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

Example 6 with PipelineState

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

the class VmExecutionLogSummary method ofFailedStages.

public static void ofFailedStages(final Storage storage, final PipelineState state) {
    List<StageOutput> failures = state.stageOutputs().stream().filter(stageOutput -> stageOutput.status().equals(PipelineStatus.FAILED)).collect(Collectors.toList());
    if (!failures.isEmpty()) {
        LOGGER.error("Failures in pipeline stages. Printing each failures full run.log here");
        for (StageOutput failure : failures) {
            for (Blob log : failure.failedLogLocations().stream().map(GoogleStorageLocation::asBlobId).map(storage::get).collect(Collectors.toList())) {
                LOGGER.error("========================================== start {} ==========================================", log.getName());
                LOGGER.error(new String(log.getContent()));
                LOGGER.error("========================================== end {} ==========================================", log.getName());
            }
        }
    }
}

Example 7 with PipelineState

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

the class LocalSomaticMetadataTest method publishesEventIfSpecifiedInArguments.

@Test
public void publishesEventIfSpecifiedInArguments() {
    PipelineState state = mock(PipelineState.class);
    SomaticRunMetadata metadata = mock(SomaticRunMetadata.class);
    new LocalSomaticMetadata(Arguments.testDefaultsBuilder().setId(setId).publishDbLoadEvent(true).build(), jsonSampleSource, stagedOutputPublisher).complete(state, metadata);
    verify(stagedOutputPublisher).publish(state, metadata);
}

Example 8 with PipelineState

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

the class ResearchMetadataApiTest method setsStatusAndEndTimeOnComplete.

@Test
public void setsStatusAndEndTimeOnComplete() {
    ArgumentCaptor<Long> runIdArgumentCaptor = ArgumentCaptor.forClass(Long.class);
    ArgumentCaptor<UpdateRun> updateRunArgumentCaptor = ArgumentCaptor.forClass(UpdateRun.class);
    when(runApi.update(runIdArgumentCaptor.capture(), updateRunArgumentCaptor.capture())).thenReturn(run);
    PipelineState state = new PipelineState();
    state.add(TestOutput.builder().status(PipelineStatus.FAILED).build());
    victim.complete(state, TestInputs.defaultSomaticRunMetadata());
    assertThat(runIdArgumentCaptor.getValue()).isEqualTo(RUN_ID);
    UpdateRun updateRun = updateRunArgumentCaptor.getValue();
    assertThat(updateRun.getEndTime()).isNotNull();
    assertThat(updateRun.getStatus()).isEqualTo(Status.FAILED);
}

Example 9 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, @SuppressWarnings("OptionalUsedAsFieldOrParameterType") final Optional<String> targetedRegionsBed, final RefGenomeVersion refGenomeVersion) throws Exception {
    final PipelineMain victim = new PipelineMain();
    final String version = version();
    final String setName = noDots(inputMode + "-" + version);
    final String fixtureDir = "smoke_test/" + inputMode + "/";
    @SuppressWarnings("deprecation") 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(findCloudSdk()).setId(setName).runId(randomRunId).runGermlineCaller(false).cleanup(false).outputBucket("smoketest-pipeline-output-pilot-1").context(Context.DIAGNOSTIC).useTargetRegions(false).refGenomeVersion(refGenomeVersion);
    if (whoami.equals("root")) {
        String privateKeyPath = workingDir() + "/google-key.json";
        builder.privateKeyPath(privateKeyPath).uploadPrivateKeyPath(privateKeyPath);
    }
    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);
    if (inputMode.equals("tumor-reference")) {
        ComparAssert.assertThat(storage, arguments.outputBucket(), outputDir).isEqualToTruthset(Resources.testResource(fixtureDir + "/truthset")).cleanup();
    }
    cleanupBucket(outputDir, arguments.outputBucket(), storage);
}