Major fixes, returns only hits founds in all words for now. Logging changes.

.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src/test/java"/>
-	<classpathentry kind="src" path="src/main/java"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
@@ -12,5 +22,10 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

bin/searchClient.bsh

+#!/bin/bash
+java -cp target/test-classes:target/classes:target/umlsIndex-0.0.2-SNAPSHOT-jar-with-dependencies.jar -Dlog4j.configuration=log4j.properties edu.uab.ccts.nlp.umlsIndex.SearchClient "multiple ulcers"

src/main/java/edu/uab/ccts/nlp/umlsIndex/SearchClient.java

+package edu.uab.ccts.nlp.umlsIndex;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.lucene.analysis.standard.StandardAnalyzer;
+import org.apache.lucene.document.Document;
+import org.apache.lucene.index.DirectoryReader;
+import org.apache.lucene.queryparser.classic.ParseException;
+import org.apache.lucene.queryparser.classic.QueryParser;
+import org.apache.lucene.search.IndexSearcher;
+import org.apache.lucene.search.Query;
+import org.apache.lucene.search.ScoreDoc;
+import org.apache.lucene.search.TopDocs;
+import org.apache.lucene.store.FSDirectory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.google.common.collect.HashMultiset;
+
+public class SearchClient {
+	private IndexSearcher word2termSearcher = null;
+	private IndexSearcher term2conceptSearcher = null;
+	private QueryParser wordParser = null;
+	private QueryParser termParser = null;
+	private static final Logger LOG  = LoggerFactory.getLogger(SearchClient.class);
+
+	public static void main(String[] args) throws Exception {
+		File f = new File(Config.UMLS_WORD2TERM_INDEX_DIR);
+		if(!(f.isDirectory() && f.list().length>0)) { System.err.println("Missing "+f); }
+		
+		SearchClient sc = new SearchClient();
+
+		TopDocs td = sc.performSearch(sc.getWordParser(),sc.getWord2termSearcher(),args[0], 100);
+		ScoreDoc[] hits = td.scoreDocs;
+		LOG.info(args[0]+ "has " + hits.length+" word hits");
+		HashMultiset<String> searchsummary = sc.doIndexSearch(hits);
+		System.out.println("Got back "+searchsummary.elementSet().size()+" results from "+args[0]);
+		for(String s : searchsummary.elementSet()) {
+			System.out.println(s);
+		}
+	}
+	
+	
+	public SearchClient() throws IOException
+	{
+		word2termSearcher = new IndexSearcher(DirectoryReader.open(FSDirectory.open(Paths.get(Config.UMLS_WORD2TERM_INDEX_DIR))));
+		term2conceptSearcher = new IndexSearcher(DirectoryReader.open(FSDirectory.open(Paths.get(Config.UMLS_TERM2CONCEPT_INDEX_DIR))));
+		wordParser = new QueryParser("word", new StandardAnalyzer());
+		termParser = new QueryParser("concept", new StandardAnalyzer());
+	}
+
+	
+	
+	public HashMultiset<String> doIndexSearch(ScoreDoc[] hits) throws IOException, ParseException {
+		HashMultiset<String> searchsummary = HashMultiset.create();
+		for (int i = 0; i < hits.length; i++) {
+	        Document hitDoc = word2termSearcher.doc(hits[i].doc);
+	        String theword = hitDoc.get("word");
+	        String allconcept_text = hitDoc.get("conceptText");
+	        String[] allcons = allconcept_text.split(" ");
+	        LOG.debug(theword+" id:"+hits[i].doc+" with score:"+hits[i].score
+	        +" is associated with "+allcons.length+" concepts, see::"+allconcept_text);
+
+	        HashMultiset<String> hitsummary = HashMultiset.create();
+	        for(int j=0;j<allcons.length;j++) {
+	        	TopDocs topcons = performSearch(termParser,term2conceptSearcher,allcons[j], 1);
+	        	ScoreDoc[] conhits = topcons.scoreDocs;
+	        	Document conDoc = term2conceptSearcher.doc(conhits[0].doc);
+	        	String cui = conDoc.get("cui");
+	        	LOG.debug(conDoc.get("concept")+" with concept score:"+
+	        	conhits[0].score+" and cui: "+cui);
+	        	hitsummary.add(cui);
+	        }
+	        if(searchsummary.size()==0) searchsummary.addAll(hitsummary);
+	        else {
+	        	searchsummary.retainAll(hitsummary);
+	        }
+	      }
+		return searchsummary;
+	}
+	
+	
+	public TopDocs performSearch(QueryParser qp, IndexSearcher is, String queryString, int n)
+			throws IOException, ParseException {
+		Query query = qp.parse(queryString);
+		return is.search(query, n);
+	}
+	
+	
+	public Document getDocument(int docId)
+			throws IOException {
+		return word2termSearcher.doc(docId);
+	}
+
+
+	public IndexSearcher getWord2termSearcher() {
+		return word2termSearcher;
+	}
+
+
+	public void setWord2termSearcher(IndexSearcher word2termSearcher) {
+		this.word2termSearcher = word2termSearcher;
+	}
+
+
+	public QueryParser getWordParser() {
+		return wordParser;
+	}
+
+
+	public void setWordParser(QueryParser wordParser) {
+		this.wordParser = wordParser;
+	}
+
+
+	
+
+}

src/main/resources/log4j.properties

-# Set root logger level to DEBUG and its only appender to A1.
-log4j.rootLogger=INFO, A1
-
-# A1 is set to be a ConsoleAppender.
-log4j.appender.A1=org.apache.log4j.ConsoleAppender
-
-# A1 uses PatternLayout.
-log4j.appender.A1.layout=org.apache.log4j.PatternLayout
-log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n

