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package eu.dnetlib.data.mapreduce.hbase.dedup;
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import java.io.IOException;
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import java.nio.charset.Charset;
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import java.util.Map;
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import org.apache.commons.collections.MapUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.hbase.client.Result;
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import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
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import org.apache.hadoop.hbase.mapreduce.TableMapper;
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import org.apache.hadoop.hbase.util.Bytes;
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import com.google.common.collect.Iterables;
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import eu.dnetlib.data.mapreduce.JobParams;
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import eu.dnetlib.data.mapreduce.util.DedupUtils;
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import eu.dnetlib.data.mapreduce.util.OafDecoder;
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import eu.dnetlib.pace.config.DedupConfig;
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public class DedupRootsToCsvMapper extends TableMapper<ImmutableBytesWritable, ImmutableBytesWritable> {
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/**
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* logger.
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*/
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private static final Log log = LogFactory.getLog(DedupRootsToCsvMapper.class); // NOPMD by marko on 11/24/08 5:02 PM
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private DedupConfig dedupConf;
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private ImmutableBytesWritable key;
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private ImmutableBytesWritable value;
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@Override
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protected void setup(final Context context) {
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dedupConf = DedupConfig.load(context.getConfiguration().get(JobParams.DEDUP_CONF));
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System.out.println("dedup buildRoots mapper\nwf conf: " + dedupConf.toString());
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key = new ImmutableBytesWritable();
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value = new ImmutableBytesWritable();
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}
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@Override
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protected void map(final ImmutableBytesWritable rowkey, final Result result, final Context context) throws IOException, InterruptedException {
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if (DedupUtils.isRoot(rowkey)) {
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context.getCounter(dedupConf.getWf().getEntityType(), "root row skipped").increment(1);
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return;
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}
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final Map<byte[], byte[]> entityCf = result.getFamilyMap(Bytes.toBytes(dedupConf.getWf().getEntityType()));
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if (MapUtils.isEmpty(entityCf) && (entityCf.get(DedupUtils.BODY_B) == null)) {
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context.getCounter(dedupConf.getWf().getEntityType(), "missing body").increment(1);
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return;
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}
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final Map<byte[], byte[]> mergedIn = result.getFamilyMap(DedupUtils.getDedupCF_mergedInBytes(dedupConf.getWf().getEntityType()));
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if (MapUtils.isEmpty(mergedIn)) {
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context.getCounter(dedupConf.getWf().getEntityType(), "missing mergedIn relationship").increment(1);
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return;
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}
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final String rootId = new String(Iterables.getOnlyElement(mergedIn.keySet()), Charset.forName("UTF-8"));
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final byte[] body = entityCf.get(DedupUtils.BODY_B);
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key.set(Bytes.toBytes(rootId));
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value.set(Bytes.toBytes(Iterables.getOnlyElement(OafDecoder.decode(body).getEntity().getOriginalIdList())));
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context.write(key, value);
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context.getCounter(dedupConf.getWf().getEntityType(), "root entity").increment(1);
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}
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}
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