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

Example 1 with SampleSet

use of com.hartwig.api.model.SampleSet in project platinum by hartwigmedical.

the class ApiRerun method create.

Long create(final String sampleId) {
    try {
        List<Sample> samples = sampleApi.list(null, null, null, null, SampleType.TUMOR, sampleId);
        for (Sample sample : samples) {
            Optional<SampleSet> maybeSampleSet = OnlyOne.ofNullable(setApi.list(null, sample.getId(), true), SampleSet.class);
            if (maybeSampleSet.isPresent()) {
                SampleSet sampleSet = maybeSampleSet.get();
                if (runApi.list(null, null, sampleSet.getId(), null, null, null, null, null).stream().anyMatch(r1 -> r1.getStatus().equals(Status.VALIDATED))) {
                    return OnlyOne.ofNullable(runApi.list(null, Ini.RERUN_INI, sampleSet.getId(), version, version, null, null, null), Run.class).filter(r -> !r.getStatus().equals(Status.INVALIDATED)).map(r -> {
                        LOGGER.info("Using existing run for sample [{}] id [{}]", sampleId, r.getId());
                        return r.getId();
                    }).orElseGet(() -> {
                        final Long id = runApi.create(new CreateRun().bucket(bucket).cluster("gcp").context("RESEARCH").ini(Ini.RERUN_INI).version(version).status(Status.PENDING).setId(sampleSet.getId())).getId();
                        LOGGER.info("Created API run for sample [{}] id [{}]", sampleId, id);
                        return id;
                    });
                }
            }
        }
    } catch (Exception e) {
        LOGGER.error("Unable to create run for [{}] reason [{}]", sampleId, e.getMessage());
        return null;
    }
    return null;
}

Example 2 with SampleSet

use of com.hartwig.api.model.SampleSet 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 3 with SampleSet

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

the class ResearchMetadataApi method get.

@Override
public SomaticRunMetadata get() {
    List<Sample> possibleTumors = sampleApi.list(null, null, null, null, SampleType.TUMOR, biopsyName);
    SampleSet set = possibleTumors.stream().flatMap(sample -> setApi.list(null, sample.getId(), true).stream()).collect(Collectors.toList()).stream().max(Comparator.comparing(SampleSet::getName)).orElseThrow(() -> new IllegalStateException(String.format("No viable set found for biopsy [%s]", biopsyName)));
    Sample ref = OnlyOne.of(sampleApi.list(null, null, null, set.getId(), SampleType.REF, null), Sample.class);
    Sample tumor = OnlyOne.of(sampleApi.list(null, null, null, set.getId(), SampleType.TUMOR, null), Sample.class);
    return SomaticRunMetadata.builder().bucket(arguments.outputBucket()).set(set.getName()).maybeTumor(singleSample(tumor, SingleSampleRunMetadata.SampleType.TUMOR, set.getName())).maybeReference(singleSample(ref, SingleSampleRunMetadata.SampleType.REFERENCE, set.getName())).build();
}

Example 4 with SampleSet

use of com.hartwig.api.model.SampleSet 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;
}