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.Collection; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.LinkedHashMap; import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Set; import java.util.StringTokenizer; import java.util.regex.Matcher; import java.util.regex.Pattern; import nl.cwi.helpers.NGramExtractor; //import nl.cwi.json2012.run.Filter_run; import nl.cwi.json2013.run.Run_info; import nl.cwi.json2013.topics.Filter_topics; import nl.cwi.json2013.topics.Targets; import nl.cwi.kba2013.thrift.Target; 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.FSDataInputStream; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.Counters; 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.output.TextOutputFormat; import org.apache.hadoop.thirdparty.guava.common.collect.Sets; import org.apache.hadoop.util.LineReader; 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 FeatureExtractor extends Configured implements Tool { public static final String QUERYFILEPATH_HDFS = "kba.topicfilelocation"; public static final String WIKI_HDFS = "wiki"; public static final String CONTEXT_HDFS = "context"; public static final String LABELSFILEPATH_HDFS = "kba.labels"; public static final String ANNOFILEPATH_HDFS = "kba.anno"; public static final String PPR_HDFS = "ppr"; public static final String MYVER = "myver"; public static final String GCLD_HDFS = "gcld"; public static Path anno_file; public static Map<String, String> all_attr = new LinkedHashMap<String, String>(); public static Map<String, HashSet<String>> DbPedia = new LinkedHashMap<String, HashSet<String>>(); public static Map<String, Integer> Annotation = new LinkedHashMap<String, Integer>(); public static Map<String, HashMap<String, Double>> Ppr = new LinkedHashMap<String, HashMap<String, Double>>(); public static Map<String, HashMap<String, Double>> Gcld = new LinkedHashMap<String, HashMap<String, Double>>(); public static Map<String, String> MyVer = new HashMap<String, String>(); public static Map<String, String> ContextL = new LinkedHashMap<String, String>(); public static Map<String, String> ContextR = new LinkedHashMap<String, String>(); public static Map<String, HashMap<String, Integer>> ContextFreqsL = new LinkedHashMap<String, HashMap<String, Integer>>(); public static Map<String, HashMap<String, Integer>> ContextFreqsR = new LinkedHashMap<String, HashMap<String, Integer>>(); public static Map<String, String> WikiContent = new LinkedHashMap<String, String>(); // public static Map<String, String> Attr ; public static final String RUNTAG = "kba.runtag"; public static final String TEAMNAME = "kba.teamname"; protected enum Counter { documents, doc_with_body, body_raw, body_with_clean_html, body_with_clean_vissible }; private static final Logger LOG = Logger.getLogger(FeatureExtractor.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(""); private String runtag; private String teamname; @Override public void reduce(Text date, Iterable<Text> values, Context context) throws IOException, InterruptedException { context.write(out, none); } } /** * Emits date, PairOfStringLong pairs, where the string contains the docno * and the topic and the long contains the score. * * @author emeij * */ public static class MyMapper extends Mapper<Text, StreamItemWritable, Text, Text> { private static final Text stream_doc_id = new 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 Filter_topics ft = null; /** * Used to load the queries. */ @Override public void setup(Context context) throws IOException, InterruptedException { super.setup(context); // String ppr_f = new // Path(context.getConfiguration().get(PPR_HDFS)).toString(); anno_file = new Path(context.getConfiguration().get(ANNOFILEPATH_HDFS)); DbPedia = loadLabels(LABELSFILEPATH_HDFS); // for (String kk : DbPedia.keySet()) { // System.out.println(kk + "\t" + DbPedia.get(kk)); // } // System.out.println("The size of DbPedia" + DbPedia.size()); //Annotation = loadAnnotation(ANNOFILEPATH_HDFS); // MyVer = loadMyVer(MYVER); Ppr = loadPPR(PPR_HDFS); Gcld = loadGCLD(GCLD_HDFS); WikiContent = loadWiki(WIKI_HDFS); //System.out.println("Wiki Content:" + WikiContent.size()); loadContext(CONTEXT_HDFS); extractNgrmFrequency(); /* * System.out.println("What are the strings:\n"); for(String k: * DbPedia.keySet()) System.out.println(k + "\t"+ * DbPedia.get(k).size() ); */ //System.out.println("Annotations size :" // + Annotation.keySet().size()); //System.out.println("DbPEdia Keys :" + DbPedia.keySet().size()); 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); all_attr.put("gcld", "0"); all_attr.put("jac", "0"); all_attr.put("cos", "0"); all_attr.put("kl", "0"); all_attr.put("ppr", "0"); all_attr.put("s_form", "0"); all_attr.put("contxR", "0"); all_attr.put("contxL", "0"); all_attr.put("FirstPos", "0"); all_attr.put("LastPos", "0"); all_attr.put("LengthBody", "0"); all_attr.put("FirstPosNorm", "0"); all_attr.put("MentionsBody", "0"); all_attr.put("RelatedBody", "0"); all_attr.put("Spread", "0"); all_attr.put("LastPosNorm", "0"); all_attr.put("SpreadNorm", "0"); all_attr.put("LengthAnchor", "0"); all_attr.put("Source", "0"); all_attr.put("LengthTitle", "0"); all_attr.put("partial", "0"); all_attr.put("MentionsAnchor", "0"); all_attr.put("Relatedtitle", "0"); all_attr.put("English", "0"); all_attr.put("RelatedAnchor", "0"); all_attr.put("MentionsTitle", "0"); all_attr.put("Class", "0"); Integer raw_length = 0; Integer clean_html_length = 0; Integer clean_vissible_length = 0; if (value.getBody() != null) { if (value.getBody().getClean_visible() != null) { if (value.getBody().getRaw() != null) raw_length = value.getBody().getRaw().length; if (value.getBody().getClean_html() != null) clean_html_length = value.getBody().getClean_html().length(); if (value.getBody().getClean_visible() != null) clean_vissible_length = value.getBody().getClean_visible().length(); String body = new String(value.getBody().getClean_visible()); //System.out.print("Body Body :" + body); //Get title and anchor String title = null; String anchor = null; if (value.getOther_content() != null) { 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 streamid = value.getStream_id(); all_attr.put("English", "0"); Integer lengthTitle = new StringTokenizer(title).countTokens(); Integer lengthBody = new StringTokenizer(body).countTokens(); Integer lengthAnchor = new StringTokenizer(anchor).countTokens(); all_attr.put("LengthTitle", lengthTitle.toString()); all_attr.put("LengthBody", lengthBody.toString()); all_attr.put("LengthAnchor", lengthAnchor.toString()); String sourcevalue = new String(value.getSource()); Integer source = 0; if (sourcevalue == "news") { source = 0; } else if (sourcevalue == "social") { source = 1; } else if (sourcevalue == "linking") { source = 2; } all_attr.put("Source", source.toString()); all_attr.put("RelatedBody", entityMentionCounter(body)); all_attr.put("Relatedtitle", entityMentionCounter(title)); all_attr.put("RelatedAnchor", entityMentionCounter(anchor)); String title_body_anchor = body + " " + title + " " + anchor; for (String topic : topicregexes.keySet()) { // int relde=0; // long count = 0; String topic_head = ""; if (topic.startsWith("https://twitter.com/")) { topic_head = topic.split("/")[3]; } else { topic_head = topic.split("/")[4]; } String stream_id_doc_id = streamid + "\t" + topic; stream_doc_id.set(streamid + "_" + topic); int anno_value = 0; // if (Annotation.containsKey(stream_doc_id.toString())) { /* * if (Annotation.get(stream_doc_id.toString()).intValue() * == 2) { anno_value = 1; // relevant * * } else if (Annotation.get(stream_doc_id.toString()) * .intValue() == 1) { anno_value = -3; * * } */ /* * all_attr.put( "Class", new Integer(Annotation.get( * stream_doc_id.toString()).intValue()) .toString()); */ if (containsMention(title_body_anchor, DbPedia.get(topic)) == 1) { // if (containsMention(body+title+anchor, new // HashSet<String> (Arrays.asList(topic.replaceAll("_", // " ")))) == 1) { double temp = 0.0; for (String partial : partialtopics.get(topic)) { if (containsMention(title_body_anchor, new HashSet<String>(Arrays.asList(partial))) == 1) { temp = temp + (double) partial.length() / topic_head.length(); } } temp = temp * scale; all_attr.put("partial", new Double(temp).toString()); temp = 0.0; //Log.info("What is failing here: topic +topic head:" + topic //+ topic_head); for (String s_form : DbPedia.get(topic)) { if (containsMention(title_body_anchor, new HashSet<String>(Arrays.asList(s_form))) == 1) { temp = temp + (double) s_form.length() / topic_head.length(); } } temp = temp * scale; all_attr.put("s_form", new Double(temp).toString()); temp = 0.0; if (!topic.startsWith("https://twitter.com/")) { //Log.info("See from gcld:" + topic); if (Gcld.get(topic_head) != null) { for (String gcld_key : Gcld.get(topic_head).keySet()) { if (containsMention(title_body_anchor, new HashSet<String>(Arrays.asList(gcld_key))) == 1) { temp = temp + Gcld.get(topic_head).get(gcld_key); } } } temp = temp * scale; all_attr.put("gcld", new Double(temp).toString()); temp = 0.0; if (Ppr.get(topic_head) != null) { for (String ppr_key : Ppr.get(topic_head).keySet()) { if (containsMention(title_body_anchor, new HashSet<String>(Arrays.asList(ppr_key))) == 1) { temp = temp + Ppr.get(topic_head).get(ppr_key); } } } temp = temp * scale; all_attr.put("ppr", new Double(temp).toString()); temp = 0.0; if (ContextFreqsL.containsKey(topic_head)) { for (String contxL_key : ContextFreqsL.get(topic_head).keySet()) { if (containsMention(title_body_anchor, new HashSet<String>(Arrays.asList(contxL_key))) == 1) { temp = temp + ContextFreqsL.get(topic_head).get(contxL_key); } } temp = temp * scale; all_attr.put("contxL", new Double(temp).toString()); temp = 0.0; } if (ContextFreqsR.containsKey(topic_head)) { for (String contxR_key : ContextFreqsR.get(topic_head).keySet()) { if (containsMention(title_body_anchor, new HashSet<String>(Arrays.asList(contxR_key))) == 1) { temp = temp + ContextFreqsR.get(topic_head).get(contxR_key); } } temp = temp * scale; all_attr.put("contxR", new Double(temp).toString()); temp = 0.0; } /**************************** * Add some similarity metrics * */ HashMap<String, Integer> doc_map = new HashMap<String, Integer>(); HashMap<String, Integer> wiki_map = new HashMap<String, Integer>(); doc_map = ReturnFreqs(title_body_anchor); wiki_map = ReturnFreqs(WikiContent.get(topic_head)); // Add cosine similarity temp = cosine_similarity(wiki_map, doc_map); all_attr.put("cos", new Double(temp).toString()); temp = 0.0; // Add kl -diveregence temp = klDivergence(wiki_map, doc_map); all_attr.put("kl", new Double(temp).toString()); temp = 0.0; // Add Jaccard temp = jaccardSimilarity(wiki_map.keySet(), doc_map.keySet()); all_attr.put("jac", new Double(temp).toString()); temp = 0.0; } Integer firstPos = returnFirstIndex(body, DbPedia.get(topic)); Integer lastPos = returnLastIndex(body, DbPedia.get(topic)); Integer spread = lastPos - firstPos; Integer firstPosNorm = firstPos.intValue() / (lengthBody.intValue() + 1); Integer lastPosNorm = lastPos.intValue() / (lengthBody.intValue() + 1); Integer spreadNorm = spread / (lengthBody.intValue() + 1); all_attr.put("FirstPos", firstPos.toString()); all_attr.put("LastPos", lastPos.toString()); all_attr.put("Spread", spread.toString()); all_attr.put("FirstPosNorm", firstPosNorm.toString()); all_attr.put("LastPosNorm", lastPosNorm.toString()); all_attr.put("SpreadNorm", spreadNorm.toString()); all_attr.put("MentionsTitle", frequencyCounter(title, DbPedia.get(topic))); all_attr.put("MentionsBody", frequencyCounter(body, DbPedia.get(topic))); all_attr.put("MentionsAnchor", frequencyCounter(anchor, DbPedia.get(topic))); if (anno_file.toString() .contains("trec-kba-ccr-2012-judgments-2012JUN22-final.filter-run.txt")) { // all_attr.put("Class", "?"); //System.out.println("Is it working ? "); // anno_value = 0; } String all_values = ""; for (String key1 : all_attr.keySet()) { if (all_values.equalsIgnoreCase("")) { all_values = all_attr.get(key1); } else { all_values = all_values + "," + all_attr.get(key1); } } //String[] key_split = key.toString().split("/"); String columns = "CWI" + "\t" + "two-step" + "\t" + streamid + "\t" + topic + "\t" + "1000" + "\t" + "2" + "\t" + "1" + "\t" + key.toString().replace(".gz", ".xz.gpg|(") .replace("hdfs://p-head03.alley.sara.nl/data/private/trec_kba/", "") + raw_length + "," + clean_html_length + "," + clean_vissible_length + ")" + "\t" + "NULL" + "\t" + "-1" + "\t" + "0-0" + "\t"; // if (anno_value != -3) { context.write(new Text(columns), new Text(all_values)); // } } } } } } public int containsMention(String str, HashSet<String> hs) { int i = 0; for (String entity : hs) { if (str.contains(entity)) { i = 1; } } return i; } public int returnFirstIndex(String str, HashSet<String> hs) { int f_index = 0; for (String entity : hs) { if (str.indexOf(entity) > f_index) { f_index = str.indexOf(entity); } } return f_index; } public int returnLastIndex(String str, HashSet<String> hs) { int l_index = 0; for (String entity : hs) { if (str.lastIndexOf(entity) > l_index) { l_index = str.lastIndexOf(entity); } } return l_index; } public String frequencyCounter(String str, HashSet<String> hs) { Integer