Cleaned up code

Author: nilshoffmann

.gitignore

@@ -5,3 +5,4 @@
 /parsers/target/
 /parsers/nbproject/
 .vscode/
+/cli/nbproject/

cli/pom.xml

@@ -36,6 +36,24 @@
             <artifactId>logback-classic</artifactId>
             <version>1.2.12</version>
         </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.6.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-params</artifactId>
+            <version>5.6.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.6.0</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
     <build>
         <resources>

cli/src/main/java/org/lifstools/jgoslin/cli/CmdLineParser.java

@@ -191,7 +191,7 @@ public static void main(String[] args) throws Exception {
         }
     }
 
-    private static enum Grammar {
+    private enum Grammar {
         GOSLIN, GOSLINFRAGMENTS, LIPIDMAPS, SWISSLIPIDS, HMDB, SHORTHAND2020, FATTYACIDS, NONE
     };
 
@@ -220,7 +220,6 @@ private static boolean writeToStdOut(List<Pair<String, List<ValidationResult>>>
                 writeToWriter(bw, results);
             }
             sw.flush();
-            sw.close();
             log.info(sw.toString());
             return true;
         } catch (IOException ex) {

parsers/src/main/java/org/lifstools/jgoslin/parser/SwissLipidsParserEventHandler.java

@@ -38,9 +38,9 @@
  */
 public class SwissLipidsParserEventHandler extends LipidBaseParserEventHandler {
 
-    public int dbPosition;
-    public String dbCistrans;
-    public int suffixNumber;
+    private int dbPosition;
+    private String dbCistrans;
+    private int suffixNumber;
 
     /**
      * Create a new {@code SwissLipidsParserEventHandler}.

parsers/src/test/java/org/lifstools/jgoslin/parser/SwissLipidsParserTest.java

@@ -15,9 +15,10 @@
  */
 package org.lifstools.jgoslin.parser;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import org.lifstools.jgoslin.domain.LipidAdduct;
 import org.junit.jupiter.api.Test;
-import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import org.junit.jupiter.api.BeforeAll;