Examples with AnalysisSubmission ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission used on opensource projects

Example 76 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission 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);
    }
}

Example 77 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisSubmissionServiceImpl method createSingleSampleSubmission.

/**
 * {@inheritDoc}
 */
@Override
@Transactional
@PreAuthorize("hasRole('ROLE_USER')")
public Collection<AnalysisSubmission> createSingleSampleSubmission(IridaWorkflow workflow, Long ref, List<SingleEndSequenceFile> sequenceFiles, List<SequenceFilePair> sequenceFilePairs, Map<String, String> params, IridaWorkflowNamedParameters namedParameters, String name, String analysisDescription, List<Project> projectsToShare, boolean writeResultsToSamples) {
    final Collection<AnalysisSubmission> createdSubmissions = new HashSet<AnalysisSubmission>();
    // Single end reads
    IridaWorkflowDescription description = workflow.getWorkflowDescription();
    if (description.acceptsSingleSequenceFiles()) {
        final Map<Sample, SingleEndSequenceFile> samplesMap = sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(sequenceFiles));
        for (final Map.Entry<Sample, SingleEndSequenceFile> entry : samplesMap.entrySet()) {
            Sample s = entry.getKey();
            SingleEndSequenceFile file = entry.getValue();
            // Build the analysis submission
            AnalysisSubmission.Builder builder = AnalysisSubmission.builder(workflow.getWorkflowIdentifier());
            builder.name(name + "_" + s.getSampleName());
            builder.inputFiles(ImmutableSet.of(file));
            builder.updateSamples(writeResultsToSamples);
            builder.priority(AnalysisSubmission.Priority.MEDIUM);
            // Add reference file
            if (ref != null && description.requiresReference()) {
                // Note: This cannot be empty if through the UI if the
                // pipeline required a reference file.
                ReferenceFile referenceFile = referenceFileRepository.findOne(ref);
                builder.referenceFile(referenceFile);
            }
            if (description.acceptsParameters()) {
                if (namedParameters != null) {
                    builder.withNamedParameters(namedParameters);
                } else {
                    if (!params.isEmpty()) {
                        // Note: This cannot be empty if through the UI if
                        // the pipeline required params.
                        builder.inputParameters(params);
                    }
                }
            }
            // Create the submission
            createdSubmissions.add(create(builder.build()));
        }
    }
    // Paired end reads
    if (description.acceptsPairedSequenceFiles()) {
        final Map<Sample, SequenceFilePair> samplesMap = sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(sequenceFilePairs));
        for (final Map.Entry<Sample, SequenceFilePair> entry : samplesMap.entrySet()) {
            Sample s = entry.getKey();
            SequenceFilePair filePair = entry.getValue();
            // Build the analysis submission
            AnalysisSubmission.Builder builder = AnalysisSubmission.builder(workflow.getWorkflowIdentifier());
            builder.name(name + "_" + s.getSampleName());
            builder.inputFiles(ImmutableSet.of(filePair));
            builder.updateSamples(writeResultsToSamples);
            // Add reference file
            if (ref != null && description.requiresReference()) {
                ReferenceFile referenceFile = referenceFileRepository.findOne(ref);
                builder.referenceFile(referenceFile);
            }
            if (description.acceptsParameters()) {
                if (namedParameters != null) {
                    builder.withNamedParameters(namedParameters);
                } else {
                    if (!params.isEmpty()) {
                        // Note: This cannot be empty if through the UI if
                        // the pipeline required params.
                        builder.inputParameters(params);
                    }
                }
            }
            // Add description to submission, can be null
            builder.analysisDescription(analysisDescription);
            // Create the submission
            createdSubmissions.add(create(builder.build()));
        }
    }
    // Share with the required projects
    for (AnalysisSubmission submission : createdSubmissions) {
        for (Project project : projectsToShare) {
            pasRepository.save(new ProjectAnalysisSubmissionJoin(project, submission));
        }
    }
    return createdSubmissions;
}

Example 78 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisSubmissionServiceImpl method delete.

