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

Example 61 with Sample

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

the class ProjectEventHandlerTest method testDelegateSampleAdded.

@Test
public void testDelegateSampleAdded() {
    Class<? extends ProjectEvent> clazz = SampleAddedProjectEvent.class;
    Project project = new Project();
    Sample sample = new Sample();
    ProjectSampleJoin returnValue = new ProjectSampleJoin(project, sample, true);
    Object[] args = { project, sample };
    MethodEvent methodEvent = new MethodEvent(clazz, returnValue, args);
    when(eventRepository.save(any(ProjectEvent.class))).thenReturn(new SampleAddedProjectEvent(returnValue));
    handler.delegate(methodEvent);
    ArgumentCaptor<ProjectEvent> captor = ArgumentCaptor.forClass(ProjectEvent.class);
    verify(eventRepository).save(captor.capture());
    ProjectEvent event = captor.getValue();
    assertTrue(event instanceof SampleAddedProjectEvent);
    verify(projectRepository).save(any(Project.class));
}

Example 62 with Sample

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

the class SampleTest method testBlacklists.

private void testBlacklists(char[] blacklist) {
    for (char c : blacklist) {
        Sample s = new Sample();
        s.setSampleName("ATLEAST3" + c);
        Set<ConstraintViolation<Sample>> violations = validator.validate(s);
        assertEquals("Wrong number of violations.", 1, violations.size());
    }
}

Example 63 with Sample

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

the class SampleTest method testInvalidSampleName.

@Test
public void testInvalidSampleName() {
    Sample s = new Sample();
    s.setSampleName("This name has a single quote ' and spaces and a period.");
    Set<ConstraintViolation<Sample>> violations = validator.validate(s);
    assertEquals("Wrong number of violations.", 3, violations.size());
}

Example 64 with Sample

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

the class SampleRepositoryIT method testFindSamplesForAnalysisSubmissionSingleSample.

@Test
@WithMockUser(username = "fbristow", roles = "ADMIN")
public void testFindSamplesForAnalysisSubmissionSingleSample() {
    AnalysisSubmission a = analysisSubmissionRepository.findOne(10L);
    Set<Sample> samples = sampleRepository.findSamplesForAnalysisSubmission(a);
    assertEquals("Sample ids are equal", Sets.newHashSet(11L), samples.stream().map(Sample::getId).collect(Collectors.toSet()));
}

Example 65 with Sample

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

the class AnalysisCollectionServiceGalaxyIT method testGetSequenceFilePairSamplesSuccess.

/**
 * Tests successfully getting a map of samples and sequence files (pair).
 *
 * @throws DuplicateSampleException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetSequenceFilePairSamplesSuccess() throws DuplicateSampleException {
    Set<SequenceFilePair> sequenceFiles = Sets.newHashSet(databaseSetupGalaxyITService.setupSampleSequenceFileInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A));
    Sample sample = sampleRepository.findOne(1L);
    SequenceFilePair sequenceFilePair = sequenceFiles.iterator().next();
    Map<Sample, SequenceFilePair> sampleSequenceFilePairs = sequencingObjectService.getUniqueSamplesForSequencingObjects(sequenceFiles);
    assertEquals("sampleSequenceFiles map has size != 1", 1, sampleSequenceFilePairs.size());
    assertEquals("sampleSequenceFiles map does not have sequenceFilePair " + sequenceFilePair + " corresponding to sample " + sample, sequenceFilePair, sampleSequenceFilePairs.get(sample));
}