Examples with ExecutionManagerException ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException used on opensource projects

Example 1 with ExecutionManagerException

use of ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException 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 ExecutionManagerException

use of ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException in project irida by phac-nml.

the class AnalysisSubmissionServiceImplTest method testDeleteSubmissionWorkflowError.

/**
 * Tests that deleting a submission deletes the submission even if an
 * execution manager exception is thrown.
 *
 * @throws ExecutionManagerException
 */
@Test
public void testDeleteSubmissionWorkflowError() throws ExecutionManagerException {
    when(analysisSubmissionRepository.findOne(ID)).thenReturn(analysisSubmission);
    when(analysisSubmissionRepository.exists(ID)).thenReturn(true);
    when(analysisExecutionService.cleanupSubmission(analysisSubmission)).thenThrow(new ExecutionManagerException());
    when(analysisSubmission.getAnalysisCleanedState()).thenReturn(AnalysisCleanedState.NOT_CLEANED);
    analysisSubmissionServiceImpl.delete(ID);
    verify(analysisExecutionService).cleanupSubmission(analysisSubmission);
    verify(analysisSubmissionRepository).delete(ID);
}

Example 3 with ExecutionManagerException

use of ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxyTest method testHistoriesFailure.

@Test(expected = ExecutionManagerException.class)
public void testHistoriesFailure() throws ExecutionManagerException {
    when(galaxyHistoriesService.showHistoryContents(any(String.class))).thenThrow(new ExecutionManagerException());
    provenanceService.buildToolExecutionForOutputFile(analysisSubmission(), analysisOutputFile());
}

Example 4 with ExecutionManagerException

use of ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxy method buildToolExecutionForHistoryStep.

/**
 * Build up a complete *tree* of ToolExecution from Galaxy's history
 * contents provenance objects. Recursively follows predecessors from the
 * current history.
 *
 * @param toolDetails
 *            the details of the current tool to build up tool execution
 *            details for.
 * @param currentProvenance
 *            the provenance that corresponds to the tool details.
 * @param historyId
 *            the Galaxy ID we should use to extract tool execution
 *            information.
 * @return the entire tree of ToolExecutions for the tool and its
 *         provenance.
 * @throws ExecutionManagerException
 *             if we could not get the history contents provenance or the
 *             tool details for a predecessor of the current tool details or
 *             provenance.
 */
private ToolExecution buildToolExecutionForHistoryStep(final Tool toolDetails, final HistoryContentsProvenance currentProvenance, final String historyId) throws ExecutionManagerException {
    final Map<String, Set<String>> predecessors = getPredecessors(currentProvenance);
    final Map<String, Object> parameters = currentProvenance.getParameters();
    // remove keys from parameters that are Galaxy-related (and thus
    // ignorable), or keys that *match* input keys (as mentioned in
    // getPredecessors, the input keys are going to have a numeric
    // suffix and so don't equal the key that we want to remove from the
    // key set):
    /* @formatter:off */
    final Set<String> parameterKeys = parameters.keySet().stream().filter(k -> !PARAMETERS_TO_IGNORE.contains(k)).filter(k -> !predecessors.keySet().stream().anyMatch(p -> k.contains(p))).collect(Collectors.toSet());
    /* @formatter:on */
    final Map<String, Object> paramValues = new HashMap<>();
    for (final String parameterKey : parameterKeys) {
        paramValues.put(parameterKey, parameters.get(parameterKey));
    }
    final Set<ToolExecution> prevSteps = new HashSet<>();
    final String toolName = toolDetails.getName();
    final String toolVersion = toolDetails.getVersion();
    final String jobId = currentProvenance.getJobId();
    final JobDetails jobDetails = jobsClient.showJob(jobId);
    final String commandLine = jobDetails.getCommandLine();
    final Map<String, String> paramStrings = buildParamMap(paramValues);
    for (final String predecessorKey : predecessors.keySet()) {
        // arbitrarily select one of the predecessors from the set, then
        // recurse on that predecessor:
        final String predecessor = predecessors.get(predecessorKey).iterator().next();
        final HistoryContentsProvenance previousProvenance = galaxyHistoriesService.showProvenance(historyId, predecessor);
        final Tool previousToolDetails = toolsClient.showTool(previousProvenance.getToolId());
        final ToolExecution toolExecution = buildToolExecutionForHistoryStep(previousToolDetails, previousProvenance, historyId);
        prevSteps.add(toolExecution);
    }
    return new ToolExecution(prevSteps, toolName, toolVersion, jobId, paramStrings, commandLine);
}

Example 5 with ExecutionManagerException

use of ca.corefacility.bioinformatics.irida.exceptions.ExecutionManagerException in project irida by phac-nml.

the class AnalysisExecutionScheduledTaskImpl method transferAnalysesResults.

/**
 * {@inheritDoc}
 */
@Override
public Set<Future<AnalysisSubmission>> transferAnalysesResults() {
    synchronized (transferAnalysesResultsLock) {
        logger.trace("Running transferAnalysesResults");
        List<AnalysisSubmission> analysisSubmissions = analysisSubmissionRepository.findByAnalysisState(AnalysisState.FINISHED_RUNNING);
        Set<Future<AnalysisSubmission>> submissions = Sets.newHashSet();
        for (AnalysisSubmission analysisSubmission : analysisSubmissions) {
            logger.debug("Transferring results for " + analysisSubmission);
            try {
                submissions.add(analysisExecutionService.transferAnalysisResults(analysisSubmission));
            } catch (ExecutionManagerException | IOException | IridaWorkflowException e) {
                logger.error("Error transferring submission " + analysisSubmission, e);
            }
        }
        return submissions;
    }
}