/**
 * {@inheritDoc}
 */
@Override
@PreAuthorize("hasRole('ROLE_ADMIN') or hasPermission(#id, 'canUpdateAnalysisSubmission')")
@Transactional
public void delete(Long id) throws EntityNotFoundException {
    final AnalysisSubmission submission = read(id);
    if (AnalysisCleanedState.NOT_CLEANED.equals(submission.getAnalysisCleanedState())) {
        // We're "CLEANING" it right now!
        submission.setAnalysisCleanedState(AnalysisCleanedState.CLEANING);
        try {
            analysisExecutionService.cleanupSubmission(submission).get();
        } catch (final ExecutionManagerException e) {
            logger.error("Failed to cleanup analysis submission before deletion," + " but proceeding with deletion anyway.", e);
        } catch (final Throwable e) {
            logger.error("An unexpected exception happened when cleaning the analysis submission," + " but proceeding with deletion anyway.", e);
        }
    } else {
        logger.debug("Not cleaning submission [" + id + "] when deleting, it's already cleaned.");
    }
    super.delete(id);
}

Example 79 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisSubmissionServiceImpl method createMultipleSampleSubmission.

/**
 * {@inheritDoc}
 */
@Transactional
@PreAuthorize("hasRole('ROLE_USER')")
public AnalysisSubmission createMultipleSampleSubmission(IridaWorkflow workflow, Long ref, List<SingleEndSequenceFile> sequenceFiles, List<SequenceFilePair> sequenceFilePairs, Map<String, String> params, IridaWorkflowNamedParameters namedParameters, String name, String newAnalysisDescription, List<Project> projectsToShare, boolean writeResultsToSamples) {
    AnalysisSubmission.Builder builder = AnalysisSubmission.builder(workflow.getWorkflowIdentifier());
    builder.name(name);
    builder.priority(AnalysisSubmission.Priority.MEDIUM);
    builder.updateSamples(writeResultsToSamples);
    IridaWorkflowDescription description = workflow.getWorkflowDescription();
    // Add reference file
    if (ref != null && description.requiresReference()) {
        ReferenceFile referenceFile = referenceFileRepository.findOne(ref);
        builder.referenceFile(referenceFile);
    }
    // Add any single end sequencing files.
    if (description.acceptsSingleSequenceFiles()) {
        if (!sequenceFiles.isEmpty()) {
            builder.inputFiles(Sets.newHashSet(sequenceFiles));
        }
    }
    // Add any paired end sequencing files.
    if (description.acceptsPairedSequenceFiles()) {
        if (!sequenceFilePairs.isEmpty()) {
            builder.inputFiles(Sets.newHashSet(sequenceFilePairs));
        }
    }
    if (description.acceptsParameters()) {
        if (namedParameters != null) {
            builder.withNamedParameters(namedParameters);
        } else {
            if (!params.isEmpty()) {
                // Note: This cannot be empty if through the UI if
                // the pipeline required params.
                builder.inputParameters(params);
            }
        }
    }
    // Add description to submission, can be null
    builder.analysisDescription(newAnalysisDescription);
    // Create the submission
    AnalysisSubmission submission = create(builder.build());
    // Share with the required projects
    for (Project project : projectsToShare) {
        pasRepository.save(new ProjectAnalysisSubmissionJoin(project, submission));
    }
    return submission;
}

Example 80 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class RESTAnalysisSubmissionController method getAnalysisInputUnpairedFiles.

/**
 * get the {@link SequenceFile}s not in {@link SequenceFilePair}s used for
 * the {@link AnalysisSubmission}
 *
 * @param identifier
 *            the {@link AnalysisSubmission} id
 * @return list of {@link SequenceFile}s
 */
@RequestMapping("/{identifier}/sequenceFiles/unpaired")
public ModelMap getAnalysisInputUnpairedFiles(@PathVariable Long identifier) {
    ModelMap map = new ModelMap();
    AnalysisSubmission analysisSubmission = analysisSubmissionService.read(identifier);
    Set<SingleEndSequenceFile> inputFilesSingleEnd = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    ResourceCollection<SequencingObject> resources = new ResourceCollection<>(inputFilesSingleEnd.size());
    for (SingleEndSequenceFile file : inputFilesSingleEnd) {
        SampleSequencingObjectJoin join = sampleService.getSampleForSequencingObject(file);
        if (join != null) {
            SequencingObject sequencingObject = join.getObject();
            RESTSampleSequenceFilesController.addSequencingObjectLinks(sequencingObject, join.getSubject().getId());
            resources.add(sequencingObject);
        }
    }
    resources.add(linkTo(methodOn(RESTAnalysisSubmissionController.class).getAnalysisInputUnpairedFiles(identifier)).withSelfRel());
    map.addAttribute(RESTGenericController.RESOURCE_NAME, resources);
    return map;
}