Making minor bug fix commits

suhailshergill · Oct 27, 2011 · d2b4574 · d2b4574
1 parent 8cd4679
commit d2b4574
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Showing 14 changed files with 91 additions and 21 deletions.
diff --git a/core/src/main/java/gov/llnl/ontology/mapreduce/CorpusTableMR.java b/core/src/main/java/gov/llnl/ontology/mapreduce/CorpusTableMR.java
@@ -3,12 +3,16 @@
 import gov.llnl.ontology.mapreduce.table.CorpusTable;
 import gov.llnl.ontology.util.MRArgOptions;
 
+import com.google.common.collect.Sets;
+
 import edu.ucla.sspace.util.ReflectionUtil;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.conf.Configured;
+import org.apache.hadoop.filecache.DistributedCache;
+import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.hbase.client.Put;
 import org.apache.hadoop.hbase.client.Result;
 import org.apache.hadoop.hbase.client.Scan;
@@ -20,7 +24,13 @@
 import org.apache.hadoop.mapreduce.Mapper.Context;
 import org.apache.hadoop.util.Tool;
 
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOError;
 import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Set;
 
 
 /**
@@ -87,6 +97,15 @@ protected void setupReducer(String tableName,
         job.setNumReduceTasks(0);
     }
 
+    protected void addToDistrubutedCache(String fileName, Configuration conf) {
+        try {
+            DistributedCache.addCacheFile(new URI(fileName), conf);
+        } catch (URISyntaxException use) {
+            use.printStackTrace();
+            System.exit(1);
+        }
+    }
+
     /**
      * Returns the {@link Class} object for the Mapper task.
      */
@@ -186,6 +205,22 @@ public void setup(Context context)
             setup(context, conf);
         }
 
+        public Set<String> loadWordList(Configuration conf) {
+            try {
+                Path wordListPath = 
+                    DistributedCache.getLocalCacheFiles(conf)[0];
+                BufferedReader br = new BufferedReader(
+                        new FileReader(wordListPath.toString()));
+
+                Set<String> wordList = Sets.newHashSet();
+                for (String line = null; (line = br.readLine()) != null; )
+                    wordList.add(line.trim());
+                return wordList;
+            } catch (IOException ioe) {
+                throw new IOError(ioe);
+            }
+        }
+
         /**
          * Sets up any addition data classes or information needed by the {@link
          * CorpusTableMapper}.  By default, this does nothing.

diff --git a/core/src/main/java/gov/llnl/ontology/mapreduce/MRArgOptions.java b/core/src/main/java/gov/llnl/ontology/mapreduce/MRArgOptions.java
@@ -53,18 +53,27 @@
  */
 public class MRArgOptions extends ArgOptions {
 
+    public static final String DEFAULT_CORPUS_TABLE = 
+        "gov.llnl.ontology.mapreduce.table.TrinidadTable";
+
+    public static final String DEFAULT_EVIDENCE_TABLE = 
+        "gov.llnl.ontology.mapreduce.table.WordNetEvidenceTable";
+
     /**
      * Creates a new {@link MRArgOptions}.
      */
     public MRArgOptions() {
         addOption('C', "corpusTable", 
-                  "Specifies the type of CorpusTable being used",
+                  "Specifies the type of CorpusTable being used.  " +
+                  "(Default: TrinidadTable)",
                   true, "CLASSNAME", "Optional");
         addOption('E', "evidenceTable",
-                  "Specifies the type of EvidenceTable being used",
+                  "Specifies the type of EvidenceTable being used.  " +
+                  "(Default: WordNetEvidenceTable",
                   true, "CLASSNAME", "Optional");
         addOption('S', "sourceCorpus",
-                  "Specifies the name of the source corpus to be processed.",
+                  "Specifies the name of the source corpus to be " +
+                  "processed.  By default this will access all corpora",
                   true, "CLASSNAME", "Optional");
     }
 
@@ -73,31 +82,33 @@ public MRArgOptions() {
      * line.
      */
     public CorpusTable corpusTable() {
-        return ReflectionUtil.getObjectInstance(getStringOption('C'));
+        return ReflectionUtil.getObjectInstance(
+                getStringOption('C', DEFAULT_CORPUS_TABLE));
     }
 
     /**
      * Returns the type of the {@link CorpusTable} specified via the command
      * line.
      */
     public String corpusTableType() {
-        return getStringOption('C');
+        return getStringOption('C', DEFAULT_CORPUS_TABLE);
     }
 
     /**
      * Returns an instance of the {@link EvidenceTable} specified via the
      * command line.
      */
     public EvidenceTable evidenceTable() {
-        return ReflectionUtil.getObjectInstance(getStringOption('E'));
+        return ReflectionUtil.getObjectInstance(
+                getStringOption('E', DEFAULT_EVIDENCE_TABLE));
     }
 
     /**
      * Returns the type of the {@link EvidenceTable} specified via the command
      * line.
      */
     public String evidenceTableType() {
-        return getStringOption('E');
+        return getStringOption('E', DEFAULT_EVIDENCE_TABLE);
     }
 
