Examples with AnalysisState ca.corefacility.bioinformatics.irida.model.enums.AnalysisState used on opensource projects

Example 1 with AnalysisState

use of ca.corefacility.bioinformatics.irida.model.enums.AnalysisState in project irida by phac-nml.

the class AnalysisController method getAjaxStatusUpdateForAnalysisSubmission.

/**
 * Get the current status for a given {@link AnalysisSubmission}
 *
 * @param submissionId The {@link UUID} id for a given {@link AnalysisSubmission}
 * @param locale       The users current {@link Locale}
 * @return {@link HashMap} containing the status and the percent complete for the {@link AnalysisSubmission}
 */
@RequestMapping(value = "/ajax/status/{submissionId}", produces = MediaType.APPLICATION_JSON_VALUE)
@ResponseBody
public Map<String, String> getAjaxStatusUpdateForAnalysisSubmission(@PathVariable Long submissionId, Locale locale) {
    Map<String, String> result = new HashMap<>();
    AnalysisSubmission analysisSubmission = analysisSubmissionService.read(submissionId);
    AnalysisState state = analysisSubmission.getAnalysisState();
    result.put("state", state.toString());
    result.put("stateLang", messageSource.getMessage("analysis.state." + state.toString(), null, locale));
    if (!state.equals(AnalysisState.ERROR)) {
        float percentComplete = 0;
        try {
            percentComplete = analysisSubmissionService.getPercentCompleteForAnalysisSubmission(analysisSubmission.getId());
            result.put("percentComplete", Float.toString(percentComplete));
        } catch (ExecutionManagerException e) {
            logger.error("Error getting the percentage complete", e);
            result.put("percentageComplete", "");
        }
    }
    return result;
}

Example 2 with AnalysisState

use of ca.corefacility.bioinformatics.irida.model.enums.AnalysisState in project irida by phac-nml.

the class AnalysesListingService method createDataTablesAnalysis.

/**
 * Convert a {@link AnalysisSubmission} to a {@link DTAnalysis} to be used by DataTables on the client.
 *
 * @param submission {@link AnalysisSubmission}
 * @param locale     {@link Locale}
 * @return {@link DTAnalysis}
 * @throws IridaWorkflowNotFoundException If the requested workflow doesn't exist
 * @throws ExecutionManagerException      If the submission cannot be read properly
 */
private DTAnalysis createDataTablesAnalysis(AnalysisSubmission submission, Locale locale) throws IridaWorkflowNotFoundException, ExecutionManagerException {
    Long id = submission.getId();
    String name = submission.getName();
    String submitter = submission.getSubmitter().getLabel();
    Date createdDate = submission.getCreatedDate();
    float percentComplete = 0;
    AnalysisState analysisState = submission.getAnalysisState();
    JobError error = null;
    if (analysisState.equals(AnalysisState.ERROR)) {
        error = getFirstJobError(submission);
    } else {
        percentComplete = analysisSubmissionService.getPercentCompleteForAnalysisSubmission(submission.getId());
    }
    String workflowType = iridaWorkflowsService.getIridaWorkflow(submission.getWorkflowId()).getWorkflowDescription().getAnalysisType().toString();
    String workflow = messageSource.getMessage("workflow." + workflowType + ".title", null, locale);
    String state = messageSource.getMessage("analysis.state." + analysisState.toString(), null, locale);
    Long duration = 0L;
    if (analysisState.equals(AnalysisState.COMPLETED)) {
        duration = getDurationInMilliseconds(submission.getCreatedDate(), submission.getAnalysis().getCreatedDate());
    }
    Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
    boolean updatePermission = updateAnalysisPermission.isAllowed(authentication, submission);
    return new DTAnalysis(id, name, submitter, percentComplete, createdDate, workflow, state, error, duration, updatePermission);
}

Example 3 with AnalysisState

use of ca.corefacility.bioinformatics.irida.model.enums.AnalysisState in project irida by phac-nml.

the class AnalysisSubmissionServiceImplIT method searchAnalyses.

