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

Example 1 with PortalDonorMetadata

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

the class DonorDao method createDonorDao.

public static DonorDao createDonorDao(Iterable<PortalDonorMetadata> portalDonorMetadataIterable) {
    val map = Maps.<String, PortalDonorMetadata>newHashMap();
    for (val portalDonorMetadata : portalDonorMetadataIterable) {
        val donorId = DonorConverter.getDonorId(portalDonorMetadata);
        checkArgument(!map.containsKey(donorId), "Map cannot have duplicates for donorId [%s]", donorId);
        map.put(donorId, portalDonorMetadata);
    }
    return createDonorDao(ImmutableMap.copyOf(map));
}

Example 2 with PortalDonorMetadata

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

the class DonorFetcher method fetchPortalDonorMetadataSet.

public Set<PortalDonorMetadata> fetchPortalDonorMetadataSet(List<PortalFileMetadata> portalFileMetadataList) {
    val donorSet = ImmutableSet.<PortalDonorMetadata>builder();
    val donorIdSet = Sets.<String>newHashSet();
    int numErrorDonorIds = 0;
    for (val portalFileMetadata : portalFileMetadataList) {
        val donorId = portalFileMetadata.getDonorId();
        val fileId = portalFileMetadata.getFileId();
        if (!donorIdSet.contains(donorId)) {
            // Want to minimize redundant network traffic (fetching)
            try {
                val portalDonorMetadata = fetchPortalDonorMetadata(donorId);
                donorSet.add(portalDonorMetadata);
            } catch (Throwable t) {
                log.error("DONOR_FETCH_ERROR[{}]: donorId [{}] data is malformed in FileId [{}]. Error recorded", ++numErrorDonorIds, donorId, fileId);
            }
            donorIdSet.add(donorId);
        }
    }
    return donorSet.build();
}