Examples with PipelineState com.hartwig.pipeline.PipelineState used on opensource projects

Example 1 with PipelineState

use of com.hartwig.pipeline.PipelineState in project pipeline5 by hartwigmedical.

the class PipelineResultsTest method onlyWritesStagedFileWhenPipelineFailsSingleSample.

@Test
public void onlyWritesStagedFileWhenPipelineFailsSingleSample() {
    ArgumentCaptor<String> createBlobCaptor = ArgumentCaptor.forClass(String.class);
    PipelineState state = new PipelineState();
    state.add(BamMetricsOutput.builder().sample("reference").status(PipelineStatus.FAILED).build());
    victim.compose(TestInputs.referenceRunMetadata(), false, state);
    verify(outputBucket, times(1)).create(createBlobCaptor.capture(), (byte[]) any());
    assertThat(createBlobCaptor.getAllValues().get(0)).isEqualTo("reference-tag/STAGED");
}

Example 2 with PipelineState

use of com.hartwig.pipeline.PipelineState in project pipeline5 by hartwigmedical.

the class SmokeTest method runFullPipelineAndCheckFinalStatus.

public void runFullPipelineAndCheckFinalStatus(final String inputMode, final PipelineStatus expectedStatus) throws Exception {
    PipelineMain victim = new PipelineMain();
    String version = version();
    String setName = noDots(inputMode + "-" + version);
    final String fixtureDir = "smoke_test/" + inputMode + "/";
    final String randomRunId = noDots(RandomStringUtils.random(5, true, false));
    final ImmutableArguments.Builder builder = Arguments.defaultsBuilder(Arguments.DefaultsProfile.DEVELOPMENT.toString()).sampleJson(Resources.testResource(fixtureDir + "samples.json")).cloudSdkPath(CLOUD_SDK_PATH).setId(setName).runId(randomRunId).runGermlineCaller(false).cleanup(true).outputBucket("smoketest-pipeline-output-pilot-1").context(Context.DIAGNOSTIC);
    final String username = System.getProperty("user.name");
    if (username.equals("root")) {
        String privateKeyPath = workingDir() + "/google-key.json";
        builder.privateKeyPath(privateKeyPath).uploadPrivateKeyPath(privateKeyPath);
    } else {
        builder.cloudSdkPath(String.format("/Users/%s/google-cloud-sdk/bin", username));
    }
    Arguments arguments = builder.build();
    Storage storage = StorageProvider.from(arguments, CredentialProvider.from(arguments).get()).get();
    cleanupBucket(inputMode, arguments.outputBucket(), storage);
    PipelineState state = victim.start(arguments);
    assertThat(state.status()).isEqualTo(expectedStatus);
    File expectedFilesResource = new File(Resources.testResource(fixtureDir + "expected_output_files"));
    List<String> expectedFiles = FileUtils.readLines(expectedFilesResource, FILE_ENCODING);
    final String outputDir = setName + "-" + randomRunId;
    List<String> actualFiles = listOutput(outputDir, arguments.outputBucket(), storage);
    assertThat(actualFiles).containsOnlyElementsOf(expectedFiles);
    cleanupBucket(outputDir, arguments.outputBucket(), storage);
}

Example 3 with PipelineState

use of com.hartwig.pipeline.PipelineState in project pipeline5 by hartwigmedical.

the class StagedOutputPublisher method publish.

public void publish(final PipelineState state, final SomaticRunMetadata metadata) {
    if (state.status() != PipelineStatus.FAILED && run.isPresent()) {
        List<AddDatatype> addDatatypes = state.stageOutputs().stream().map(StageOutput::datatypes).flatMap(List::stream).collect(Collectors.toList());
        SampleSet set = setResolver.resolve(metadata.set(), useOnlyDBSets);
        Optional<String> tumorSampleName = metadata.maybeTumor().map(SingleSampleRunMetadata::sampleName);
        Optional<String> refSampleName = metadata.maybeReference().map(SingleSampleRunMetadata::sampleName);
        ImmutableAnalysis.Builder alignedReadsAnalysis = eventBuilder(Type.ALIGNMENT);
        ImmutableAnalysis.Builder somaticAnalysis = eventBuilder(Type.SOMATIC);
        ImmutableAnalysis.Builder germlineAnalysis = eventBuilder(Type.GERMLINE);
        OutputIterator.from(blob -> {
            Optional<AddDatatype> dataType = addDatatypes.stream().filter(d -> blob.getName().endsWith(d.path())).findFirst();
            Blob blobWithMd5 = sourceBucket.get(blob.getName());
            if (isSecondary(blobWithMd5)) {
                alignedReadsAnalysis.addOutput(createBlob(tumorSampleName, refSampleName, dataType, blobWithMd5));
            } else {
                if (isGermline(blobWithMd5)) {
                    germlineAnalysis.addOutput(createBlob(tumorSampleName, refSampleName, dataType, blobWithMd5));
                } else if (notSecondary(blobWithMd5)) {
                    somaticAnalysis.addOutput(createBlob(tumorSampleName, refSampleName, dataType, blobWithMd5));
                }
            }
        }, sourceBucket).iterate(metadata);
        publish(PipelineComplete.builder().pipeline(ImmutablePipeline.builder().sample(tumorSampleName.orElseGet(() -> refSampleName.orElseThrow())).bucket(sourceBucket.getName()).runId(run.get().getId()).setId(set.getId()).context(context).addAnalyses(alignedReadsAnalysis.build(), somaticAnalysis.build(), germlineAnalysis.build()).version(Versions.pipelineMajorMinorVersion()).build()).build());
    }
}

Example 4 with PipelineState

use of com.hartwig.pipeline.PipelineState in project pipeline5 by hartwigmedical.

the class ResearchMetadataApiTest method pipelineCompleteWithFile.

@NotNull
public ArgumentCaptor<PubsubMessage> pipelineCompleteWithFile(final String s, final StageOutput stageOutput) {
    PipelineState state = new PipelineState();
    state.add(stageOutput);
    ArgumentCaptor<PubsubMessage> pubsubMessageArgumentCaptor = ArgumentCaptor.forClass(PubsubMessage.class);
    SomaticRunMetadata metadata = TestInputs.defaultSomaticRunMetadata();
    when(setResolver.resolve(metadata.set(), true)).thenReturn(new SampleSet().id(SET_ID));
    Blob outputBlob = mock(Blob.class);
    when(outputBlob.getBucket()).thenReturn("bucket");
    when(outputBlob.getName()).thenReturn(s);
    when(outputBlob.getSize()).thenReturn(1L);
    when(outputBlob.getMd5()).thenReturn("md5");
    when(bucket.get(s)).thenReturn(outputBlob);
    Page<Blob> page = TestBlobs.pageOf(outputBlob);
    when(bucket.list(Storage.BlobListOption.prefix("set/"))).thenReturn(page);
    // noinspection unchecked
    when(publisher.publish(pubsubMessageArgumentCaptor.capture())).thenReturn(mock(ApiFuture.class));
    victim.complete(state, metadata);
    return pubsubMessageArgumentCaptor;
}

Example 5 with PipelineState

use of com.hartwig.pipeline.PipelineState in project pipeline5 by hartwigmedical.

the class ResearchMetadataApiTest method doesNothingOnFailedPipeline.

@Test
public void doesNothingOnFailedPipeline() {
    PipelineState state = new PipelineState();
    state.add(TestOutput.builder().status(PipelineStatus.FAILED).build());
    victim.complete(state, TestInputs.defaultSomaticRunMetadata());
    verify(publisher, never()).publish(any());
}