fix: handle the smb over mac edge case about closing file channels failing after a successful write.

Author: cmhulbert

src/main/java/org/janelia/saalfeldlab/n5/FsIoPolicy.java

@@ -52,16 +52,44 @@ static FileChannel openFileChannel(final Path path, final boolean forWriting) th
         }
     }
 
+
+    /**
+     * This method is necessary to handle the situtation where writing is successful, but `close` fails on the file channel.
+     * This has been observed to happen fairly consistently on MacOS when writing to a file mounted over SMB.
+     *
+     * @param readData to write to the {@code Path}
+     * @param path to write to
+     * @throws IOException if writing failed.
+     */
+    private static void writeToPathIgnoreCloseException(ReadData readData, Path path) throws IOException {
+
+        FileChannel channel = openFileChannel(path, true);
+        OutputStream os = Channels.newOutputStream(channel);
+
+        try {
+            readData.writeTo(os);
+            os.flush();
+            channel.force(true);
+        } catch (Throwable e) {
+            os.close();
+            channel.close();
+            throw e;
+        }
+
+        /* if we get here, the write succeeded, and the os/channel may not be closed yet */
+        try {
+            os.close();
+            channel.close();
+        } catch (IOException | UncheckedIOException ignore) {
+            /* Ignore; we know the data was written already. */
+        }
+    }
+
     public static class Unsafe implements IoPolicy {
         @Override
         public void write(String key, ReadData readData) throws IOException {
             final Path path = Paths.get(key);
-            try (
-                    FileChannel channel = openFileChannel(path, true);
-                    OutputStream os = Channels.newOutputStream(channel);
-            ) {
-                readData.writeTo(os);
-            }
+            writeToPathIgnoreCloseException(readData, path);
         }
 
         @Override

src/test/java/org/janelia/saalfeldlab/n5/shard/ShardTest.java

@@ -632,14 +632,13 @@ public void testPartialReadAggregationBehavior() {
 			writer.resetNumMaterializeCalls();
 			writer.readBlocks(dataset, datasetAttributes, ptList);
 
-			// TODO change this if and when we implement aggregation of read calls
-			// one for the index, one for each of the four blocks
-			assertEquals(5, writer.getNumMaterializeCalls());
+			// one for the index, one for the four blocks (aggregated)
+			assertEquals(2, writer.getNumMaterializeCalls());
 
 			writer.resetNumMaterializeCalls();
 			writer.readShard(dataset, datasetAttributes, new long[] {0,0});
-			// one for the index, one for each of the four blocks
-			assertEquals(5, writer.getNumMaterializeCalls());
+			// one for the index, one for the four blocks (aggregated)
+			assertEquals(2, writer.getNumMaterializeCalls());
 
 
 			/**