Examples with SampleSequencingObjectJoin ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin used on opensource projects

Example 16 with SampleSequencingObjectJoin

use of ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin in project irida by phac-nml.

the class RESTSampleSequenceFilesController method listSequencingObjectsOfTypeForSample.

/**
 * List all {@link SequencingObject}s of a given type for a {@link Sample}
 *
 * @param sampleId
 *            ID of the {@link Sample} to read from
 * @param objectType
 *            {@link SequencingObject} type
 * @return The {@link SequencingObject}s of the given type for the
 *         {@link Sample}
 */
@RequestMapping(value = "/api/samples/{sampleId}/{objectType}", method = RequestMethod.GET)
public ModelMap listSequencingObjectsOfTypeForSample(@PathVariable Long sampleId, @PathVariable String objectType) {
    ModelMap modelMap = new ModelMap();
    logger.debug("Reading seq file  for sample " + sampleId);
    Sample sample = sampleService.read(sampleId);
    Class<? extends SequencingObject> type = objectLabels.inverse().get(objectType);
    Collection<SampleSequencingObjectJoin> unpairedSequenceFilesForSample = sequencingObjectService.getSequencesForSampleOfType(sample, type);
    ResourceCollection<SequencingObject> resources = new ResourceCollection<>(unpairedSequenceFilesForSample.size());
    for (SampleSequencingObjectJoin join : unpairedSequenceFilesForSample) {
        SequencingObject sequencingObject = join.getObject();
        sequencingObject = addSequencingObjectLinks(sequencingObject, sampleId);
        resources.add(sequencingObject);
    }
    // add a link to this collection
    resources.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).listSequencingObjectsOfTypeForSample(sampleId, objectType)).withSelfRel());
    // add a link back to the sample
    resources.add(linkTo(methodOn(RESTProjectSamplesController.class).getSample(sampleId)).withRel(RESTSampleSequenceFilesController.REL_SAMPLE));
    modelMap.addAttribute(RESTGenericController.RESOURCE_NAME, resources);
    return modelMap;
}

Example 17 with SampleSequencingObjectJoin

use of ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin 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 18 with SampleSequencingObjectJoin

use of ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin in project irida by phac-nml.

the class ProjectEventHandlerTest method testHandleSequenceFileAddedEventMultipleReturn.

@SuppressWarnings("unchecked")
@Test
public void testHandleSequenceFileAddedEventMultipleReturn() {
    Class<? extends ProjectEvent> clazz = DataAddedToSampleProjectEvent.class;
    Project project = new Project();
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile();
    SingleEndSequenceFile seqObj1 = new SingleEndSequenceFile(file);
    SingleEndSequenceFile seqObj2 = new SingleEndSequenceFile(file);
    SampleSequencingObjectJoin join1 = new SampleSequencingObjectJoin(sample, seqObj1);
    SampleSequencingObjectJoin join2 = new SampleSequencingObjectJoin(sample, seqObj2);
    when(psjRepository.getProjectForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true)));
    when(eventRepository.save(any(ProjectEvent.class))).thenReturn(new DataAddedToSampleProjectEvent(project, sample));
    Object[] args = {};
    MethodEvent methodEvent = new MethodEvent(clazz, Lists.newArrayList(join1, join2), args);
    handler.delegate(methodEvent);
    ArgumentCaptor<ProjectEvent> captor = ArgumentCaptor.forClass(ProjectEvent.class);
    verify(eventRepository).save(captor.capture());
    ProjectEvent event = captor.getValue();
    assertTrue(event instanceof DataAddedToSampleProjectEvent);
    verify(projectRepository).save(any(Project.class));
    verify(sampleRepository).save(any(Sample.class));
}

Example 19 with SampleSequencingObjectJoin

use of ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin in project irida by phac-nml.

the class SequencingObjectServiceImplIT method testGetSequenceFilePairForSample.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testGetSequenceFilePairForSample() {
    Sample s = sampleService.read(2L);
    Set<Long> fileIds = Sets.newHashSet(3L, 4L);
    Collection<SampleSequencingObjectJoin> sequenceFilePairsForSample = objectService.getSequencesForSampleOfType(s, SequenceFilePair.class);
    assertEquals(1, sequenceFilePairsForSample.size());
    SequencingObject pair = sequenceFilePairsForSample.iterator().next().getObject();
    for (SequenceFile file : pair.getFiles()) {
        assertTrue("file id should be in set", fileIds.contains(file.getId()));
        fileIds.remove(file.getId());
    }
    assertTrue("all file ids should have been found", fileIds.isEmpty());
}

Example 20 with SampleSequencingObjectJoin

use of ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin in project irida by phac-nml.

the class SequencingObjectServiceImplIT method testGetSequencefilesForSampleAsSequencer.

@Test
@WithMockUser(username = "fbristow", roles = "SEQUENCER")
public void testGetSequencefilesForSampleAsSequencer() throws IOException {
    Sample s = sampleService.read(1L);
    Collection<SampleSequencingObjectJoin> sequencingObjectsForSample = objectService.getSequencingObjectsForSample(s);
    assertEquals(1, sequencingObjectsForSample.size());
}