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

Example 6 with MiseqRun

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

the class SequencingRunControllerTest method testGetFilesPage.

@SuppressWarnings("rawtypes")
@Test
public void testGetFilesPage() throws IOException {
    Long runId = 1L;
    ExtendedModelMap model = new ExtendedModelMap();
    SequencingRun sequencingRunEntity = new MiseqRun(SequencingRun.LayoutType.PAIRED_END, "");
    ImmutableSet<SequencingObject> files = ImmutableSet.of(new SingleEndSequenceFile(new SequenceFile()));
    when(sequencingRunService.read(runId)).thenReturn(sequencingRunEntity);
    when(objectService.getSequencingObjectsForSequencingRun(sequencingRunEntity)).thenReturn(files);
    String filesPage = controller.getFilesPage(runId, model);
    assertEquals(SequencingRunController.FILES_VIEW, filesPage);
    assertFalse(((Collection) model.get("sequencingObjects")).isEmpty());
    assertEquals(sequencingRunEntity, model.get("run"));
    assertTrue(model.containsKey("fileCount"));
    verify(sequencingRunService).read(runId);
    verify(objectService).getSequencingObjectsForSequencingRun(sequencingRunEntity);
}

Example 7 with MiseqRun

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

the class SequencingRunServiceImplIT method testCreateMiseqRunAsUser.

@Test
@WithMockUser(username = "user", password = "password1", roles = "USER")
public void testCreateMiseqRunAsUser() {
    MiseqRun mr = new MiseqRun(LayoutType.PAIRED_END, "workflow");
    SequencingRun create = miseqRunService.create(mr);
    assertEquals("user", create.getUser().getUsername());
}

Example 8 with MiseqRun

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

the class SequencingObjectServiceTest method testCreateSequenceFileInSampleWrongType.

@Test(expected = IllegalArgumentException.class)
public void testCreateSequenceFileInSampleWrongType() throws IOException {
    Sample s = new Sample();
    SingleEndSequenceFile so = TestDataFactory.constructSingleEndSequenceFile();
    SequencingRun run = new MiseqRun(LayoutType.PAIRED_END, "workflow");
    so.setSequencingRun(run);
    when(repository.save(so)).thenReturn(so);
    service.createSequencingObjectInSample(so, s);
}

Example 9 with MiseqRun

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

the class SequencingObjectServiceTest method testCreateSequenceFilePairInSampleWrongType.

@Test(expected = IllegalArgumentException.class)
public void testCreateSequenceFilePairInSampleWrongType() throws IOException {
    Sample s = new Sample();
    SequencingRun run = new MiseqRun(LayoutType.SINGLE_END, "workflow");
    SequenceFilePair so = TestDataFactory.constructSequenceFilePair();
    so.setSequencingRun(run);
    when(repository.save(so)).thenReturn(so);
    service.createSequencingObjectInSample(so, s);
}