ExtractIsATool.java

package com.ontology2.bakemono.entityCentric;

import com.google.common.base.Joiner;
import com.google.common.collect.Lists;
import com.ontology2.bakemono.configuration.HadoopTool;
import com.ontology2.bakemono.mapred.ToolBase;
import com.ontology2.centipede.errors.UsageException;
import com.ontology2.centipede.parser.OptionParser;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.NullWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.mapreduce.lib.output.TextOutputFormat;

import java.util.List;

@HadoopTool("extractIsA")
public class ExtractIsATool extends ToolBase {

    @Override
    public int run(String[] strings) throws Exception {
        ExtractIsAOptions options = extractOptions(Lists.newArrayList(strings));
        configureOutputCompression();

        List<String> nodes=Lists.newArrayList();
        for(String link:options.type)
            nodes.add("<"+link+">");
        getConf().set(EntityIsAReducer.TYPE_LIST, Joiner.on(",").join(nodes));

        Job job=new Job(getConf(),"extractIsA");
        job.setJarByClass(this.getClass());
        job.setMapperClass(EntityCentricMapper.class);
        job.setReducerClass(EntityIsAReducer.class);

        job.setNumReduceTasks(options.reducerCount);
        job.setMapOutputKeyClass(Text.class);
        job.setMapOutputValueClass(Text.class);
        job.setOutputKeyClass(NullWritable.class);
        job.setOutputValueClass(Text.class);

        for(String path: options.input) {
            FileInputFormat.addInputPath(job, new Path(path));
        }

        FileOutputFormat.setOutputPath(job, new Path(options.output));
        FileOutputFormat.setCompressOutput(job,true);
        FileOutputFormat.setOutputCompressorClass(job,GzipCodec.class);
        job.setOutputFormatClass(TextOutputFormat.class);

        return job.waitForCompletion(true) ? 0 : 1;
    }

    ExtractIsAOptions extractOptions(List<String> strings) throws IllegalAccessException {
        OptionParser parser=new OptionParser(ExtractIsAOptions.class);
        applicationContext.getAutowireCapableBeanFactory().autowireBean(parser);

        ExtractIsAOptions options=(ExtractIsAOptions) parser.parse(Lists.newArrayList(strings));
        if (options.input.isEmpty())
            throw new UsageException("You did not specify a value for -input");

        if (options.output==null || options.output.isEmpty())
            throw new UsageException("You did not specify a value for -output");

        if (options.type.isEmpty())
            throw new UsageException("You did not specify a value for -type");

        if(options.reducerCount<1) {
            options.reducerCount=1;
        }
        return options;
    }
}