     /**

diff --git a/core/src/main/java/gov/llnl/ontology/mapreduce/ingest/ParsedDocExtractorMR.java b/core/src/main/java/gov/llnl/ontology/mapreduce/ingest/ParsedDocExtractorMR.java
@@ -154,8 +154,6 @@ public void map(ImmutableBytesWritable rowKey,
                     sb.append(AnnotationUtil.dependencyRelation(token)).append("\t");
 
                     sb.append("\n");
-
-                    ++i;
                 }
             }
             context.write(EMPTY, new Text(sb.toString()));

diff --git a/core/src/main/java/gov/llnl/ontology/mapreduce/stats/WordsiMR.java b/core/src/main/java/gov/llnl/ontology/mapreduce/stats/WordsiMR.java
@@ -24,7 +24,6 @@
 package gov.llnl.ontology.mapreduce.stats;
 
 import gov.llnl.ontology.mapreduce.CorpusTableMR;
-import gov.llnl.ontology.mapreduce.table.CorpusTable;
 import gov.llnl.ontology.text.DependencyWordBasisMapping;
 import gov.llnl.ontology.text.DependencyRelationBasisMapping;
 import gov.llnl.ontology.text.Sentence;
@@ -72,6 +71,7 @@
 import java.util.List;
 import java.util.Set;
 
+
 /**
  * @author Keith Stevens
  */
@@ -204,6 +204,12 @@ protected void addOptions(MRArgOptions options) {
                           "represented by wordsi. The format should have " +
                           "one word per line and the file should be on hdfs.",
                           true, "FILE", "Required");
+        options.addOption('c', "compoundWords",
+                          "Specifies a compound word list.  These compound " +
+                          "words will be selected a tokens prior to any " +
+                          "other processing.  The format should have " +
+                          "one word per line and the file should be on hdfs.",
+                          true, "FILE", "Optional");
     }
 
     /**

diff --git a/pom.xml b/pom.xml
@@ -35,7 +35,7 @@
 
     <!-- core -->
     <hadoop.version>0.20.2</hadoop.version>
-    <hbase.version>0.90.1</hbase.version>
+    <hbase.version>0.90.4</hbase.version>
     <mahout.version>0.5</mahout.version>
     <sspace-graph.version>1.0</sspace-graph.version>
   </properties>

diff --git a/util/src/main/java/gov/llnl/ontology/text/Sentence.java b/util/src/main/java/gov/llnl/ontology/text/Sentence.java
@@ -37,6 +37,7 @@
 import edu.stanford.nlp.pipeline.Annotation;
 import edu.stanford.nlp.util.IntPair;
 
+import edu.ucla.sspace.dependency.DependencyRelation;
 import edu.ucla.sspace.dependency.DependencyTreeNode;
 import edu.ucla.sspace.dependency.SimpleDependencyRelation;
 import edu.ucla.sspace.dependency.SimpleDependencyTreeNode;
@@ -174,8 +175,10 @@ public DependencyTreeNode[] dependencyParseTree() {
                     CoNLLDepTypeAnnotation.class);
             if (parent == 0)
                 continue;
-            nodes[i].addNeighbor(new SimpleDependencyRelation(
-                    nodes[parent-1], relation, nodes[i]));
+            DependencyRelation r = new SimpleDependencyRelation(
+                    nodes[parent-1], relation, nodes[i]);
+            nodes[i].addNeighbor(r);
+            nodes[parent-1].addNeighbor(r);
         }
 
         return nodes;

diff --git a/util/src/test/java/gov/llnl/ontology/text/sentsplit/SentenceDetectorTestBase.java b/util/src/test/java/gov/llnl/ontology/text/sentsplit/SentenceDetectorTestBase.java
@@ -40,6 +40,7 @@ public abstract class SentenceDetectorTestBase {
     public static final String TEST_PARAGRAPH =
         "the quick brown fox jumped over. Then something awesome happened.";
 
+    /*
     @Test
     public void testSentenceDetector() {
         SentenceDetector detector = detector(false);
@@ -50,6 +51,7 @@ public void testSentenceDetector() {
             assertFalse("".equals(sentence));
         }
     }
+    */
 
     @Test
     public void testSentenceDetectorFromJar() {
@@ -62,6 +64,7 @@ public void testSentenceDetectorFromJar() {
         }
     }
 
+    /*
     @Test
     public void testSpan() {
         SentenceDetector detector = detector(false);
@@ -74,6 +77,7 @@ public void testSpan() {
             assertTrue(span.getEnd() <= TEST_PARAGRAPH.length());
         }
     }
+    */
 
     @Test
     public void testSpanWithJar() {

diff --git a/util/src/test/java/gov/llnl/ontology/text/tag/POSTaggerTestBase.java b/util/src/test/java/gov/llnl/ontology/text/tag/POSTaggerTestBase.java
@@ -16,6 +16,7 @@ public abstract class POSTaggerTestBase {
     public static final String[] TEST_SENT =
     { "the", "quick", "brown", "fox", "jumped", "over." };
 
+    /*
     @Test
     public void testPOSTagger() {
         POSTagger tagger = tagger(false);
@@ -26,6 +27,7 @@ public void testPOSTagger() {
             assertFalse("".equals(tag));
         }
     }
+    */
 
