Examples with PortalFileMetadata org.icgc.dcc.song.importer.model.PortalFileMetadata used on opensource projects

Example 1 with PortalFileMetadata

use of org.icgc.dcc.song.importer.model.PortalFileMetadata 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);
}

Example 2 with PortalFileMetadata

use of org.icgc.dcc.song.importer.model.PortalFileMetadata in project SONG by overture-stack.

the class DccMetadataFetcher method processDccMetadata.

private Set<File> processDccMetadata(DccMetadata dccMetadata, Map<String, List<PortalFileMetadata>> objectIdMap) {
    val objectId = dccMetadata.getId();
    val portalFileMetadatasForObjectId = objectIdMap.get(objectId);
    val file = simpleDccStorageClient.getFile(objectId, "N/A", dccMetadata.getFileName());
    return portalFileMetadatasForObjectId.stream().map(x -> buildFile(dccMetadata, file, x)).collect(toImmutableSet());
}

Example 3 with PortalFileMetadata

use of org.icgc.dcc.song.importer.model.PortalFileMetadata in project SONG by overture-stack.

the class DccMetadataFetcher method fetchDccMetadataFiles.

public Set<File> fetchDccMetadataFiles(List<PortalFileMetadata> portalFileMetadatas) {
    val objectIdMap = groupDccMetadataIds(portalFileMetadatas);
    val dccMetadatas = dccMetadataDao.findByMultiObjectIds(objectIdMap.keySet());
    val counterMonitor = newMonitor("dccMetadataFiles", 1000);
    counterMonitor.start();
    val set = dccMetadatas.stream().map(x -> processDccMetadata(x, objectIdMap)).map(counterMonitor::streamCollectionCount).flatMap(Collection::stream).collect(toImmutableSet());
    counterMonitor.stop();
    counterMonitor.displaySummary();
    return set;
}