Examples with GalaxyWorkflowStatus ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus used on opensource projects

Example 36 with GalaxyWorkflowStatus

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowStatus in project irida by phac-nml.

the class AnalysisExecutionScheduledTaskImpl method monitorRunningAnalyses.

/**
 * {@inheritDoc}
 */
@Override
public Set<Future<AnalysisSubmission>> monitorRunningAnalyses() {
    synchronized (monitorRunningAnalysesLock) {
        logger.trace("Running monitorRunningAnalyses");
        List<AnalysisSubmission> analysisSubmissions = analysisSubmissionRepository.findByAnalysisState(AnalysisState.RUNNING);
        Set<Future<AnalysisSubmission>> submissions = Sets.newHashSet();
        for (AnalysisSubmission analysisSubmission : analysisSubmissions) {
            logger.trace("Checking state of " + analysisSubmission);
            try {
                GalaxyWorkflowStatus workflowStatus = analysisExecutionService.getWorkflowStatus(analysisSubmission);
                submissions.add(handleWorkflowStatus(workflowStatus, analysisSubmission));
            } catch (ExecutionManagerException | RuntimeException e) {
                logger.error("Error checking state for " + analysisSubmission, e);
                analysisSubmission.setAnalysisState(AnalysisState.ERROR);
                submissions.add(new AsyncResult<>(analysisSubmissionRepository.save(analysisSubmission)));
            }
        }
        return submissions;
    }
}