counter = 0; for (String entity : hs) { Pattern pattern = Pattern.compile(entity); Matcher matcher = pattern.matcher(str); while (matcher.find()) counter++; } return counter.toString(); } public String entityMentionCounter(String str) { Integer rel = 0; for (String topic : topicregexes.keySet()) { if (containsMention(str, DbPedia.get(topic)) == 1) { //Log.info("Null pointer" + str + " " + DbPedia.get(topic)); rel++; } } return rel.toString(); } private void loadTopics(String xcontext) { DataInputStream in = null; try { in = new DataInputStream(new FileInputStream(xcontext)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); ft = new Filter_topics.Factory().loadTopics(br); LOG.info(ft.getTopic_set_id()); Targets[] t = ft.getTargets(); Iterator it = Arrays.asList(t).iterator(); // for (Target t : Arrays.asList(t))) { while (it.hasNext()) { Targets targ = (Targets) it.next(); Pattern p; // add the full name p = Pattern.compile(".*\\b+" + targ.target_id.replaceAll("_", " ") + "\\b+.*", Pattern.CASE_INSENSITIVE); topicregexes.put(targ.target_id, p); // add the individual terms HashSet<String> pset = new HashSet<String>(); pset.addAll(new HashSet<String>(Arrays.asList(targ.target_id.split("_")))); pset.add(targ.target_id.replaceAll("_", " ")); partialtopics.put(targ.target_id, pset); } } 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(); } } } } private Map<String, HashSet<String>> loadLabels(String xcontext) { // Hashtable<String, Hashtable> prep = new Hashtable(); Map<String, HashSet<String>> prep = new LinkedHashMap<String, HashSet<String>>(); Hashtable<String, HashSet<String>> tmp = new Hashtable<String, HashSet<String>>(); DataInputStream in = null; // System.out.println("This is from LoadLabels"); //System.out.println("\nwhat am I opening :" + xcontext); 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]; // System.out.println("length " + str.length); 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()); // keys.add(temp_value); } br.close(); for (Object entity : tmp.keySet()) { prep.put((String) entity, tmp.get(entity)); } } 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; } /*** * This method takes an annotation file and returns a map whose key is * doc-entity and its value the annotation value assigned. In case there * is multiple annotations, it takes the lowest annotation value * * @param xcontext * @return */ private Map<String, Integer> loadAnnotation(String xcontext) { Map<String, Integer> prep = new LinkedHashMap<String, Integer>(); 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[2] + "_" + str[3]; temp_value = str[5]; // if (Integer.parseInt(str[6]) == 1) { if (prep.containsKey(temp_key)) { if (prep.get(temp_key).intValue() > Integer.parseInt(temp_value)) { prep.put(temp_key, Integer.parseInt(temp_value)); } } else { prep.put(temp_key, Integer.parseInt(temp_value)); } // } } br.close(); } catch (IOException e) { e.printStackTrace(); LOG.error("read from distributed cache: read instances"); } catch (Exception e) { e.printStackTrace(); LOG.error("File not found: " + e); } finally { if (in != null) { try { in.close(); } catch (IOException e1) { e1.printStackTrace(); } } } return prep; } private Map<String, HashMap<String, Double>> loadPPR(String xcontext) { // Hashtable<String, Hashtable> prep = new Hashtable(); Map<String, HashMap<String, Double>> prep = new LinkedHashMap<String, HashMap<String, Double>>(); DataInputStream in = null; try { in = new DataInputStream(new FileInputStream(xcontext)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; // Read File Line By Line String key_check = ""; HashMap<String, Double> intermediat = new HashMap<String, Double>(); while ((strLine = br.readLine()) != null) { String temp_key; Double temp_value; String temp_str; String[] str = new String(strLine.getBytes("UTF-8"), "UTF-8").split("\t"); String[] entity = str[1].split(" "); int i = 0; temp_key = entity[i]; while (++i < entity.length) { temp_key = temp_key + "_" + entity[i]; } temp_str = str[3].toLowerCase(); // temp_str = str[3]; if (key_check == "") { key_check = temp_key; // System.out.println( " Executed ! :) "+ key_check ); } temp_value = Double.parseDouble(str[4]); if (!key_check.equalsIgnoreCase(temp_key)) { // System.out.println(" When: " + temp_key); if (key_check.equalsIgnoreCase("William_H._Gates,_Sr.")) { key_check = "William_H._Gates,_Sr"; } HashMap<String, Double> temp = new