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

Example 1 with Sample

use of com.hartwig.api.model.Sample 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 Sample

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

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

the class DiagnosticSomaticMetadataApi method get.

@Override
public SomaticRunMetadata get() {
    String runBucket = ofNullable(run.getBucket()).orElseThrow();
    RunSet set = run.getSet();
    List<Sample> samplesBySet = sampleApi.list(null, null, null, set.getId(), null, null);
    return SomaticRunMetadata.builder().bucket(runBucket).set(set.getName()).maybeReference(find(SampleType.REF, samplesBySet).map(referenceSample -> toMetadata(referenceSample, run, SingleSampleRunMetadata.SampleType.REFERENCE, anonymizer))).maybeTumor(find(SampleType.TUMOR, samplesBySet).map(referenceSample1 -> toMetadata(referenceSample1, run, SingleSampleRunMetadata.SampleType.TUMOR, anonymizer))).build();
}