Examples with SequencingObject ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject used on opensource projects

Example 21 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject in project irida by phac-nml.

the class TestDataFactory method constructAnalysisSubmission.

public static AnalysisSubmission constructAnalysisSubmission() {
    Set<SequencingObject> files = new HashSet<>();
    files.add(constructSingleEndSequenceFile());
    Long id = 5L;
    final ReferenceFile rf = new ReferenceFile(files.iterator().next().getFiles().iterator().next().getFile());
    rf.setId(id);
    AnalysisSubmission analysisSubmission = AnalysisSubmission.builder(UUID.randomUUID()).name("submission-" + id).inputFiles(files).referenceFile(rf).build();
    analysisSubmission.setId(id);
    analysisSubmission.setAnalysisState(AnalysisState.COMPLETED);
    try {
        analysisSubmission.setAnalysis(constructAnalysis());
    } catch (final AnalysisAlreadySetException e) {
        // this should *never* happen, we just constructed
        // AnalysisSubmission above.
        fail();
    }
    return analysisSubmission;
}

Example 22 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject in project irida by phac-nml.

the class SequencingObjectServiceImpl method create.

/**
 * {@inheritDoc}
 */
@Override
@Transactional
@PreAuthorize("hasAnyRole('ROLE_SEQUENCER', 'ROLE_USER')")
public SequencingObject create(SequencingObject object) throws ConstraintViolationException, EntityExistsException {
    SequencingRun sequencingRun = object.getSequencingRun();
    if (sequencingRun != null) {
        if (object instanceof SingleEndSequenceFile && sequencingRun.getLayoutType() != LayoutType.SINGLE_END) {
            throw new IllegalArgumentException("Attempting to add a single end file to a non single end run");
        } else if (object instanceof SequenceFilePair && sequencingRun.getLayoutType() != LayoutType.PAIRED_END) {
            throw new IllegalArgumentException("Attempting to add a paired end file to a non paired end run");
        }
    }
    for (SequenceFile file : object.getFiles()) {
        file = sequenceFileRepository.save(file);
    }
    SequencingObject so = super.create(object);
    fileProcessingChainExecutor.execute(new SequenceFileProcessorLauncher(fileProcessingChain, so.getId(), SecurityContextHolder.getContext()));
    return so;
}

Example 23 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject in project irida by phac-nml.

the class SampleServiceImpl method mergeSamples.

/**
 * {@inheritDoc}
 */
@Override
@Transactional
@PreAuthorize("hasPermission(#project, 'isProjectOwner') and hasPermission(#mergeInto, 'canUpdateSample') and hasPermission(#toMerge, 'canUpdateSample')")
public Sample mergeSamples(Project project, Sample mergeInto, Collection<Sample> toMerge) {
    // confirm that all samples are part of the same project:
    confirmProjectSampleJoin(project, mergeInto);
    logger.debug("Merging samples " + toMerge.stream().map(t -> t.getId()).collect(Collectors.toList()) + " into sample [" + mergeInto.getId() + "]");
    for (Sample s : toMerge) {
        confirmProjectSampleJoin(project, s);
        List<SampleSequencingObjectJoin> sequencesForSample = ssoRepository.getSequencesForSample(s);
        for (SampleSequencingObjectJoin join : sequencesForSample) {
            SequencingObject sequencingObject = join.getObject();
            ssoRepository.delete(join);
            addSequencingObjectToSample(mergeInto, sequencingObject);
        }
        Collection<SampleGenomeAssemblyJoin> genomeAssemblyJoins = getAssembliesForSample(s);
        for (SampleGenomeAssemblyJoin join : genomeAssemblyJoins) {
            GenomeAssembly genomeAssembly = join.getObject();
            logger.trace("Removing genome assembly [" + genomeAssembly.getId() + "] from sample [" + s.getId() + "]");
            sampleGenomeAssemblyJoinRepository.delete(join);
            logger.trace("Adding genome assembly [" + genomeAssembly.getId() + "] to sample [" + mergeInto.getId() + "]");
            SampleGenomeAssemblyJoin newJoin = new SampleGenomeAssemblyJoin(mergeInto, genomeAssembly);
            sampleGenomeAssemblyJoinRepository.save(newJoin);
        }
        // have to remove the sample to be deleted from its project:
        ProjectSampleJoin readSampleForProject = psjRepository.readSampleForProject(project, s);
        psjRepository.delete(readSampleForProject);
        sampleRepository.delete(s.getId());
    }
    return mergeInto;
}

Example 24 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject 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;
}

Example 25 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject in project irida by phac-nml.

the class AssemblyFileProcessor method shouldAssemble.

/**
 * Check whether any {@link Project} associated with the
 * {@link SequencingObject} is set to assemble
 *
 * @param object
 *            {@link SequencingObject} to check ot assemble
 * @return true if it should assemble, false otherwise
 */
private boolean shouldAssemble(SequencingObject object) {
    boolean assemble = false;
    SampleSequencingObjectJoin sampleForSequencingObject = ssoRepository.getSampleForSequencingObject(object);
    /*
		 * This is something that should only ever happen in tests, but added
		 * check with a warning
		 */
    if (sampleForSequencingObject != null) {
        List<Join<Project, Sample>> projectForSample = psjRepository.getProjectForSample(sampleForSequencingObject.getSubject());
        assemble = projectForSample.stream().anyMatch(j -> j.getSubject().getAssembleUploads());
    } else {
        logger.warn("Cannot find sample for sequencing object.  Not assembling");
    }
    return assemble;
}