Examples with SpecimenSampleTuple org.icgc.dcc.song.importer.convert.SpecimenSampleConverter.SpecimenSampleTuple used on opensource projects

Example 1 with SpecimenSampleTuple

use of org.icgc.dcc.song.importer.convert.SpecimenSampleConverter.SpecimenSampleTuple in project SONG by overture-stack.

the class Importer method processSpecimensAndSamples.

private void processSpecimensAndSamples(List<PortalFileMetadata> portalFileMetadataList) {
    log.info("Converting Specimen and Samples...");
    val specimenSampleTuples = SPECIMEN_SAMPLE_CONVERTER.convertSpecimenSampleTuples(portalFileMetadataList);
    // Aggregating specimens
    val specimens = specimenSampleTuples.stream().collect(groupingBy(SpecimenSampleTuple::getSpecimen)).keySet();
    log.info("Updating SpecimenRepository with {} specimens", specimens.size());
    specimens.forEach(repositoryDao::createSpecimen);
    // Aggregating samples
    val samples = specimenSampleTuples.stream().collect(groupingBy(x -> x.getSample().getSampleId())).entrySet().stream().map(// TODO: why??
    x -> x.getValue().get(0).getSample()).collect(toImmutableSet());
    log.info("Updating SampleRepository with {} samples", samples.size());
    samples.forEach(repositoryDao::createSample);
}