Merge branch 'stable-5.1' into stable-5.2

* stable-5.1:
  Prepare 5.1.8-SNAPSHOT builds
  JGit v5.1.7.201904200442-r
  ObjectUploadListener: Add callback interface
  Prepare 4.11.9-SNAPSHOT builds
  JGit v4.11.8.201904181247-r
  Prepare 4.9.11-SNAPSHOT builds
  JGit v4.9.10.201904181027-r
  Prepare 4.7.10-SNAPSHOT builds
  JGit v4.7.9.201904161809-r
  Prepare 4.5.8-SNAPSHOT builds
  JGit v4.5.7.201904151645-r
  Remember the cause for invalidating a packfile
  Fix API problem filters
  Fix pack files scan when filesnapshot isn't modified

Change-Id: I76761002eedf360e93d0559942ebc927a40428d6
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit.lfs.server/.settings/.api_filters

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<component id="org.eclipse.jgit.lfs.server" version="2">
+    <resource path="META-INF/MANIFEST.MF">
+        <filter id="924844039">
+            <message_arguments>
+                <message_argument value="5.2.2"/>
+                <message_argument value="5.2.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/lfs/server/fs/ObjectUploadListener.java" type="org.eclipse.jgit.lfs.server.fs.ObjectUploadListener">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.7"/>
+                <message_argument value="setCallback(ObjectUploadListener.Callback)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/lfs/server/fs/ObjectUploadListener.java" type="org.eclipse.jgit.lfs.server.fs.ObjectUploadListener$Callback">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.7"/>
+                <message_argument value="Callback"/>
+            </message_arguments>
+        </filter>
+    </resource>
+</component>

org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/ObjectUploadListener.java

@@ -48,6 +48,7 @@ import java.nio.ByteBuffer;
 import java.nio.channels.Channels;
 import java.nio.channels.ReadableByteChannel;
 import java.nio.channels.WritableByteChannel;
+import java.nio.file.Path;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -87,6 +88,29 @@ public class ObjectUploadListener implements ReadListener {
 
 	private final ByteBuffer buffer = ByteBuffer.allocateDirect(8192);
 
+	private final Path path;
+
+	private long uploaded;
+
+	private Callback callback;
+
+	/**
+	 * Callback invoked after object upload completed.
+	 *
+	 * @since 5.1.7
+	 */
+	public interface Callback {
+		/**
+		 * Notified after object upload completed.
+		 *
+		 * @param path
+		 *            path to the object on the backend
+		 * @param size
+		 *            uploaded size in bytes
+		 */
+		void uploadCompleted(String path, long size);
+	}
+
 	/**
 	 * Constructor for ObjectUploadListener.
 	 *
@@ -113,9 +137,24 @@ public class ObjectUploadListener implements ReadListener {
 		this.inChannel = Channels.newChannel(in);
 		this.out = repository.getOutputStream(id);
 		this.channel = Channels.newChannel(out);
+		this.path = repository.getPath(id);
+		this.uploaded = 0L;
 		response.setContentType(Constants.CONTENT_TYPE_GIT_LFS_JSON);
 	}
 
+	/**
+	 * Set the callback to invoke after upload completed.
+	 *
+	 * @param callback
+	 *            the callback
+	 * @return {@code this}.
+	 * @since 5.1.7
+	 */
+	public ObjectUploadListener setCallback(Callback callback) {
+		this.callback = callback;
+		return this;
+	}
+
 	/**
 	 * {@inheritDoc}
 	 *
@@ -126,12 +165,13 @@ public class ObjectUploadListener implements ReadListener {
 		while (in.isReady()) {
 			if (inChannel.read(buffer) > 0) {
 				buffer.flip();
-				channel.write(buffer);
+				uploaded += Integer.valueOf(channel.write(buffer)).longValue();
 				buffer.compact();
 			} else {
 				buffer.flip();
 				while (buffer.hasRemaining()) {
-					channel.write(buffer);
+					uploaded += Integer.valueOf(channel.write(buffer))
+							.longValue();
 				}
 				close();
 				return;
@@ -159,6 +199,9 @@ public class ObjectUploadListener implements ReadListener {
 			if (!response.isCommitted()) {
 				response.setStatus(HttpServletResponse.SC_OK);
 			}
+			if (callback != null) {
+				callback.uploadCompleted(path.toString(), uploaded);
+			}
 		} finally {
 			context.complete();
 		}

org.eclipse.jgit/.settings/.api_filters

@@ -8,6 +8,20 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/errors/PackInvalidException.java" type="org.eclipse.jgit.errors.PackInvalidException">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="4.5.7"/>
+                <message_argument value="PackInvalidException(File, Throwable)"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="4.5.7"/>
+                <message_argument value="PackInvalidException(String, Throwable)"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/transport/TransferConfig.java" type="org.eclipse.jgit.transport.TransferConfig">
         <filter id="1159725059">
             <message_arguments>

