/*
* 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.app;
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.MedlineCitationInputFormat;
import edu.umd.cloud9.collection.medline.MedlineDocnoMapping;
import edu.umd.cloud9.collection.medline.MedlineDocnoMappingBuilder;
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);
} else {
LOG.info("Index directory " + p + " already exists!");
return -1;
}
RetrievalEnvironment env = new RetrievalEnvironment(indexPath, fs);
Path mappingFile = env.getDocnoMappingData();
new MedlineDocnoMappingBuilder().build(new Path(collection), mappingFile, conf);
conf.set(Constants.CollectionName, "Medline");
conf.set(Constants.CollectionPath, collection);
conf.set(Constants.IndexPath, indexPath);
conf.set(Constants.InputFormat, MedlineCitationInputFormat.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);
}
}