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

Example 91 with Sample

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

the class SampleServiceImplIT method testGetBasesForSample.

/**
 * Tests getting the total bases for a sample as an admin user.
 *
 * @throws SequenceFileAnalysisException
 */
@Test
@WithMockUser(username = "fbristow", roles = "ADMIN")
public void testGetBasesForSample() throws SequenceFileAnalysisException {
    Long sampleID = 1L;
    Sample s = sampleService.read(sampleID);
    long bases = sampleService.getTotalBasesForSample(s);
    assertEquals(1000, bases);
}

Example 92 with Sample

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

the class SampleServiceImplIT method testGetBasesForSampleInvalidUser.

/**
 * Tests failing to get bases for a sample for a user not on the project.
 *
 * @throws SequenceFileAnalysisException
 */
@Test(expected = AccessDeniedException.class)
@WithMockUser(username = "dr-evil", roles = "USER")
public void testGetBasesForSampleInvalidUser() throws SequenceFileAnalysisException {
    Sample s = new Sample();
    s.setId(1L);
    sampleService.getTotalBasesForSample(s);
}

Example 93 with Sample

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

the class SampleServiceImplIT method testCreateSample.

@Test
@WithMockUser(username = "fbristow", roles = "ADMIN")
public void testCreateSample() {
    Sample s = new Sample();
    String sampleName = "sampleName";
    s.setSampleName(sampleName);
    Sample saved = sampleService.create(s);
    assertEquals("Wrong name was saved.", sampleName, saved.getSampleName());
}

Example 94 with Sample

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

the class SampleServiceImplIT method testRemoveGenomeAssemblyFromSampleSuccess.

@Test
@WithMockUser(username = "fbristow", roles = "USER")
public void testRemoveGenomeAssemblyFromSampleSuccess() {
    Sample s = sampleService.read(1L);
    assertNotNull(sampleService.getGenomeAssemblyForSample(s, 1L));
    sampleService.removeGenomeAssemblyFromSample(s, 1L);
    try {
        sampleService.getGenomeAssemblyForSample(s, 1L);
    } catch (EntityNotFoundException e) {
        return;
    }
    fail("Did not catch " + EntityNotFoundException.class);
}

Example 95 with Sample

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

the class SampleServiceImplIT method testEstimateCoverageForSampleReferenceFile.

/**
 * Tests esimating coverage with a reference file.
 *
 * @throws SequenceFileAnalysisException
 */
@Test
@WithMockUser(username = "fbristow", roles = "USER")
public void testEstimateCoverageForSampleReferenceFile() throws SequenceFileAnalysisException {
    Long sampleID = 1L;
    Sample s = sampleService.read(sampleID);
    ReferenceFile referenceFile = new ReferenceFile();
    referenceFile.setFileLength(500L);
    double coverage = sampleService.estimateCoverageForSample(s, referenceFile);
    assertEquals(2.0, coverage, deltaFloatEquality);
}