/*
* Cloud9: A MapReduce Library for Hadoop
*
* 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 edu.umd.cloud9.collection.medline;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.util.LineReader;
import org.apache.log4j.Logger;
import com.google.common.base.Preconditions;
import com.google.common.collect.Lists;
import edu.umd.cloud9.collection.DocnoMapping;
/**
* Object that maps between MEDLINE docids (PMIDs) to docnos (sequentially-numbered ints).
* The {@code main} of this class provides a simple program for accessing docno mappings.
* Command-line arguments are as follows:
*
* <ul>
* <li>list, getDocno, getDocid: the command—list all mappings; get docno from docid; or, get
* docid from docno</li>
* <li>[mappings-file]: the mappings file</li>
* <li>[docid/docno]: the docid or docno (optional)</li>
* </ul>
*
* @author Jimmy Lin
*/
public class MedlineDocnoMapping implements DocnoMapping {
private static final Logger LOG = Logger.getLogger(MedlineDocnoMapping.class);
private int[] pmids;
/**
* Creates a <code>MedlineDocnoMapping</code> object
*/
public MedlineDocnoMapping() {
}
public int getDocno(String docid) {
// docnos are numbered starting from one
return Arrays.binarySearch(pmids, Integer.parseInt(docid));
}
public String getDocid(int docno) {
// docnos are numbered starting from one
return new Integer(pmids[docno]).toString();
}
public void loadMapping(Path p, FileSystem fs) throws IOException {
pmids = MedlineDocnoMapping.readDocidData(p, fs);
}
/**
* Creates a mappings file from the contents of a flat text file containing docid to docno
* mappings. This method is used by {@link MedlineDocnoMappingBuilder} internally.
*
* @param input flat text file containing docid to docno mappings
* @param output output mappings file
* @param fs reference to the file system
* @throws IOException
*/
static public void writeMappingData(Path input, Path output, FileSystem fs)
throws IOException {
Preconditions.checkNotNull(input);
Preconditions.checkNotNull(output);
Preconditions.checkNotNull(fs);
LOG.info("Writing docids to " + output);
LineReader reader = new LineReader(fs.open(input));
List<Integer> list = Lists.newArrayList();
LOG.info("Reading " + input);
int cnt = 0;
Text line = new Text();
while (reader.readLine(line) > 0) {
String[] arr = line.toString().split("\\t");
list.add(Integer.parseInt(arr[0]));
cnt++;
if (cnt % 500000 == 0) {
LOG.info(cnt);
}
}
reader.close();
LOG.info("Done! Total of " + cnt + " docids read.");
cnt = 0;
LOG.info("Writing " + output);
FSDataOutputStream out = fs.create(output, true);
out.writeInt(list.size());
for (int i = 0; i < list.size(); i++) {
out.writeInt(list.get(i));
cnt++;
if (cnt % 500000 == 0) {
LOG.info(cnt);
}
}
out.close();
LOG.info("Done! Total of " + cnt + " docids written.");
}
/**
* Reads a mappings file into memory.
*
* @param p path to the mappings file
* @param fs appropriate FileSystem
* @return an array of docids; the index position of each docid is its docno
* @throws IOException
*/
static public int[] readDocidData(Path p, FileSystem fs) throws IOException {
LOG.info("Reading docid mapping...");
FSDataInputStream in = fs.open(p);
// docnos start at one, so we need an array that's one larger than
// number of docs
int sz = in.readInt() + 1;
int[] arr = new int[sz];
int cnt = 0;
for (int i = 1; i < sz; i++) {
arr[i] = in.readInt();
if (i % 500000 == 0) {
LOG.info(i);
}
cnt++;
}
in.close();
LOG.info(cnt + " docid mappings read");
return arr;
}
@Override
public Builder getBuilder() {
return new MedlineDocnoMappingBuilder();
}
/**
* Simple program the provides access to the docno/docid mappings.
*
* @param args command-line arguments
* @throws IOException
*/
public static void main(String[] args) throws IOException {
if (args.length < 2) {
System.out.println("usage: (list|getDocno|getDocid) [mapping-file] [docid/docno]");
System.exit(-1);
}
Configuration conf = new Configuration();
FileSystem fs = FileSystem.get(conf);
System.out.println("loading mapping file " + args[1]);
MedlineDocnoMapping mapping = new MedlineDocnoMapping();
mapping.loadMapping(new Path(args[1]), fs);
if (args[0].equals("list")) {
for (int i = 1; i < mapping.pmids.length; i++) {
System.out.println(i + "\t" + mapping.pmids[i]);
}
} else if (args[0].equals("getDocno")) {
System.out.println("looking up docno for \"" + args[2] + "\"");
int idx = mapping.getDocno(args[2]);
if (idx > 0) {
System.out.println(mapping.getDocno(args[2]));
} else {
System.err.print("Invalid docid!");
}
} else if (args[0].equals("getDocid")) {
try {
System.out.println("looking up docid for " + args[2]);
System.out.println(mapping.getDocid(Integer.parseInt(args[2])));
} catch (Exception e) {
System.err.print("Invalid docno!");
}
} else {
System.out.println("Invalid command!");
System.out.println("usage: (list|getDocno|getDocid) [mappings-file] [docid/docno]");
}
}
}