Examples with Run com.hartwig.api.model.Run used on opensource projects

Example 6 with Run

use of com.hartwig.api.model.Run in project pipeline5 by hartwigmedical.

the class DiagnosticSomaticMetadataApiTest method throwsIllegalStateIfNoBucketInRun.

@Test(expected = IllegalStateException.class)
public void throwsIllegalStateIfNoBucketInRun() {
    victim = new DiagnosticSomaticMetadataApi(new Run().bucket(null), runApi, sampleApi, publisher, new Anonymizer(Arguments.testDefaults()));
    when(pipelineState.status()).thenReturn(PipelineStatus.FAILED);
    victim.complete(pipelineState, somaticRunMetadata);
}

Example 7 with Run

use of com.hartwig.api.model.Run in project pipeline5 by hartwigmedical.

the class ResearchMetadataApiTest method setUp.

@Before
public void setUp() throws Exception {
    sampleApi = mock(SampleApi.class);
    setApi = mock(SetApi.class);
    bucket = mock(Bucket.class);
    when(bucket.getName()).thenReturn("bucket");
    runApi = mock(RunApi.class);
    run = new Run().id(RUN_ID);
    publisher = mock(Publisher.class);
    ObjectMapper objectMapper = ObjectMappers.get();
    setResolver = mock(SetResolver.class);
    victim = new ResearchMetadataApi(sampleApi, setApi, runApi, Optional.of(run), BIOPSY, Arguments.testDefaults(), new StagedOutputPublisher(setResolver, bucket, publisher, objectMapper, Optional.of(run), Context.RESEARCH, false, true), new Anonymizer(Arguments.testDefaults()));
}

Example 8 with Run

use of com.hartwig.api.model.Run in project pipeline5 by hartwigmedical.

the class StagedOutputPublisherTest method setUp.

@Before
public void setUp() throws Exception {
    bucket = mock(Bucket.class);
    when(bucket.getName()).thenReturn("bucket");
    publisher = mock(Publisher.class);
    state = mock(PipelineState.class);
    setResolver = mock(SetResolver.class);
    victim = new StagedOutputPublisher(setResolver, bucket, publisher, OBJECT_MAPPER, Optional.of(new Run().ini(Ini.SOMATIC_INI.getValue()).id(1L)), Context.DIAGNOSTIC, true, false);
}