ivory.core.driver.PreprocessMedline.java Source code

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

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/*
 * 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.core.driver;

import ivory.core.Constants;
import ivory.core.RetrievalEnvironment;
import ivory.core.preprocess.BuildDictionary;
import ivory.core.preprocess.BuildIntDocVectors;
import ivory.core.preprocess.BuildIntDocVectorsForwardIndex;
import ivory.core.preprocess.BuildTermDocVectors;
import ivory.core.preprocess.BuildTermDocVectorsForwardIndex;
import ivory.core.preprocess.ComputeGlobalTermStatistics;
import ivory.core.tokenize.GalagoTokenizer;

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.MedlineCitationInputFormat2;
import edu.umd.cloud9.collection.medline.MedlineDocnoMapping;
import edu.umd.cloud9.collection.medline.NumberMedlineCitations2;

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

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

    /**
     * Runs this tool.
     */
    public int run(String[] args) throws Exception {
        if (args.length != 2) {
            printUsage();
            return -1;
        }

        String collection = args[0];
        String indexPath = args[1];

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

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

        // Create the index directory if it doesn't already exist.
        Path p = new Path(indexPath);
        if (!fs.exists(p)) {
            LOG.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();
        Path mappingDir = env.getDocnoMappingDirectory();

        if (!fs.exists(mappingFile)) {
            LOG.info(mappingFile + " doesn't exist, creating...");
            String[] arr = new String[] { collection, mappingDir.toString(), mappingFile.toString() };
            NumberMedlineCitations2 tool = new NumberMedlineCitations2();
            tool.setConf(conf);
            tool.run(arr);

            fs.delete(mappingDir, true);
        }

        conf.set(Constants.CollectionName, "Medline");
        conf.set(Constants.CollectionPath, collection);
        conf.set(Constants.IndexPath, indexPath);
        conf.set(Constants.InputFormat, MedlineCitationInputFormat2.class.getCanonicalName());
        conf.set(Constants.Tokenizer, GalagoTokenizer.class.getCanonicalName());
        conf.set(Constants.DocnoMappingClass, MedlineDocnoMapping.class.getCanonicalName());
        conf.set(Constants.DocnoMappingFile, env.getDocnoMappingData().toString());

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

        new BuildTermDocVectors(conf).run();
        new ComputeGlobalTermStatistics(conf).run();
        new BuildDictionary(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}.
     */
    public static void main(String[] args) throws Exception {
        ToolRunner.run(new Configuration(), new PreprocessMedline(), args);
    }
}