Examples with SequencingRun ca.corefacility.bioinformatics.irida.model.run.SequencingRun used on opensource projects

Example 1 with SequencingRun

use of ca.corefacility.bioinformatics.irida.model.run.SequencingRun in project irida by phac-nml.

the class SequencingRunController method getPageDetails.

private Model getPageDetails(Long runId, Model model) {
    SequencingRun run = sequencingRunService.read(runId);
    Set<SequencingObject> sequencingObjectsForSequencingRun = objectService.getSequencingObjectsForSequencingRun(run);
    int fileCount = sequencingObjectsForSequencingRun.stream().mapToInt(o -> o.getFiles().size()).sum();
    model.addAttribute("sequencingObjects", sequencingObjectsForSequencingRun);
    model.addAttribute("fileCount", fileCount);
    model.addAttribute("run", run);
    return model;
}

Example 2 with SequencingRun

use of ca.corefacility.bioinformatics.irida.model.run.SequencingRun in project irida by phac-nml.

the class SequencingObjectServiceImplIT method testCoverage.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testCoverage() throws IOException, InterruptedException {
    Project project = projectService.read(1L);
    project.setGenomeSize(3L);
    project.setMinimumCoverage(2);
    project = projectService.update(project);
    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);
    // Wait 10 seconds. file processing should have run by then.
    Thread.sleep(10000);
    Sample readSample = sampleService.read(s.getId());
    List<QCEntry> qcEntries = sampleService.getQCEntriesForSample(readSample);
    assertEquals("should be one qc entry", 1, qcEntries.size());
    QCEntry qcEntry = qcEntries.iterator().next();
    qcEntry.addProjectSettings(project);
    assertTrue("should be coverage entry", qcEntry instanceof CoverageQCEntry);
    assertEquals("qc should have passed", QCEntryStatus.POSITIVE, qcEntry.getStatus());
    assertEquals("should be 6x coverage", "6x", qcEntry.getMessage());
    project.setMinimumCoverage(10);
    project = projectService.update(project);
    // Wait 10 seconds. file processing should have run by then.
    Thread.sleep(10000);
    qcEntries = sampleService.getQCEntriesForSample(readSample);
    assertEquals("should be one qc entry", 1, qcEntries.size());
    qcEntry = qcEntries.iterator().next();
    qcEntry.addProjectSettings(project);
    assertTrue("should be coverage entry", qcEntry instanceof CoverageQCEntry);
    assertEquals("qc should have failed", QCEntryStatus.NEGATIVE, qcEntry.getStatus());
}

Example 3 with SequencingRun

use of ca.corefacility.bioinformatics.irida.model.run.SequencingRun in project irida by phac-nml.

the class SequencingRunServiceImplIT method testAddDetachedRunToSequenceFile.

/**
 * This test simulates a bug that happens from the REST API when uploading
 * sequence files to samples, where a new sequence file is created, then
 * detached from a transaction.
 *
 * @throws IOException
 * @throws InterruptedException
 */
@Test
@WithMockUser(username = "fbristow", password = "password1", roles = "ADMIN")
public void testAddDetachedRunToSequenceFile() throws IOException, InterruptedException {
    final String SEQUENCE = "ACGTACGTN";
    final byte[] FASTQ_FILE_CONTENTS = ("@testread\n" + SEQUENCE + "\n+\n?????????\n@testread2\n" + SEQUENCE + "\n+\n?????????").getBytes();
    Path p = Files.createTempFile(null, null);
    Files.write(p, FASTQ_FILE_CONTENTS);
    SequenceFile sf = new SequenceFile();
    sf.setFile(p);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    Sample sample = sampleService.read(1L);
    SequencingRun run = miseqRunService.read(2L);
    objectService.createSequencingObjectInSample(so, sample);
    miseqRunService.addSequencingObjectToSequencingRun(run, so);
    AnalysisFastQC analysis = null;
    do {
        try {
            analysis = analysisService.getFastQCAnalysisForSequenceFile(so, sf.getId());
        } catch (final EntityNotFoundException e) {
            logger.info("Fastqc still isn't finished, sleeping a bit.");
            Thread.sleep(1000);
        }
    } while (analysis == null);
    assertNotNull("FastQC analysis should have been created for sequence file.", analysis);
}

Example 4 with SequencingRun

use of ca.corefacility.bioinformatics.irida.model.run.SequencingRun in project irida by phac-nml.

the class SequencingRunServiceImplIT method testFindAll.

@Test
@WithMockUser(username = "user", password = "password1", roles = "USER")
public void testFindAll() {
    Iterable<SequencingRun> findAll = miseqRunService.findAll();
    List<SequencingRun> runs = Lists.newArrayList(findAll);
    assertEquals("user should be able to see 1 run", 1, runs.size());
    SequencingRun run = runs.iterator().next();
    assertEquals("id should be 1", new Long(1), run.getId());
}

Example 5 with SequencingRun

use of ca.corefacility.bioinformatics.irida.model.run.SequencingRun in project irida by phac-nml.

the class SequencingRunServiceImplIT method testUpdateMiseqRunAsUserFail.

@Test(expected = AccessDeniedException.class)
@WithMockUser(username = "user", password = "password1", roles = "USER")
public void testUpdateMiseqRunAsUserFail() {
    // run 2 is not owned by "user"
    SequencingRun mr = miseqRunService.read(2L);
    mr.setDescription("different description");
    miseqRunService.update(mr);
}