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

Example 6 with CoverageQCEntry

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