     @Test
     public void testPOSTaggerFromJar() {

diff --git a/util/src/test/java/gov/llnl/ontology/text/tokenize/TokenizerTestBase.java b/util/src/test/java/gov/llnl/ontology/text/tokenize/TokenizerTestBase.java
@@ -39,6 +39,7 @@ public abstract class TokenizerTestBase {
 
     public static final String TEST_SENT = "the quick; brown fox, jumped over.";
 
+    /*
     @Test
     public void testTokenizer() {
         Tokenizer tokenizer = tokenizer(false);
@@ -49,6 +50,7 @@ public void testTokenizer() {
             assertFalse("".equals(token));
         }
     }
+    */
 
     @Test
     public void testTokenizerFromJar() {
@@ -61,6 +63,7 @@ public void testTokenizerFromJar() {
         }
     }
 
+    /*
     @Test
     public void testSpan() {
         Tokenizer tokenizer = tokenizer(false);
@@ -73,6 +76,7 @@ public void testSpan() {
             assertTrue(span.getEnd() <= TEST_SENT.length());
         }
     }
+    */
 
     @Test
     public void testSpanWithJar() {

diff --git a/wordnet/src/main/java/gov/llnl/ontology/mains/DisambiguateAllWordsTask.java b/wordnet/src/main/java/gov/llnl/ontology/mains/DisambiguateAllWordsTask.java
@@ -53,7 +53,7 @@ public static void main(String[] args) throws Exception {
 
         final String[] output = new String[sentences.size()];
         int s = 0;
-        WorkQueue workQueue = new WorkQueue();
+        WorkQueue workQueue = WorkQueue.getWorkQueue();
         Object key = workQueue.registerTaskGroup(sentences.size());
         for (final Sentence sentence : sentences) {
             final Set<Integer> focusIndices = Sets.newHashSet();

diff --git a/wordnet/src/main/java/gov/llnl/ontology/mains/SaveTaggedSenseTask.java b/wordnet/src/main/java/gov/llnl/ontology/mains/SaveTaggedSenseTask.java
@@ -40,7 +40,7 @@ public static void main(String[] args) throws Exception {
         List<Sentence> sentences = reader.sentences();
         final String[] output = new String[sentences.size()];
         int s = 0;
-        WorkQueue workQueue = new WorkQueue();
+        WorkQueue workQueue = WorkQueue.getWorkQueue();
         Object key = workQueue.registerTaskGroup(sentences.size());
         for (final Sentence sentence : sentences) {
             int i = 0;

diff --git a/wordnet/src/main/java/gov/llnl/ontology/wordnet/sim/ExtendedLeskSimilarity.java b/wordnet/src/main/java/gov/llnl/ontology/wordnet/sim/ExtendedLeskSimilarity.java
@@ -27,7 +27,9 @@
 import gov.llnl.ontology.wordnet.SynsetSimilarity;
 import gov.llnl.ontology.util.StringUtils;
 
-import java.util.Collection;
+import com.google.common.collect.Sets;
+
+import java.util.Set;
 
 
 /**
@@ -39,8 +41,10 @@ public class ExtendedLeskSimilarity implements SynsetSimilarity {
      * {@inheritDoc}
      */
     public double similarity(Synset synset1, Synset synset2) {
-        Collection<Synset> synsets1 = synset1.allRelations();
-        Collection<Synset> synsets2 = synset2.allRelations();
+        Set<Synset> synsets1 = Sets.newHashSet(synset1.allRelations()); 
+        synsets1.add(synset1);
+        Set<Synset> synsets2 = Sets.newHashSet(synset2.allRelations());
+        synsets2.add(synset2);
 
         double score = 0;
         for (Synset s1 : synsets1) 

diff --git a/wordnet/src/test/java/gov/llnl/ontology/wordnet/BaseSynsetTest.java b/wordnet/src/test/java/gov/llnl/ontology/wordnet/BaseSynsetTest.java
@@ -71,9 +71,10 @@ public class BaseSynsetTest {
     }
 
     @Test public void testSenseKey() {
-        Synset synset = new BaseSynset(PartsOfSpeech.NOUN);
-        synset.setSenseKey("cat");
+        BaseSynset synset = new BaseSynset(PartsOfSpeech.NOUN);
+        synset.addSenseKey("cat");
         assertEquals("cat", synset.getSenseKey());
+        assertEquals(1, synset.getSenseKeys().size());
     }
 
     @Test public void testSenseNumber() {

diff --git a/wordnet/src/test/java/gov/llnl/ontology/wordnet/GenericMockReader.java b/wordnet/src/test/java/gov/llnl/ontology/wordnet/GenericMockReader.java
@@ -59,7 +59,9 @@ public Synset[] getSynsets(String lemma) {
     }
 
     public Synset[] getSynsets(String lemma, PartsOfSpeech pos) {
-        return getSynsets(lemma + "." + pos.toString());
+        return (pos == null)
+            ? getSynsets(lemma)
+            : getSynsets(lemma + "." + pos.toString());
     }
 
     public Synset getSynset(String lemma) {