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

Example 56 with Sample

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

the class RESTSampleMetadataController method addSampleMetadata.

/**
 * Add select new metadata fields to the {@link Sample}. Note this will only
 * overwrite duplicate terms. Existing metadata will not be affected.
 *
 * @param sampleId
 *            the {@link Sample} to add metadata to
 * @param metadataMap
 *            the new metadata
 * @return the updated {@link Sample}
 */
@RequestMapping(value = "/api/samples/{sampleId}/metadata", method = RequestMethod.PUT)
public ModelMap addSampleMetadata(@PathVariable Long sampleId, @RequestBody Map<String, MetadataEntry> metadataMap) {
    Sample s = sampleService.read(sampleId);
    Map<MetadataTemplateField, MetadataEntry> metadata = metadataTemplateService.getMetadataMap(metadataMap);
    s.mergeMetadata(metadata);
    sampleService.update(s);
    return getSampleMetadata(sampleId);
}

Example 57 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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 58 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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 59 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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 60 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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));
}