstance().isMac()){
    // throw new RuntimeException("parameter estimation not currently available on Mac\n\n   try Windows or Linux.\n\n   coming soon on Mac.");
    // }
    copasiOptCallbacks.reset();
    updateMath(parameterEstimationTask.getSimulationContext(), NetworkGenerationRequirements.ComputeFullStandardTimeout);
    StringBuffer issueText = new StringBuffer();
    java.util.Vector<Issue> issueList = new java.util.Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    parameterEstimationTask.gatherIssues(issueContext, issueList);
    boolean bFailed = false;
    for (int i = 0; i < issueList.size(); i++) {
        Issue issue = (Issue) issueList.elementAt(i);
        issueText.append(issue.getMessage() + "\n");
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            bFailed = true;
            break;
        }
    }
    if (bFailed) {
        throw new OptimizationException(issueText.toString());
    }
    parameterEstimationTask.refreshMappings();
    OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(new ParameterEstimationTaskSimulatorIDA(), parameterEstimationTask, copasiOptCallbacks, callback);
    return optResultSet;
}

Example 7 with IssueContext

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

the class WorkflowTest 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(repository, 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);
        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);
    }
}

Example 8 with IssueContext

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

the class BioCartoonTool method pasteReactionsAndRules.

public static final void pasteReactionsAndRules(Component requester, ReactionSpeciesCopy rsCopy, Model pasteModel, Structure structTo, RXPasteInterface rxPasteInterface) {
    PasteHelper[] pasteHelper = new PasteHelper[1];
    AsynchClientTask issueTask = new AsynchClientTask("Checking Issues...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Model clonedModel = (Model) org.vcell.util.BeanUtils.cloneSerializable(pasteModel);
            clonedModel.refreshDependencies();
            // Model clonedModel = pasteModel;
            IssueContext issueContext = new IssueContext(ContextType.Model, clonedModel, null);
            Vector<Issue> issues = new Vector<>();
            checkStructuresCompatibility(rsCopy, clonedModel, structTo, issues, issueContext);
            Set<MolecularType> mtFromListStrict = getMoleculesFromStrict(rsCopy, clonedModel, issues, issueContext);
            if (issues.size() != 0) {
                // at this point we can only have fatal error issues or no issues at all
                if (!printIssues(issues, requester)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
            // map all the structures of the reactions, rules and their participants to existing structures, at need make new structures
            // key is the "from" structure, value is the name of the equivalent "to" structure
            // on the first position we have the struct from where we copy (key) and the struct where we paste (value)
            Map<Structure, String> structuresMap;
            if (rsCopy.getStructuresArr().length > 1) {
                // throws CANCEL_GENERIC if the user cancels
                structuresMap = mapStructures(requester, rsCopy, clonedModel, structTo, issueContext);
            } else {
                // if length == 1 it's just structFrom which automatically maps to structTo
                structuresMap = new LinkedHashMap<>();
                structuresMap.put(rsCopy.getFromStructure(), structTo.getName());
            }
            pasteMolecules(mtFromListStrict, clonedModel, structuresMap);
            List<ReactionRule> rulesTo = pasteRules(rsCopy, clonedModel, structTo, issues, issueContext, structuresMap);
            // for(ReactionRule rr : rulesTo) {
            // clonedModel.getRbmModelContainer().addReactionRule(rr);
            // }
            clonedModel.getRbmModelContainer().addReactionRules(rulesTo);
            // TODO: make any final verifications in the cloned model here
            // if anything is wrong exit here with some helpful message
            // .....
            // otherwise go directly to populating the real model
            mapStructures(structuresMap, pasteModel);
            pasteMolecules(mtFromListStrict, pasteModel, structuresMap);
            // we repeat all the steps to paste the rules in the real model instead of the clone
            rulesTo = pasteRules(rsCopy, pasteModel, structTo, issues, issueContext, structuresMap);
            // for(ReactionRule rr : rulesTo) {
            // pasteModel.getRbmModelContainer().addReactionRule(rr);
            // }
            pasteModel.getRbmModelContainer().addReactionRules(rulesTo);
            System.out.println("done");
        }
    };
    AsynchClientTask pasteRXTask = new AsynchClientTask("Pasting Reaction...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            IssueContext issueContext = new IssueContext(ContextType.Model, pasteModel, null);
        // if (pasteHelper[0].issues.size() != 0) {
        // printIssues(pasteHelper[0].issues, requester);
        // }
        // if(rxPasteInterface != null){
        // for(BioModelEntityObject newBioModelEntityObject:pasteHelper[0].reactionsAndSpeciesContexts.keySet()) {
        // ReactionCartoonTool.copyRelativePosition(rxPasteInterface.getGraphPane().getGraphModel(), pasteHelper[0].reactionsAndSpeciesContexts.get(newBioModelEntityObject), newBioModelEntityObject);
        // }
        // ReactionCartoonTool.selectAndSaveDiagram(rxPasteInterface, new ArrayList<BioModelEntityObject>(pasteHelper[0].reactionsAndSpeciesContexts.keySet()));
        // //					//Setup to allow dispatcher to set focus on a specified component after it closes the ProgressPopup
        // setFinalWindow(hashTable, rxPasteInterface.getGraphPane());
        // }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<>(), new AsynchClientTask[] { issueTask, pasteRXTask }, false);
}

