boa.runtime.BoaCombiner.java Source code

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Here is the source code for boa.runtime.BoaCombiner.java

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/*
 * Copyright 2015, Anthony Urso, Hridesh Rajan, Robert Dyer,
 *                 and Iowa State University of Science and Technology
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package boa.runtime;

import java.io.IOException;
import java.util.HashMap;
import java.util.Map;

import org.apache.hadoop.conf.Configurable;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.mapreduce.Reducer;
import org.apache.log4j.Logger;

import boa.aggregators.Aggregator;
import boa.aggregators.FinishedException;
import boa.io.EmitKey;
import boa.io.EmitValue;

/**
 * A {@link Reducer} that pre-reduces the outputs from a single mapper node in
 * order to save I/O.
 * 
 * @author anthonyu
 * @author rdyer
 */
public abstract class BoaCombiner extends Reducer<EmitKey, EmitValue, EmitKey, EmitValue> implements Configurable {
    /**
     * A {@link Logger} that log entries can be written to.
     * 
     */
    protected static final Logger LOG = Logger.getLogger(BoaCombiner.class);

    /**
     * A {@link Map} from {@link String} to {@link Aggregator} indexing instantiated
     * aggregators to their Boa identifiers.
     */
    protected Map<String, Aggregator> aggregators;

    private Configuration conf;
    private boolean robust;

    /**
     * Construct a {@link BoaCombiner}.
     */
    protected BoaCombiner() {
        this.aggregators = new HashMap<String, Aggregator>();
    }

    /** {@inheritDoc} */
    @Override
    public Configuration getConf() {
        return this.conf;
    }

    /** {@inheritDoc} */
    @Override
    public void setConf(final Configuration conf) {
        this.conf = conf;
        this.robust = conf.getBoolean("boa.runtime.robust", false);
    }

    /** {@inheritDoc} */
    @Override
    protected void reduce(final EmitKey key, final Iterable<EmitValue> values, final Context context)
            throws IOException, InterruptedException {
        // if we can't combine, just pass the output through
        // TODO: find away to avoid combiner entirely when non-associative
        if (!this.aggregators.containsKey(key.getKey())) {
            for (final EmitValue value : values)
                context.write(key, value);

            return;
        }

        // get the aggregator named by the emit key
        final Aggregator a = this.aggregators.get(key.getKey());

        a.setCombining(true);
        a.start(key);
        a.setContext(context);

        for (final EmitValue value : values)
            try {
                for (final String s : value.getData())
                    a.aggregate(s, value.getMetadata());
            } catch (final FinishedException e) {
                // we are done
                return;
            } catch (final Throwable e) {
                throw new RuntimeException(e);
            }

        a.finish();
    }
}