ivory.driver.PreprocessMedline.java Source code

Introduction

Here is the source code for ivory.driver.PreprocessMedline.java

Source

/*
 * Ivory: A Hadoop toolkit for Web-scale information retrieval
 * 
 * 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 ivory.driver;

import ivory.preprocess.BuildIntDocVectors;
import ivory.preprocess.BuildIntDocVectorsForwardIndex;
import ivory.preprocess.BuildTermDocVectors;
import ivory.preprocess.BuildTermDocVectorsForwardIndex;
import ivory.preprocess.BuildTermIdMap;
import ivory.preprocess.GetTermCount;
import ivory.util.RetrievalEnvironment;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
import org.apache.log4j.Logger;

import edu.umd.cloud9.collection.medline.NumberMedlineCitations;

public class PreprocessMedline extends Configured implements Tool {
    private static final Logger sLogger = Logger.getLogger(PreprocessMedline.class);

    private static int printUsage() {
        System.out.println("usage: [input-path] [index-path] [num-of-mappers] [num-of-reducers]");
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }

    /**
     * Runs this tool.
     */
    public int run(String[] args) throws Exception {
        if (args.length != 4) {
            printUsage();
            return -1;
        }

        String collection = args[0];
        String indexPath = args[1];
        int numMappers = Integer.parseInt(args[2]);
        int numReducers = Integer.parseInt(args[3]);

        sLogger.info("Tool name: ProcessMedline");
        sLogger.info(" - Collection path: " + collection);
        sLogger.info(" - Index path: " + indexPath);

        Configuration conf = new Configuration();
        FileSystem fs = FileSystem.get(conf);

        // Create the index directory if it doesn't already exist.
        Path p = new Path(indexPath);
        if (!fs.exists(p)) {
            sLogger.info("index path doesn't exist, creating...");
            fs.mkdirs(p);
        }

        RetrievalEnvironment env = new RetrievalEnvironment(indexPath, fs);

        // Look for the docno mapping, which maps from docid (String) to docno
        // (sequentially-number integer). If it doesn't exist create it.
        Path mappingFile = env.getDocnoMappingData();
        if (!fs.exists(mappingFile)) {
            sLogger.info(mappingFile + " doesn't exist, creating...");
            String[] arr = new String[] { collection, indexPath + "/medline-docid-tmp", mappingFile.toString(),
                    new Integer(numMappers).toString() };
            NumberMedlineCitations tool = new NumberMedlineCitations();
            tool.setConf(conf);
            tool.run(arr);

            fs.delete(new Path(indexPath + "/medline-docid-tmp"), true);
        }

        // Now we're ready to start the preprocessing pipeline... set
        // appropriate properties.
        conf.setInt("Ivory.NumMapTasks", numMappers);
        conf.setInt("Ivory.NumReduceTasks", numReducers);

        conf.set("Ivory.CollectionName", "Medline");
        conf.set("Ivory.CollectionPath", collection);
        conf.set("Ivory.IndexPath", indexPath);
        conf.set("Ivory.Tokenizer", "ivory.tokenize.GalagoTokenizer");
        conf.set("Ivory.InputFormat", "edu.umd.cloud9.collection.medline.MedlineCitationInputFormat");
        conf.set("Ivory.DocnoMappingFile", indexPath + "docno.mapping");
        conf.set("Ivory.DocnoMappingClass", "edu.umd.cloud9.collection.medline.MedlineDocnoMapping");

        conf.setInt("Ivory.DocnoOffset", 0); // docnos start at 1
        conf.setInt("Ivory.MinDf", 2); // toss away singleton terms
        conf.setInt("Ivory.MaxDf", Integer.MAX_VALUE);
        conf.setInt("Ivory.TermIndexWindow", 8);

        new BuildTermDocVectors(conf).run();
        new GetTermCount(conf).run();
        new BuildTermIdMap(conf).run();
        new BuildIntDocVectors(conf).run();

        new BuildIntDocVectorsForwardIndex(conf).run();
        new BuildTermDocVectorsForwardIndex(conf).run();

        return 0;
    }

    /**
     * Dispatches command-line arguments to the tool via the
     * <code>ToolRunner</code>.
     */
    public static void main(String[] args) throws Exception {
        int res = ToolRunner.run(new Configuration(), new PreprocessMedline(), args);
        System.exit(res);
    }
}