HashMap<String, Double>(); temp.putAll(intermediat); prep.put(key_check, temp); intermediat.clear(); key_check = temp_key; } if (intermediat.containsKey(temp_str)) { intermediat.put(temp_str, intermediat.get(temp_str) + temp_value); } else { intermediat.put(temp_str, temp_value); } } if (key_check.equalsIgnoreCase("William_H._Gates,_Sr.")) { key_check = "William_H._Gates,_Sr"; } prep.put(key_check, intermediat); 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; } private Map<String, String> loadWiki(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]; // int i = 0; // temp_key = entity[i]; // while (++i < entity.length) { // temp_key = temp_key + "_" + entity[i]; // } // // if (temp_key.equalsIgnoreCase("William_H._Gates,_Sr.")) { // temp_key = "William_H._Gates,_Sr"; // } // Log.info("From Load Wiki "+ temp_key); prep.put(temp_key, str[3]); } 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; } private Map<String, HashMap<String, Double>> loadGCLD(String xcontext) { Map<String, HashMap<String, Double>> prep = new LinkedHashMap<String, HashMap<String, Double>>(); DataInputStream in = null; try { in = new DataInputStream(new FileInputStream(xcontext)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; String key_check = ""; HashMap<String, Double> intermediat = new HashMap<String, Double>(); while ((strLine = br.readLine()) != null) { String temp_key; Double temp_value; String temp_str; String[] str = new String(strLine.getBytes("UTF-8"), "UTF-8").split("\t"); temp_str = str[0].toLowerCase(); // temp_str = str[0]; temp_key = str[2]; temp_value = Double.parseDouble(str[1]) * Double.parseDouble(str[4]); if (key_check == "") { key_check = temp_key; // System.out.println( " Executed ! :) "+ key_check ); } if (!key_check.equalsIgnoreCase(temp_key)) { // System.out.println(" When ! :) " + temp_key); HashMap<String, Double> temp = new HashMap<String, Double>(); temp.putAll(intermediat); prep.put(key_check, temp); intermediat.clear(); key_check = temp_key; } if (intermediat.containsKey(temp_str)) { intermediat.put(temp_str, intermediat.get(temp_str) + temp_value); } else { intermediat.put(temp_str, temp_value); } // lastValue_Holder = intermediat; } prep.put(key_check, intermediat); 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; } private Map<String, String> loadMyVer(String xcontext) { // Hashtable<String, Hashtable> prep = new Hashtable(); Map<String, String> prep = new HashMap<String, String>(); DataInputStream in = null; try { in = new DataInputStream(new FileInputStream(xcontext)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; while ((strLine = br.readLine()) != null) { String[] str = new String(strLine.getBytes("UTF-8"), "UTF-8").split("\t"); prep.put(str[0], 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; } private void loadContext(String xcontext) { DataInputStream in = null; try { in = new DataInputStream(new FileInputStream(xcontext)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; while ((strLine = br.readLine()) != null) { String[] str = new String(strLine.getBytes("UTF-8"), "UTF-8").split("\t"); String temp_str1 = str[1].toLowerCase(); String temp_str2 = str[2].toLowerCase(); /* * String temp_str1 = str[1]; String temp_str2 = str[2]; */ if (ContextL.containsKey(str[0])) { // System.out.println(Context.get(str[0])); ContextL.put(str[0], ContextL.get(str[0]) + "===" + temp_str1); ContextR.put(str[0], ContextR.get(str[0]) + "===" + temp_str2); } else { ContextL.put(str[0], temp_str1); ContextR.put(str[0], temp_str2); } } 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(); } } } } /****************************************************************/ private HashMap<String, Integer> ReturnFreqs(String str) { HashMap<String, Integer> temp = new HashMap<String, Integer>(); try { NGramExtractor extractor = new NGramExtractor(); // get the uni-grams extractor.extract(str, 1, 1, true); LinkedList<String> ngrams = extractor.getUniqueNGrams(); for (String s : ngrams) { if (temp.containsKey(s)) { temp.put(s, temp.get(s) + extractor.getNGramFrequency(s)); } else { temp.put(s, extractor.getNGramFrequency(s)); } } // Repeat it for ngarsms extractor.extract(str.toString(), 2, 4, false); ngrams = extractor.getUniqueNGrams(); for (String s : ngrams) { // System.out.println( s + " \t\t " + // extractorL.getNGramFrequency(s) ); if (temp.containsKey(s)) { temp.put(s, temp.get(s) + extractor.getNGramFrequency(s)); } else { temp.put(s, extractor.getNGramFrequency(s)); } } } catch (Exception e) { // System.err.println("Did Not work: " + e.toString()); e.printStackTrace(); } return temp; } /*************************************************************/ private Double cosine_similarity(Map<String, Integer> v1, Map<String, Integer> v2) { Set<String> both = Sets.newHashSet(v1.keySet()); both.retainAll(v2.keySet()); double sclar = 0.0, norm1 = 0.0, norm2 = 0.0; for (String k : both) sclar += v1.get(k).doubleValue() * v2.get(k).doubleValue(); for (String k : v1.keySet()) norm1 += v1.get(k).doubleValue() * v1.get(k).doubleValue(); for (String k : v2.keySet()) norm2 += v2.get(k).doubleValue() * v2.get(k).doubleValue(); return sclar / Math.sqrt(norm1 * norm2); } /**************************************/ private Double klDivergence(Map<String, Integer> v1, Map<String, Integer> v2) { double log2 = Math.log(2); double klDiv = 0.0; for (String k : v1.keySet()) { if (v1.get(k) == 0) { continue; } if (v2.containsKey(k)) if (v2.get(k) == 0) { continue; } // Limin else { ; } else { continue; } klDiv += v1.get(k).doubleValue() * Math.log(v1.get(k).doubleValue() / v2.get(k).doubleValue()); } klDiv = klDiv / log2; // moved this division out of the loop -DM /* * if (klDiv == Double.POSITIVE_INFINITY || klDiv == * Double.NEGATIVE_INFINITY) klDiv = 0; */ return klDiv; } /********************/ public double jaccardSimilarity(Set<String> h1, Set<String> h2) { int sizeh1 = h1.size(); // Retains all elements in h3 that are contained in h2 ie // intersection h1.retainAll(h2); // h1 now contains the intersection of h1 and h2 // System.out.println("Intersection " + h1); h2.removeAll(h1); // h2 now contains unique elements // System.out.println("Unique in h2 " + h2); // Union int union = sizeh1 + h2.size(); int intersection = h1.size(); return (double) intersection / union; } /**************************************************************************/ private void extractNgrmFrequency() { for (String k : ContextL.keySet()) { // System.out.println("This is the id: \n" + ContextL.get(k)); HashMap<String, Integer> tempL = new HashMap<String, Integer>(); HashMap<String, Integer> tempR = new HashMap<String, Integer>(); String[] leftContexts = ContextL.get(k).split("==="); String[] rightContexts = ContextR.get(k).split("==="); for (int i = 0; i < leftContexts.length; i++) { tempL.putAll(ReturnFreqs(leftContexts[i])); tempR.putAll(ReturnFreqs(rightContexts[i])); } ContextFreqsL.put(k, tempL); ContextFreqsR.put(k, tempR); } // Only keep the 10 best from each n-gram int top_n = 5; Map<String, HashMap<String, Integer>> tempL = new LinkedHashMap<String, HashMap<String, Integer>>(); Map<String, HashMap<String, Integer>> tempR = new LinkedHashMap<String, HashMap<String, Integer>>(); for (String k : ContextFreqsR.keySet()) { List<Integer> l = new ArrayList<Integer>(ContextFreqsR.get(k).values()); Collections.sort(l); int leng = l.size(); List<Integer> top_values = l.subList(leng - top_n, leng); HashMap<String, Integer> hs = new HashMap<String, Integer>(); for (String k2 : ContextFreqsR.get(k).keySet()) { if (top_values.contains(ContextFreqsR.get(k).get(k2))) { hs.put(k2, ContextFreqsR.get(k).get(k2)); } } tempR.put(k, hs); } for (String k : ContextFreqsL.keySet()) { List<Integer> l = new ArrayList<Integer>(ContextFreqsL.get(k).values()); Collections.sort(l); int leng = l.size(); List<Integer> top_values = l.subList(leng - top_n, leng); HashMap<String, Integer> hs = new HashMap<String, Integer>(); for (String k2 : ContextFreqsL.get(k).keySet()) { if (top_values.contains(ContextFreqsL.get(k).get(k2))) { hs.put(k2, ContextFreqsL.get(k).get(k2)); } } tempL.put(k, hs); } ContextFreqsR = tempR; ContextFreqsL = tempL; } } /** * Loads the JSON topic file. * * @param context */ private static void loadTopicData(String queryfile, Run_info fr, FileSystem fs, HashMap<String, Object> run_info) { FSDataInputStream in = null; try { in = fs.open(new Path(queryfile)); BufferedReader br = new BufferedReader(new InputStreamReader(in)); Filter_topics ft = new Filter_topics.Factory().loadTopics(br); fr.setTopic_set_id(ft.getTopic_set_id()); run_info.put("num_entities", ft.getTargets().length); } catch (IOException e1) { e1.printStackTrace(); } catch (Exception e1) { e1.