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

Example 16 with Sample

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

the class DefaultSampleServiceTest method testValidateRelationshipForSimpleSample.

@Test
public void testValidateRelationshipForSimpleSample() throws Exception {
    // Simple sample has no DetailedSample attributes.
    Sample child = new SampleImpl();
    // Simple sample has no parent.
    Sample parent = null;
    assertTrue("Simple sample with a null parent and null DetailedSample is a valid relationship", sut.isValidRelationship(parent, child));
}

Example 17 with Sample

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

the class DefaultSampleServiceTest method notTemporarySampleNameTest.

@Test
public void notTemporarySampleNameTest() throws Exception {
    Sample sample = new SampleImpl();
    sample.setName("RealSampleName");
    assertFalse("Real sample names must return false.", hasTemporaryName(sample));
}

Example 18 with Sample

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

the class DefaultSampleServiceTest method makePlainSample.

private Sample makePlainSample() {
    Sample sample = new SampleImpl();
    sample.setId(77L);
    sample.setAlias("alias");
    sample.setName("name");
    return sample;
}

Example 19 with Sample

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

the class DefaultSampleServiceTest method testPlainSampleAliasGeneration.

@Test
public void testPlainSampleAliasGeneration() throws Exception {
    Sample sample = new SampleImpl();
    mockShellProjectWithRealLookup(sample);
    String expectedAlias = "generated_alias";
    Mockito.when(namingScheme.hasSampleAliasGenerator()).thenReturn(true);
    Mockito.when(namingScheme.generateSampleAlias((Sample) Mockito.any())).thenReturn(expectedAlias);
    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();
    assertEquals("alias should be generated", expectedAlias, updated.getAlias());
}

Example 20 with Sample

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

the class DefaultTransferService method addTransferSample.

@Override
public void addTransferSample(TransferSample transferSample) throws IOException {
    Transfer managedTransfer = get(transferSample.getTransfer().getId());
    Sample managedSample = sampleService.get(transferSample.getItem().getId());
    transferSample.setTransfer(managedTransfer);
    transferSample.setItem(managedSample);
    validateAddition(managedTransfer, transferSample);
    transferStore.update(managedTransfer);
    sampleService.update(managedSample);
}