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

Example 66 with SequenceFile

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

the class RESTSampleSequenceFilesController method addNewSequenceFileToSample.

/**
 * Add a new {@link SequenceFile} to a {@link Sample}.
 *
 * @param sampleId
 *            the identifier for the {@link Sample}.
 * @param file
 *            the content of the {@link SequenceFile}.
 * @param fileResource
 *            the parameters for the file
 * @param response
 *            the servlet response.
 * @return a response indicating the success of the submission.
 * @throws IOException
 *             if we can't write the file to disk.
 */
@RequestMapping(value = "/api/samples/{sampleId}/sequenceFiles", method = RequestMethod.POST, consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
public ModelMap addNewSequenceFileToSample(@PathVariable Long sampleId, @RequestPart("file") MultipartFile file, @RequestPart(value = "parameters", required = false) SequenceFileResource fileResource, HttpServletResponse response) throws IOException {
    ModelMap modelMap = new ModelMap();
    logger.debug("Adding sequence file to sample " + sampleId);
    logger.trace("Uploaded file size: " + file.getSize() + " bytes");
    // load the sample from the database
    Sample sample = sampleService.read(sampleId);
    logger.trace("Read sample " + sampleId);
    // prepare a new sequence file using the multipart file supplied by the
    // caller
    Path temp = Files.createTempDirectory(null);
    Path target = temp.resolve(file.getOriginalFilename());
    // Changed to MultipartFile.transerTo(File) because it was truncating
    // large files to 1039956336 bytes
    // target = Files.write(target, file.getBytes());
    file.transferTo(target.toFile());
    logger.trace("Wrote temp file to " + target);
    SequenceFile sf;
    SequencingRun miseqRun = null;
    if (fileResource != null) {
        sf = fileResource.getResource();
        Long miseqRunId = fileResource.getMiseqRunId();
        if (miseqRunId != null) {
            miseqRun = miseqRunService.read(miseqRunId);
            logger.trace("Read miseq run " + miseqRunId);
        }
    } else {
        sf = new SequenceFile();
    }
    sf.setFile(target);
    SingleEndSequenceFile singleEndSequenceFile = new SingleEndSequenceFile(sf);
    if (miseqRun != null) {
        singleEndSequenceFile.setSequencingRun(miseqRun);
        logger.trace("Added seqfile to miseqrun");
    }
    // save the seqobject and sample
    SampleSequencingObjectJoin createSequencingObjectInSample = sequencingObjectService.createSequencingObjectInSample(singleEndSequenceFile, sample);
    singleEndSequenceFile = (SingleEndSequenceFile) createSequencingObjectInSample.getObject();
    logger.trace("Created seqfile in sample " + createSequencingObjectInSample.getObject().getId());
    // clean up the temporary files.
    Files.deleteIfExists(target);
    Files.deleteIfExists(temp);
    logger.trace("Deleted temp file");
    // prepare a link to the sequence file itself (on the sequence file
    // controller)
    String objectType = objectLabels.get(SingleEndSequenceFile.class);
    Long sequenceFileId = singleEndSequenceFile.getSequenceFile().getId();
    Link selfRel = linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequenceFileForSequencingObject(sampleId, objectType, singleEndSequenceFile.getId(), sequenceFileId)).withSelfRel();
    // Changed, because sfr.setResource(sf)
    // and sfr.setResource(sampleSequenceFileRelationship.getObject())
    // both will not pass a GET-POST comparison integration test.
    singleEndSequenceFile = (SingleEndSequenceFile) sequencingObjectService.read(singleEndSequenceFile.getId());
    SequenceFile sequenceFile = singleEndSequenceFile.getFileWithId(sequenceFileId);
    // add links to the resource
    sequenceFile.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).getSampleSequenceFiles(sampleId)).withRel(REL_SAMPLE_SEQUENCE_FILES));
    sequenceFile.add(selfRel);
    sequenceFile.add(linkTo(methodOn(RESTProjectSamplesController.class).getSample(sampleId)).withRel(REL_SAMPLE));
    sequenceFile.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequencingObject(sampleId, objectType, singleEndSequenceFile.getId())).withRel(REL_SEQ_OBJECT));
    modelMap.addAttribute(RESTGenericController.RESOURCE_NAME, sequenceFile);
    // add a location header.
    response.addHeader(HttpHeaders.LOCATION, selfRel.getHref());
    // set the response status.
    response.setStatus(HttpStatus.CREATED.value());
    // respond to the client
    return modelMap;
}

Example 67 with SequenceFile

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

the class RESTSampleSequenceFilesController method addNewSequenceFilePairToSample.

