Examples with Sample uk.ac.bbsrc.tgac.miso.core.data.Sample used on opensource projects

Example 11 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class DefaultSampleServiceTest method nullSampleObjectNameTest.

@Test
public void nullSampleObjectNameTest() throws Exception {
    Sample sample = null;
    assertFalse("A null sample object does not contain a temporary name so must return false.", hasTemporaryName(sample));
}

Example 12 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class DefaultSampleServiceTest method testUpdatePlainSample.

@Test
public void testUpdatePlainSample() throws Exception {
    Sample old = makePlainSample();
    Mockito.when(sampleStore.getSample(old.getId())).thenReturn(old);
    Sample updated = makePlainSample();
    // modifiable attributes
    updated.setAlias("newAlias");
    updated.setDescription("newDesc");
    updated.setSampleType("newType");
    updated.setDetailedQcStatus(mockDetailedQcStatus(5L, "Ready", false));
    updated.setQcUser(mockUser());
    updated.setScientificName(mockScientificName(2L, "newSciName"));
    updated.setTaxonIdentifier("newTaxonId");
    updated.setVolume(new BigDecimal("5.5"));
    updated.setVolumeUnits(VolumeUnit.MICROLITRES);
    // unmodifiable
    updated.setName("newName");
    mockShellProjectWithRealLookup(updated);
    sut.update(updated);
    ArgumentCaptor<Sample> updatedCapture = ArgumentCaptor.forClass(Sample.class);
    Mockito.verify(sampleStore).update(updatedCapture.capture());
    Sample result = updatedCapture.getValue();
    assertEquals("Sample sampleType should be modifiable", updated.getSampleType(), result.getSampleType());
    assertEquals("Sample description should be modifiable", updated.getDescription(), result.getDescription());
    assertEquals("Sample sampleType should be modifiable", updated.getSampleType(), result.getSampleType());
    assertEquals("Sample detailedQcStatus should be modifiable", updated.getDetailedQcStatus(), result.getDetailedQcStatus());
    assertEquals("Sample scientificName should be modifiable", updated.getScientificName(), result.getScientificName());
    assertEquals("Sample taxonIdentifier should be modifiable", updated.getTaxonIdentifier(), result.getTaxonIdentifier());
    assertEquals("Sample volume should be modifiable", updated.getVolume(), result.getVolume());
    assertEquals("Sample project should be modifiable", updated.getProject().getId(), result.getProject().getId());
    assertEquals("Sample name should NOT be modifiable", old.getName(), result.getName());
}

Example 13 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class DefaultSampleServiceTest method testCreateDetailedSampleNoParent.

@Test
public void testCreateDetailedSampleNoParent() throws Exception {
    SampleTissue sample = makeUnsavedChildTissue();
    SampleIdentity fakeParent = new SampleIdentityImpl();
    fakeParent.setExternalName("non-existing");
    sample.setParent(fakeParent);
    mockShellProjectWithRealLookup(sample);
    mockUser();
    // because of mocked dao, we can't actually continue with the same parent sample that should be created, but the partial
    // parent sample that gets created is caught and examined below
    SampleIdentity parent = makeParentIdentityWithLookup();
    Mockito.when(sampleStore.create(Mockito.any(Sample.class))).thenReturn(parent.getId());
    mockValidRelationship(parent.getSampleClass(), sample.getSampleClass());
    Long newId = 31L;
    Mockito.when(sampleStore.create(sample)).thenReturn(newId);
    Mockito.when(sampleStore.getSample(newId)).thenReturn(sample);
    sut.create(sample);
    ArgumentCaptor<Sample> createdCapture = ArgumentCaptor.forClass(Sample.class);
    Mockito.verify(sampleStore, Mockito.times(2)).create(createdCapture.capture());
    Sample partialParent = createdCapture.getAllValues().get(0);
    assertTrue(LimsUtils.isIdentitySample(partialParent));
    Sample partialChild = createdCapture.getAllValues().get(1);
    assertTrue(LimsUtils.isTissueSample(partialChild));
    ArgumentCaptor<Sample> updatedCapture = ArgumentCaptor.forClass(Sample.class);
    Mockito.verify(sampleStore, Mockito.times(3)).update(updatedCapture.capture());
    // note: finalParent is not actually derived from partialParent because of mocked dao (above), but it should be the parent
    // linked to finalChild
    Sample finalParent = updatedCapture.getAllValues().get(0);
    Sample finalChild = updatedCapture.getAllValues().get(1);
    assertNotNull("Child sample should have parent", ((SampleTissue) finalChild).getParent());
    assertEquals("Unexpected parent ID", ((SampleTissue) finalChild).getParent().getId(), finalParent.getId());
}

Example 14 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class DefaultSampleServiceTest method testPlainSampleIdentificationBarcodeGeneration.

@Test
public void testPlainSampleIdentificationBarcodeGeneration() throws Exception {
    Sample sample = new SampleImpl();
    sample.setAlias("alias");
    mockShellProjectWithRealLookup(sample);
    assertNull("identificationBarcode should be null before save for test", sample.getIdentificationBarcode());
    sut.setAutoGenerateIdBarcodes(true);
    Mockito.when(sampleStore.getSample(Mockito.anyLong())).thenReturn(sample);
    sut.create(sample);
    ArgumentCaptor<Sample> updatedCapture = ArgumentCaptor.forClass(Sample.class);
    Mockito.verify(sampleStore).update(updatedCapture.capture());
    Sample updated = updatedCapture.getValue();
    assertNotNull("identificationBarcode should be generated", updated.getIdentificationBarcode());
}

Example 15 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class DefaultSampleServiceTest method testCreatePlainSample.

@Test
public void testCreatePlainSample() throws Exception {
    Sample sample = new SampleImpl();
    String expectedAlias = "not_generated";
    sample.setAlias(expectedAlias);
    Project expectedProject = mockShellProjectWithRealLookup(sample);
    User expectedLastModifier = mockUser();
    String expectedName = "generated_name";
    Mockito.when(namingScheme.generateNameFor((Sample) Mockito.any())).thenReturn(expectedName);
    Mockito.when(namingScheme.generateSampleAlias((Sample) Mockito.any())).thenReturn("bad");
    Mockito.when(sampleStore.getSample(Mockito.anyLong())).thenReturn(sample);
    sut.create(sample);
    ArgumentCaptor<Sample> createdCapture = ArgumentCaptor.forClass(Sample.class);
    Mockito.verify(sampleStore).create(createdCapture.capture());
    Sample created = createdCapture.getValue();
    assertEquals("shell project should be replaced by real project", expectedProject.getAlias(), created.getProject().getAlias());
    assertNotNull("modification details should be added", created.getLastModifier());
    assertEquals("modification details should be added", expectedLastModifier.getId(), created.getLastModifier().getId());
    assertTrue("expected a plain sample", LimsUtils.isPlainSample(created));
    // name generators get called after initial save
    ArgumentCaptor<Sample> updatedCapture = ArgumentCaptor.forClass(Sample.class);
    Mockito.verify(sampleStore).update(updatedCapture.capture());
    Sample updated = updatedCapture.getValue();
    assertEquals("name should be generated", expectedName, updated.getName());
    assertEquals("alias should not be generated", expectedAlias, updated.getAlias());
    assertNull("identificationBarcode should not be generated", updated.getIdentificationBarcode());
    assertTrue("expected a plain sample", LimsUtils.isPlainSample(updated));
}