Examples with JsonSampleSource com.hartwig.pipeline.alignment.sample.JsonSampleSource used on opensource projects

Example 1 with JsonSampleSource

use of com.hartwig.pipeline.alignment.sample.JsonSampleSource in project pipeline5 by hartwigmedical.

the class LocalSomaticMetadataTest method setUp.

@Before
public void setUp() throws Exception {
    setId = "setId";
    tumorName = "CORE123T";
    refName = "CORE123R";
    jsonSampleSource = mock(JsonSampleSource.class);
    tumorSample = mock(Sample.class);
    final Sample refSample = mock(Sample.class);
    stagedOutputPublisher = mock(StagedOutputPublisher.class);
    victim = new LocalSomaticMetadata(Arguments.testDefaultsBuilder().setId(setId).build(), jsonSampleSource, stagedOutputPublisher);
    when(jsonSampleSource.sample(SampleType.REFERENCE)).thenReturn(Optional.of(refSample));
    when(tumorSample.name()).thenReturn(tumorName);
    when(refSample.name()).thenReturn(refName);
}