WIP: Update to new API changes

Author: gab1one

src/main/java/org/scijava/io/handle/DefaultBufferedStreamHandle.java

@@ -105,7 +105,7 @@ public void seek(final long pos) throws IOException {
 	}
 
 	private long maxBuf() throws IOException {
-		return getBufferIfOpen().getMaxPos();
+		return getBufferIfOpen().size();
 	}
 
 	@Override
@@ -231,4 +231,9 @@ private ByteBank getBufferIfOpen() throws IOException {
 		}
 		return buffer;
 	}
+
+	@Override
+	public boolean exists() throws IOException {
+		return false;
+	}
 }

src/main/java/org/scijava/io/location/AbstractCompressedHandle.java

@@ -35,9 +35,10 @@
 import java.io.InputStream;
 import java.io.OutputStream;
 
-import org.scijava.io.DataHandle;
-import org.scijava.io.DataHandleService;
-import org.scijava.io.Location;
+import org.scijava.io.handle.AbstractStreamHandle;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.handle.DataHandleService;
+import org.scijava.io.handle.ResettableStreamHandle;
 import org.scijava.plugin.Parameter;
 
 /**
@@ -79,6 +80,13 @@ public InputStream in() throws IOException {
 		return inputStream;
 	}
 
+	@Override
+	public long skip(long n) throws IOException {
+		long skipped = in().skip(n);
+		setOffset(offset() + skipped);
+		return skipped; 
+	}
+
 	protected abstract void initInputStream() throws IOException;
 
 	@Override
@@ -101,6 +109,11 @@ public long length() throws IOException {
 		return raw().length();
 	}
 
+	@Override
+	public boolean exists() throws IOException {
+		return raw().exists();
+	}
+
 	@Override
 	public void setLength(long length) throws IOException {
 		throw new IOException("This handle " + this.getClass().getSimpleName() +

src/main/java/org/scijava/io/location/AbstractHigherOrderLocation.java

@@ -0,0 +1,15 @@
+
+package org.scijava.io.location;
+
+public abstract class AbstractHigherOrderLocation implements Location {
+
+	private final Location baseLocation;
+
+	public AbstractHigherOrderLocation(final Location location) {
+		this.baseLocation = location;
+	}
+
+	public Location getBaseLocation() {
+		return baseLocation;
+	}
+}

src/main/java/org/scijava/io/location/bzip2/BZip2Handle.java

@@ -33,7 +33,7 @@
 
 import java.io.IOException;
 
-import org.scijava.io.DataHandle;
+import org.scijava.io.handle.DataHandle;
 import org.scijava.io.location.AbstractCompressedHandle;
 import org.scijava.plugin.Plugin;
 
@@ -60,5 +60,4 @@ protected void initInputStream() throws IOException {
 	public Class<BZip2Location> getType() {
 		return BZip2Location.class;
 	}
-
 }

src/main/java/org/scijava/io/location/bzip2/BZip2Location.java

@@ -1,9 +1,9 @@
 
 package org.scijava.io.location.bzip2;
 
-import org.scijava.io.DataHandle;
-import org.scijava.io.Location;
+import org.scijava.io.handle.DataHandle;
 import org.scijava.io.location.AbstractHigherOrderLocation;
+import org.scijava.io.location.Location;
 
 /**
  * {@link Location} backed by a {@link DataHandle} that is BZip2 compressed.

src/main/java/org/scijava/io/location/bzip2/CBZip2InputStream.java

@@ -56,8 +56,8 @@
 import java.io.IOException;
 import java.io.InputStream;
 
-import org.scijava.io.DataHandle;
-import org.scijava.io.Location;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.location.Location;
 import org.scijava.log.LogService;
 
 /**

src/main/java/org/scijava/io/location/gzip/GZipHandle.java

@@ -33,8 +33,8 @@
 import java.io.IOException;
 import java.util.zip.GZIPInputStream;
 
