fix major issues from sonarqube

Author: Christopher Gross cogross

core/connection-pool/src/main/java/datawave/core/common/cache/SharedCacheCoordinator.java

@@ -726,11 +726,17 @@ protected void reapEvictions() {
                         String recursiveDeletePath = ZKPaths.makePath(curatorClient.getNamespace(), path);
                         ZKUtil.deleteRecursive(curatorClient.getZookeeperClient().getZooKeeper(), recursiveDeletePath);
                     } catch (Exception e) {
+                        if (e instanceof InterruptedException) {
+                            Thread.currentThread().interrupt();
+                        }
                         log.trace("Problem deleting " + path + " (this may be ok): " + e.getMessage(), e);
                     }
                 }
             }
         } catch (Exception e) {
+            if (e instanceof InterruptedException) {
+                Thread.currentThread().interrupt();
+            }
             log.warn("Error cleaning up eviction notices: " + e.getMessage(), e);
         }
     }

core/map-reduce/src/main/java/datawave/core/mapreduce/bulkresults/map/BulkResultsFileOutputMapper.java

@@ -118,6 +118,9 @@ protected void map(Key key, Value value, org.apache.hadoop.mapreduce.Mapper<Key,
                     }
                     context.write(key, val);
                 } catch (Exception e) {
+                    if (e instanceof InterruptedException) {
+                        Thread.currentThread().interrupt();
+                    }
                     throw new RuntimeException("Unable to serialize response of class: " + response.getClass().getName(), e);
                 }
                 context.progress();

core/map-reduce/src/main/java/datawave/core/mapreduce/bulkresults/map/BulkResultsTableOutputMapper.java

@@ -89,6 +89,9 @@ protected void map(Key key, Value value, org.apache.hadoop.mapreduce.Mapper<Key,
                     m.put(key.getColumnFamily(), key.getColumnQualifier(), new ColumnVisibility(key.getColumnVisibility()), key.getTimestamp(), val);
                     context.write(this.tableName, m);
                 } catch (Exception e) {
+                    if (e instanceof InterruptedException) {
+                        Thread.currentThread().interrupt();
+                    }
                     throw new RuntimeException("Unable to serialize response of class: " + response.getClass().getName(), e);
                 }
                 context.progress();

core/query/src/main/java/datawave/core/query/logic/composite/CompositeQueryLogic.java

@@ -150,6 +150,7 @@ public void run() {
                             log.debug(Thread.currentThread().getName() + ": Got null result");
                         }
                     } catch (InterruptedException e) {
+                        Thread.currentThread().interrupt();
                         // if this was on purpose, then just log and the loop will naturally exit
                         if (interrupted) {
                             log.warn("QueryLogic thread interrupted", e);
@@ -478,6 +479,7 @@ public void close() {
             try {
                 holder.join();
             } catch (InterruptedException e) {
+                Thread.currentThread().interrupt();
                 log.error("Error joining query logic thread", e);
                 throw new RuntimeException("Error joining query logic thread", e);
             }

core/query/src/main/java/datawave/core/query/logic/composite/CompositeQueryLogicResultsIterator.java

@@ -68,6 +68,7 @@ public boolean hasNext() {
                     if (failure != null) {
                         Throwables.propagate(failure);
                     }
+                    Thread.currentThread().interrupt();
                     throw new RuntimeException(e);
                 }
             }

warehouse/assemble/webservice/src/main/java/datawave/webservice/mr/input/SecureEventSequenceFileInputFormat.java

@@ -17,6 +17,7 @@ public RecordReader<K,RawRecordContainer> createRecordReader(InputSplit split, T
         try {
             reader.initialize(split, context);
         } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
             throw new IOException("Error initializing SecureEventSequenceFileRecordReader", e);
         }
         return reader;

warehouse/ingest-core/src/main/java/datawave/ingest/data/tokenize/TokenizationHelper.java

@@ -1,6 +1,7 @@
 package datawave.ingest.data.tokenize;
 
 import java.io.IOException;
+import java.util.concurrent.atomic.AtomicInteger;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.log4j.Logger;
@@ -25,6 +26,7 @@ public static class HeartBeatThread extends Thread {
 
         public static final long INTERVAL = 500; // half second resolution
         public static volatile int counter = 0;
+
         public static long lastRun;
 
         static {
@@ -41,6 +43,7 @@ public void run() {
                 try {
                     Thread.sleep(INTERVAL);
                 } catch (InterruptedException e) {
+                    Thread.currentThread().interrupt();
                     throw new RuntimeException(e);
                 }
 

warehouse/ingest-core/src/main/java/datawave/ingest/input/reader/AbstractEventRecordReader.java

@@ -175,6 +175,9 @@ public RawRecordContainer getEvent() {
 
         try {
             event.setRawRecordNumber(getCurrentKey().get());
+        } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
+            throw new RuntimeException("Unable to get current key", e);
         } catch (Exception e) {
             throw new RuntimeException("Unable to get current key", e);
         }

warehouse/ingest-core/src/main/java/datawave/ingest/mapreduce/EventMapper.java

@@ -253,6 +253,9 @@ public void setup(Context context) throws IOException, InterruptedException {
         try {
             contextWriter = contextWriterClass.getDeclaredConstructor().newInstance();
             contextWriter.setup(filterConf, filterConf.getBoolean(CONTEXT_WRITER_OUTPUT_TABLE_COUNTERS, false));
+        } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
+            throw new IOException("Failed to initialized " + contextWriterClass + " from property " + CONTEXT_WRITER_CLASS, e);
         } catch (Exception e) {
             throw new IOException("Failed to initialized " + contextWriterClass + " from property " + CONTEXT_WRITER_CLASS, e);
         }
@@ -480,7 +483,11 @@ public void map(K1 key, V1 value, Context context) throws IOException, Interrupt
                     NDC.push(origFiles.iterator().next());
                     reprocessedNDCPush = true;
                 }
-
+            } catch (InterruptedException e) {
+                contextWriter.rollback();
+                Thread.currentThread().interrupt();
+                log.error("Failed to clean event from error table.  Terminating map", e);
+                throw new IOException("Failed to clean event from error table, Terminating map", e);
             } catch (Exception e) {
                 contextWriter.rollback();
                 log.error("Failed to clean event from error table.  Terminating map", e);

warehouse/ingest-core/src/main/java/datawave/ingest/mapreduce/handler/facet/HashTableFunction.java

@@ -107,7 +107,10 @@ public Collection<NormalizedContentInterface> apply(@Nullable Collection<Normali
 
             try {
                 contextWriter.write(map, context);
-            } catch (IOException | InterruptedException e) {
+            } catch (InterruptedException e) {
+                Thread.currentThread().interrupt();
+                throw new RuntimeException(e);
+            } catch (IOException e) {
                 throw new RuntimeException(e);
             }