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

Example 31 with SequenceFile

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

the class GzipFileProcessorTest method handleCompressedFileWithoutGzExtension.

@Test
public void handleCompressedFileWithoutGzExtension() throws IOException {
    // the file processor should decompress the file, then update the
    // sequence file in the database.
    SequenceFile sf = constructSequenceFile();
    SequenceFile sfUpdated = new SequenceFile();
    sfUpdated.setFile(sf.getFile());
    final Long id = 1L;
    sf.setId(id);
    // compress the file, update the sequence file reference
    Path uncompressed = sf.getFile();
    Path compressed = Files.createTempFile(null, null);
    GZIPOutputStream out = new GZIPOutputStream(Files.newOutputStream(compressed));
    Files.copy(uncompressed, out);
    out.close();
    sf.setFile(compressed);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    fileProcessor.process(so);
    ArgumentCaptor<SequenceFile> argument = ArgumentCaptor.forClass(SequenceFile.class);
    verify(sequenceFileRepository).save(argument.capture());
    SequenceFile modified = argument.getValue();
    String uncompressedFileContents = new String(Files.readAllBytes(modified.getFile()));
    assertEquals("uncompressed file and file in database should be the same.", FILE_CONTENTS, uncompressedFileContents);
    Files.delete(uncompressed);
    if (Files.exists(compressed)) {
        Files.delete(compressed);
    }
}

Example 32 with SequenceFile

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

the class RESTSampleSequenceFilesController method getSampleSequenceFiles.

/**
 * Get the {@link SequenceFile} entities associated with a specific
 * {@link Sample}.
 *
 * @param sampleId
 *            the identifier for the {@link Sample}.
 * @return the {@link SequenceFile} entities associated with the
 *         {@link Sample}.
 */
@RequestMapping(value = "/api/samples/{sampleId}/sequenceFiles", method = RequestMethod.GET)
public ModelMap getSampleSequenceFiles(@PathVariable Long sampleId) {
    ModelMap modelMap = new ModelMap();
    logger.debug("Reading seq files for sample " + sampleId);
    Sample sample = sampleService.read(sampleId);
    Collection<SampleSequencingObjectJoin> sequencingObjectsForSample = sequencingObjectService.getSequencingObjectsForSample(sample);
    ResourceCollection<SequenceFile> resources = new ResourceCollection<>();
    /*
		 * Note: This is a kind of antiquated seeing we should be referencing
		 * sequencing objects instead. At the very least the link we're pointing
		 * to here should be going through the sequencing object
		 */
    for (SampleSequencingObjectJoin r : sequencingObjectsForSample) {
        for (SequenceFile sf : r.getObject().getFiles()) {
            String fileLabel = objectLabels.get(r.getObject().getClass());
            sf.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequenceFileForSequencingObject(sampleId, fileLabel, r.getObject().getId(), sf.getId())).withSelfRel());
            resources.add(sf);
        }
    }
    // add a link to this collection
    resources.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).getSampleSequenceFiles(sampleId)).withSelfRel());
    // add a link back to the sample
    resources.add(linkTo(methodOn(RESTProjectSamplesController.class).getSample(sampleId)).withRel(RESTSampleSequenceFilesController.REL_SAMPLE));
    resources.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).listSequencingObjectsOfTypeForSample(sample.getId(), RESTSampleSequenceFilesController.objectLabels.get(SequenceFilePair.class))).withRel(RESTSampleSequenceFilesController.REL_SAMPLE_SEQUENCE_FILE_PAIRS));
    resources.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).listSequencingObjectsOfTypeForSample(sample.getId(), RESTSampleSequenceFilesController.objectLabels.get(SingleEndSequenceFile.class))).withRel(RESTSampleSequenceFilesController.REL_SAMPLE_SEQUENCE_FILE_UNPAIRED));
    modelMap.addAttribute(RESTGenericController.RESOURCE_NAME, resources);
    return modelMap;
}

Example 33 with SequenceFile

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

the class RESTSampleSequenceFilesController method readSequenceFileForSequencingObject.

/**
 * Read a single {@link SequenceFile} for a given {@link Sample} and
 * {@link SequencingObject}
 *
 * @param sampleId
 *            ID of the {@link Sample}
 * @param objectType
 *            type of {@link SequencingObject}
 * @param objectId
 *            id of the {@link SequencingObject}
 * @param fileId
 *            ID of the {@link SequenceFile} to read
 * @return a {@link SequenceFile}
 */
@RequestMapping(value = "/api/samples/{sampleId}/{objectType}/{objectId}/files/{fileId}", method = RequestMethod.GET)
public ModelMap readSequenceFileForSequencingObject(@PathVariable Long sampleId, @PathVariable String objectType, @PathVariable Long objectId, @PathVariable Long fileId) {
    ModelMap modelMap = new ModelMap();
    Sample sample = sampleService.read(sampleId);
    SequencingObject readSequenceFilePairForSample = sequencingObjectService.readSequencingObjectForSample(sample, objectId);
    Optional<SequenceFile> findFirst = readSequenceFilePairForSample.getFiles().stream().filter(f -> f.getId().equals(fileId)).findFirst();
    if (!findFirst.isPresent()) {
        throw new EntityNotFoundException("File with id " + fileId + " is not associated with this sequencing object");
    }
    SequenceFile file = findFirst.get();
    file.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).getSampleSequenceFiles(sampleId)).withRel(REL_SAMPLE_SEQUENCE_FILES));
    file.add(linkTo(methodOn(RESTProjectSamplesController.class).getSample(sampleId)).withRel(REL_SAMPLE));
    file.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequencingObject(sampleId, objectType, objectId)).withRel(REL_SEQ_OBJECT));
    file.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readQCForSequenceFile(sampleId, objectType, objectId, fileId)).withRel(REL_SEQ_QC));
    file.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequenceFileForSequencingObject(sampleId, objectType, objectId, fileId)).withSelfRel());
    modelMap.addAttribute(RESTGenericController.RESOURCE_NAME, file);
    return modelMap;
}

Example 34 with SequenceFile

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

the class FastaView 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 35 with SequenceFile

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

the class GenbankView 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();
}