Fix self-suppression problem with exception handling in AbstractAsync…

…Writer

An exception thrown during synchronousWrite() by the underlying thread
is typically picked up during write()'s invocation of checkAndRethrow().
Subsequent calling of close() (e.g. by try-with-resources) would result
in an attempt to throw the same exception instance.

This commit ensures that the underlying exception is only thrown once,
by clearing the AtomicReference to the Throwable before throwing.

Includes a unit test which demonstrates the problem.

src/main/java/htsjdk/samtools/util/AbstractAsyncWriter.java

@@ -14,6 +14,10 @@
  * NOTE: Objects of subclasses of this class are not intended to be shared between threads.
  * In particular there must be only one thread that calls {@link #write} and {@link #close}.
  *
+ * NOTE: Any exception thrown by the underlying Writer will be propagated back to the caller
+ * during the next available call to {@link #write} or {@link #close}. After the exception
+ * has been thrown to the caller, it is not safe to attempt further operations on the instance.
+ *
  * @author Tim Fennell
  */
 public abstract class AbstractAsyncWriter<T> implements Closeable {
@@ -92,8 +96,9 @@ public void close() {
      * or RuntimeException as appropriate.
      */
     private final void checkAndRethrow() {
-        final Throwable t = this.ex.get();
+        final Throwable t = this.ex.getAndSet(null);
         if (t != null) {
+            this.isClosed.set(true); // Ensure no further attempts to write
             if (t instanceof Error) throw (Error) t;
             if (t instanceof RuntimeException) throw (RuntimeException) t;
             else throw new RuntimeException(t);

src/test/java/htsjdk/samtools/util/AsyncWriterTest.java

@@ -0,0 +1,77 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2016 Len Trigg
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package htsjdk.samtools.util;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class AsyncWriterTest {
+    private static class MyException extends RuntimeException {
+        final Integer item;
+        public MyException(Integer item) {
+            this.item = item;
+        }
+    }
+    private static class TestAsyncWriter extends AbstractAsyncWriter<Integer> {
+        protected TestAsyncWriter() {
+            super(1); // Queue size of 1 to give us more control over the order of events
+        }
+
+        @Override
+        protected String getThreadNamePrefix() {
+            return "TestAsyncWriter";
+        }
+
+        @Override
+        protected void synchronouslyWrite(Integer item) {
+            throw new MyException(item);
+        }
+
+        @Override
+        protected void synchronouslyClose() {
+            // Nothing
+        }
+    }
+    @Test
+    public void testNoSelfSuppression() {
+        try (TestAsyncWriter t = new TestAsyncWriter()) {
+            try {
+                t.write(1); // Will trigger exception in writing thread
+                t.write(2); // Will block if the above write has not been executed, but may not trigger checkAndRethrow()
+                t.write(3); // Will trigger checkAndRethrow() if not already done by the above write
+                Assert.fail("Expected exception");
+            } catch (MyException e) {
+                // Pre-bug fix, this was a "Self-suppression not permitted" exception from Java, rather than MyException
+                Assert.assertEquals(1, e.item.intValue());
+            }
+            // Verify that attempts to write after exception will fail
+            try {
+                t.write(4);
+                Assert.fail("Expected exception");
+            } catch (RuntimeIOException e) {
+                // Expected
+            }
+        }
+    }
+}