Example 9 with IssueContext

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

the class BioCartoonTool method pasteReactionSteps.

/**
 * pasteReactionSteps : this method clones the model argument and calls the private pasteReationSteps0 method with the cloned model to see if
 * there are any issues with the paste operation. If so, the issue list is popped up in a warning dialog, and user is given the option of proceeding
 * with the paste or cancelling the operation.
 *
 * @param reactionStepsArr : reactions to be pasted
 * @param model : model where reactions are to be pasted
 * @param struct : strucure in 'model' where the reactions should be pasted
 * @param bNew : is it 'paste' or 'paste new' reaction (new reaction Participants are created if 'bNew' is <true>).
 * @param guiRequestComponent : the parent component for the warning dialog that pops up the issues, if any, encountered in the pasting process
 * @throws Exception
 */
public static final void pasteReactionSteps(Component requester, ReactionStep[] reactionStepsArrOrig, Model pasteModel, Structure struct, boolean bNew, /*boolean bUseDBSpecies,*/
UserResolvedRxElements userResolvedRxElements, RXPasteInterface rxPasteInterface) {
    PasteHelper[] pasteHelper = new PasteHelper[1];
    AsynchClientTask issueTask = new AsynchClientTask("Checking Issues...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Model clonedModel = (Model) org.vcell.util.BeanUtils.cloneSerializable(pasteModel);
            clonedModel.refreshDependencies();
            IssueContext issueContext = new IssueContext(ContextType.Model, clonedModel, null);
            pasteHelper[0] = pasteReactionSteps0(null, requester, issueContext, reactionStepsArrOrig, clonedModel, clonedModel.getStructure(struct.getName()), bNew, /*bUseDBSpecies,*/
            UserResolvedRxElements.createCompatibleUserResolvedRxElements(userResolvedRxElements, clonedModel));
            if (pasteHelper[0].issues.size() != 0) {
                if (!printIssues(pasteHelper[0].issues, requester)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
            if (pasteHelper[0].rxPartMapStruct != null) {
                // Convert rxPartMapStruct instances from cloned to pasteModel
                HashMap<String, HashMap<ReactionParticipant, Structure>> new_rxPartMapStruct = new HashMap<>();
                for (int i = 0; reactionStepsArrOrig != null && i < reactionStepsArrOrig.length; i++) {
                    new_rxPartMapStruct.put(reactionStepsArrOrig[i].getName(), new HashMap<ReactionParticipant, Structure>());
                    for (ReactionParticipant rxPart : pasteHelper[0].rxPartMapStruct.get(reactionStepsArrOrig[i].getName()).keySet()) {
                        ReactionParticipant[] origRXParts = reactionStepsArrOrig[i].getReactionParticipants();
                        for (int j = 0; j < origRXParts.length; j++) {
                            if (origRXParts[j].getName().equals(rxPart.getName())) {
                                new_rxPartMapStruct.get(reactionStepsArrOrig[i].getName()).put(origRXParts[j], pasteModel.getStructure(pasteHelper[0].rxPartMapStruct.get(reactionStepsArrOrig[i].getName()).get(rxPart).getName()));
                            }
                        }
                    }
                }
                pasteHelper[0].rxPartMapStruct = new_rxPartMapStruct;
            }
        }
    };
    AsynchClientTask pasteRXTask = new AsynchClientTask("Pasting Reaction...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            IssueContext issueContext = new IssueContext(ContextType.Model, pasteModel, null);
            pasteHelper[0] = pasteReactionSteps0(pasteHelper[0].rxPartMapStruct, requester, issueContext, reactionStepsArrOrig, pasteModel, struct, bNew, /*bUseDBSpecies,*/
            userResolvedRxElements);
            if (pasteHelper[0].issues.size() != 0) {
                printIssues(pasteHelper[0].issues, requester);
            }
            if (rxPasteInterface != null) {
                for (BioModelEntityObject newBioModelEntityObject : pasteHelper[0].reactionsAndSpeciesContexts.keySet()) {
                    ReactionCartoonTool.copyRelativePosition(rxPasteInterface.getGraphPane().getGraphModel(), pasteHelper[0].reactionsAndSpeciesContexts.get(newBioModelEntityObject), newBioModelEntityObject);
                }
                ReactionCartoonTool.selectAndSaveDiagram(rxPasteInterface, new ArrayList<BioModelEntityObject>(pasteHelper[0].reactionsAndSpeciesContexts.keySet()));
                // //Setup to allow dispatcher to set focus on a specified component after it closes the ProgressPopup
                setFinalWindow(hashTable, rxPasteInterface.getGraphPane());
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<>(), new AsynchClientTask[] { issueTask, pasteRXTask }, false);
}

