Make Snappy technically an optional dependency

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

@@ -25,25 +25,22 @@
 
 import htsjdk.samtools.Defaults;
 import htsjdk.samtools.SAMException;
-import org.xerial.snappy.SnappyError;
-import org.xerial.snappy.SnappyInputStream;
-import org.xerial.snappy.SnappyOutputStream;
 
-import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 
 /**
- * Checks if Snappy is available, and provides methods for wrapping InputStreams and OutputStreams with Snappy if so.
+ * Checks if Snappy is available, and provides methods for wrapping InputStreams and OutputStreams with Snappy if it is.
+ *
+ * @implNote this class must not import Snappy code in order to prevent exceptions if the Snappy Library is not available.
+ * Snappy code is handled by {@link SnappyLoaderInternal}.
  */
 public class SnappyLoader {
-    private static final int SNAPPY_BLOCK_SIZE = 32768;  // keep this as small as can be without hurting compression ratio.
     private static final Log logger = Log.getInstance(SnappyLoader.class);
 
     private final boolean snappyAvailable;
 
-
     public SnappyLoader() {
         this(Defaults.DISABLE_SNAPPY_COMPRESSOR);
     }
@@ -52,24 +49,18 @@ public SnappyLoader() {
         if (disableSnappy) {
             logger.debug("Snappy is disabled via system property.");
             snappyAvailable = false;
-        }
-        else {
-            boolean tmpSnappyAvailable = false;
-            try (final OutputStream test = new SnappyOutputStream(new ByteArrayOutputStream(1000))){
-                test.write("Hello World!".getBytes());
-                tmpSnappyAvailable = true;
-                logger.debug("Snappy successfully loaded.");
-            }
-            /*
-             * ExceptionInInitializerError: thrown by Snappy if native libs fail to load.
-             * IllegalStateException: thrown within the `test.write` call above if no UTF-8 encoder is found.
-             * IOException: potentially thrown by the `test.write` and `test.close` calls.
-             * SnappyError: potentially thrown for a variety of reasons by Snappy.
-             */
-            catch (final ExceptionInInitializerError | IllegalStateException | IOException | SnappyError e) {
-                logger.warn(e, "Snappy native library failed to load.");
+        } else {
+            boolean tmpAvailable;
+            try {
+                //This triggers trying to import Snappy code, which causes an exception if the library is missing.
+                tmpAvailable = SnappyLoaderInternal.tryToLoadSnappy();
+            } catch (NoClassDefFoundError e){
+                tmpAvailable = false;
+                logger.error(e, "Snappy java library was requested but not found. If Snappy is " +
+                        "intentionally missing, this message may be suppressed by setting " +
+                        "-D"+ Defaults.SAMJDK_PREFIX + Defaults.DISABLE_SNAPPY_PROPERTY_NAME + "=true " );
             }
-            snappyAvailable = tmpSnappyAvailable;
+            snappyAvailable = tmpAvailable;
         }
     }
 
@@ -81,18 +72,21 @@ public SnappyLoader() {
      * @throws SAMException if Snappy is not available will throw an exception.
      */
     public InputStream wrapInputStream(final InputStream inputStream) {
-        return wrapWithSnappyOrThrow(inputStream, SnappyInputStream::new);
+        return wrapWithSnappyOrThrow(inputStream, SnappyLoaderInternal.getInputStreamWrapper());
     }
 
     /**
      * Wrap an OutputStream in a SnappyOutputStream.
      * @throws SAMException if Snappy is not available
      */
     public OutputStream wrapOutputStream(final OutputStream outputStream) {
-        return wrapWithSnappyOrThrow(outputStream, (stream) -> new SnappyOutputStream(stream, SNAPPY_BLOCK_SIZE));
+        return wrapWithSnappyOrThrow(outputStream, SnappyLoaderInternal.getOutputStreamWrapper());
     }
 
-    private interface IOFunction<T,R> {
+    /**
+     * Function which can throw IOExceptions
+     */
+    interface IOFunction<T,R> {
         R apply(T input) throws IOException;
     }
 
@@ -111,4 +105,5 @@ private <T,R> R wrapWithSnappyOrThrow(T stream, IOFunction<T, R> wrapper){
             throw new SAMException(errorMessage);
         }
     }
+
 }

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

@@ -0,0 +1,69 @@
+package htsjdk.samtools.util;
+
+import htsjdk.annotations.InternalAPI;
+import org.xerial.snappy.SnappyError;
+import org.xerial.snappy.SnappyInputStream;
+import org.xerial.snappy.SnappyOutputStream;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+/**
+ * This class is the only one which should actually import Snappy Classes.  It is separated from SnappyLoader to allow
+ * snappy to be an optional dependency. Referencing snappy classes directly if the library is unavailable causes a
+ * NoClassDefFoundError, so use this instead.
+ *
+ * This should only be referenced by {@link SnappyLoader} in order to prevent accidental imports of Snappy classes.
+ *
+ */
+@InternalAPI
+class SnappyLoaderInternal {
+    private static final Log logger = Log.getInstance(SnappyLoaderInternal.class);
+    private static final int SNAPPY_BLOCK_SIZE = 32768;  // keep this as small as can be without hurting compression ratio.
+
+    /**
+     * Try to load Snappy's native library.
+     *
+     * Note that calling this when snappy is not available will throw NoClassDefFoundError!
+     *
+     * @return true iff Snappy's native libraries are loaded and functioning.
+     */
+    static boolean tryToLoadSnappy() {
+        final boolean snappyAvailable;
+        boolean tmpSnappyAvailable = false;
+        try (final OutputStream test = new SnappyOutputStream(new ByteArrayOutputStream(1000))){
+            test.write("Hello World!".getBytes());
+            tmpSnappyAvailable = true;
+            logger.debug("Snappy successfully loaded.");
+        }
+        /*
+         * ExceptionInInitializerError: thrown by Snappy if native libs fail to load.
+         * IllegalStateException: thrown within the `test.write` call above if no UTF-8 encoder is found.
+         * IOException: potentially thrown by the `test.write` and `test.close` calls.
+         * SnappyError: potentially thrown for a variety of reasons by Snappy.
+         */
+        catch (final ExceptionInInitializerError | IllegalStateException | IOException | SnappyError e) {
+            logger.warn(e, "Snappy native library failed to load.");
+        }
+        snappyAvailable = tmpSnappyAvailable;
+        return snappyAvailable;
+    }
+
+
+    /**
+     * @return a function which wraps an InputStream in a new SnappyInputStream
+     */
+    static SnappyLoader.IOFunction<InputStream, InputStream> getInputStreamWrapper(){
+        return SnappyInputStream::new;
+    }
+
+    /**
+     * @return a function which wraps an OutputStream in a new SnappyOutputStream with an appropriate block size
+     */
+    static SnappyLoader.IOFunction<OutputStream, OutputStream> getOutputStreamWrapper(){
+        return (stream) -> new SnappyOutputStream(stream, SNAPPY_BLOCK_SIZE);
+    }
+
+}