Java tutorial
/******************************************************************************* * Copyright 2013 Gebre * * 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 nl.cwi.kba2013.apps; import java.io.BufferedReader; import java.io.DataInputStream; import java.io.FileInputStream; import java.io.IOException; import java.io.InputStreamReader; import java.net.URI; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.LinkedHashMap; import java.util.LinkedHashSet; import java.util.List; import java.util.Map; import java.util.Set; import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; import nl.cwi.json2013.topics.Filter_topics; import nl.cwi.json2013.topics.Targets; import nl.cwi.kba2013.thrift.ContentItem; import nl.cwi.kba2013.thrift.Sentence; import nl.cwi.kba2013.thrift.Token; import nl.cwi.kba2013.thrift.Tagging; import nl.cwi.kba2013.thrift.bin.StreamItemWritable; import nl.cwi.kba2013.thrift.bin.ThriftFileInputFormat; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configured; import org.apache.hadoop.filecache.DistributedCache; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.Job; import org.apache.hadoop.mapreduce.Mapper; import org.apache.hadoop.mapreduce.Reducer; import org.apache.hadoop.mapreduce.lib.input.FileInputFormat; import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat; import org.apache.hadoop.mapreduce.lib.output.LazyOutputFormat; import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; import org.apache.hadoop.mapreduce.lib.output.TextOutputFormat; import org.apache.hadoop.util.Tool; import org.apache.hadoop.util.ToolRunner; import org.apache.log4j.Logger; import org.mortbay.log.Log; /** * TThis program extracts features from either the training set or test set. * documents based on mere lexical matching. * * @author Gebremeskel * */ public class KBANER extends Configured implements Tool { public static final String QUERYFILEPATH_HDFS = "kba.topicfilelocation"; public static final String TrainTest_HDFS = "tt"; public static final String LABELSFILEPATH_HDFS = "kba.labels"; public static Map<String, HashSet<String>> DbPedia = new LinkedHashMap<String, HashSet<String>>(); public static Map<String, String> TrainTest = new LinkedHashMap<String, String>(); // public static Map<String, String> Attr ; protected enum Counter { documents, doc_with_body, body_raw, body_with_clean_html, body_with_clean_vissible }; private static final Logger LOG = Logger.getLogger(KBANER.class); public static class MyReducer extends Reducer<Text, Text, Text, Text> { //private static final Text out = new Text(); //private static final Text none = new Text(""); @Override public void reduce(Text key, Iterable<Text> values, Context context) throws IOException, InterruptedException { Integer a_p = 0, a = 0, c_p = 0, c = 0, l = 0; for (Text value : values) { String[] v_s = value.toString().split("\t"); a_p = a_p + Integer.parseInt(v_s[0]); a = a + Integer.parseInt(v_s[1]); c_p = c_p + Integer.parseInt(v_s[2]); c = c + Integer.parseInt(v_s[3]); l = l + Integer.parseInt(v_s[4]); } context.write(key, new Text(a_p.toString() + "\t" + a.toString() + "\t" + c_p.toString() + "\t" + c.toString() + "\t" + l.toString())); } } /** * Emits date, PairOfStringLong pairs, where the string contains the docno * and the topic and the long contains the score. * * */ public static class MyMapper extends Mapper<Text, StreamItemWritable, Text, Text> { public static final int scale = 1000; // private static final Text featurLine = new Text(); //private Map<String, Pattern> topicregexes = new LinkedHashMap<String, Pattern>(); //private Map<String, HashSet<String>> partialtopics = new LinkedHashMap<String, HashSet<String>>(); private Set<String> topicSet = new LinkedHashSet<String>(); private Filter_topics ft = null; /** * Used to load the queries. */ @Override public void setup(Context context) throws IOException, InterruptedException { super.setup(context); DbPedia = loadLabels(LABELSFILEPATH_HDFS); topicSet = DbPedia.keySet(); //TrainTest = loadTrainTest(TrainTest_HDFS); // //loadTopics(QUERYFILEPATH_HDFS); } /** * Loads the queries from the JSON topic file. * * @param context */ /** * Not used */ @Override protected void cleanup(Context context) throws IOException, InterruptedException { super.cleanup(context); } @Override public void map(Text key, StreamItemWritable value, Context context) throws IOException, InterruptedException { context.getCounter(Counter.documents).increment(1); //Log.info("watch streamid "+key.toString().split("/")[7]); if (value.getBody() != null) { // if (value.getBody().getRaw()!