/**
 * Add a pair of {@link SequenceFile}s to a {@link Sample}
 *
 * @param sampleId
 *            The {@link Sample} id to add to
 * @param file1
 *            The first multipart file
 * @param fileResource1
 *            The metadata for the first file
 * @param file2
 *            The second multipart file
 * @param fileResource2
 *            the metadata for the second file
 * @param response
 *            a reference to the servlet response.
 * @return Response containing the locations for the created files
 * @throws IOException
 *             if we can't write the files to disk
 */
@RequestMapping(value = "/api/samples/{sampleId}/pairs", method = RequestMethod.POST, consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
public ModelMap addNewSequenceFilePairToSample(@PathVariable Long sampleId, @RequestPart("file1") MultipartFile file1, @RequestPart(value = "parameters1") SequenceFileResource fileResource1, @RequestPart("file2") MultipartFile file2, @RequestPart(value = "parameters2") SequenceFileResource fileResource2, HttpServletResponse response) throws IOException {
    logger.debug("Adding pair of sequence files to sample " + sampleId);
    logger.trace("First uploaded file size: " + file1.getSize() + " bytes");
    logger.trace("Second uploaded file size: " + file2.getSize() + " bytes");
    ModelMap modelMap = new ModelMap();
    // confirm that a relationship exists between the project and the sample
    Sample sample = sampleService.read(sampleId);
    logger.trace("Read sample " + sampleId);
    // create temp files
    Path temp1 = Files.createTempDirectory(null);
    Path target1 = temp1.resolve(file1.getOriginalFilename());
    Path temp2 = Files.createTempDirectory(null);
    Path target2 = temp2.resolve(file2.getOriginalFilename());
    // transfer the files to temp directories
    file1.transferTo(target1.toFile());
    file2.transferTo(target2.toFile());
    // create the model objects
    SequenceFile sf1 = fileResource1.getResource();
    SequenceFile sf2 = fileResource2.getResource();
    sf1.setFile(target1);
    sf2.setFile(target2);
    // get the sequencing run
    SequencingRun sequencingRun = null;
    if (!Objects.equal(fileResource1.getMiseqRunId(), fileResource2.getMiseqRunId())) {
        throw new IllegalArgumentException("Cannot upload a pair of files from different sequencing runs");
    }
    Long runId = fileResource1.getMiseqRunId();
    SequenceFilePair sequenceFilePair = new SequenceFilePair(sf1, sf2);
    if (runId != null) {
        sequencingRun = miseqRunService.read(runId);
        sequenceFilePair.setSequencingRun(sequencingRun);
        logger.trace("Added sequencing run to files" + runId);
    }
    // add the files and join
    SampleSequencingObjectJoin createSequencingObjectInSample = sequencingObjectService.createSequencingObjectInSample(sequenceFilePair, sample);
    // clean up the temporary files.
    Files.deleteIfExists(target1);
    Files.deleteIfExists(temp1);
    Files.deleteIfExists(target2);
    Files.deleteIfExists(temp2);
    logger.trace("Deleted temp files");
    SequencingObject sequencingObject = createSequencingObjectInSample.getObject();
    sequencingObject = addSequencingObjectLinks(sequencingObject, sampleId);
    sequencingObject.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).getSampleSequenceFiles(sampleId)).withRel(REL_SAMPLE_SEQUENCE_FILES));
    // add location header
    response.addHeader(HttpHeaders.LOCATION, sequencingObject.getLink("self").getHref());
    // set the response status.
    response.setStatus(HttpStatus.CREATED.value());
    modelMap.addAttribute(RESTGenericController.RESOURCE_NAME, sequencingObject);
    // respond to the client
    return modelMap;
}

Example 68 with SequenceFile

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

the class RESTSampleSequenceFilesController method addSequencingObjectLinks.

