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

Example 6 with QCEntry

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

the class SequencingObjectServiceImplIT method testCreateSequenceFileInSample.

@Test
@WithMockUser(username = "fbristow", roles = "SEQUENCER")
public void testCreateSequenceFileInSample() throws IOException, InterruptedException {
    Sample s = sampleService.read(1L);
    SequenceFile sf = new SequenceFile();
    Path sequenceFile = Files.createTempFile("TEMPORARY-SEQUENCE-FILE", ".gz");
    OutputStream gzOut = new GZIPOutputStream(Files.newOutputStream(sequenceFile));
    gzOut.write(FASTQ_FILE_CONTENTS);
    gzOut.close();
    sf.setFile(sequenceFile);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    objectService.createSequencingObjectInSample(so, s);
    SequencingRun mr = sequencingRunService.read(1L);
    sequencingRunService.addSequencingObjectToSequencingRun(mr, so);
    // Sleeping for a bit to let file processing run
    Thread.sleep(10000);
    Sample readSample = sampleService.read(s.getId());
    List<QCEntry> qcEntries = sampleService.getQCEntriesForSample(readSample);
    assertEquals("should be one qc entries", 1, qcEntries.size());
    QCEntry qcEntry = qcEntries.iterator().next();
    assertTrue("should be coverage entry", qcEntry instanceof CoverageQCEntry);
    CoverageQCEntry coverage = (CoverageQCEntry) qcEntry;
    assertEquals("should be 18 bases", 18, coverage.getTotalBases());
}

Example 7 with QCEntry

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

the class ProjectSamplesController method buildProjectSampleDataTablesModel.

/**
 * Build a {@link ProjectSampleModel} object for a given {@link Sample}
 *
 * @param sso    a {@link ProjectSampleJoin} to build the {@link ProjectSampleModel} from
 * @param locale of the current user.
 * @return a newly constructed {@link ProjectSampleModel}
 */
private DTProjectSamples buildProjectSampleDataTablesModel(ProjectSampleJoin sso, Locale locale) {
    Project p = sso.getSubject();
    List<QCEntry> qcEntriesForSample = sampleService.getQCEntriesForSample(sso.getObject());
    List<String> list = new ArrayList<>();
    for (QCEntry q : qcEntriesForSample) {
        q.addProjectSettings(p);
        String status = q.getStatus().toString();
        if (q.getStatus() == QCEntry.QCEntryStatus.NEGATIVE) {
            list.add(messageSource.getMessage("sample.files.qc." + q.getType(), new Object[] { q.getMessage() }, locale));
        }
    }
    return new DTProjectSamples(sso, list);
}

Example 8 with QCEntry

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

the class DefaultFileProcessingChainTest method testFailWriteQCEntry.

@Test
public void testFailWriteQCEntry() throws FileProcessorTimeoutException {
    FileProcessingChain fileProcessingChain = new DefaultFileProcessingChain(objectRepository, qcRepository, new FailingFileProcessorNoContinue());
    when(objectRepository.exists(objectId)).thenReturn(true);
    boolean exceptionCaught = false;
    try {
        fileProcessingChain.launchChain(1L);
    } catch (FileProcessorException e) {
        exceptionCaught = true;
    }
    assertTrue("File process should have thrown exception", exceptionCaught);
    ArgumentCaptor<QCEntry> captor = ArgumentCaptor.forClass(QCEntry.class);
    verify(qcRepository).save(captor.capture());
    QCEntry qcEntry = captor.getValue();
    assertEquals("should have saved qc entry for sample", seqObject, qcEntry.getSequencingObject());
}