=null){ // //if (value.getBody().getClean_visible() != null){ // String body = new String () ; // if (value.getBody().getRaw().length != 0){ // // //byte [] encoded =Base64.encodeBase64(value.getBody().getRaw()); // body = new String(value.getBody().getRaw(), "UTF-8"); // //Log.info("raw body:" +body); // // } //if (value.getBody().getRaw()!=null){ if (value.getBody().getClean_visible() != null) { String body = new String(); // ContentItem b = value.getBody(); // byte[] r = b.getRaw(); // String encoding; // if (b.getEncoding()!=null){ // encoding=b.getEncoding(); // } // else{ // encoding="UTF-8"; // } // if (r.length != 0){ // // //byte [] encoded =Base64.encodeBase64(value.getBody().getRaw()); // body = new String(r, encoding); // //Log.info("raw body:" +body); // // } if ((value.getBody().getClean_visible() != null)) { body = value.getBody().getClean_visible().toString(); //Log.info("clean_visible value "+ value.getBody().getClean_visible().toString()); } // System.out.print("Body Body :" + body); // Get title and anchor String title = null; String anchor = null; Map<String, ContentItem> c = null; if (value.getOther_content() != null) { c = value.getOther_content(); if (value.getOther_content().get("title") != null) { if (value.getOther_content().get("title").getClean_visible() != null) { title = new String(value.getOther_content().get("title").getClean_visible()); } else if (value.getOther_content().get("title").getClean_html() != null) { title = new String(value.getOther_content().get("title").getClean_html()); } else if (value.getOther_content().get("title").getRaw() != null) { title = new String(value.getOther_content().get("title").getRaw()); } else title = ""; } if (value.getOther_content().get("anchor") != null) { if (value.getOther_content().get("anchor").getClean_visible() != null) { anchor = new String(value.getOther_content().get("anchor").getClean_visible()); } else if (value.getOther_content().get("anchor").getClean_html() != null) { anchor = new String(value.getOther_content().get("anchor").getClean_html()); } else if (value.getOther_content().get("anchor").getRaw() != null) { anchor = new String(value.getOther_content().get("anchor").getRaw()); } else { anchor = ""; } } } if (title == null) title = ""; if (anchor == null) anchor = ""; // lowercase all body = body.toLowerCase(); title = title.toLowerCase(); anchor = anchor.toLowerCase(); String url = new String(); String source = new String(); if (value.getSource() != null) { source = value.getSource(); } String streamid = value.getStream_id(); String title_body_anchor = body + " " + title + " " + anchor; title_body_anchor = title_body_anchor.replaceAll("\\s+", " "); Log.info("title_body_anchor" + title_body_anchor); for (String topic : topicSet) { HashSet<String> canonical = new HashSet<String>(); if (!topic.startsWith("https://twitter.com/")) { Log.info("The topic at hand" + topic); //canonical.add(topic.split("/")[4].replace("_", " ")); canonical.add(topic.split("/")[4].replaceAll("_", " ").replace("(", "").replace(")", "") .replaceAll("\\s+", " ").toLowerCase()); //Log.info("hmmmmm" +canonical); } else { canonical.add(topic.split("/")[3].replaceAll("\\s+", " ").toLowerCase()); } HashSet<String> canonical_partial = new HashSet<String>(); if (!topic.startsWith("https://twitter.com/")) { canonical_partial .addAll(Arrays.asList(topic.split("/")[4].replaceAll("_", " ").replace("(", "") .replace(")", "").replaceAll("\\s+", " ").toLowerCase().split(" "))); //canonical_partial.addAll(listremove(Arrays.asList(topic.split("/")[4].replaceAll("_", " ").replace("(", "").replace(")", "").replaceAll("\\s+"," ").toLowerCase().split(" ")))); } else { canonical_partial.addAll(Arrays .asList(topic.split("/")[3].replaceAll("\\s+", " ").toLowerCase().split(" "))); //canonical_partial.addAll(listremove(Arrays.asList(topic.split("/")[3].replaceAll("\\s+"," ").toLowerCase().split(" ")))); } HashSet<String> label_name_redirect_canonical_partial = new HashSet<String>(); try { for (String all_str : DbPedia.get(topic)) { label_name_redirect_canonical_partial .addAll(Arrays.asList(all_str.replaceAll(",", " ").split(" "))); //label_name_redirect_canonical_partial.addAll(listremove(Arrays.asList(all_str.replaceAll(",", " ").split(" ")))); } } catch (NullPointerException e) { //Log.info("what what " +topic+ "\t" ); } HashSet<String> label_name_redirect_canonical = new HashSet<String>(); label_name_redirect_canonical = DbPedia.get(topic); //if (containsMention(title_body_anchor, // label_name_redirect_canonical_partial) == 1) { Integer all_part = 1; Integer all = 0; Integer cano_part = 0; Integer cano = 0; Integer labelMentionCount = 0; if (containsMention(title_body_anchor, label_name_redirect_canonical) == 1) { all = 1; } if (containsMention(title_body_anchor, canonical_partial) == 1) { cano_part = 1; } if (containsMention(title_body_anchor, canonical) == 1) { cano = 1; } labelMentionCount = frequencyCounter(title_body_anchor, label_name_redirect_canonical); for (String doc : c.keySet()) { Map<String, List<Sentence>> mmm = c.get(doc).getSentences(); for (String tag : mmm.keySet()) { Iterator it = mmm.get(tag).iterator(); while (it.hasNext()) { Sentence sen = (Sentence) it.next(); Iterator tokens = sen.getTokens().iterator(); while (tokens.hasNext()) { Token tok = (Token) tokens.next(); context.write(new Text(tok.getToken()), new Text(new String(tok.getEntity_type() + "\t" + tok.getPos()))); } } } } //if(TrainTest.containsKey(streamid) && TrainTest.get(streamid).equalsIgnoreCase(key.toString())){ //context.write(new Text( topic), new Text( all_part.toString()+"\t"+ all.toString()+"\t"+ cano_part.toString()+"\t"+ cano.toString()+"\t" +labelMentionCount.toString())); //} //} } } } } public int containsMention(String str, HashSet<String> hs) { int i = 0; for (String entity : hs) { if (str.contains(entity)) { i = 1; } } return i; } public List<String> listremove(List<String> ls) { Iterator<String> i = ls.iterator(); //List <List> lst2 =new ArrayList <String>(); List<String> list = new ArrayList<String>(); while (i.hasNext()) { String s = i.next(); // must be called before you can call i.remove() s = s.replace("(", "").replace(")", ""); if (s.length() > 2) { list.add(s); } } return list; } private Map<String, HashSet<String>> loadLabels(String xcontext) { Map<String, HashSet<String>> prep = new LinkedHashMap<String, HashSet<String>>(); Hashtable<String, HashSet<String>> tmp = new Hashtable<String, HashSet<String>>(); DataInputStream in = null; try { in = new DataInputStream(new FileInputStream(xcontext)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; // Read File Line By Line while ((strLine = br.readLine()) != null) { // Print the content on the console String temp_key; String temp_value; String[] str = new String(strLine.getBytes("UTF-8"), "UTF-8").split("\t"); temp_key = str[0]; temp_value = str[1]; HashSet<String> keys = (HashSet<String>) tmp.get(temp_key); if (keys == null) { keys = new HashSet<String>(); tmp.put(temp_key, keys); } keys.add(temp_value.toLowerCase()); } br.close(); for (Object entity : tmp.keySet()) { prep.put((String) entity, tmp.get(entity)); } } catch (IOException e) { e.printStackTrace(); LOG.error(""); } catch (Exception e) { e.printStackTrace(); LOG.error("" + e); } finally { if (in != null) { try { in.close(); } catch (IOException e1) { e1.printStackTrace(); } } } return prep; } private Map<String, String> loadTrainTest(String xcontext) { // Hashtable<String, Hashtable> prep = new Hashtable(); Map<String, String> prep = new