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

Example 6 with SequencingObject

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

the class CoverageFileProcessorTest method testBadCoverage.

@Test
public void testBadCoverage() {
    Project p = new Project();
    p.setGenomeSize(100L);
    p.setMinimumCoverage(5);
    SequenceFile file = new SequenceFile();
    SequencingObject o = new SingleEndSequenceFile(file);
    AnalysisFastQC fqc = mock(AnalysisFastQC.class);
    Long baseCount = 300L;
    when(analysisRepository.findFastqcAnalysisForSequenceFile(file)).thenReturn(fqc);
    when(fqc.getTotalBases()).thenReturn(baseCount);
    processor.process(o);
    ArgumentCaptor<CoverageQCEntry> qcCaptor = ArgumentCaptor.forClass(CoverageQCEntry.class);
    verify(qcEntryRepository, times(0)).delete(any(QCEntry.class));
    verify(qcEntryRepository).save(qcCaptor.capture());
    CoverageQCEntry qc = qcCaptor.getValue();
    qc.addProjectSettings(p);
    assertEquals("should show 3 times coverage", 3, qc.getCoverage());
    assertEquals("should be bad coverage", QCEntryStatus.NEGATIVE, qc.getStatus());
}

Example 7 with SequencingObject

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

the class CoverageFileProcessorTest method testRemoveExistingEntry.

@Test
public void testRemoveExistingEntry() {
    Project p = new Project();
    p.setGenomeSize(100L);
    p.setMinimumCoverage(2);
    SequenceFile file = new SequenceFile();
    SequencingObject o = new SingleEndSequenceFile(file);
    AnalysisFastQC fqc = mock(AnalysisFastQC.class);
    Long baseCount = 300L;
    QCEntry existingQc = new CoverageQCEntry();
    o.setQcEntries(Sets.newHashSet(existingQc));
    when(analysisRepository.findFastqcAnalysisForSequenceFile(file)).thenReturn(fqc);
    when(fqc.getTotalBases()).thenReturn(baseCount);
    processor.process(o);
    ArgumentCaptor<CoverageQCEntry> qcCaptor = ArgumentCaptor.forClass(CoverageQCEntry.class);
    verify(qcEntryRepository).delete(existingQc);
    verify(qcEntryRepository).save(qcCaptor.capture());
    CoverageQCEntry qc = qcCaptor.getValue();
    qc.addProjectSettings(p);
    assertEquals("should show 3 times coverage", 3, qc.getCoverage());
    assertEquals("should be positive coverage", QCEntryStatus.POSITIVE, qc.getStatus());
}

Example 8 with SequencingObject

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

the class CoverageFileProcessorTest method testGoodCoverage.

@Test
public void testGoodCoverage() {
    Project p = new Project();
    p.setGenomeSize(100L);
    p.setMinimumCoverage(2);
    SequenceFile file = new SequenceFile();
    SequencingObject o = new SingleEndSequenceFile(file);
    AnalysisFastQC fqc = mock(AnalysisFastQC.class);
    Long baseCount = 300L;
    when(analysisRepository.findFastqcAnalysisForSequenceFile(file)).thenReturn(fqc);
    when(fqc.getTotalBases()).thenReturn(baseCount);
    processor.process(o);
    ArgumentCaptor<CoverageQCEntry> qcCaptor = ArgumentCaptor.forClass(CoverageQCEntry.class);
    verify(qcEntryRepository, times(0)).delete(any(QCEntry.class));
    verify(qcEntryRepository).save(qcCaptor.capture());
    CoverageQCEntry qc = qcCaptor.getValue();
    qc.addProjectSettings(p);
    assertEquals("should show 3 times coverage", 3, qc.getCoverage());
    assertEquals("should be positive coverage", QCEntryStatus.POSITIVE, qc.getStatus());
}

Example 9 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject 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 10 with SequencingObject

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