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e1) { e1.printStackTrace(); } } } } public static void main(String[] args) throws Exception { int res = ToolRunner.run(new Configuration(), new FeatureExtractor(), args); System.exit(res); } static int printUsage() { System.out.println("Usage: " + FeatureExtractor.class.getName() + " -i input \n" + "-o output\n " + "-q query_file (hdfs) \n" + "-l labels file\n " + "-a annotation file \n" + "-p ppr file \n" + "-g gcld file \n" + "-c context File \n" + "-w wiki File\n \n" + "[-c corpus_id -r runtag -t teamname -d description -ds description short] \n\n " + "Example usage: hadoop jar trec-kba.jar " + FeatureExtractor.class.getName() + " " + "-i kba/tiny-kba-stream-corpus/*/* " + "-i KBA/Data/kba-stream-corpus-2012-cleansed-only-testing-out/*/*" + "-o KBA/OutPut/Kba_2012/testing_features_normalized.topic.ppr.gcld.sfrom.cl.cr.cos.kl.jac " + "-q KBA/Data/trec-kba-ccr-2012.filter-topics.json" + "-l KBA/Data/entity-surface-forms_merged.txt" + "-a KBA/Data/trec-kba-ccr-2012-judgments-2012JUN22-final.filter-run.txt" + "-p KBA/Data/trec-kba-ccr-topics-2012.ppr-top100.txt " + "-g KBA/Data/dictionary.txt" + "-c KBA/Data/wikilink-context.txt" + "-w KBA/Data/trec-kba-ccr-topics-2012-wiki.txt\n\n"); ToolRunner.printGenericCommandUsage(System.out); return -1; } @Override public int run(String[] args) throws Exception { String in = null; String out = null; String queryfile = null; String contextFile = null; String systemdescription = null; String systemdescription_short = null; String corpus_id = null; String runtag = null; String teamname = null; String annoFile = null; String gcldFile = null; String labelsFile = null; String pprFile = null; String myverFile = null; String wikiFile = null; HashMap<String, Object> run_info = new HashMap<String, Object>(); 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 ("-q".equals(args[i])) { queryfile = args[++i]; } else if ("-r".equals(args[i])) { runtag = args[++i]; } else if ("-l".equals(args[i])) { labelsFile = args[++i]; } else if ("-a".equals(args[i])) { annoFile = args[++i]; } else if ("-t".equals(args[i])) { teamname = args[++i]; } else if ("-d".equals(args[i])) { systemdescription = args[++i]; } else if ("-ds".equals(args[i])) { systemdescription_short = args[++i]; } else if ("-p".equals(args[i])) { pprFile = args[++i]; } else if ("-g".equals(args[i])) { gcldFile = args[++i]; } else if ("-s".equals(args[i])) { myverFile = args[++i]; } else if ("-c".equals(args[i])) { contextFile = args[++i]; } else if ("-w".equals(args[i])) { wikiFile = 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 || queryfile == null) return printUsage(); if (runtag == null) runtag = "toy_1"; if (teamname == null) teamname = "CompInsights"; if (corpus_id == null) corpus_id = "kba-stream-corpus-2012-cleansed-only"; if (systemdescription == null) systemdescription = "Description intentionally left blank."; if (systemdescription_short == null) systemdescription_short = "a two -step classification approach"; LOG.info("Tool: " + this.getClass().getName()); LOG.info(" - input path: " + in); LOG.info(" - output path: " + out); LOG.info(" - runtag: " + runtag); LOG.info(" - teamname: " + teamname); LOG.info(" - corpus_id: " + corpus_id); LOG.info(" - run description: " + systemdescription); Run_info fr = new Run_info.Factory().create(teamname, runtag, systemdescription, systemdescription_short, corpus_id); Map<String, String> Attr = new LinkedHashMap<String, String>(); // Attr.put("trec-kba", ""); /* * Attr.put("LengthTitle", ""); Attr.put("LengthBody", ""); * Attr.put("LengthAnchor", ""); Attr.put("Source", ""); * Attr.put("English", ""); Attr.put("MentionsTitle", ""); * Attr.put("MentionsBody", ""); Attr.put("MentionsAnchor", ""); * Attr.put("FirstPos", ""); Attr.put("LastPos", ""); Attr.put("Spread", * ""); Attr.put("FirstPosNorm", ""); Attr.put("LastPosNorm", ""); * Attr.put("SpreadNorm", ""); // Attr.put("Related", ""); * Attr.put("Relatedtitle", ""); Attr.put("RelatedBody", ""); * Attr.put("RelatedAnchor", ""); Attr.put("ppr", ""); Attr.put("gcld", * ""); Attr.put("partial", ""); Attr.put("s_form", ""); * Attr.put("contxL", "0"); Attr.put("contxR", "0"); Attr.put("cos", * "0"); Attr.put("kl", "0"); Attr.put("jac", "0"); Attr.put("Class", * ""); */ Attr.put("gcld", "0"); Attr.put("jac", "0"); Attr.put("cos", "0"); Attr.put("kl", "0"); Attr.put("ppr", "0"); Attr.put("s_form", "0"); Attr.put("contxR", "0"); Attr.put("contxL", "0"); Attr.put("FirstPos", "0"); Attr.put("LastPos", "0"); Attr.put("LengthBody", "0"); Attr.put("FirstPosNorm", "0"); Attr.put("MentionsBody", "0"); Attr.put("RelatedBody", "0"); Attr.put("Spread", "0"); Attr.put("LastPosNorm", "0"); Attr.put("SpreadNorm", "0"); Attr.put("LengthAnchor", "0"); Attr.put("Source", "0"); Attr.put("LengthTitle", "0"); Attr.put("partial", "0"); Attr.put("MentionsAnchor", "0"); Attr.put("Relatedtitle", "0"); Attr.put("English", "0"); Attr.put("RelatedAnchor", "0"); Attr.put("MentionsTitle", "0"); Attr.put("Class", "0"); Configuration conf = getConf(); conf.set(QUERYFILEPATH_HDFS, new Path(queryfile).toUri().toString()); conf.set(LABELSFILEPATH_HDFS, new Path(labelsFile).toUri().toString()); conf.set(ANNOFILEPATH_HDFS, new Path(annoFile).toUri().toString()); conf.set(PPR_HDFS, new Path(pprFile).toUri().toString()); conf.set(MYVER, new Path(myverFile).toUri().toString()); conf.set(GCLD_HDFS, new Path(gcldFile).toUri().toString()); conf.set(CONTEXT_HDFS, new Path(contextFile).toUri().toString()); conf.set(WIKI_HDFS, new Path(wikiFile).toUri().toString()); conf.set(RUNTAG, runtag); conf.set(TEAMNAME, teamname); // 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"); FileSystem fs = FileSystem.get(conf); // Lookup required data from the topic file loadTopicData(queryfile, fr, fs, run_info); Job job = new Job(conf, "Feature Extractor"); job.setJarByClass(FeatureExtractor.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(queryfile) + "#" + QUERYFILEPATH_HDFS), job.getConfiguration()); DistributedCache.addCacheFile(new URI(new Path(labelsFile) + "#" + LABELSFILEPATH_HDFS), job.getConfiguration()); DistributedCache.addCacheFile(new URI(new Path(annoFile) + "#" + ANNOFILEPATH_HDFS), job.getConfiguration()); DistributedCache.addCacheFile(new URI(new Path(pprFile) + "#" + PPR_HDFS), job.getConfiguration()); DistributedCache.addCacheFile(new URI(new Path(gcldFile) + "#" + GCLD_HDFS), job.getConfiguration()); DistributedCache.addCacheFile(new URI(new Path(contextFile) + "#" + CONTEXT_HDFS), job.getConfiguration()); DistributedCache.addCacheFile(new URI(new Path(wikiFile) + "#" + WIKI_HDFS), job.getConfiguration()); DistributedCache.addCacheFile(new URI(new Path(myverFile) + "#" + MYVER), job.getConfiguration()); DistributedCache.createSymlink(job.getConfiguration()); job.setInputFormatClass(ThriftFileInputFormat.class); job.setMapperClass(MyMapper.class); FileInputFormat.addInputPath(job, new Path(in)); job.setMapOutputKeyClass(Text.class); job.setMapOutputValueClass(Text.class); // job.setCombinerClass(MyReducer.class); // job.setReducerClass(MyReducer.class); job.setNumReduceTasks(1); FileSystem.get(conf).delete(new Path(out), true); TextOutputFormat.setOutputPath(job, new Path(out)); job.setOutputFormatClass(TextOutputFormat.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(Text.class); // Let's go int status = job.waitForCompletion(true) ? 0 : 1; Counters c = job.getCounters(); long cputime = c.findCounter(org.apache.hadoop.mapred.Task.Counter.CPU_MILLISECONDS).getValue(); run_info.put("elapsed_time", ((double) cputime)); long num_filter_results = c.findCounter(org.apache.hadoop.mapred.Task.Counter.MAP_OUTPUT_RECORDS) .getValue(); run_info.put("num_filter_results", num_filter_results); long num_entity_doc_compares = c.findCounter(org.apache.hadoop.mapred.Task.Counter.MAP_INPUT_RECORDS) .getValue(); run_info.put("num_entity_doc_compares", num_entity_doc_compares); long hours = c.findCounter(org.apache.hadoop.mapred.Task.Counter.REDUCE_INPUT_GROUPS).getValue(); run_info.put("num_stream_hours", hours); fr.setAdditionalProperties("run_info", run_info); System.out.println("#" + new Run_info.Factory().toJSON(fr)); System.out.println("@RELATION" + " trec-kba" + " "); for (String key : Attr.keySet()) { if (key.equalsIgnoreCase("English")) { System.out.println("@ATTRIBUTE " + key + " " + "{0,1,2}"); } else if (key.equalsIgnoreCase("Class")) { System.out.println("@ATTRIBUTE " + key + " " + "{0,1}"); } else { System.out.println("@ATTRIBUTE " + key + " " + "NUMERIC"); } } System.out.println("\n@DATA"); // Text line = new Text(); // LineReader reader = new LineReader(fs.open(new Path(out // + "/part-r-00000"))); // for (int i = 0; i < num_filter_results; i++) { // reader.readLine(line); // System.out.println(line.toString().split("\t\t")[1]); // } System.out.println("#" + new Run_info.Factory().toPrettyJSON(fr).replaceAll("\\n", "\n#")); return status; } }