/**
 * Add the links for a {@link SequencingObject} to its sample, self, to each
 * individual {@link SequenceFile}
 *
 * @param sequencingObject {@link SequencingObject} to enhance
 * @param sampleId         ID of the {@link Sample} for the object
 * @param <T>              The subclass of {@link SequencingObject} being enhanced by this method
 * @return the enhanced {@link SequencingObject}
 */
@SuppressWarnings("unchecked")
public static <T extends SequencingObject> T addSequencingObjectLinks(T sequencingObject, Long sampleId) {
    String objectType = objectLabels.get(sequencingObject.getClass());
    // link to self
    sequencingObject.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequencingObject(sampleId, objectType, sequencingObject.getId())).withSelfRel());
    // link to the sample
    sequencingObject.add(linkTo(methodOn(RESTProjectSamplesController.class).getSample(sampleId)).withRel(RESTSampleSequenceFilesController.REL_SAMPLE));
    // link to the individual files
    for (SequenceFile file : sequencingObject.getFiles()) {
        file.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequenceFileForSequencingObject(sampleId, objectType, sequencingObject.getId(), file.getId())).withSelfRel());
    }
    AnalysisSubmission automatedAssembly = sequencingObject.getAutomatedAssembly();
    if (automatedAssembly != null) {
        sequencingObject.add(linkTo(methodOn(RESTAnalysisSubmissionController.class).getResource(automatedAssembly.getId())).withRel(REL_AUTOMATED_ASSEMBLY));
    }
    AnalysisSubmission sistrTyping = sequencingObject.getSistrTyping();
    if (sistrTyping != null) {
        sequencingObject.add(linkTo(methodOn(RESTAnalysisSubmissionController.class).getResource(sistrTyping.getId())).withRel(REL_SISTR_TYPING));
    }
    // if it's a pair, add forward/reverse links
    if (sequencingObject instanceof SequenceFilePair) {
        sequencingObject = (T) addSequenceFilePairLinks((SequenceFilePair) sequencingObject, sampleId);
    }
    return sequencingObject;
}

Example 69 with SequenceFile

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

the class FastqView method renderMergedOutputModel.

/**
 * {@inheritDoc}
 */
@Override
protected void renderMergedOutputModel(Map<String, Object> model, HttpServletRequest request, HttpServletResponse response) throws Exception {
    SequenceFile sfr = (SequenceFile) model.get(RESTGenericController.RESOURCE_NAME);
    Path fileContent = sfr.getFile();
    String filename = fileContent.getFileName().toString();
    logger.trace("Sending file to client [" + filename + "]");
    response.setHeader(HttpHeaders.CONTENT_DISPOSITION, "attachment; filename=\"" + filename + "\"");
    response.setHeader(HttpHeaders.CONTENT_TYPE, DEFAULT_CONTENT_TYPE);
    response.setHeader(HttpHeaders.CONTENT_LENGTH, String.valueOf(Files.size(fileContent)));
    OutputStream os = response.getOutputStream();
    Files.copy(fileContent, os);
    os.flush();
    os.close();
}

Example 70 with SequenceFile

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

the class ProjectEventHandlerTest method testHandleSequenceFileAddedEventMultipleProjects.

@SuppressWarnings("unchecked")
@Test
public void testHandleSequenceFileAddedEventMultipleProjects() {
    Class<? extends ProjectEvent> clazz = DataAddedToSampleProjectEvent.class;
    Project project = new Project("p1");
    Project project2 = new Project("p2");
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile();
    SingleEndSequenceFile seqObj = new SingleEndSequenceFile(file);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(sample, seqObj);
    when(psjRepository.getProjectForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true), new ProjectSampleJoin(project2, sample, true)));
    when(eventRepository.save(any(ProjectEvent.class))).thenReturn(new DataAddedToSampleProjectEvent(project, sample));
    Object[] args = {};
    MethodEvent methodEvent = new MethodEvent(clazz, join, args);
    handler.delegate(methodEvent);
    ArgumentCaptor<ProjectEvent> captor = ArgumentCaptor.forClass(ProjectEvent.class);
    verify(eventRepository, times(2)).save(captor.capture());
    List<ProjectEvent> allValues = captor.getAllValues();
    Set<Project> projects = Sets.newHashSet(project, project2);
    for (ProjectEvent event : allValues) {
        assertTrue(event instanceof DataAddedToSampleProjectEvent);
        Project eventProject = event.getProject();
        assertTrue(projects.contains(eventProject));
        projects.remove(eventProject);
    }
    verify(projectRepository, times(2)).save(project);
}