src/test/java/edu/uab/ccts/nlp/umlsIndex/test/integration/LuceneIndexIT.java

@@ -3,34 +3,26 @@ package edu.uab.ccts.nlp.umlsIndex.test.integration;
 
 import java.io.IOException;
 import java.io.File;
-import java.nio.file.Paths;
-
-import org.apache.lucene.analysis.standard.StandardAnalyzer;
-import org.apache.lucene.document.Document;
-import org.apache.lucene.index.DirectoryReader;
-import org.apache.lucene.queryparser.classic.ParseException;
-import org.apache.lucene.queryparser.classic.QueryParser;
-import org.apache.lucene.search.IndexSearcher;
-import org.apache.lucene.search.Query;
 import org.apache.lucene.search.ScoreDoc;
 import org.apache.lucene.search.TopDocs;
-import org.apache.lucene.store.FSDirectory;
 
 import com.google.common.collect.HashMultiset;
 
 import edu.uab.ccts.nlp.umlsIndex.Config;
+import edu.uab.ccts.nlp.umlsIndex.SearchClient;
 
-import org.junit.Assume;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Unit test for simple App.
  */
 public class LuceneIndexIT 
 {
-	private IndexSearcher word2termSearcher = null;
-	private IndexSearcher term2conceptSearcher = null;
-	private QueryParser wordParser = null;
-	private QueryParser termParser = null;
+	
+	SearchClient searchClient = null;
+
+	private static final Logger LOG  = LoggerFactory.getLogger(LuceneIndexIT.class);
 	/**
 	 * Create the test case
 	 *
@@ -38,10 +30,7 @@ public class LuceneIndexIT
 	 */
 	public LuceneIndexIT() throws IOException
 	{
-		word2termSearcher = new IndexSearcher(DirectoryReader.open(FSDirectory.open(Paths.get(Config.UMLS_WORD2TERM_INDEX_DIR))));
-		term2conceptSearcher = new IndexSearcher(DirectoryReader.open(FSDirectory.open(Paths.get(Config.UMLS_TERM2CONCEPT_INDEX_DIR))));
-		wordParser = new QueryParser("word", new StandardAnalyzer());
-		termParser = new QueryParser("concept", new StandardAnalyzer());
+		searchClient = new SearchClient();
 	}
 
 	
@@ -53,43 +42,16 @@ public class LuceneIndexIT
 		File f = new File(Config.UMLS_WORD2TERM_INDEX_DIR);
 		org.junit.Assume.assumeTrue(!(f.isDirectory() && f.list().length>0));
 
-		TopDocs td = performSearch(wordParser,word2termSearcher,"multiple ulcers", 100);
-		ScoreDoc[] hits = td.scoreDocs;
-		System.out.println("Number of hits: " + hits.length);
-		HashMultiset<String> searchsummary = HashMultiset.create();
-	    for (int i = 0; i < hits.length; i++) {
-	        Document hitDoc = word2termSearcher.doc(hits[i].doc);
-	        String theword = hitDoc.get("word");
-	        String allconcept_text = hitDoc.get("conceptText");
-	        String[] allcons = allconcept_text.split(" ");
-	        System.out.println(theword+" id:"+hits[i].doc+" with score:"+hits[i].score
-	        +" is associated with "+allcons.length+" concepts, see::"+allconcept_text);
+		TopDocs td = searchClient.performSearch(searchClient.getWordParser(),
+		searchClient.getWord2termSearcher(),"multiple ulcers", 100);
 
-	        HashMultiset<String> hitsummary = HashMultiset.create();
-	        for(int j=0;j<allcons.length;j++) {
-	        	TopDocs topcons = performSearch(termParser,term2conceptSearcher,allcons[j], 1);
-	        	ScoreDoc[] conhits = topcons.scoreDocs;
-	        	Document conDoc = term2conceptSearcher.doc(conhits[0].doc);
-	        	String cui = conDoc.get("cui");
-	        	System.out.println(conDoc.get("concept")+" with concept score:"+
-	        	conhits[0].score+" and cui: "+cui);
-	        	hitsummary.add(cui);
-	        }
-	        searchsummary.addAll(hitsummary);
-	      }
-          assert(searchsummary.contains("C1265815"));
+		ScoreDoc[] hits = td.scoreDocs;
+		LOG.info("Number of hits: " + hits.length);
+		HashMultiset<String> searchsummary = searchClient.doIndexSearch(hits);
+        assert(searchsummary.contains("C1265815"));
 	}
 
 
-	public TopDocs performSearch(QueryParser qp, IndexSearcher is, String queryString, int n)
-			throws IOException, ParseException {
-		Query query = qp.parse(queryString);
-		return is.search(query, n);
-	}
-
 
-	public Document getDocument(int docId)
-			throws IOException {
-		return word2termSearcher.doc(docId);
-	}
+	
 }

src/test/resources/log4j.properties

+#log4j.rootLogger=DEBUG
+#log4j.rootLogger=DEBUG, file
+log4j.rootLogger=INFO, file
+#log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.file=org.apache.log4j.RollingFileAppender
+log4j.appender.file.File=log/umlsIndex.log
+log4j.appender.file.MaxFileSize=100MB
+log4j.appender.file.MaxBackupIndex=10
+#log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.file.layout=org.apache.log4j.PatternLayout
+log4j.appender.file.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n