LinkedHashMap<String, String>(); DataInputStream in = null; try { in = new DataInputStream(new FileInputStream(xcontext)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; // Read File Line By Line while ((strLine = br.readLine()) != null) { String temp_key; String[] str = new String(strLine.getBytes("UTF-8"), "UTF-8").split("\t"); temp_key = str[0]; prep.put(temp_key, str[1]); } br.close(); } catch (IOException e) { e.printStackTrace(); LOG.error("read from distributed cache: read instances"); } catch (Exception e) { e.printStackTrace(); LOG.error("read from distributed cache: " + e); } finally { if (in != null) { try { in.close(); } catch (IOException e1) { e1.printStackTrace(); } } } return prep; } public int frequencyCounter(String str, HashSet<String> hs) { Integer counter = 0; for (String entity : hs) { try { Pattern pattern = Pattern.compile(entity); Matcher matcher = pattern.matcher(str); while (matcher.find()) counter++; } catch (PatternSyntaxException e) { //Log.info("what what what "+ entity); } } return counter; } } public static void main(String[] args) throws Exception { int res = ToolRunner.run(new Configuration(), new KBANER(), args); System.exit(res); } static int printUsage() { System.out.println("Usage: " + KBANER.class.getName() + "-i input \n" + "-o output \n " + "-l labels file\n " + "Example usage: hadoop jar cwi-trec/TRECKBA/TRECKBA2013-in_2014.jar nl.cwi.kba2013.apps.KbaNameVariantMatch " + KBANER.class.getName() + " " + "-i KBA/Data/kba2013/kba2013-seq-cleansed-anno/*/* " + "-o KBA/OutPut/kba2013-seq-cleansed-raw-with-short-count " + "-l KBA/Data/kba2013/all-combined-wiki-and-twitte-and-cano.txt"); ToolRunner.printGenericCommandUsage(System.out); return -1; } @Override public int run(String[] args) throws Exception { String in = null; String out = null; String labelsFile = null; List<String> other_args = new ArrayList<String>(); for (int i = 0; i < args.length; ++i) { try { if ("-i".equals(args[i])) { in = args[++i]; } else if ("-o".equals(args[i])) { out = args[++i]; } else if ("-l".equals(args[i])) { labelsFile = args[++i]; } else if ("-h".equals(args[i]) || "--help".equals(args[i])) { return printUsage(); } else { other_args.add(args[i]); } } catch (ArrayIndexOutOfBoundsException except) { System.out.println("ERROR: Required parameter missing from " + args[i - 1]); return printUsage(); } } if (other_args.size() > 0 || in == null || out == null || labelsFile == null) return printUsage(); LOG.info("Tool: " + this.getClass().getName()); LOG.info(" - input path: " + in); LOG.info(" - output path: " + out); Configuration conf = getConf(); conf.set(LABELSFILEPATH_HDFS, new Path(labelsFile).toUri().toString()); // set time conf.setLong("mapred.task.timeout", 40 * 600000); conf.set("mapred.map.child.java.opts", "-Xmx4g -XX:-UseGCOverheadLimit"); conf.set("mapred.child.java.opts", "-Xmx4096m"); Job job = new Job(conf, "Feature Extractor"); job.setJarByClass(KBANER.class); // some weird issues with Thrift classes in the Hadoop distro. job.setUserClassesTakesPrecedence(true); // make the query file available to each mapper. DistributedCache.addCacheFile(new URI(new Path(labelsFile) + "#" + LABELSFILEPATH_HDFS), job.getConfiguration()); DistributedCache.createSymlink(job.getConfiguration()); job.setInputFormatClass(ThriftFileInputFormat.class); //job.setInputFormatClass(SequenceFileInputFormat.class); job.setMapperClass(MyMapper.class); job.setCombinerClass(MyReducer.class); job.setReducerClass(MyReducer.class); FileInputFormat.addInputPath(job, new Path(in)); job.setNumReduceTasks(0); FileSystem.get(conf).delete(new Path(out), true); TextOutputFormat.setOutputPath(job, new Path(out)); //job.setOutputFormatClass(SequenceFileOutputFormat.class); job.setOutputKeyClass(Text.class); //job.setOutputValueClass(StreamItemWritable.class); job.setOutputValueClass(Text.class); //LazyOutputFormat.setOutputFormatClass(job, SequenceFileOutputFormat.class); LazyOutputFormat.setOutputFormatClass(job, TextOutputFormat.class); int status = job.waitForCompletion(true) ? 0 : 1; return status; } }