@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void searchAnalyses() {
    Page<AnalysisSubmission> paged = analysisSubmissionService.listAllSubmissions(null, null, null, null, new PageRequest(0, 10, new Sort(Direction.ASC, "createdDate")));
    assertEquals(10, paged.getContent().size());
    // Try filtering a by names
    String name = "My";
    paged = analysisSubmissionService.listAllSubmissions(null, name, null, null, new PageRequest(0, 10, new Sort(Direction.ASC, "createdDate")));
    assertEquals(8, paged.getContent().size());
    // Add a state filter
    AnalysisState state = AnalysisState.COMPLETED;
    paged = analysisSubmissionService.listAllSubmissions(null, name, state, null, new PageRequest(0, 10, new Sort(Direction.ASC, "createdDate")));
    assertEquals(2, paged.getContent().size());
}

Example 4 with AnalysisState

use of ca.corefacility.bioinformatics.irida.model.enums.AnalysisState in project irida by phac-nml.

the class AnalysisSubmissionCleanupServiceImpl method switchInconsistentSubmissionsToError.

/**
 * {@inheritDoc}
 */
@Override
@PreAuthorize("hasRole('ROLE_ADMIN')")
public int switchInconsistentSubmissionsToError() {
    if (ranSwitchInconsistentSubmissionsToError) {
        throw new RuntimeException("already ran this method once");
    } else {
        int numberSubmissionsSwitched = 0;
        ranSwitchInconsistentSubmissionsToError = true;
        for (AnalysisState state : inconsistentStates) {
            List<AnalysisSubmission> submissions = analysisSubmissionRepository.findByAnalysisState(state);
            for (AnalysisSubmission submission : submissions) {
                logger.error("AnalysisSubmission [id=" + submission.getId() + ", name=" + submission.getName() + ", state=" + submission.getAnalysisState() + "] left in inconsistent state.  Switching to " + AnalysisState.ERROR + ".");
                submission.setAnalysisState(AnalysisState.ERROR);
                analysisSubmissionRepository.save(submission);
                numberSubmissionsSwitched++;
            }
        }
        return numberSubmissionsSwitched;
    }
}

Example 5 with AnalysisState

use of ca.corefacility.bioinformatics.irida.model.enums.AnalysisState in project irida by phac-nml.

the class AnalysisSubmissionServiceImpl method getPercentCompleteForAnalysisSubmission.

/**
 * {@inheritDoc}
 */
@Override
@PreAuthorize("hasRole('ROLE_ADMIN') or hasPermission(#id, 'canReadAnalysisSubmission')")
public float getPercentCompleteForAnalysisSubmission(Long id) throws EntityNotFoundException, ExecutionManagerException, NoPercentageCompleteException {
    AnalysisSubmission analysisSubmission = read(id);
    AnalysisState analysisState = analysisSubmission.getAnalysisState();
    switch(analysisState) {
        case NEW:
        case PREPARING:
        case PREPARED:
        case SUBMITTING:
            return STATE_PERCENTAGE.get(analysisState);
        /**
         * If the analysis is in a state of {@link AnalysisState.RUNNING}
         * then we are able to ask Galaxy for the proportion of jobs that
         * are complete. We can scale this value between RUNNING_PERCENT
         * (10%) and FINISHED_RUNNING_PERCENT (90%) so that after all jobs
         * are complete we are only at 90%. The remaining 10% involves
         * transferring files back to Galaxy.
         *
         * For example, if there are 10 out of 20 jobs finished on Galaxy,
         * then the proportion of jobs complete is 10/20 = 0.5. So, the
         * percent complete for the overall analysis is: percentComplete =
         * 10 + (90 - 10) * 0.5 = 50%.
         *
         * If there are 20 out of 20 jobs finished in Galaxy, then the
         * percent complete is: percentComplete = 10 + (90 - 10) * 1.0 =
         * 90%.
         */
        case RUNNING:
            String workflowHistoryId = analysisSubmission.getRemoteAnalysisId();
            GalaxyWorkflowStatus workflowStatus = galaxyHistoriesService.getStatusForHistory(workflowHistoryId);
            return RUNNING_PERCENT + (FINISHED_RUNNING_PERCENT - RUNNING_PERCENT) * workflowStatus.getProportionComplete();
        case FINISHED_RUNNING:
        case COMPLETING:
        case TRANSFERRED:
        case POST_PROCESSING:
        case COMPLETED:
            return STATE_PERCENTAGE.get(analysisState);
        default:
            throw new NoPercentageCompleteException("No valid percent complete for state " + analysisState);
    }
}