From 95c5f3e02244f8deebda1acc78b04b8630c5e9c8 Mon Sep 17 00:00:00 2001
From: Jonas Schaub <44881147+JonasSchaub@users.noreply.github.com>
Date: Wed, 20 Dec 2023 11:14:24 +0100
Subject: [PATCH] Fixed bugs SonarCloud complained about;

---
 .../cdk/tools/ErtlFunctionalGroupsFinder.java     |  2 +-
 ...ctionalGroupsFinderPerformanceSnapshotApp.java | 15 ++++++++++++---
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/openscience/cdk/tools/ErtlFunctionalGroupsFinder.java b/src/main/java/org/openscience/cdk/tools/ErtlFunctionalGroupsFinder.java
index 6ee66d4..43c471b 100644
--- a/src/main/java/org/openscience/cdk/tools/ErtlFunctionalGroupsFinder.java
+++ b/src/main/java/org/openscience/cdk/tools/ErtlFunctionalGroupsFinder.java
@@ -605,7 +605,7 @@ private void expandFullEnvironments(List<IAtomContainer> fGroups) {
             for(int i = 0; i < atomCount; i++) {
                 IAtom atom = fGroup.getAtom(i);
 
-                if(isDbg()) log.debug(String.format(" - Atom #%d:%   - Expanding environment...", i));
+                if(isDbg()) log.debug(String.format(" - Atom #%d   - Expanding environment...", i));
                 expandEnvironment(atom, fGroup);
 
                 int hCount = atom.getImplicitHydrogenCount();
diff --git a/src/main/java/org/openscience/cdk/tools/efgf/app/ErtlFunctionalGroupsFinderPerformanceSnapshotApp.java b/src/main/java/org/openscience/cdk/tools/efgf/app/ErtlFunctionalGroupsFinderPerformanceSnapshotApp.java
index cbdd185..721103b 100644
--- a/src/main/java/org/openscience/cdk/tools/efgf/app/ErtlFunctionalGroupsFinderPerformanceSnapshotApp.java
+++ b/src/main/java/org/openscience/cdk/tools/efgf/app/ErtlFunctionalGroupsFinderPerformanceSnapshotApp.java
@@ -52,6 +52,7 @@
 import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Objects;
 import java.util.Random;
 import java.util.Set;
 import java.util.concurrent.ExecutorService;
@@ -138,6 +139,7 @@ public ErtlFunctionalGroupsFinderPerformanceSnapshotApp(String[] anArgs) throws
         tmpExceptionsPrintWriter.println();
         tmpExceptionsPrintWriter.flush();
         tmpExceptionsPrintWriter.close();
+        ExecutorService executor = null;
         try {
             if (anArgs.length != 2) {
                 throw new IllegalArgumentException("Two arguments (a file name and the number of threads to use) are required.");
@@ -211,13 +213,14 @@ public ErtlFunctionalGroupsFinderPerformanceSnapshotApp(String[] anArgs) throws
                 IAtomContainer[] tmpMoleculesArrayForThread = Arrays.copyOfRange(this.moleculesArray, i, i + tmpNumberOfMoleculesPerThread);
                 tmpListOfThreads.add(new ExtractFunctionalGroupsTask(tmpMoleculesArrayForThread));
             }
-            ExecutorService executor = Executors.newFixedThreadPool(this.numberOfThreadsToUse);
+            executor = Executors.newFixedThreadPool(this.numberOfThreadsToUse);
             List<Future<Integer>> tmpFuturesList = new LinkedList<>();
             long tmpStartTime = System.currentTimeMillis();
             try {
                 tmpFuturesList = executor.invokeAll(tmpListOfThreads);
             } catch (Exception ex) {
                 this.appendToLogfile(ex);
+                throw ex;
             }
             long tmpEndTime = System.currentTimeMillis();
             tmpResultsPrintWriter.println("Divided molecules onto " + this.numberOfThreadsToUse
@@ -230,13 +233,17 @@ public ErtlFunctionalGroupsFinderPerformanceSnapshotApp(String[] anArgs) throws
             }
             tmpResultsPrintWriter.println(tmpExceptionsCounter + " molecules produced an exception.");
             tmpResultsPrintWriter.flush();
-            executor.shutdown();
+            executor.close();
             tmpResultsPrintWriter.println();
             tmpResultsPrintWriter.flush();
             tmpResultsPrintWriter.close();
         } catch (Exception anException) {
             this.appendToLogfile(anException);
             anException.printStackTrace(System.err);
+            if (!Objects.isNull(executor)) {
+                executor.close();
+            }
+            Thread.currentThread().interrupt();
             System.exit(1);
         }
     }
@@ -265,7 +272,9 @@ private IAtomContainer applyFiltersAndPreprocessing(IAtomContainer aMolecule) th
                     tmpBiggestFragment = tmpFragment;
                 }
             }
-            aMolecule = tmpBiggestFragment;
+            if (!Objects.isNull(tmpBiggestFragment)) {
+                aMolecule = tmpBiggestFragment;
+            }
         }
         for (IAtom tmpAtom : aMolecule.atoms()) {
             if (!this.nonMetallicAtomicNumbersSet.contains(tmpAtom.getAtomicNumber())) {