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

Example 1 with IssueContext

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

the class ParameterEstimationRunTaskPanel method solve.

private void solve() throws NumberFormatException {
    CopasiOptimizationMethod com = optimizationMethodParameterTableModel.copasiOptimizationMethod;
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(com);
    // get num runs for stochstic opt mehtods before starting solving...
    if (com.getType().isStochasticMethod()) {
        int numRuns = Integer.parseInt(((String) numberOfRunComboBox.getSelectedItem()));
        optSolverSpec.setNumOfRuns(numRuns);
    }
    parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    parameterEstimationTask.getModelOptimizationSpec().setComputeProfileDistributions(computeProfileDistributionsCheckBox.isSelected());
    optSolverCallbacks.reset();
    Double endValue = com.getEndValue();
    optSolverCallbacks.setEvaluation(0, Double.POSITIVE_INFINITY, 0, endValue, 0);
    // (endValue != null);
    getRunStatusDialog().showProgressBar(com);
    Collection<AsynchClientTask> taskList = ClientRequestManager.updateMath(this, parameterEstimationTask.getSimulationContext(), false, NetworkGenerationRequirements.ComputeFullStandardTimeout);
    AsynchClientTask task1 = new AsynchClientTask("checking issues", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            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();
        }
    };
    taskList.add(task1);
    AsynchClientTask task2 = new AsynchClientTask("solving", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
            // OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(new ParameterEstimationTaskSimulatorIDA(),parameterEstimationTask,optSolverCallbacks,mathMappingCallback);
            OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveRemoteApi(new ParameterEstimationTaskSimulatorIDA(), parameterEstimationTask, optSolverCallbacks, mathMappingCallback);
            hashTable.put(ORS_KEY, optResultSet);
        }
    };
    taskList.add(task2);
    AsynchClientTask setResultTask = new AsynchClientTask("set results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            OptimizationResultSet optResultSet = (OptimizationResultSet) hashTable.get(ORS_KEY);
            parameterEstimationTask.setOptimizationResultSet(optResultSet);
        }
    };
    taskList.add(setResultTask);
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), taskList.toArray(new AsynchClientTask[taskList.size()]), getRunStatusDialog(), true, true, true, null, false);
}

Example 2 with IssueContext

use of org.vcell.util.IssueContext 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 3 with IssueContext

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

the class MathDescription method isValid.

public boolean isValid() {
    IssueContext issueContext = new IssueContext(ContextType.MathDescription, this, null);
    ArrayList<Issue> issueList = new ArrayList<Issue>();
    gatherIssues(issueContext, issueList);
    if (issueList.size() > 0) {
        setWarning(issueList.get(0).getMessage());
    }
    return issueList.size() == 0;
}

Example 4 with IssueContext

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

the class IssueManager method updateIssues0.

/**
 * @param immediate update now, skip check of {@link #LAST_DIRTY_MILLISECONDS}
 */
private void updateIssues0(boolean immediate) {
    if (vcDocument == null) {
        return;
    }
    if (!immediate) {
        if (dirtyTimestamp == 0) {
            return;
        }
        long elapsedTime = System.currentTimeMillis() - dirtyTimestamp;
        if (elapsedTime < LAST_DIRTY_MILLISECONDS) {
            return;
        }
    }
    try {
        VCDocumentDecorator decorator = VCDocumentDecorator.getDecorator(vcDocument);
        numErrors = 0;
        numWarnings = 0;
        ArrayList<Issue> oldIssueList = new ArrayList<Issue>(issueList);
        ArrayList<Issue> tempIssueList = new ArrayList<Issue>();
        IssueContext issueContext = new ManagerContext();
        decorator.gatherIssues(issueContext, tempIssueList);
        // vcDocument.gatherIssues(issueContext,tempIssueList);
        issueList = new ArrayList<Issue>();
        for (Issue issue : tempIssueList) {
            if (issue instanceof SimpleBoundsIssue) {
                continue;
            }
            issueList.add(issue);
            Severity severity = issue.getSeverity();
            if (severity == Issue.Severity.ERROR) {
                numErrors++;
            } else if (severity == Issue.Severity.WARNING) {
                numWarnings++;
            }
        }
        fireIssueEventListener(new IssueEvent(vcDocument, oldIssueList, issueList));
    // System.out.println("\n................... update performed .................." + System.currentTimeMillis());
    } finally {
        dirtyTimestamp = 0;
        if (bMoreTime) {
            setDirty();
            bMoreTime = false;
        }
    }
}

Example 5 with IssueContext

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

the class MathOverrides method hasUnusedOverrides.

public boolean hasUnusedOverrides() {
    ArrayList<Issue> issueList = new ArrayList<Issue>();
    IssueContext issueContext = new IssueContext(ContextType.Simulation, getSimulation(), null);
    gatherIssues(issueContext, issueList);
    for (Issue issue : issueList) {
        if (issue.getSeverity() == Issue.SEVERITY_ERROR && (issue.getCategory().equals(IssueCategory.Simulation_Override_NotFound) || issue.getCategory().equals(IssueCategory.Simulation_Override_NotSupported))) {
            return true;
        }
    }
    return false;
}