org.eclipse.jgit/src/org/eclipse/jgit/errors/PackInvalidException.java

@@ -60,9 +60,24 @@ public class PackInvalidException extends IOException {
 	 *
 	 * @param path
 	 *            path of the invalid pack file.
+	 * @deprecated Use {@link #PackInvalidException(File, Throwable)}.
 	 */
+	@Deprecated
 	public PackInvalidException(File path) {
-		this(path.getAbsolutePath());
+		this(path, null);
+	}
+
+	/**
+	 * Construct a pack invalid error with cause.
+	 *
+	 * @param path
+	 *            path of the invalid pack file.
+	 * @param cause
+	 *            cause of the pack file becoming invalid.
+	 * @since 4.5.7
+	 */
+	public PackInvalidException(File path, Throwable cause) {
+		this(path.getAbsolutePath(), cause);
 	}
 
 	/**
@@ -70,8 +85,23 @@ public class PackInvalidException extends IOException {
 	 *
 	 * @param path
 	 *            path of the invalid pack file.
+	 * @deprecated Use {@link #PackInvalidException(String, Throwable)}.
 	 */
+	@Deprecated
 	public PackInvalidException(String path) {
-		super(MessageFormat.format(JGitText.get().packFileInvalid, path));
+		this(path, null);
+	}
+
+	/**
+	 * Construct a pack invalid error with cause.
+	 *
+	 * @param path
+	 *            path of the invalid pack file.
+	 * @param cause
+	 *            cause of the pack file becoming invalid.
+	 * @since 4.5.7
+	 */
+	public PackInvalidException(String path, Throwable cause) {
+		super(MessageFormat.format(JGitText.get().packFileInvalid, path), cause);
 	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java

@@ -84,6 +84,9 @@ abstract class BlockBasedFile {
 	/** True once corruption has been detected that cannot be worked around. */
 	volatile boolean invalid;
 
+	/** Exception that caused the packfile to be flagged as invalid */
+	protected volatile Exception invalidatingCause;
+
 	BlockBasedFile(DfsBlockCache cache, DfsPackDescription desc, PackExt ext) {
 		this.cache = cache;
 		this.key = desc.getStreamKey(ext);
@@ -135,8 +138,9 @@ abstract class BlockBasedFile {
 
 	DfsBlock readOneBlock(long pos, DfsReader ctx,
 			@Nullable ReadableChannel fileChannel) throws IOException {
-		if (invalid)
+		if (invalid) {
-			throw new PackInvalidException(getFileName());
+			throw new PackInvalidException(getFileName(), invalidatingCause);
+		}
 
 		ctx.stats.readBlock++;
 		long start = System.nanoTime();

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java

@@ -181,8 +181,9 @@ public final class DfsPackFile extends BlockBasedFile {
 				return idx;
 		}
 
-		if (invalid)
+		if (invalid) {
-			throw new PackInvalidException(getFileName());
+			throw new PackInvalidException(getFileName(), invalidatingCause);
+		}
 
 		Repository.getGlobalListenerList()
 				.dispatch(new BeforeDfsPackIndexLoadedEvent(this));
@@ -224,11 +225,13 @@ public final class DfsPackFile extends BlockBasedFile {
 				}
 			} catch (EOFException e) {
 				invalid = true;
+				invalidatingCause = e;
 				throw new IOException(MessageFormat.format(
 						DfsText.get().shortReadOfIndex,
 						desc.getFileName(INDEX)), e);
 			} catch (IOException e) {
 				invalid = true;
+				invalidatingCause = e;
 				throw new IOException(MessageFormat.format(
 						DfsText.get().cannotReadIndex,
 						desc.getFileName(INDEX)), e);
@@ -720,8 +723,10 @@ public final class DfsPackFile extends BlockBasedFile {
 
 	private IOException packfileIsTruncated() {
 		invalid = true;
-		return new IOException(MessageFormat.format(
+		IOException exc = new IOException(MessageFormat.format(
 				JGitText.get().packfileIsTruncated, getFileName()));
+		invalidatingCause = exc;
+		return exc;
 	}
 
 	private void readFully(long position, byte[] dstbuf, int dstoff, int cnt,

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java

@@ -132,8 +132,6 @@ public class ObjectDirectory extends FileObjectDatabase {
 
 	private final File alternatesFile;
 
-	private final AtomicReference<PackList> packList;
-
 	private final FS fs;
 
 	private final AtomicReference<AlternateHandle[]> alternates;
@@ -146,6 +144,8 @@ public class ObjectDirectory extends FileObjectDatabase {
 
 	private Set<ObjectId> shallowCommitsIds;
 