Example 10 with IssueContext

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

the class MolecularComponentLargeShape method setComponentColor.

private Color setComponentColor() {
    boolean highlight = isHighlighted();
    if (owner == null) {
        return highlight == true ? componentBad.brighter() : componentBad;
    }
    Color componentColor = highlight == true ? componentBad.brighter() : componentBad;
    if (owner instanceof MolecularType) {
        componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
    } else if (owner instanceof SpeciesContext) {
        if (shapePanel != null && !shapePanel.isShowNonTrivialOnly()) {
            componentColor = componentHidden;
        } else {
            componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
        }
    } else if (mcp != null && owner instanceof RbmObservable) {
        if (shapePanel != null && !shapePanel.isEditable()) {
            componentColor = componentHidden;
        } else {
            componentColor = highlight == true ? componentHidden.brighter() : componentHidden;
        }
        if (mcp.getBondType() != BondType.Possible) {
            componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
        }
    } else if (owner instanceof ReactionRule) {
        ReactionRule reactionRule = (ReactionRule) owner;
        if (shapePanel.getDisplayMode() == DisplayMode.participantSignatures) {
            componentColor = componentHidden;
            if (shapePanel.isShowNonTrivialOnly() == true) {
                if (mcp.getBondType() != BondType.Possible) {
                    componentColor = componentPaleYellow;
                } else {
                    componentColor = componentHidden;
                }
            }
            if (shapePanel.isShowDifferencesOnly()) {
                switch(shapePanel.hasBondChanged(reactionRule.getName(), mcp)) {
                    case CHANGED:
                        componentColor = Color.orange;
                        break;
                    case ANALYSISFAILED:
                        ArrayList<Issue> issueList = new ArrayList<Issue>();
                        reactionRule.gatherIssues(new IssueContext(), issueList);
                        boolean bRuleHasErrorIssues = false;
                        for (Issue issue : issueList) {
                            if (issue.getSeverity() == Severity.ERROR) {
                                bRuleHasErrorIssues = true;
                                break;
                            }
                        }
                        if (bRuleHasErrorIssues) {
                            componentColor = componentHidden;
                        } else {
                            System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                            componentColor = Color.red.darker();
                        }
                        break;
                    default:
                        break;
                }
            }
        } else if (shapePanel.getDisplayMode() == DisplayMode.rules) {
            componentColor = componentHidden;
            if (shapePanel.isShowNonTrivialOnly() == true) {
                if (mcp.getBondType() != BondType.Possible) {
                    componentColor = componentPaleYellow;
                } else {
                    componentColor = componentHidden;
                }
            }
            if (shapePanel.isShowDifferencesOnly()) {
                switch(shapePanel.hasBondChanged(mcp)) {
                    case CHANGED:
                        componentColor = Color.orange;
                        break;
                    case ANALYSISFAILED:
                        ArrayList<Issue> issueList = new ArrayList<Issue>();
                        reactionRule.gatherIssues(new IssueContext(), issueList);
                        boolean bRuleHasErrorIssues = false;
                        for (Issue issue : issueList) {
                            if (issue.getSeverity() == Severity.ERROR) {
                                bRuleHasErrorIssues = true;
                                break;
                            }
                        }
                        if (bRuleHasErrorIssues) {
                            componentColor = componentHidden;
                        } else {
                            System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                            componentColor = Color.red.darker();
                        }
                        break;
                    default:
                        break;
                }
            }
        } else {
            componentColor = highlight == true ? componentHidden.brighter() : componentHidden;
            if (mcp.getBondType() != BondType.Possible) {
                componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
            }
        }
    }
    if (hasErrorIssues(owner, mcp, mc)) {
        componentColor = highlight == true ? componentBad.brighter() : componentBad;
    }
    return componentColor;
}