-import org.scijava.io.DataHandle;
-import org.scijava.io.DataHandleInputStream;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.handle.DataHandleInputStream;
 import org.scijava.io.location.AbstractCompressedHandle;
 import org.scijava.plugin.Plugin;
 

src/main/java/org/scijava/io/location/gzip/GZipLocation.java

@@ -1,9 +1,9 @@
 
 package org.scijava.io.location.gzip;
 
-import org.scijava.io.DataHandle;
-import org.scijava.io.Location;
+import org.scijava.io.handle.DataHandle;
 import org.scijava.io.location.AbstractHigherOrderLocation;
+import org.scijava.io.location.Location;
 
 /**
  * {@link Location} backed by a {@link DataHandle} that is <code>gzip</code>

src/main/java/org/scijava/io/location/zip/ZipHandle.java

@@ -35,12 +35,12 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
-import org.scijava.io.DataHandle;
-import org.scijava.io.DataHandleInputStream;
-import org.scijava.io.Location;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.handle.DataHandleInputStream;
+import org.scijava.io.handle.ResettableStreamHandle;
+import org.scijava.io.handle.StreamHandle;
 import org.scijava.io.location.AbstractCompressedHandle;
-import org.scijava.io.location.ResettableStreamHandle;
-import org.scijava.io.location.StreamHandle;
+import org.scijava.io.location.Location;
 import org.scijava.plugin.Plugin;
 
 /**
@@ -202,4 +202,16 @@ protected void initInputStream() throws IOException {
 			resetStream();
 		}
 	}
+
+	@Override
+	public long length() throws IOException {
+		if (entry == null) {
+			return -1;
+		}
+		return entry.getSize();
+	}
+
+	public long getEntryLength() {
+		return entryLength;
+	}
 }

src/main/java/org/scijava/io/location/zip/ZipLocation.java

@@ -33,9 +33,9 @@
 
 import java.util.zip.ZipEntry;
 
-import org.scijava.io.DataHandle;
-import org.scijava.io.Location;
+import org.scijava.io.handle.DataHandle;
 import org.scijava.io.location.AbstractHigherOrderLocation;
+import org.scijava.io.location.Location;
 import org.scijava.plugin.Plugin;
 
 /**

src/test/java/org/scijava/io/BZip2HandleTest.java src/test/java/org/scijava/io/handle/BZip2HandleTest.java

@@ -29,15 +29,19 @@
  * #L%
  */
 
-package org.scijava.io;
+package org.scijava.io.handle;
 
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 
+import org.junit.Ignore;
+import org.junit.Test;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.location.FileLocation;
+import org.scijava.io.location.Location;
 import org.scijava.io.location.bzip2.BZip2Handle;
 import org.scijava.io.location.bzip2.BZip2Location;
-import org.scijava.io.location.file.FileLocation;
 
 /**
  * Tests {@link BZip2Handle}.
@@ -76,16 +80,19 @@ public Location createLocation() throws IOException {
 		return new BZip2Location(new FileLocation(bzip2File));
 	}
 
+	@Test
 	@Override
-	protected <L extends Location> void checkWrites(DataHandle<L> handle)
-		throws IOException
-	{
-		// NB Handle is read only
+	public void testWriting() throws IOException {
+		// no Op
 	}
 
 	@Override
-	protected void setup() {
-		checkLength = false;
+	@Test
+	public void testReading() throws IOException {
+		try (final DataHandle<? extends Location> handle = createHandle()) {
+			checkBasicReadMethods(handle, false);
+			checkEndiannessReading(handle);
+		}
 	}
 
 }

src/test/java/org/scijava/io/handle/DataHandleTest.java

@@ -113,7 +113,7 @@ public void testEndianesSettings() throws IOException {
 	@Test
 	public void testReading() throws IOException {
 		try (final DataHandle<? extends Location> handle = createHandle()) {
-			checkBasicReadMethods(handle);
+			checkBasicReadMethods(handle, true);
 			checkEndiannessReading(handle);
 		}
 	}
@@ -168,13 +168,16 @@ public void populateData(final OutputStream out) throws IOException {
 	 * Checks basic byte reading methods.
 	 *
 	 * @param handle the handle to test
+	 * @param checkLength whether to check the total length of the handle
 	 * @throws IOException
 	 */
 	public <L extends Location> void checkBasicReadMethods(
-		final DataHandle<L> handle) throws IOException
+		final DataHandle<L> handle, boolean checkLength) throws IOException
 	{
 		assertEquals(0, handle.offset());
-		assertEquals(BYTES.length, handle.length());
+		if (checkLength) {
+			assertEquals(BYTES.length, handle.length());
+		}
 		assertEquals("UTF-8", handle.getEncoding());
 