+	final AtomicReference<PackList> packList;
+
 	/**
 	 * Initialize a reference to an on-disk object directory.
 	 *
@@ -674,13 +674,8 @@ public class ObjectDirectory extends FileObjectDatabase {
 			transientErrorCount = p.incrementTransientErrorCount();
 		}
 		if (warnTmpl != null) {
-			if (LOG.isDebugEnabled()) {
+			LOG.warn(MessageFormat.format(warnTmpl,
-				LOG.debug(MessageFormat.format(warnTmpl,
+					p.getPackFile().getAbsolutePath()), e);
-						p.getPackFile().getAbsolutePath()), e);
-			} else {
-				LOG.warn(MessageFormat.format(warnTmpl,
-						p.getPackFile().getAbsolutePath()));
-			}
 		} else {
 			if (doLogExponentialBackoff(transientErrorCount)) {
 				// Don't remove the pack from the list, as the error may be
@@ -767,7 +762,7 @@ public class ObjectDirectory extends FileObjectDatabase {
 		return InsertLooseObjectResult.FAILURE;
 	}
 
-	private boolean searchPacksAgain(PackList old) {
+	boolean searchPacksAgain(PackList old) {
 		// Whether to trust the pack folder's modification time. If set
 		// to false we will always scan the .git/objects/pack folder to
 		// check for new pack files. If set to true (default) we use the
@@ -917,7 +912,8 @@ public class ObjectDirectory extends FileObjectDatabase {
 			final String packName = base + PACK.getExtension();
 			final File packFile = new File(packDirectory, packName);
 			final PackFile oldPack = forReuse.remove(packName);
-			if (oldPack != null && oldPack.getFileSnapshot().isModified(packFile)) {
+			if (oldPack != null
+					&& !oldPack.getFileSnapshot().isModified(packFile)) {
 				list.add(oldPack);
 				continue;
 			}
@@ -1074,7 +1070,7 @@ public class ObjectDirectory extends FileObjectDatabase {
 		return new File(new File(getDirectory(), d), f);
 	}
 
-	private static final class PackList {
+	static final class PackList {
 		/** State just before reading the pack directory. */
 		final FileSnapshot snapshot;
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java

@@ -135,6 +135,8 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 
 	private volatile boolean invalid;
 
+	private volatile Exception invalidatingCause;
+
 	private boolean invalidBitmap;
 
 	private AtomicInteger transientErrorCount = new AtomicInteger();
@@ -184,7 +186,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 				idx = loadedIdx;
 				if (idx == null) {
 					if (invalid) {
-						throw new PackInvalidException(packFile);
+						throw new PackInvalidException(packFile, invalidatingCause);
 					}
 					try {
 						idx = PackIndex.open(extFile(INDEX));
@@ -208,6 +210,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 						throw e;
 					} catch (IOException e) {
 						invalid = true;
+						invalidatingCause = e;
 						throw e;
 					}
 				}
@@ -661,7 +664,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 
 	private void doOpen() throws IOException {
 		if (invalid) {
-			throw new PackInvalidException(packFile);
+			throw new PackInvalidException(packFile, invalidatingCause);
 		}
 		try {
 			synchronized (readLock) {
@@ -671,13 +674,13 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 			}
 		} catch (InterruptedIOException e) {
 			// don't invalidate the pack, we are interrupted from another thread
-			openFail(false);
+			openFail(false, e);
 			throw e;
 		} catch (FileNotFoundException fn) {
 			// don't invalidate the pack if opening an existing file failed
 			// since it may be related to a temporary lack of resources (e.g.
 			// max open files)
-			openFail(!packFile.exists());
+			openFail(!packFile.exists(), fn);
 			throw fn;
 		} catch (EOFException | AccessDeniedException | NoSuchFileException
 				| CorruptObjectException | NoPackSignatureException
@@ -685,20 +688,21 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 				| UnsupportedPackIndexVersionException
 				| UnsupportedPackVersionException pe) {
 			// exceptions signaling permanent problems with a pack
-			openFail(true);
+			openFail(true, pe);
 			throw pe;
 		} catch (IOException | RuntimeException ge) {
 			// generic exceptions could be transient so we should not mark the
 			// pack invalid to avoid false MissingObjectExceptions
-			openFail(false);
+			openFail(false, ge);
 			throw ge;
 		}
 	}
 
-	private void openFail(boolean invalidate) {
+	private void openFail(boolean invalidate, Exception cause) {
 		activeWindows = 0;
 		activeCopyRawData = 0;
 		invalid = invalidate;
+		invalidatingCause = cause;
 		doClose();
 	}
 
@@ -725,7 +729,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 				// Detect the situation and throw a proper exception so that can be properly
 				// managed by the main packfile search loop and the Git client won't receive
 				// any failures.
-				throw new PackInvalidException(packFile);
+				throw new PackInvalidException(packFile, invalidatingCause);
 			}
 			if (length < pos + size)
 				size = (int) (length - pos);