restore logging

otter606 · otter606 · commit 4a7d768039e0 · 2021-09-18T11:11:03.000+01:00
diff --git a/biojava-ontology/src/main/java/demo/ParseGO.java b/biojava-ontology/src/main/java/demo/ParseGO.java
@@ -27,6 +27,8 @@
 import org.biojava.nbio.ontology.Ontology;
 import org.biojava.nbio.ontology.Term;
 import org.biojava.nbio.ontology.io.OboParser;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.BufferedReader;
 import java.io.InputStream;
@@ -37,31 +39,29 @@
 
 public class ParseGO {
 
+	static final Logger logger = LoggerFactory.getLogger(ParseGO.class);
+
 	/**
-	 * Parses Biosapiens OBO file and prints out name/description
-	 * pairs
+	 * Parses Biosapiens OBO file and logs name/description at INFO level
 	 * 
 	 * @param args
 	 */
 	public static void main(String[] args) {
 
-		try {
-
-			OboParser parser = new OboParser();
-			InputStream inStream = OboParser.class.getResourceAsStream("/ontology/biosapiens.obo");
-
-			BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream));
-
+		OboParser parser = new OboParser();
+		try (InputStream inStream = OboParser.class.getResourceAsStream("/ontology/bio sapiens.obo");
+				BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream))) {
 			Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");
-
 			Set<Term> keys = ontology.getTerms();
 			Iterator<Term> iter = keys.iterator();
 			while (iter.hasNext()) {
 				Term t = iter.next();
-				System.out.println(t.getName() + " " + t.getDescription());
+				logger.info("{} [{}]", t.getName(), t.getDescription());
 			}
+
 		} catch (Exception e) {
-			System.err.println("Exception: " + e);
+			logger.error("Exception: " + e);
+			System.exit(1);
 		}
 	}
 }