 		// test read()

src/test/java/org/scijava/io/GZipHandleTest.java src/test/java/org/scijava/io/handle/GZipHandleTest.java

@@ -29,14 +29,17 @@
  * #L%
  */
 
-package org.scijava.io;
+package org.scijava.io.handle;
 
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.zip.GZIPOutputStream;
 
-import org.scijava.io.location.file.FileLocation;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.scijava.io.location.FileLocation;
+import org.scijava.io.location.Location;
 import org.scijava.io.location.gzip.GZipHandle;
 import org.scijava.io.location.gzip.GZipLocation;
 
@@ -68,14 +71,18 @@ public Location createLocation() throws IOException {
 		return new GZipLocation(new FileLocation(tmpFile));
 	}
 
+	@Test
 	@Override
-	protected <L extends Location> void checkWrites(DataHandle<L> handle)
-		throws IOException
-	{
-		// NB Handle is read only
+	public void testWriting() throws IOException {
+		// no Op
 	}
+
 	@Override
-	protected void setup() {
-		checkLength = false;
+	@Test
+	public void testReading() throws IOException {
+		try (final DataHandle<? extends Location> handle = createHandle()) {
+			checkBasicReadMethods(handle, false);
+			checkEndiannessReading(handle);
+		}
 	}
 }

src/test/java/org/scijava/io/handle/ReadBufferDataHandleTest.java

@@ -64,7 +64,7 @@ public void testSmallBuffer() throws IOException {
 					new ReadBufferDataHandle(handle, 5))
 		{
 			// check with small buffersize
-			checkBasicReadMethods(bufferedHandle);
+			checkBasicReadMethods(bufferedHandle, true);
 			checkEndiannessReading(bufferedHandle);
 		}
 	}
@@ -127,7 +127,6 @@ public void testLargeRead() throws Exception {
 	}
 
 	@Test
-	@Ignore
 	@Override
 	public void testWriting() throws IOException {
 		// nothing to do here

src/test/java/org/scijava/io/handle/WriteBufferDataHandleTest.java

@@ -64,14 +64,12 @@ public DataHandle<? extends Location> createHandle() {
 	}
 
 	@Test
-	@Ignore
 	@Override
 	public void testReading() throws IOException {
 		// nothing to do
 	}
 
 	@Test
-	@Ignore
 	@Override
 	public void checkSkip() throws IOException {
 		// nothing to do

src/test/java/org/scijava/io/ZipHandleTest.java src/test/java/org/scijava/io/handle/ZipHandleTest.java

@@ -29,15 +29,19 @@
  * #L%
  */
 
-package org.scijava.io;
+package org.scijava.io.handle;
 
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
-import org.scijava.io.location.file.FileLocation;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.location.FileLocation;
+import org.scijava.io.location.Location;
 import org.scijava.io.location.zip.ZipHandle;
 import org.scijava.io.location.zip.ZipLocation;
 
@@ -69,15 +73,18 @@ public Location createLocation() throws IOException {
 		return new ZipLocation(new FileLocation(tmpFile));
 	}
 
+	@Test
 	@Override
-	protected <L extends Location> void checkWrites(DataHandle<L> handle)
-		throws IOException
-	{
-		// NB Handle is read only
+	public void testWriting() throws IOException {
+		// no Op
 	}
 
 	@Override
-	protected void setup() {
-		checkLength = false;
+	@Test
+	public void testReading() throws IOException {
+		try (final DataHandle<? extends Location> handle = createHandle()) {
+			checkBasicReadMethods(handle, false);
+			checkEndiannessReading(handle);
+		}
 	}
 }