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

Example 1 with RunSet

use of com.hartwig.api.model.RunSet 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();
}