SNOMED CT querying, don't do IT unless index is populated

README.md

 # umlsIndex
-Short code to do some simple indexing of UMLS.
+Short code to do some simple indexing of SNOMEDCT via UMLS.
+FIXME - Should pull all synonyms, not just the most common/largest/smallest. Should have memory for it, order query by CUI and write after all synonyms have been pulled

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

@@ -231,8 +231,8 @@ Text fields are useful for keyword search.
 	 */
 	public List<String> dropStopWords(List<String> allWords) throws URISyntaxException{
 		List<String> stops = new ArrayList<String>();
-		//try (Stream<String> stream = Files.lines(Paths.get(getClass().getResource("/StopWords.txt").toURI()))) {
-		try (Stream<String> stream = new BufferedReader(new InputStreamReader(ClassLoader.getSystemResourceAsStream("StopWords.txt"))).lines()){
+		try (Stream<String> stream = Files.lines(Paths.get(getClass().getResource("/StopWords.txt").toURI()))) {
+		//try (Stream<String> stream = new BufferedReader(new InputStreamReader(ClassLoader.getSystemResourceAsStream("StopWords.txt"))).lines()){
 			stops = stream
 			.filter(line -> !line.startsWith("#"))
 			.collect(Collectors.toList());

src/main/resources/sql/oracle/umlsConceptDefSelect.sql

@@ -19,8 +19,9 @@ WHERE mrconso.LAT='ENG'
 -- AND mrconso.ts = 'P'
 -- AND mrconso.stt = 'PF'
 -- AND mrconso.ispref = 'Y'
-AND tui IN ('T046')
+-- AND tui IN ('T046')
 -- AND tui IN ('T046','T047')
+AND mrconso.SAB LIKE 'SNOMEDCT%'
 -- AND mrconso.cui='C0814136'
 GROUP BY mrconso.cui
 ) thetable

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

@@ -2,6 +2,7 @@ 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;
@@ -19,6 +20,7 @@ import com.google.common.collect.HashMultiset;
 
 import edu.uab.ccts.nlp.umlsIndex.Config;
 
+import org.junit.Assume;
 
 /**
  * Unit test for simple App.
@@ -48,6 +50,9 @@ public class LuceneIndexIT
 	@org.junit.Test
 	public void testIndex() throws Exception
 	{
+		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);